A simple numerical model for predicting organic matter decomposition in a fed-batch composting operation.

PubMed

Nakasaki, Kiyohiko; Ohtaki, Akihito

2002-01-01

Using dog food as a model of the organic waste that comprises composting raw material, the degradation pattern of organic materials was examined by continuously measuring the quantity of CO2 evolved during the composting process in both batch and fed-batch operations. A simple numerical model was made on the basis of three suppositions for describing the organic matter decomposition in the batch operation. First, a certain quantity of carbon in the dog food was assumed to be recalcitrant to degradation in the composting reactor within the retention time allowed. Second, it was assumed that the decomposition rate of carbon is proportional to the quantity of easily degradable carbon, that is, the carbon recalcitrant to degradation was subtracted from the total carbon remaining in the dog food. Third, a certain lag time is assumed to occur before the start of active decomposition of organic matter in the dog food; this lag corresponds to the time required for microorganisms to proliferate and become active. It was then ascertained that the decomposition pattern for the organic matter in the dog food during the fed-batch operation could be predicted by the numerical model with the parameters obtained from the batch operation. This numerical model was modified so that the change in dry weight of composting materials could be obtained. The modified model was found suitable for describing the organic matter decomposition pattern in an actual fed-batch composting operation of the garbage obtained from a restaurant, approximately 10 kg d(-1) loading for 60 d.

Influence of dissolved organic carbon content on modelling natural organic matter acid-base properties.

PubMed

Garnier, Cédric; Mounier, Stéphane; Benaïm, Jean Yves

2004-10-01

Natural organic matter (NOM) behaviour towards proton is an important parameter to understand NOM fate in the environment. Moreover, it is necessary to determine NOM acid-base properties before investigating trace metals complexation by natural organic matter. This work focuses on the possibility to determine these acid-base properties by accurate and simple titrations, even at low organic matter concentrations. So, the experiments were conducted on concentrated and diluted solutions of extracted humic and fulvic acid from Laurentian River, on concentrated and diluted model solutions of well-known simple molecules (acetic and phenolic acids), and on natural samples from the Seine river (France) which are not pre-concentrated. Titration experiments were modelled by a 6 acidic-sites discrete model, except for the model solutions. The modelling software used, called PROSECE (Programme d'Optimisation et de SpEciation Chimique dans l'Environnement), has been developed in our laboratory, is based on the mass balance equilibrium resolution. The results obtained on extracted organic matter and model solutions point out a threshold value for a confident determination of the studied organic matter acid-base properties. They also show an aberrant decreasing carboxylic/phenolic ratio with increasing sample dilution. This shift is neither due to any conformational effect, since it is also observed on model solutions, nor to ionic strength variations which is controlled during all experiments. On the other hand, it could be the result of an electrode troubleshooting occurring at basic pH values, which effect is amplified at low total concentration of acidic sites. So, in our conditions, the limit for a correct modelling of NOM acid-base properties is defined as 0.04 meq of total analysed acidic sites concentration. As for the analysed natural samples, due to their high acidic sites content, it is possible to model their behaviour despite the low organic carbon concentration.

A 360° Vision for Virtual Organizations Characterization and Modelling: Two Intentional Level Aspects

NASA Astrophysics Data System (ADS)

Priego-Roche, Luz-María; Rieu, Dominique; Front, Agnès

Nowadays, organizations aiming to be successful in an increasingly competitive market tend to group together into virtual organizations. Designing the information system (IS) of such virtual organizations on the basis of the IS of those participating is a real challenge. The IS of a virtual organization plays an important role in the collaboration and cooperation of the participants organizations and in reaching the common goal. This article proposes criteria allowing virtual organizations to be identified and classified at an intentional level, as well as the information necessary for designing the organizations’ IS. Instantiation of criteria for a specific virtual organization and its participants, will allow simple graphical models to be generated in a modelling tool. The models will be used as bases for the IS design at organizational and operational levels. The approach is illustrated by the example of the virtual organization UGRT (a regional stockbreeders union in Tabasco, Mexico).

Dynamical system with plastic self-organized velocity field as an alternative conceptual model of a cognitive system.

PubMed

Janson, Natalia B; Marsden, Christopher J

2017-12-05

It is well known that architecturally the brain is a neural network, i.e. a collection of many relatively simple units coupled flexibly. However, it has been unclear how the possession of this architecture enables higher-level cognitive functions, which are unique to the brain. Here, we consider the brain from the viewpoint of dynamical systems theory and hypothesize that the unique feature of the brain, the self-organized plasticity of its architecture, could represent the means of enabling the self-organized plasticity of its velocity vector field. We propose that, conceptually, the principle of cognition could amount to the existence of appropriate rules governing self-organization of the velocity field of a dynamical system with an appropriate account of stimuli. To support this hypothesis, we propose a simple non-neuromorphic mathematical model with a plastic self-organized velocity field, which has no prototype in physical world. This system is shown to be capable of basic cognition, which is illustrated numerically and with musical data. Our conceptual model could provide an additional insight into the working principles of the brain. Moreover, hardware implementations of plastic velocity fields self-organizing according to various rules could pave the way to creating artificial intelligence of a novel type.

Deterministic models for traffic jams

NASA Astrophysics Data System (ADS)

Nagel, Kai; Herrmann, Hans J.

1993-10-01

We study several deterministic one-dimensional traffic models. For integer positions and velocities we find the typical high and low density phases separated by a simple transition. If positions and velocities are continuous variables the model shows self-organized critically driven by the slowest car.

Tenax extraction as a simple approach to improve environmental risk assessments.

PubMed

Harwood, Amanda D; Nutile, Samuel A; Landrum, Peter F; Lydy, Michael J

2015-07-01

It is well documented that using exhaustive chemical extractions is not an effective means of assessing exposure of hydrophobic organic compounds in sediments and that bioavailability-based techniques are an improvement over traditional methods. One technique that has shown special promise as a method for assessing the bioavailability of hydrophobic organic compounds in sediment is the use of Tenax-extractable concentrations. A 6-h or 24-h single-point Tenax-extractable concentration correlates to both bioaccumulation and toxicity. This method has demonstrated effectiveness for several hydrophobic organic compounds in various organisms under both field and laboratory conditions. In addition, a Tenax bioaccumulation model was developed for multiple compounds relating 24-h Tenax-extractable concentrations to oligochaete tissue concentrations exposed in both the laboratory and field. This model has demonstrated predictive capacity for additional compounds and species. Use of Tenax-extractable concentrations to estimate exposure is rapid, simple, straightforward, and relatively inexpensive, as well as accurate. Therefore, this method would be an invaluable tool if implemented in risk assessments. © 2015 SETAC.

An OpenMI Implementation of a Water Resources System using Simple Script Wrappers

NASA Astrophysics Data System (ADS)

Steward, D. R.; Aistrup, J. A.; Kulcsar, L.; Peterson, J. M.; Welch, S. M.; Andresen, D.; Bernard, E. A.; Staggenborg, S. A.; Bulatewicz, T.

2013-12-01

This team has developed an adaption of the Open Modelling Interface (OpenMI) that utilizes Simple Script Wrappers. Code is made OpenMI compliant through organization within three modules that initialize, perform time steps, and finalize results. A configuration file is prepared that specifies variables a model expects to receive as input and those it will make available as output. An example is presented for groundwater, economic, and agricultural production models in the High Plains Aquifer region of Kansas. Our models use the programming environments in Scilab and Matlab, along with legacy Fortran code, and our Simple Script Wrappers can also use Python. These models are collectively run within this interdisciplinary framework from initial conditions into the future. It will be shown that by applying model constraints to one model, the impact may be accessed on changes to the water resources system.

Sensory Perception and Aging in Model Systems: From the Outside In

PubMed Central

Linford, Nancy J.; Kuo, Tsung-Han; Chan, Tammy P.; Pletcher, Scott D.

2014-01-01

Sensory systems provide organisms from bacteria to human with the ability to interact with the world. Numerous senses have evolved that allow animals to detect and decode cues from sources in both their external and internal environments. Recent advances in understanding the central mechanisms by which the brains of simple organisms evaluate different cues and initiate behavioral decisions, coupled with observations that sensory manipulations are capable of altering organism lifespan, have opened the door for powerful new research into aging. While direct links between sensory perception and aging have been established only recently, here we discuss these initial discoveries and evaluate the potential for different forms of sensory processing to modulate lifespan across taxa. Harnessing the neurobiology of simple model systems to study the biological impact of sensory experiences will yield insights into the broad influence of sensory perception in mammals and may help uncover new mechanisms of healthy aging. PMID:21756108

Pre-Modeling Ensures Accurate Solid Models

ERIC Educational Resources Information Center

Gow, George

2010-01-01

Successful solid modeling requires a well-organized design tree. The design tree is a list of all the object's features and the sequential order in which they are modeled. The solid-modeling process is faster and less prone to modeling errors when the design tree is a simple and geometrically logical definition of the modeled object. Few high…

A dynamical systems approach to actin-based motility in Listeria monocytogenes

NASA Astrophysics Data System (ADS)

Hotton, S.

2010-11-01

A simple kinematic model for the trajectories of Listeria monocytogenes is generalized to a dynamical system rich enough to exhibit the resonant Hopf bifurcation structure of excitable media and simple enough to be studied geometrically. It is shown how L. monocytogenes trajectories and meandering spiral waves are organized by the same type of attracting set.

Artificial neural network study on organ-targeting peptides

NASA Astrophysics Data System (ADS)

Jung, Eunkyoung; Kim, Junhyoung; Choi, Seung-Hoon; Kim, Minkyoung; Rhee, Hokyoung; Shin, Jae-Min; Choi, Kihang; Kang, Sang-Kee; Lee, Nam Kyung; Choi, Yun-Jaie; Jung, Dong Hyun

2010-01-01

We report a new approach to studying organ targeting of peptides on the basis of peptide sequence information. The positive control data sets consist of organ-targeting peptide sequences identified by the peroral phage-display technique for four organs, and the negative control data are prepared from random sequences. The capacity of our models to make appropriate predictions is validated by statistical indicators including sensitivity, specificity, enrichment curve, and the area under the receiver operating characteristic (ROC) curve (the ROC score). VHSE descriptor produces statistically significant training models and the models with simple neural network architectures show slightly greater predictive power than those with complex ones. The training and test set statistics indicate that our models could discriminate between organ-targeting and random sequences. We anticipate that our models will be applicable to the selection of organ-targeting peptides for generating peptide drugs or peptidomimetics.

Tier 1 Rice Model for Estimating Pesticide Concentrations in Rice Paddies

EPA Science Inventory

The Tier 1 Rice Model estimates screening level aquatic concentrations of pesticides in rice paddies. It is a simple pesticide soil:water partitioning model with default values for water volume, soil mass, and organic carbon. Pesticide degradation is not considered in the mode...

Emergence of heterogeneity and political organization in information exchange networks

NASA Astrophysics Data System (ADS)

Guttenberg, Nicholas; Goldenfeld, Nigel

2010-04-01

We present a simple model of the emergence of the division of labor and the development of a system of resource subsidy from an agent-based model of directed resource production with variable degrees of trust between the agents. The model has three distinct phases corresponding to different forms of societal organization: disconnected (independent agents), homogeneous cooperative (collective state), and inhomogeneous cooperative (collective state with a leader). Our results indicate that such levels of organization arise generically as a collective effect from interacting agent dynamics and may have applications in a variety of systems including social insects and microbial communities.

Emergence of heterogeneity and political organization in information exchange networks.

PubMed

Guttenberg, Nicholas; Goldenfeld, Nigel

2010-04-01

We present a simple model of the emergence of the division of labor and the development of a system of resource subsidy from an agent-based model of directed resource production with variable degrees of trust between the agents. The model has three distinct phases corresponding to different forms of societal organization: disconnected (independent agents), homogeneous cooperative (collective state), and inhomogeneous cooperative (collective state with a leader). Our results indicate that such levels of organization arise generically as a collective effect from interacting agent dynamics and may have applications in a variety of systems including social insects and microbial communities.

Chemical Defects, Electronic Structure, and Transport in N-type and P-type Organic Semiconductors: First Principles Theory

DTIC Science & Technology

2012-11-29

of localized states extending into the gap. We also introduced a simple model allowing estimates of the upper limit of the intra-grain mobility in...well as to pentacene , and DATT. This research will be described below. In addition to our work on the electronic structure and charge mobility, we have...stacking distance gives rise to a tail of localized states which act as traps for electrons and holes. We introduced a simple effective Hamiltonian model

Calibration of the soil conditioning index (SCI) to soil organic carbon in the southeastern USA

USDA-ARS?s Scientific Manuscript database

Prediction of soil organic C sequestration with adoption of various conservation agricultural management approaches is needed to meet the emerging market for environmental services provided by agricultural land stewardship. The soil conditioning index (SCI) is a relatively simple model used by the ...

Simple, stable and reliable modeling of gas properties of organic working fluids in aerodynamic designs of turbomachinery for ORC and VCC

NASA Astrophysics Data System (ADS)

Kawakubo, T.

2016-05-01

A simple, stable and reliable modeling of the real gas nature of the working fluid is required for the aerodesigns of the turbine in the Organic Rankine Cycle and of the compressor in the Vapor Compression Cycle. Although many modern Computational Fluid Dynamics tools are capable of incorporating real gas models, simulations with such a gas model tend to be more time-consuming than those with a perfect gas model and even can be unstable due to the simulation near the saturation boundary. Thus a perfect gas approximation is still an attractive option to stably and swiftly conduct a design simulation. In this paper, an effective method of the CFD simulation with a perfect gas approximation is discussed. A method of representing the performance of the centrifugal compressor or the radial-inflow turbine by means of each set of non-dimensional performance parameters and translating the fictitious perfect gas result to the actual real gas performance is presented.

An Universal and Easy-to-Use Model for the Pressure of Arbitrary-Shape 3D Multifunctional Integumentary Cardiac Membranes.

PubMed

Su, Yewang; Liu, Zhuangjian; Xu, Lizhi

2016-04-20

Recently developed concepts for 3D, organ-mounted electronics for cardiac applications require a universal and easy-to-use mechanical model to calculate the average pressure associated with operation of the device, which is crucial for evaluation of design efficacy and optimization. This work proposes a simple, accurate, easy-to-use, and universal model to quantify the average pressure for arbitrary-shape organs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural Preferential Attachment: Network Organization beyond the Link

NASA Astrophysics Data System (ADS)

Hébert-Dufresne, Laurent; Allard, Antoine; Marceau, Vincent; Noël, Pierre-André; Dubé, Louis J.

2011-10-01

We introduce a mechanism which models the emergence of the universal properties of complex networks, such as scale independence, modularity and self-similarity, and unifies them under a scale-free organization beyond the link. This brings a new perspective on network organization where communities, instead of links, are the fundamental building blocks of complex systems. We show how our simple model can reproduce social and information networks by predicting their community structure and more importantly, how their nodes or communities are interconnected, often in a self-similar manner.

Drift mobility of photo-electrons in organic molecular crystals: Quantitative comparison between theory and experiment

NASA Astrophysics Data System (ADS)

Reineker, P.; Kenkre, V. M.; Kühne, R.

1981-08-01

A quantitative comparison of a simple theoretical prediction for the drift mobility of photo-electrons in organic molecular crystals, calculated within the model of the coupled band-like and hopping motion, with experiments in napthalene of Schein et al. and Karl et al. is given.

A detailed comparison of optimality and simplicity in perceptual decision-making

PubMed Central

Shen, Shan; Ma, Wei Ji

2017-01-01

Two prominent ideas in the study of decision-making have been that organisms behave near-optimally, and that they use simple heuristic rules. These principles might be operating in different types of tasks, but this possibility cannot be fully investigated without a direct, rigorous comparison within a single task. Such a comparison was lacking in most previous studies, because a) the optimal decision rule was simple; b) no simple suboptimal rules were considered; c) it was unclear what was optimal, or d) a simple rule could closely approximate the optimal rule. Here, we used a perceptual decision-making task in which the optimal decision rule is well-defined and complex, and makes qualitatively distinct predictions from many simple suboptimal rules. We find that all simple rules tested fail to describe human behavior, that the optimal rule accounts well for the data, and that several complex suboptimal rules are indistinguishable from the optimal one. Moreover, we found evidence that the optimal model is close to the true model: first, the better the trial-to-trial predictions of a suboptimal model agree with those of the optimal model, the better that suboptimal model fits; second, our estimate of the Kullback-Leibler divergence between the optimal model and the true model is not significantly different from zero. When observers receive no feedback, the optimal model still describes behavior best, suggesting that sensory uncertainty is implicitly represented and taken into account. Beyond the task and models studied here, our results have implications for best practices of model comparison. PMID:27177259

Role of demographic stochasticity in a speciation model with sexual reproduction

NASA Astrophysics Data System (ADS)

Lafuerza, Luis F.; McKane, Alan J.

2016-03-01

Recent theoretical studies have shown that demographic stochasticity can greatly increase the tendency of asexually reproducing phenotypically diverse organisms to spontaneously evolve into localized clusters, suggesting a simple mechanism for sympatric speciation. Here we study the role of demographic stochasticity in a model of competing organisms subject to assortative mating. We find that in models with sexual reproduction, noise can also lead to the formation of phenotypic clusters in parameter ranges where deterministic models would lead to a homogeneous distribution. In some cases, noise can have a sizable effect, rendering the deterministic modeling insufficient to understand the phenotypic distribution.

Intelligent traffic signals : extending the range of self-organization in the BML model.

DOT National Transportation Integrated Search

2013-04-01

The two-dimensional traffic model of Biham, Middleton and Levine (Phys. Rev. A, 1992) is : a simple cellular automaton that exhibits a wide range of complex behavior. It consists of both : northbound and eastbound cars traveling on a rectangular arra...

Overview of a simple model describing variation of dissolved organic carbon in an upland catchment

USGS Publications Warehouse

Boyer, Elizabeth W.; Hornberger, George M.; Bencala, Kenneth E.; McKnight, Diane M.

1996-01-01

Hydrological mechanisms controlling the variation of dissolved organic carbon (DOC) were investigated in the Deer Creek catchment located near Montezuma, CO. Patterns of DOC in streamflow suggested that increased flows through the upper soil horizon during snowmelt are responsible for flushing this DOC-enriched interstitial water to the streams. We examined possible hydrological mechanisms to explain the observed variability of DOC in Deer Creek by first simulating the hydrological response of the catchment using TOPMODEL and then routing the predicted flows through a simple model that accounted for temporal changes in DOC. Conceptually the DOC model can be taken to represent a terrestrial (soil) reservoir in which DOC builds up during low flow periods and is flushed out when infiltrating meltwaters cause the water table to rise into this “reservoir”. Concentrations of DOC measured in the upper soil and in streamflow were compared to model simulations. The simulated DOC response provides a reasonable reproduction of the observed dynamics of DOC in the stream at Deer Creek.

The initial establishment and epithelial morphogenesis of the esophagus: a new model of tracheal–esophageal separation and transition of simple columnar into stratified squamous epithelium in the developing esophagus

PubMed Central

Que, Jianwen

2016-01-01

The esophagus and trachea are tubular organs that initially share a single common lumen in the anterior foregut. Several models have been proposed to explain how this single-lumen developmental intermediate generates two tubular organs. However, new evidence suggests that these models are not comprehensive. I will first briefly review these models and then propose a novel ‘splitting and extension’ model based on our in vitro modeling of the foregut separation process. Signaling molecules (e.g., SHHs, WNTs, BMPs) and transcription factors (e.g., NKX2.1 and SOX2) are critical for the separation of the foregut. Intriguingly, some of these molecules continue to play essential roles during the transition of simple columnar into stratified squamous epithelium in the developing esophagus, and they are also closely involved in epithelial maintenance in the adults. Alterations in the levels of these molecules have been associated with the initiation and progression of several esophageal diseases and cancer in adults. PMID:25727889

Calibration of a simple and a complex model of global marine biogeochemistry

NASA Astrophysics Data System (ADS)

Kriest, Iris

2017-11-01

The assessment of the ocean biota's role in climate change is often carried out with global biogeochemical ocean models that contain many components and involve a high level of parametric uncertainty. Because many data that relate to tracers included in a model are only sparsely observed, assessment of model skill is often restricted to tracers that can be easily measured and assembled. Examination of the models' fit to climatologies of inorganic tracers, after the models have been spun up to steady state, is a common but computationally expensive procedure to assess model performance and reliability. Using new tools that have become available for global model assessment and calibration in steady state, this paper examines two different model types - a complex seven-component model (MOPS) and a very simple four-component model (RetroMOPS) - for their fit to dissolved quantities. Before comparing the models, a subset of their biogeochemical parameters has been optimised against annual-mean nutrients and oxygen. Both model types fit the observations almost equally well. The simple model contains only two nutrients: oxygen and dissolved organic phosphorus (DOP). Its misfit and large-scale tracer distributions are sensitive to the parameterisation of DOP production and decay. The spatio-temporal decoupling of nitrogen and oxygen, and processes involved in their uptake and release, renders oxygen and nitrate valuable tracers for model calibration. In addition, the non-conservative nature of these tracers (with respect to their upper boundary condition) introduces the global bias (fixed nitrogen and oxygen inventory) as a useful additional constraint on model parameters. Dissolved organic phosphorus at the surface behaves antagonistically to phosphate, and suggests that observations of this tracer - although difficult to measure - may be an important asset for model calibration.

FUNDAMENTAL MASS TRANSFER MODEL FOR INDOOR AIR EMISSIONS FROM SURFACE COATINGS

EPA Science Inventory

Emissions from freshly applied paints and other coatings can cause elevated indoor concentrations of vapor-phase organics. Methods are needed to determine the emission rates over time for these products. Some success has been achieved using simple first-order decay models to eval...

Concentration dependence of in vivo biotransformation rates of organic sunscreen agents in rainbow trout following a dietary exposure

EPA Science Inventory

Simple diffusion lipid-partitioning models have historically described the bioaccumulation of hydrophobic chemicals in fish. While these models are sufficient to describe the bioaccumulation of recalcitrant PCBs and other non-metabolized chemicals, they are inadequate for chemica...

Statistical Mechanics of the US Supreme Court

NASA Astrophysics Data System (ADS)

Lee, Edward D.; Broedersz, Chase P.; Bialek, William

2015-07-01

We build simple models for the distribution of voting patterns in a group, using the Supreme Court of the United States as an example. The maximum entropy model consistent with the observed pairwise correlations among justices' votes, an Ising spin glass, agrees quantitatively with the data. While all correlations (perhaps surprisingly) are positive, the effective pairwise interactions in the spin glass model have both signs, recovering the intuition that ideologically opposite justices negatively influence each another. Despite the competing interactions, a strong tendency toward unanimity emerges from the model, organizing the voting patterns in a relatively simple "energy landscape." Besides unanimity, other energy minima in this landscape, or maxima in probability, correspond to prototypical voting states, such as the ideological split or a tightly correlated, conservative core. The model correctly predicts the correlation of justices with the majority and gives us a measure of their influence on the majority decision. These results suggest that simple models, grounded in statistical physics, can capture essential features of collective decision making quantitatively, even in a complex political context.

A simple approach to estimate daily loads of total, refractory, and labile organic carbon from their seasonal loads in a watershed.

PubMed

Ouyang, Ying; Grace, Johnny M; Zipperer, Wayne C; Hatten, Jeff; Dewey, Janet

2018-05-22

Loads of naturally occurring total organic carbons (TOC), refractory organic carbon (ROC), and labile organic carbon (LOC) in streams control the availability of nutrients and the solubility and toxicity of contaminants and affect biological activities through absorption of light and complex metals with production of carcinogenic compounds. Although computer models have become increasingly popular in understanding and management of TOC, ROC, and LOC loads in streams, the usefulness of these models hinges on the availability of daily data for model calibration and validation. Unfortunately, these daily data are usually insufficient and/or unavailable for most watersheds due to a variety of reasons, such as budget and time constraints. A simple approach was developed here to calculate daily loads of TOC, ROC, and LOC in streams based on their seasonal loads. We concluded that the predictions from our approach adequately match field measurements based on statistical comparisons between model calculations and field measurements. Our approach demonstrates that an increase in stream discharge results in increased stream TOC, ROC, and LOC concentrations and loads, although high peak discharge did not necessarily result in high peaks of TOC, ROC, and LOC concentrations and loads. The approach developed herein is a useful tool to convert seasonal loads of TOC, ROC, and LOC into daily loads in the absence of measured daily load data.

Charge carrier coherence and Hall effect in organic semiconductors.

PubMed

Yi, H T; Gartstein, Y N; Podzorov, V

2016-03-30

Hall effect measurements are important for elucidating the fundamental charge transport mechanisms and intrinsic mobility in organic semiconductors. However, Hall effect studies frequently reveal an unconventional behavior that cannot be readily explained with the simple band-semiconductor Hall effect model. Here, we develop an analytical model of Hall effect in organic field-effect transistors in a regime of coexisting band and hopping carriers. The model, which is supported by the experiments, is based on a partial Hall voltage compensation effect, occurring because hopping carriers respond to the transverse Hall electric field and drift in the direction opposite to the Lorentz force acting on band carriers. We show that this can lead in particular to an underdeveloped Hall effect observed in organic semiconductors with substantial off-diagonal thermal disorder. Our model captures the main features of Hall effect in a variety of organic semiconductors and provides an analytical description of Hall mobility, carrier density and carrier coherence factor.

A Behavior-Based Circuit Model of How Outcome Expectations Organize Learned Behavior in Larval "Drosophila"

ERIC Educational Resources Information Center

Schleyer, Michael; Saumweber, Timo; Nahrendorf, Wiebke; Fischer, Benjamin; von Alpen, Desiree; Pauls, Dennis; Thum, Andreas; Gerber, Bertram

2011-01-01

Drosophila larvae combine a numerically simple brain, a correspondingly moderate behavioral complexity, and the availability of a rich toolbox for transgenic manipulation. This makes them attractive as a study case when trying to achieve a circuit-level understanding of behavior organization. From a series of behavioral experiments, we suggest a…

EFFECTS OF REVERSE OSMOSIS ISOLATION ON REACTIVITY OF NATURALLY OCCURRING DISSOLVED ORGANIC MATTER IN PHYSICOCHEMICAL PROCESSES. (R828045)

EPA Science Inventory

A field reverse osmosis system was used to isolate dissolved organic matter (DOM) from two lacustrine and two riverine surface water sources. The rejection of DOM was on the order of 99% and did not vary significantly with pressure. A simple mass balance model using a single m...

Development of a simple and low cost microbioreactor for high-throughput bioprocessing.

PubMed

Rahman, Pattanathu K S M; Pasirayi, Godfrey; Auger, Vincent; Ali, Zulfiqur

2009-02-01

A simple microbioreactor for high-throughput bioprocessing made from low cost polymer polytetrafluoroethylene (PTFE) tubes with a working volume of 1.5 ml is described. We have developed a microfluidic system that handles a small population of cells of a model microorganism, Pseudomonas aeruginosa DS10-129. Under the conditions of the microbioreactor, the organism produced extracellular secondary metabolites by using nutrient broth modified with glycerol. Pyocyanins were isolated from the fermented medium as a metabolite of interest. Antibiotic properties of pyocyanin were effective against a number of microorganisms such as Staphylococcus aureus, S. epidermis, Bacillus subtilis, Micrococcus luteus and Saccharomyces cerevisiae. Batch fermentation of the model organism in the microbioreactor was compared to shake-flask and conventional bench fermenter methods. Results obtained from the microbioreactor compared favourably with the conventional processes.

Simulation studies of self-organization of microtubules and molecular motors.

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

Jian, Z.; Karpeev, D.; Aranson, I. S.

We perform Monte Carlo type simulation studies of self-organization of microtubules interacting with molecular motors. We model microtubules as stiff polar rods of equal length exhibiting anisotropic diffusion in the plane. The molecular motors are implicitly introduced by specifying certain probabilistic collision rules resulting in realignment of the rods. This approximation of the complicated microtubule-motor interaction by a simple instant collision allows us to bypass the 'computational bottlenecks' associated with the details of the diffusion and the dynamics of motors and the reorientation of microtubules. Consequently, we are able to perform simulations of large ensembles of microtubules and motors onmore » a very large time scale. This simple model reproduces all important phenomenology observed in in vitro experiments: Formation of vortices for low motor density and raylike asters and bundles for higher motor density.« less

A novel and simple model of the uptake of organic chemicals by vegetation from air and soil.

PubMed

Hung, H; Mackay, D

1997-09-01

A novel and simple three-compartment fugacity model has been developed to predict the kinetics and equilibria of the uptake of organic chemicals in herbaceous agricultural plants at various times, including the time of harvest using only readily available input data. The chemical concentration in each of the three plant compartments leaf, stem which includes fruits and seeds, and root) is expressed as a function of both time and chemical concentrations in soil and air. The model was developed using the fugacity concept; however, the final expressions are presented in terms of concentrations in soil and air, equilibrium partition coefficients and a set of transport and transformation half-lives. An illustrative application of the model is presented which describes the uptake of bromacil by a soybean plant under hydroponic conditions. The model, which is believed to give acceptably accurate prediction of the distribution of chemicals among plant tissues, air and soil, may be used for the assessment of exposure to, and risk from contaminants consumed either directly from vegetation or indirectly in natural and agricultural food chains.

Laboratory and modeling studies of chemistry in dense molecular clouds

NASA Technical Reports Server (NTRS)

Huntress, W. T., Jr.; Prasad, S. S.; Mitchell, G. F.

1980-01-01

A chemical evolutionary model with a large number of species and a large chemical library is used to examine the principal chemical processes in interstellar clouds. Simple chemical equilibrium arguments show the potential for synthesis of very complex organic species by ion-molecule radiative association reactions.

Nature of solidification of nanoconfined organic liquid layers.

PubMed

Lang, X Y; Zhu, Y F; Jiang, Q

2007-01-30

A simple model is established for solidification of a nanoconfined liquid under nonequilibrium conditions. In terms of this model, the nature of solidification is the conjunct finite size and interface effects, which is directly related to the cooling rate or the relaxation time of the undercooled liquid. The model predictions are consistent with available experimental results.

Modelling the Active Hearing Process in Mosquitoes

NASA Astrophysics Data System (ADS)

Avitabile, Daniele; Homer, Martin; Jackson, Joe; Robert, Daniel; Champneys, Alan

2011-11-01

A simple microscopic mechanistic model is described of the active amplification within the Johnston's organ of the mosquito species Toxorhynchites brevipalpis. The model is based on the description of the antenna as a forced-damped oscillator coupled to a set of active threads (ensembles of scolopidia) that provide an impulsive force when they twitch. This twitching is in turn controlled by channels that are opened and closed if the antennal oscillation reaches a critical amplitude. The model matches both qualitatively and quantitatively with recent experiments. New results are presented using mathematical homogenization techniques to derive a mesoscopic model as a simple oscillator with nonlinear force and damping characteristics. It is shown how the results from this new model closely resemble those from the microscopic model as the number of threads approach physiologically correct values.

Self-organized criticality in sandpiles - Nature of the critical phenomenon. [dynamic models in phase transition

NASA Technical Reports Server (NTRS)

Carlson, J. M.; Chayes, J. T.; Swindle, G. H.; Grannan, E. R.

1990-01-01

The scaling behavior of sandpile models is investigated analytically. First, it is shown that sandpile models contain a set of domain walls, referred to as troughs, which bound regions that can experience avalanches. It is further shown that the dynamics of the troughs is governed by a simple set of rules involving birth, death, and coalescence events. A simple trough model is then introduced, and it is proved that the model has a phase transition with the density of the troughs as an order parameter and that, in the thermodynamic limit, the trough density goes to zero at the transition point. Finally, it is shown that the observed scaling behavior is a consequence of finite-size effects.

Discrete element modeling of microstructure of nacre

NASA Astrophysics Data System (ADS)

Chandler, Mei Qiang; Cheng, Jing-Ru C.

2018-04-01

The microstructure of nacre consists of polygon-shaped aragonite mineral tablets bonded by very thin layers of organic materials and is organized in a brick-mortar morphology. In this research, the discrete element method was utilized to model this structure. The aragonite mineral tablets were modeled with three-dimensional polygon particles generated by the Voronoi tessellation method to represent the Voronoi-like patterns of mineral tablets assembly observed in experiments. The organic matrix was modeled with a group of spring elements. The constitutive relations of the spring elements were inspired from the experimental results of organic molecules from the literature. The mineral bridges were modeled with simple elastic bonds with the parameters based on experimental data from the literature. The bulk stress-strain responses from the models agreed well with experimental results. The model results show that the mineral bridges play important roles in providing the stiffness and yield strength for the nacre, while the organic matrix in providing the ductility for the nacre. This work demonstrated the suitability of particle methods for modeling microstructures of nacre.

Bak-Sneppen model: Local equilibrium and critical value.

PubMed

Fraiman, Daniel

2018-04-01

The Bak-Sneppen (BS) model is a very simple model that exhibits all the richness of self-organized criticality theory. At the thermodynamic limit, the BS model converges to a situation where all particles have a fitness that is uniformly distributed between a critical value p_{c} and 1. The p_{c} value is unknown, as are the variables that influence and determine this value. Here we study the BS model in the case in which the lowest fitness particle interacts with an arbitrary even number of m nearest neighbors. We show that p_{c} verifies a simple local equilibrium relation. Based on this relation, we can determine bounds for p_{c} of the BS model and exact results for some BS-like models. Finally, we show how transformations of the original BS model can be done without altering the model's complex dynamics.

Bak-Sneppen model: Local equilibrium and critical value

NASA Astrophysics Data System (ADS)

Fraiman, Daniel

2018-04-01

The Bak-Sneppen (BS) model is a very simple model that exhibits all the richness of self-organized criticality theory. At the thermodynamic limit, the BS model converges to a situation where all particles have a fitness that is uniformly distributed between a critical value pc and 1. The pc value is unknown, as are the variables that influence and determine this value. Here we study the BS model in the case in which the lowest fitness particle interacts with an arbitrary even number of m nearest neighbors. We show that pc verifies a simple local equilibrium relation. Based on this relation, we can determine bounds for pc of the BS model and exact results for some BS-like models. Finally, we show how transformations of the original BS model can be done without altering the model's complex dynamics.

A simple model for deep tissue attenuation correction and large organ analysis of Cerenkov luminescence imaging

NASA Astrophysics Data System (ADS)

Habte, Frezghi; Natarajan, Arutselvan; Paik, David S.; Gambhir, Sanjiv S.

2014-03-01

Cerenkov luminescence imaging (CLI) is an emerging cost effective modality that uses conventional small animal optical imaging systems and clinically available radionuclide probes for light emission. CLI has shown good correlation with PET for organs of high uptake such as kidney, spleen, thymus and subcutaneous tumors in mouse models. However, CLI has limitations for deep tissue quantitative imaging since the blue-weighted spectral characteristics of Cerenkov radiation attenuates highly by mammalian tissue. Large organs such as the liver have also shown higher signal due to the contribution of emission of light from a greater thickness of tissue. In this study, we developed a simple model that estimates the effective tissue attenuation coefficient in order to correct the CLI signal intensity with a priori estimated depth and thickness of specific organs. We used several thin slices of ham to build a phantom with realistic attenuation. We placed radionuclide sources inside the phantom at different tissue depths and imaged it using an IVIS Spectrum (Perkin-Elmer, Waltham, MA, USA) and Inveon microPET (Preclinical Solutions Siemens, Knoxville, TN). We also performed CLI and PET of mouse models and applied the proposed attenuation model to correct CLI measurements. Using calibration factors obtained from phantom study that converts the corrected CLI measurements to %ID/g, we obtained an average difference of less that 10% for spleen and less than 35% for liver compared to conventional PET measurements. Hence, the proposed model has a capability of correcting the CLI signal to provide comparable measurements with PET data.

Production of organic compounds in plasmas: A comparison among electric sparks, laser-induced plasmas and UV light

NASA Technical Reports Server (NTRS)

Scattergood, T. W.; Mckay, C. P.; Borucki, W. J.; Giver, L. P.; Vanghyseghem, H.; Parris, J. E.; Miller, S. L.

1991-01-01

In order to study the production of organic compounds in plasmas (and shocks), various mixtures of N2, CH4, and H2, modeling the atmosphere of Titan, were exposed to discrete sparks, laser-induced plasmas (LIP) and ultraviolet light. The yields of HCN and simple hydrocarbons were measured and compared to those calculated from a simple quenched thermodynamic equilibrium model. The agreement between experiment and theory was fair for HCN and C2H2. However, the yields of C2H6 and other hydrocarbons were much higher than those predicted by the model. Our experiments suggest that photolysis by ultraviolet light from the plasma is an important process in the synthesis. This was confirmed by the photolysis of gas samples exposed to the light, but not to the plasma or shock waves. The results of these experiments demonstrate that, in addition to the well-known efficient synthesis of organic compounds in plasmas, the yields of saturated species, e.g., ethane, may be higher than predicted by theory and that LIP provide a convenient and clean way of simulating planetary lightning and impact plasmas in the laboratory.

The 'cube' meta-model for the information system of large health sector organizations--a (platform neutral) mapping tool to integrate information system development with changing business functions and organizational development.

PubMed

Balkányi, László

2002-01-01

To develop information systems (IS) in the changing environment of the health sector, a simple but throughout model, avoiding the techno-jargon of informatics, might be useful for the top management. A platform neutral, extensible, transparent conceptual model should be established. Limitations of current methods lead to a simple, but comprehensive mapping, in the form of a three-dimensional cube. The three 'orthogonal' views are (a) organization functionality, (b) organizational structures and (c) information technology. Each of the cube-sides is described according to its nature. This approach enables to define any kind of an IS component as a certain point/layer/domain of the cube and enables also the management to label all IS components independently form any supplier(s) and/or any specific platform. The model handles changes in organization structure, business functionality and the serving info-system independently form each other. Practical application extends to (a) planning complex, new ISs, (b) guiding development of multi-vendor, multi-site ISs, (c) supporting large-scale public procurement procedures and the contracting, implementation phase by establishing a platform neutral reference, (d) keeping an exhaustive inventory of an existing large-scale system, that handles non-tangible aspects of the IS.

The role of noise in self-organized decision making by the true slime mold Physarum polycephalum.

PubMed

Meyer, Bernd; Ansorge, Cedrick; Nakagaki, Toshiyuki

2017-01-01

Self-organized mechanisms are frequently encountered in nature and known to achieve flexible, adaptive control and decision-making. Noise plays a crucial role in such systems: It can enable a self-organized system to reliably adapt to short-term changes in the environment while maintaining a generally stable behavior. This is fundamental in biological systems because they must strike a delicate balance between stable and flexible behavior. In the present paper we analyse the role of noise in the decision-making of the true slime mold Physarum polycephalum, an important model species for the investigation of computational abilities in simple organisms. We propose a simple biological experiment to investigate the reaction of P. polycephalum to time-variant risk factors and present a stochastic extension of an established mathematical model for P. polycephalum to analyze this experiment. It predicts that-due to the mechanism of stochastic resonance-noise can enable P. polycephalum to correctly assess time-variant risk factors, while the corresponding noise-free system fails to do so. Beyond the study of P. polycephalum we demonstrate that the influence of noise on self-organized decision-making is not tied to a specific organism. Rather it is a general property of the underlying process dynamics, which appears to be universal across a wide range of systems. Our study thus provides further evidence that stochastic resonance is a fundamental component of the decision-making in self-organized macroscopic and microscopic groups and organisms.

The role of noise in self-organized decision making by the true slime mold Physarum polycephalum

PubMed Central

Ansorge, Cedrick; Nakagaki, Toshiyuki

2017-01-01

Self-organized mechanisms are frequently encountered in nature and known to achieve flexible, adaptive control and decision-making. Noise plays a crucial role in such systems: It can enable a self-organized system to reliably adapt to short-term changes in the environment while maintaining a generally stable behavior. This is fundamental in biological systems because they must strike a delicate balance between stable and flexible behavior. In the present paper we analyse the role of noise in the decision-making of the true slime mold Physarum polycephalum, an important model species for the investigation of computational abilities in simple organisms. We propose a simple biological experiment to investigate the reaction of P. polycephalum to time-variant risk factors and present a stochastic extension of an established mathematical model for P. polycephalum to analyze this experiment. It predicts that—due to the mechanism of stochastic resonance—noise can enable P. polycephalum to correctly assess time-variant risk factors, while the corresponding noise-free system fails to do so. Beyond the study of P. polycephalum we demonstrate that the influence of noise on self-organized decision-making is not tied to a specific organism. Rather it is a general property of the underlying process dynamics, which appears to be universal across a wide range of systems. Our study thus provides further evidence that stochastic resonance is a fundamental component of the decision-making in self-organized macroscopic and microscopic groups and organisms. PMID:28355213

Hands-On! Living in the Biosphere: Production, Pattern, Population, and Diversity. Developing Active Learning Module on the Human Dimensions of Global Change.

ERIC Educational Resources Information Center

Brown, Dwight

Biogeography examines questions of organism inventory and pattern, organisms' interactions with the environment, and the processes that create and change inventory, pattern, and interactions. This learning module uses time series maps and simple simulation models to illustrate how human actions alter biological productivity patterns at local and…

in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies

USDA-ARS?s Scientific Manuscript database

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding it...

Maintenance of algal endosymbionts in Paramecium bursaria: a simple model based on population dynamics.

PubMed

Iwai, Sosuke; Fujiwara, Kenji; Tamura, Takuro

2016-09-01

Algal endosymbiosis is widely distributed in eukaryotes including many protists and metazoans, and plays important roles in aquatic ecosystems, combining phagotrophy and phototrophy. To maintain a stable symbiotic relationship, endosymbiont population size in the host must be properly regulated and maintained at a constant level; however, the mechanisms underlying the maintenance of algal endosymbionts are still largely unknown. Here we investigate the population dynamics of the unicellular ciliate Paramecium bursaria and its Chlorella-like algal endosymbiont under various experimental conditions in a simple culture system. Our results suggest that endosymbiont population size in P. bursaria was not regulated by active processes such as cell division coupling between the two organisms, or partitioning of the endosymbionts at host cell division. Regardless, endosymbiont population size was eventually adjusted to a nearly constant level once cells were grown with light and nutrients. To explain this apparent regulation of population size, we propose a simple mechanism based on the different growth properties (specifically the nutrient requirements) of the two organisms, and based from this develop a mathematical model to describe the population dynamics of host and endosymbiont. The proposed mechanism and model may provide a basis for understanding the maintenance of algal endosymbionts. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Organ Dose-Rate Calculations for Small Mammals at Maralinga, the Nevada Test Site, Hanford and Fukushima: A Comparison of Ellipsoidal and Voxelized Dosimetric Methodologies.

PubMed

Caffrey, Emily A; Johansen, Mathew P; Higley, Kathryn A

2015-10-01

Radiological dosimetry for nonhuman biota typically relies on calculations that utilize the Monte Carlo simulations of simple, ellipsoidal geometries with internal radioactivity distributed homogeneously throughout. In this manner it is quick and easy to estimate whole-body dose rates to biota. Voxel models are detailed anatomical phantoms that were first used for calculating radiation dose to humans, which are now being extended to nonhuman biota dose calculations. However, if simple ellipsoidal models provide conservative dose-rate estimates, then the additional labor involved in creating voxel models may be unnecessary for most scenarios. Here we show that the ellipsoidal method provides conservative estimates of organ dose rates to small mammals. Organ dose rates were calculated for environmental source terms from Maralinga, the Nevada Test Site, Hanford and Fukushima using both the ellipsoidal and voxel techniques, and in all cases the ellipsoidal method yielded more conservative dose rates by factors of 1.2-1.4 for photons and 5.3 for beta particles. Dose rates for alpha-emitting radionuclides are identical for each method as full energy absorption in source tissue is assumed. The voxel procedure includes contributions to dose from organ-to-organ irradiation (shown here to comprise 2-50% of total dose from photons and 0-93% of total dose from beta particles) that is not specifically quantified in the ellipsoidal approach. Overall, the voxel models provide robust dosimetry for the nonhuman mammals considered in this study, and though the level of detail is likely extraneous to demonstrating regulatory compliance today, voxel models may nevertheless be advantageous in resolving ongoing questions regarding the effects of ionizing radiation on wildlife.

Computational principles underlying recognition of acoustic signals in grasshoppers and crickets.

PubMed

Ronacher, Bernhard; Hennig, R Matthias; Clemens, Jan

2015-01-01

Grasshoppers and crickets independently evolved hearing organs and acoustic communication. They differ considerably in the organization of their auditory pathways, and the complexity of their songs, which are essential for mate attraction. Recent approaches aimed at describing the behavioral preference functions of females in both taxa by a simple modeling framework. The basic structure of the model consists of three processing steps: (1) feature extraction with a bank of 'LN models'-each containing a linear filter followed by a nonlinearity, (2) temporal integration, and (3) linear combination. The specific properties of the filters and nonlinearities were determined using a genetic learning algorithm trained on a large set of different song features and the corresponding behavioral response scores. The model showed an excellent prediction of the behavioral responses to the tested songs. Most remarkably, in both taxa the genetic algorithm found Gabor-like functions as the optimal filter shapes. By slight modifications of Gabor filters several types of preference functions could be modeled, which are observed in different cricket species. Furthermore, this model was able to explain several so far enigmatic results in grasshoppers. The computational approach offered a remarkably simple framework that can account for phenotypically rather different preference functions across several taxa.

Incorporating User Input in Template-Based Segmentation

PubMed Central

Vidal, Camille; Beggs, Dale; Younes, Laurent; Jain, Sanjay K.; Jedynak, Bruno

2015-01-01

We present a simple and elegant method to incorporate user input in a template-based segmentation method for diseased organs. The user provides a partial segmentation of the organ of interest, which is used to guide the template towards its target. The user also highlights some elements of the background that should be excluded from the final segmentation. We derive by likelihood maximization a registration algorithm from a simple statistical image model in which the user labels are modeled as Bernoulli random variables. The resulting registration algorithm minimizes the sum of square differences between the binary template and the user labels, while preventing the template from shrinking, and penalizing for the inclusion of background elements into the final segmentation. We assess the performance of the proposed algorithm on synthetic images in which the amount of user annotation is controlled. We demonstrate our algorithm on the segmentation of the lungs of Mycobacterium tuberculosis infected mice from μCT images. PMID:26146532

Sensory perception and aging in model systems: from the outside in.

PubMed

Linford, Nancy J; Kuo, Tsung-Han; Chan, Tammy P; Pletcher, Scott D

2011-01-01

Sensory systems provide organisms from bacteria to humans with the ability to interact with the world. Numerous senses have evolved that allow animals to detect and decode cues from sources in both their external and internal environments. Recent advances in understanding the central mechanisms by which the brains of simple organisms evaluate different cues and initiate behavioral decisions, coupled with observations that sensory manipulations are capable of altering organismal lifespan, have opened the door for powerful new research into aging. Although direct links between sensory perception and aging have been established only recently, here we discuss these initial discoveries and evaluate the potential for different forms of sensory processing to modulate lifespan across taxa. Harnessing the neurobiology of simple model systems to study the biological impact of sensory experiences will yield insights into the broad influence of sensory perception in mammals and may help uncover new mechanisms of healthy aging.

Construction and Testing of an 80C86 Based Communications Controller for the Petite Amateur Navy Satellite (PANSAT)

DTIC Science & Technology

1990-12-01

S) Naval Postgraduate School 6a. NAME OF PERFORMING ORGANIZATION 6b OFFICE SYMBOL 7a NAME OF MONITORING ORGANIZATION (if applicable ) Code 33 6c...FUNDING/SPONSORING Bb. OFFICE SYMBOL 9. PROCUREMENT INSTRUMENT IDENTIFICATION NUMBER ORGANIZATION (If applicable ) 8c. ADDRESS (City, State, and ZIP Code...system’s individual components. Then one derives the overall system reliability from that information, using a simple mathematical model, to be

Magnetic gaps in organic tri-radicals: From a simple model to accurate estimates.

PubMed

Barone, Vincenzo; Cacelli, Ivo; Ferretti, Alessandro; Prampolini, Giacomo

2017-03-14

The calculation of the energy gap between the magnetic states of organic poly-radicals still represents a challenging playground for quantum chemistry, and high-level techniques are required to obtain accurate estimates. On these grounds, the aim of the present study is twofold. From the one side, it shows that, thanks to recent algorithmic and technical improvements, we are able to compute reliable quantum mechanical results for the systems of current fundamental and technological interest. From the other side, proper parameterization of a simple Hubbard Hamiltonian allows for a sound rationalization of magnetic gaps in terms of basic physical effects, unraveling the role played by electron delocalization, Coulomb repulsion, and effective exchange in tuning the magnetic character of the ground state. As case studies, we have chosen three prototypical organic tri-radicals, namely, 1,3,5-trimethylenebenzene, 1,3,5-tridehydrobenzene, and 1,2,3-tridehydrobenzene, which differ either for geometric or electronic structure. After discussing the differences among the three species and their consequences on the magnetic properties in terms of the simple model mentioned above, accurate and reliable values for the energy gap between the lowest quartet and doublet states are computed by means of the so-called difference dedicated configuration interaction (DDCI) technique, and the final results are discussed and compared to both available experimental and computational estimates.

Mechanochemical pattern formation in simple models of active viscoelastic fluids and solids

NASA Astrophysics Data System (ADS)

Alonso, Sergio; Radszuweit, Markus; Engel, Harald; Bär, Markus

2017-11-01

The cytoskeleton of the organism Physarum polycephalum is a prominent example of a complex active viscoelastic material wherein stresses induce flows along the organism as a result of the action of molecular motors and their regulation by calcium ions. Experiments in Physarum polycephalum have revealed a rich variety of mechanochemical patterns including standing, traveling and rotating waves that arise from instabilities of spatially homogeneous states without gradients in stresses and resulting flows. Herein, we investigate simple models where an active stress induced by molecular motors is coupled to a model describing the passive viscoelastic properties of the cellular material. Specifically, two models for viscoelastic fluids (Maxwell and Jeffrey model) and two models for viscoelastic solids (Kelvin-Voigt and Standard model) are investigated. Our focus is on the analysis of the conditions that cause destabilization of spatially homogeneous states and the related onset of mechano-chemical waves and patterns. We carry out linear stability analyses and numerical simulations in one spatial dimension for different models. In general, sufficiently strong activity leads to waves and patterns. The primary instability is stationary for all active fluids considered, whereas all active solids have an oscillatory primary instability. All instabilities found are of long-wavelength nature reflecting the conservation of the total calcium concentration in the models studied.

Emergent organization in a model market

NASA Astrophysics Data System (ADS)

Yadav, Avinash Chand; Manchanda, Kaustubh; Ramaswamy, Ramakrishna

2017-09-01

We study the collective behaviour of interacting agents in a simple model of market economics that was originally introduced by Nørrelykke and Bak. A general theoretical framework for interacting traders on an arbitrary network is presented, with the interaction consisting of buying (namely consumption) and selling (namely production) of commodities. Extremal dynamics is introduced by having the agent with least profit in the market readjust prices, causing the market to self-organize. In addition to examining this model market on regular lattices in two-dimensions, we also study the cases of random complex networks both with and without community structures. Fluctuations in an activity signal exhibit properties that are characteristic of avalanches observed in models of self-organized criticality, and these can be described by power-law distributions when the system is in the critical state.

Soil property effects on wind erosion of organic soils

NASA Astrophysics Data System (ADS)

Zobeck, Ted M.; Baddock, Matthew; Scott Van Pelt, R.; Tatarko, John; Acosta-Martinez, Veronica

2013-09-01

Histosols (also known as organic soils, mucks, or peats) are soils that are dominated by organic matter (OM > 20%) in half or more of the upper 80 cm. Forty two states have a total of 21 million ha of Histosols in the United States. These soils, when intensively cropped, are subject to wind erosion resulting in loss of crop productivity and degradation of soil, air, and water quality. Estimating wind erosion on Histosols has been determined by USDA-Natural Resources Conservation Service (NRCS) as a critical need for the Wind Erosion Prediction System (WEPS) model. WEPS has been developed to simulate wind erosion on agricultural land in the US, including soils with organic soil material surfaces. However, additional field measurements are needed to understand how soil properties vary among organic soils and to calibrate and validate estimates of wind erosion of organic soils using WEPS. Soil properties and sediment flux were measured in six soils with high organic contents located in Michigan and Florida, USA. Soil properties observed included organic matter content, particle density, dry mechanical stability, dry clod stability, wind erodible material, and geometric mean diameter of the surface aggregate distribution. A field portable wind tunnel was used to generate suspended sediment and dust from agricultural surfaces for soils ranging from 17% to 67% organic matter. The soils were tilled and rolled to provide a consolidated, friable surface. Dust emissions and saltation were measured using an isokinetic vertical slot sampler aspirated by a regulated suction source. Suspended dust was sampled using a Grimm optical particle size analyzer. Particle density of the saltation-sized material (>106 μm) was inversely related to OM content and varied from 2.41 g cm-3 for the soil with the lowest OM content to 1.61 g cm-3 for the soil with highest OM content. Wind erodible material and the geometric mean diameter of the surface soil were inversely related to dry clod stability. The effect of soil properties on sediment flux varied among flux types. Saltation flux was adequately predicted with simple linear regression models. Dry mechanical stability was the best single soil property linearly related to saltation flux. Simple linear models with soil properties as independent variables were not well correlated with PM10E values (mass flux). A second order polynomial equation with OM as the independent variable was found to be most highly correlated with PM10E values. These results demonstrate that variations in sediment and dust emissions can be linked to soil properties using simple models based on one or more soil properties to estimate saltation mass flux and PM10E values from organic and organic-rich soils.

There Is No Simple Model of the Plasma Membrane Organization

PubMed Central

Bernardino de la Serna, Jorge; Schütz, Gerhard J.; Eggeling, Christian; Cebecauer, Marek

2016-01-01

Ever since technologies enabled the characterization of eukaryotic plasma membranes, heterogeneities in the distributions of its constituents were observed. Over the years this led to the proposal of various models describing the plasma membrane organization such as lipid shells, picket-and-fences, lipid rafts, or protein islands, as addressed in numerous publications and reviews. Instead of emphasizing on one model we in this review give a brief overview over current models and highlight how current experimental work in one or the other way do not support the existence of a single overarching model. Instead, we highlight the vast variety of membrane properties and components, their influences and impacts. We believe that highlighting such controversial discoveries will stimulate unbiased research on plasma membrane organization and functionality, leading to a better understanding of this essential cellular structure. PMID:27747212

There Is No Simple Model of the Plasma Membrane Organization.

PubMed

Bernardino de la Serna, Jorge; Schütz, Gerhard J; Eggeling, Christian; Cebecauer, Marek

2016-01-01

Ever since technologies enabled the characterization of eukaryotic plasma membranes, heterogeneities in the distributions of its constituents were observed. Over the years this led to the proposal of various models describing the plasma membrane organization such as lipid shells, picket-and-fences, lipid rafts, or protein islands, as addressed in numerous publications and reviews. Instead of emphasizing on one model we in this review give a brief overview over current models and highlight how current experimental work in one or the other way do not support the existence of a single overarching model. Instead, we highlight the vast variety of membrane properties and components, their influences and impacts. We believe that highlighting such controversial discoveries will stimulate unbiased research on plasma membrane organization and functionality, leading to a better understanding of this essential cellular structure.

Protein Folding and Self-Organized Criticality

NASA Astrophysics Data System (ADS)

Bajracharya, Arun; Murray, Joelle

Proteins are known to fold into tertiary structures that determine their functionality in living organisms. However, the complex dynamics of protein folding and the way they consistently fold into the same structures is not fully understood. Self-organized criticality (SOC) has provided a framework for understanding complex systems in various systems (earthquakes, forest fires, financial markets, and epidemics) through scale invariance and the associated power law behavior. In this research, we use a simple hydrophobic-polar lattice-bound computational model to investigate self-organized criticality as a possible mechanism for generating complexity in protein folding.

Model systems for the study of kidney development: use of the pronephros in the analysis of organ induction and patterning.

PubMed

Vize, P D; Seufert, D W; Carroll, T J; Wallingford, J B

1997-08-15

Most vertebrate organs, once formed, continue to perform the function for which they were generated until the death of the organism. The kidney is a notable exception to this rule. Vertebrates, even those that do not undergo metamorphosis, utilize a progression of more complex kidneys as they grow and develop. This is presumably due to the changing conditions to which the organism must respond to retain what Homer Smith referred to as our physiological freedom. To quote, "Recognizing that we have the kind of blood we have because we have the kind of kidneys we have, we must acknowledge that our kidneys constitute the major foundation of our physiological freedom. Only because they work the way they do has it become possible for us to have bones, muscles, glands, and brains. Superficially, it might be said that the function of the kidneys is to make urine; but in a more considered view one can say that the kidneys make the stuff of philosophy itself" ("From Fish to Philosopher," Little, Brown and Co., Boston, 1953). Different kidneys are used to make the stuff of philosophy at different stages of development depending on the age and needs of the organism, rather than the usual approach of simply making embryonic organs larger as the animal grows. Although evolution has provided the higher vertebrates with complex adult kidneys, they continue to utilize simple kidneys in embryogenesis. In lower vertebrates with simple adult kidneys, even more simple versions are used during early developmental stages. In this review the anatomy, development, and gene expression patterns of the embryonic kidney, the pronephros, will be described and compared to the more complex kidney forms. Despite some differences in anatomy, similar developmental pathways seem to be responsible for the induction and the response to induction in both evanescent and permanent kidney forms. Gene expression patterns can, therefore, be added to the morphological and functional data indicating that all forms of the kidney are closely related structures. Given the similarities between the development of simple and complex kidneys, the embryonic kidneys may be an ideal model system in which to investigate the genesis of multicomponent organ systems.

A micromechanical model to explain the mechanical properties of bovine cortical bone in tension: In vitro fluoride ion effects

NASA Astrophysics Data System (ADS)

Kotha, Shiva Prasad

Bone mineral and bone organic are assumed to be a linearly elastic, brittle material. A simple micromechanical model based on the shear lag theory is developed to model the stress transfer between the mineral platelets of bone. The bone mineral platelets carry most of the applied load while the organic primarily serves to transfer load between the overlapped mineral platelets by shear. Experiments were done to elucidate the mechanism of failure in bovine cortical bone and to decrease the mineral content of control bone with in-vitro fluoride ion treatments. It was suggested that the failure at the ultrastructural level is due to the transverse failure of bonds between the collagen microfibrils in the organic matrix. However, the shear stress transfer and the axial load bearing capacity of the organic is not impaired. Hence, it is assumed that the shear strain in the matrix increases while the shear stress remains constant at the shear yield stress once the matrix starts yielding at the ends of the bone mineral. When the shear stress over the length of the mineral platelet reaches the shear yield stress, no more applied stress is carried by the bone mineral platelets while the organic matrix carries the increased axial load. The bone fails when the axial stress in the organic reaches its ultimate stress. The bone mineral is assumed to dissolve due to in-vitro fluoride ion treatments and precipitate calcium fluoride or fluoroapatite like material. The amount of dissolution is estimated based on 19F Nuclear Magnetic Resonance or a decrease in the carbonate content of bone. The dissolution of bone mineral is assumed to increase the porosity in the organic. We assume that the elastic modulus and the ultimate strength of the organic decrease due to the increased porosity. A simple empirical model is used to model the decrease in the elastic modulus. The strength is modeled to decrease based on an increase in the cross-sectional area occupied by the porosity. The precipitate is assumed to contribute to the mechanical properties of bone due to friction generated by the poisson's contraction of the organic as it carries axial loads. The resulting stress-strain curve predicted by the model resembles the stress-strain curves obtained in the experiments.

Statistics of certain models of evolution

NASA Astrophysics Data System (ADS)

Standish, Russell K.

1999-02-01

In a recent paper, Newman [J. Theo. Bio. 189, 235 (1997)] surveys the literature on power law spectra in evolution, self-organized criticality and presents a model of his own to arrive at a conclusion that self-organized criticality is not necessary for evolution. Not only did he miss a key model (Ecolab) that has a clear self-organized critical mechanism, but also Newman's model exhibits the same mechanism that gives rise to power law behavior, as does Ecolab. Newman's model is, in fact, a ``mean field'' approximation of a self-organized critical system. In this paper, I have also implemented Newman's model using the Ecolab software, removing the restriction that the number of species must remain constant. It turns out that the requirement of constant species number is nontrivial, leading to a global coupling between species that is similar in effect to the species interactions seen in Ecolab. In fact, the model must self-organize to a state where the long time average of speciations balances that of the extinctions; otherwise, the system either collapses or explodes. In view of this, Newman's model does not provide the hoped-for counterexample to the presence of self-organized criticality in evolution, but does provide a simple, almost analytic model that can be used to understand more intricate models such as Ecolab.

Charge carrier coherence and Hall effect in organic semiconductors

DOE PAGES

Yi, H. T.; Gartstein, Y. N.; Podzorov, V.

2016-03-30

Hall effect measurements are important for elucidating the fundamental charge transport mechanisms and intrinsic mobility in organic semiconductors. However, Hall effect studies frequently reveal an unconventional behavior that cannot be readily explained with the simple band-semiconductor Hall effect model. Here, we develop an analytical model of Hall effect in organic field-effect transistors in a regime of coexisting band and hopping carriers. The model, which is supported by the experiments, is based on a partial Hall voltage compensation effect, occurring because hopping carriers respond to the transverse Hall electric field and drift in the direction opposite to the Lorentz force actingmore » on band carriers. We show that this can lead in particular to an underdeveloped Hall effect observed in organic semiconductors with substantial off-diagonal thermal disorder. Lastly, our model captures the main features of Hall effect in a variety of organic semiconductors and provides an analytical description of Hall mobility, carrier density and carrier coherence factor.« less

Charge carrier coherence and Hall effect in organic semiconductors

PubMed Central

Yi, H. T.; Gartstein, Y. N.; Podzorov, V.

2016-01-01

Hall effect measurements are important for elucidating the fundamental charge transport mechanisms and intrinsic mobility in organic semiconductors. However, Hall effect studies frequently reveal an unconventional behavior that cannot be readily explained with the simple band-semiconductor Hall effect model. Here, we develop an analytical model of Hall effect in organic field-effect transistors in a regime of coexisting band and hopping carriers. The model, which is supported by the experiments, is based on a partial Hall voltage compensation effect, occurring because hopping carriers respond to the transverse Hall electric field and drift in the direction opposite to the Lorentz force acting on band carriers. We show that this can lead in particular to an underdeveloped Hall effect observed in organic semiconductors with substantial off-diagonal thermal disorder. Our model captures the main features of Hall effect in a variety of organic semiconductors and provides an analytical description of Hall mobility, carrier density and carrier coherence factor. PMID:27025354

Development of Maps of Simple and Complex Cells in the Primary Visual Cortex

PubMed Central

Antolík, Ján; Bednar, James A.

2011-01-01

Hubel and Wiesel (1962) classified primary visual cortex (V1) neurons as either simple, with responses modulated by the spatial phase of a sine grating, or complex, i.e., largely phase invariant. Much progress has been made in understanding how simple-cells develop, and there are now detailed computational models establishing how they can form topographic maps ordered by orientation preference. There are also models of how complex cells can develop using outputs from simple cells with different phase preferences, but no model of how a topographic orientation map of complex cells could be formed based on the actual connectivity patterns found in V1. Addressing this question is important, because the majority of existing developmental models of simple-cell maps group neurons selective to similar spatial phases together, which is contrary to experimental evidence, and makes it difficult to construct complex cells. Overcoming this limitation is not trivial, because mechanisms responsible for map development drive receptive fields (RF) of nearby neurons to be highly correlated, while co-oriented RFs of opposite phases are anti-correlated. In this work, we model V1 as two topographically organized sheets representing cortical layer 4 and 2/3. Only layer 4 receives direct thalamic input. Both sheets are connected with narrow feed-forward and feedback connectivity. Only layer 2/3 contains strong long-range lateral connectivity, in line with current anatomical findings. Initially all weights in the model are random, and each is modified via a Hebbian learning rule. The model develops smooth, matching, orientation preference maps in both sheets. Layer 4 units become simple cells, with phase preference arranged randomly, while those in layer 2/3 are primarily complex cells. To our knowledge this model is the first explaining how simple cells can develop with random phase preference, and how maps of complex cells can develop, using only realistic patterns of connectivity. PMID:21559067

Exploring the patterns and evolution of self-organized urban street networks through modeling

NASA Astrophysics Data System (ADS)

Rui, Yikang; Ban, Yifang; Wang, Jiechen; Haas, Jan

2013-03-01

As one of the most important subsystems in cities, urban street networks have recently been well studied by using the approach of complex networks. This paper proposes a growing model for self-organized urban street networks. The model involves a competition among new centers with different values of attraction radius and a local optimal principle of both geometrical and topological factors. We find that with the model growth, the local optimization in the connection process and appropriate probability for the loop construction well reflect the evolution strategy in real-world cities. Moreover, different values of attraction radius in centers competition process lead to morphological change in patterns including urban network, polycentric and monocentric structures. The model succeeds in reproducing a large diversity of road network patterns by varying parameters. The similarity between the properties of our model and empirical results implies that a simple universal growth mechanism exists in self-organized cities.

Controlled recovery of phylogenetic communities from an evolutionary model using a network approach

NASA Astrophysics Data System (ADS)

Sousa, Arthur M. Y. R.; Vieira, André P.; Prado, Carmen P. C.; Andrade, Roberto F. S.

2016-04-01

This works reports the use of a complex network approach to produce a phylogenetic classification tree of a simple evolutionary model. This approach has already been used to treat proteomic data of actual extant organisms, but an investigation of its reliability to retrieve a traceable evolutionary history is missing. The used evolutionary model includes key ingredients for the emergence of groups of related organisms by differentiation through random mutations and population growth, but purposefully omits other realistic ingredients that are not strictly necessary to originate an evolutionary history. This choice causes the model to depend only on a small set of parameters, controlling the mutation probability and the population of different species. Our results indicate that for a set of parameter values, the phylogenetic classification produced by the used framework reproduces the actual evolutionary history with a very high average degree of accuracy. This includes parameter values where the species originated by the evolutionary dynamics have modular structures. In the more general context of community identification in complex networks, our model offers a simple setting for evaluating the effects, on the efficiency of community formation and identification, of the underlying dynamics generating the network itself.

Is organic matter alone sufficient to predict isoproturon sorption in calcareous soils?

PubMed

El Arfaoui, Achouak; Sayen, Stéphanie; Paris, Michaël; Keziou, Amor; Couderchet, Michel; Guillon, Emmanuel

2012-08-15

Eleven soils collected from Champagne-Ardenne area (France) were used to investigate isoproturon sorption in laboratory conditions. Our results identified the organic matter (OM) and the ratio of calcite content to OM content (Rt) as the main two parameters governing isoproturon retention in soils. While organic matter favored pesticide sorption, calcite had an antagonistic effect since it limited isoproturon retention. The Rt ratio of calcite content to organic matter content in soils appeared to be a parameter that should be considered in predictive models in addition to OM in regions presenting calcareous soils. Adsorption of isoproturon as a function of Rt and OM was successfully described through a simple empirical model. Copyright © 2012 Elsevier B.V. All rights reserved.

Towards a representation of priming on soil carbon decomposition in the global land biosphere model ORCHIDEE (version 1.9.5.2)

NASA Astrophysics Data System (ADS)

Guenet, Bertrand; Esteban Moyano, Fernando; Peylin, Philippe; Ciais, Philippe; Janssens, Ivan A.

2016-03-01

Priming of soil carbon decomposition encompasses different processes through which the decomposition of native (already present) soil organic matter is amplified through the addition of new organic matter, with new inputs typically being more labile than the native soil organic matter. Evidence for priming comes from laboratory and field experiments, but to date there is no estimate of its impact at global scale and under the current anthropogenic perturbation of the carbon cycle. Current soil carbon decomposition models do not include priming mechanisms, thereby introducing uncertainty when extrapolating short-term local observations to ecosystem and regional to global scale. In this study we present a simple conceptual model of decomposition priming, called PRIM, able to reproduce laboratory (incubation) and field (litter manipulation) priming experiments. Parameters for this model were first optimized against data from 20 soil incubation experiments using a Bayesian framework. The optimized parameter values were evaluated against another set of soil incubation data independent from the ones used for calibration and the PRIM model reproduced the soil incubations data better than the original, CENTURY-type soil decomposition model, whose decomposition equations are based only on first-order kinetics. We then compared the PRIM model and the standard first-order decay model incorporated into the global land biosphere model ORCHIDEE (Organising Carbon and Hydrology In Dynamic Ecosystems). A test of both models was performed at ecosystem scale using litter manipulation experiments from five sites. Although both versions were equally able to reproduce observed decay rates of litter, only ORCHIDEE-PRIM could simulate the observed priming (R2 = 0.54) in cases where litter was added or removed. This result suggests that a conceptually simple and numerically tractable representation of priming adapted to global models is able to capture the sign and magnitude of the priming of litter and soil organic matter.

Towards a representation of priming on soil carbon decomposition in the global land biosphere model ORCHIDEE (version 1.9.5.2)

NASA Astrophysics Data System (ADS)

Guenet, B.; Moyano, F. E.; Peylin, P.; Ciais, P.; Janssens, I. A.

2015-10-01

Priming of soil carbon decomposition encompasses different processes through which the decomposition of native (already present) soil organic matter is amplified through the addition of new organic matter, with new inputs typically being more labile than the native soil organic matter. Evidence for priming comes from laboratory and field experiments, but to date there is no estimate of its impact at global scale and under the current anthropogenic perturbation of the carbon cycle. Current soil carbon decomposition models do not include priming mechanisms, thereby introducing uncertainty when extrapolating short-term local observations to ecosystem and regional to global scale. In this study we present a simple conceptual model of decomposition priming, called PRIM, able to reproduce laboratory (incubation) and field (litter manipulation) priming experiments. Parameters for this model were first optimized against data from 20 soil incubation experiments using a Bayesian framework. The optimized parameter values were evaluated against another set of soil incubation data independent from the ones used for calibration and the PRIM model reproduced the soil incubations data better than the original, CENTURY-type soil decomposition model, whose decomposition equations are based only on first order kinetics. We then compared the PRIM model and the standard first order decay model incorporated into the global land biosphere model ORCHIDEE. A test of both models was performed at ecosystem scale using litter manipulation experiments from 5 sites. Although both versions were equally able to reproduce observed decay rates of litter, only ORCHIDEE-PRIM could simulate the observed priming (R2 = 0.54) in cases where litter was added or removed. This result suggests that a conceptually simple and numerically tractable representation of priming adapted to global models is able to capture the sign and magnitude of the priming of litter and soil organic matter.

Continuum Model for River Networks

NASA Astrophysics Data System (ADS)

Giacometti, Achille; Maritan, Amos; Banavar, Jayanth R.

1995-07-01

The effects of erosion, avalanching, and random precipitation are captured in a simple stochastic partial differential equation for modeling the evolution of river networks. Our model leads to a self-organized structured landscape and to abstraction and piracy of the smaller tributaries as the evolution proceeds. An algebraic distribution of the average basin areas and a power law relationship between the drainage basin area and the river length are found.

Incorporating redox processes improves prediction of carbon and nutrient cycling and greenhouse gas emission

NASA Astrophysics Data System (ADS)

Tang, Guoping; Zheng, Jianqiu; Yang, Ziming; Graham, David; Gu, Baohua; Mayes, Melanie; Painter, Scott; Thornton, Peter

2016-04-01

Among the coupled thermal, hydrological, geochemical, and biological processes, redox processes play major roles in carbon and nutrient cycling and greenhouse gas (GHG) emission. Increasingly, mechanistic representation of redox processes is acknowledged as necessary for accurate prediction of GHG emission in the assessment of land-atmosphere interactions. Simple organic substrates, Fe reduction, microbial reactions, and the Windermere Humic Aqueous Model (WHAM) were added to a reaction network used in the land component of an Earth system model. In conjunction with this amended reaction network, various temperature response functions used in ecosystem models were assessed for their ability to describe experimental observations from incubation tests with arctic soils. Incorporation of Fe reduction reactions improves the prediction of the lag time between CO2 and CH4 accumulation. The inclusion of the WHAM model enables us to approximately simulate the initial pH drop due to organic acid accumulation and then a pH increase due to Fe reduction without parameter adjustment. The CLM4.0, CENTURY, and Ratkowsky temperature response functions better described the observations than the Q10 method, Arrhenius equation, and ROTH-C. As electron acceptors between O2 and CO2 (e.g., Fe(III), SO42-) are often involved, our results support inclusion of these redox reactions for accurate prediction of CH4 production and consumption. Ongoing work includes improving the parameterization of organic matter decomposition to produce simple organic substrates, examining the influence of redox potential on methanogenesis under thermodynamically favorable conditions, and refining temperature response representation near the freezing point by additional model-experiment iterations. We will use the model to describe observed GHG emission at arctic and tropical sites.

On the improbability of intelligent extraterrestrials

NASA Astrophysics Data System (ADS)

Bond, A.

1982-05-01

Discussions relating to the prevalence of extraterrestrial life generally remain ambiguous due to the lack of a suitable model for the development of biology. In this paper a simple model is proposed based on neutral evolution theory which leads to quantitative values for the genome growth rate within a biosphere. It is hypothesised that the genome size is a measure of organism complexity and hence an indicator of the likelihood of intelligence. The calculations suggest that organisms with the complexity of human beings may be rare and only occur with a probability below once per galaxy.

Helping Students Assess the Relative Importance of Different Intermolecular Interactions

ERIC Educational Resources Information Center

Jasien, Paul G.

2008-01-01

A semi-quantitative model has been developed to estimate the relative effects of dispersion, dipole-dipole interactions, and H-bonding on the normal boiling points ("T[subscript b]") for a subset of simple organic systems. The model is based upon a statistical analysis using multiple linear regression on a series of straight-chain organic…

Biomat development in soil treatment units for on-site wastewater treatment.

PubMed

Winstanley, H F; Fowler, A C

2013-10-01

We provide a simple mathematical model of the bioremediation of contaminated wastewater leaching into the subsoil below a septic tank percolation system. The model comprises a description of the percolation system's flows, together with equations describing the growth of biomass and the uptake of an organic contaminant concentration. By first rendering the model dimensionless, it can be partially solved, to provide simple insights into the processes which control the efficacy of the system. In particular, we provide quantitative insight into the effect of a near surface biomat on subsoil permeability; this can lead to trench ponding, and thus propagation of effluent further down the trench. Using the computed vadose zone flow field, the model can be simply extended to include reactive transport of other contaminants of interest.

Simple extrapolation method to predict the electronic structure of conjugated polymers from calculations on oligomers

DOE PAGES

Larsen, Ross E.

2016-04-12

In this study, we introduce two simple tight-binding models, which we call fragment frontier orbital extrapolations (FFOE), to extrapolate important electronic properties to the polymer limit using electronic structure calculations on only a few small oligomers. In particular, we demonstrate by comparison to explicit density functional theory calculations that for long oligomers the energies of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and of the first electronic excited state are accurately described as a function of number of repeat units by a simple effective Hamiltonian parameterized from electronic structure calculations on monomers, dimers and, optionally,more » tetramers. For the alternating copolymer materials that currently comprise some of the most efficient polymer organic photovoltaic devices one can use these simple but rigorous models to extrapolate computed properties to the polymer limit based on calculations on a small number of low-molecular-weight oligomers.« less

Meta-analysis of pesticide sorption in subsoils

NASA Astrophysics Data System (ADS)

Jarvis, Nicholas

2017-04-01

It has been known for several decades that sorption koc values tend to be larger in soils that are low in organic carbon (i.e. subsoils). Nevertheless, in a regulatory context, the models used to assess leaching of pesticides to groundwater still rely on a constant koc value, which is usually measured on topsoil samples. This is mainly because the general applicability of any improved model approach that is also simple enough to use for regulatory purposes has not been demonstrated. The objective of this study was therefore first to summarize and generalize available literature data in order to assess the magnitude of any systematic increase of koc values in subsoil and to test an alternative model of subsoil sorption that could be useful in pesticide risk assessment and management. To this end, a database containing the results of batch sorption experiments for pesticides was compiled from published studies in the literature, which placed at least as much emphasis on measurements in subsoil horizons as in topsoil. The database includes 967 data entries from 46 studies and for 34 different active substances (15 non-ionic compounds, 13 weak acids, 6 weak bases). In order to minimize pH effects on sorption, data for weak acids and bases were only included if the soil pH was more than two units larger than the compound pKa. A simple empirical model, whereby the sorption constant is given as a power law function of the soil organic carbon content, gave good fits to most data sets. Overall, the apparent koc value, koc(app), for non-ionic compounds and weak bases roughly doubled as the soil organic carbon content decreased by a factor of ten. The typical increase in koc(app) was even larger for weak acids: on average koc(app) increased by a factor of six as soil organic carbon content decreased by a factor of ten. These results suggest the koc concept currently used in leaching models should be replaced by an alternative approach that gives a more realistic representation of pesticide sorption in subsoil. The model tested in this study appears to be widely applicable and simple enough to parameterize for risk assessment purposes. However, more data on subsoil sorption should first be included in the analysis to enable reliable estimation of worst-case percentile values of the power law exponent in the model.

Modeling human diseases with induced pluripotent stem cells: from 2D to 3D and beyond.

PubMed

Liu, Chun; Oikonomopoulos, Angelos; Sayed, Nazish; Wu, Joseph C

2018-03-08

The advent of human induced pluripotent stem cells (iPSCs) presents unprecedented opportunities to model human diseases. Differentiated cells derived from iPSCs in two-dimensional (2D) monolayers have proven to be a relatively simple tool for exploring disease pathogenesis and underlying mechanisms. In this Spotlight article, we discuss the progress and limitations of the current 2D iPSC disease-modeling platform, as well as recent advancements in the development of human iPSC models that mimic in vivo tissues and organs at the three-dimensional (3D) level. Recent bioengineering approaches have begun to combine different 3D organoid types into a single '4D multi-organ system'. We summarize the advantages of this approach and speculate on the future role of 4D multi-organ systems in human disease modeling. © 2018. Published by The Company of Biologists Ltd.

Characteristics of aperiodic sequence of slip events caused by interaction between seismic patches and that caused be self-organized stress heterogeneity

NASA Astrophysics Data System (ADS)

Kato, N.

2017-12-01

Numerical simulations of earthquake cycles are conducted to investigate the origin of complexity of earthquake recurrence. There are two main causes of the complexity. One is self-organized stress heterogeneity due to dynamical effect. The other is the effect of interaction between some fault patches. In the model, friction on the fault is assumed to obey a rate- and state-dependent friction law. Circular patches of velocity-weakening frictional property are assumed on the fault. On the remaining areas of the fault, velocity-strengthening friction is assumed. We consider three models: Single patch model, two-patch model, and three-patch model. In the first model, the dynamical effect is mainly examined. The latter two models take into consideration the effect of interaction as well as the dynamical effect. Complex multiperiodic or aperiodic sequences of slip events occur when slip behavior changes from the seismic to aseismic, and when the degree of interaction between seismic patches is intermediate. The former is observed in all the models, and the latter is observed in the two-patch model and the three-patch model. Evolution of spatial distribution of shear stress on the fault suggests that aperiodicity at the transition from seismic to aseismic slip is caused by self-organized stress heterogeneity. The iteration maps of recurrence intervals of slip events in aperiodic sequences are examined, and they are approximately expressed by simple curves for aperiodicity at the transition from seismic to aseismic slip. In contrast, the iteration maps for aperiodic sequences caused by interaction between seismic patches are scattered and they are not expressed by simple curves. This result suggests that complex sequences caused by different mechanisms may be distinguished.

Cell motility in cancer invasion and metastasis: insights from simple model organisms.

PubMed

Stuelten, Christina H; Parent, Carole A; Montell, Denise J

2018-05-01

Metastasis remains the greatest challenge in the clinical management of cancer. Cell motility is a fundamental and ancient cellular behaviour that contributes to metastasis and is conserved in simple organisms. In this Review, we evaluate insights relevant to human cancer that are derived from the study of cell motility in non-mammalian model organisms. Dictyostelium discoideum, Caenorhabditis elegans, Drosophila melanogaster and Danio rerio permit direct observation of cells moving in complex native environments and lend themselves to large-scale genetic and pharmacological screening. We highlight insights derived from each of these organisms, including the detailed signalling network that governs chemotaxis towards chemokines; a novel mechanism of basement membrane invasion; the positive role of E-cadherin in collective direction-sensing; the identification and optimization of kinase inhibitors for metastatic thyroid cancer on the basis of work in flies; and the value of zebrafish for live imaging, especially of vascular remodelling and interactions between tumour cells and host tissues. While the motility of tumour cells and certain host cells promotes metastatic spread, the motility of tumour-reactive T cells likely increases their antitumour effects. Therefore, it is important to elucidate the mechanisms underlying all types of cell motility, with the ultimate goal of identifying combination therapies that will increase the motility of beneficial cells and block the spread of harmful cells.

Proposal for a screening test to evaluate the fate of organic micropollutants in activated sludge.

PubMed

Salvetti, Roberta; Vismara, Renato; Dal Ben, Ilaria; Gorla, Elena; Romele, Laura

2011-04-01

The concentrations of organic micropollutants are usually low in wastewaters (order of magnitude of mg L(-1)). However, their emission standards, especially in the case of carcinogenic and bioaccumulating substances, are often much lower (order of magnitude of microg L(-1)). Since these substances, in some cases, can be adsorbable or volatile, their removal via volatilization, biodegradation or sludge adsorption in a wastewater treatment plant (WWTP) becomes a significant feature to include in the usual design process, in order to verify the emission standards in gas and sludge too. In this study a simple screening batch test for the evaluation of the fate of organic micropollutants in water, air and sludge is presented. The test is set up by means of simple laboratory instruments and simulates an activated sludge tank process. In this study the results obtained for four substances with different chemical properties (i.e. toluene, benz(a)anthracene, phenol and benzene) are presented. The screening test proposed can be a useful tool to assess in about one month the fate of organic micropollutants in an activated sludge tank of a WWTP. Moreover, the test can constitute a useful support in the use of mathematical models, since it allows the verification of model results and the calibration of the reactions involved in the removal process.

An interfacial mechanism for cloud droplet formation on organic aerosols

DOE PAGES

Ruehl, C. R.; Davies, J. F.; Wilson, K. R.

2016-03-25

Accurate predictions of aerosol/cloud interactions require simple, physically accurate parameterizations of the cloud condensation nuclei (CCN) activity of aerosols. Current models assume that organic aerosol species contribute to CCN activity by lowering water activity. We measured droplet diameters at the point of CCN activation for particles composed of dicarboxylic acids or secondary organic aerosol and ammonium sulfate. Droplet activation diameters were 40 to 60% larger than predicted if the organic was assumed to be dissolved within the bulk droplet, suggesting that a new mechanism is needed to explain cloud droplet formation. A compressed film model explains how surface tension depressionmore » by interfacial organic molecules can alter the relationship between water vapor supersaturation and droplet size (i.e., the Köhler curve), leading to the larger diameters observed at activation.« less

An interfacial mechanism for cloud droplet formation on organic aerosols

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

Ruehl, C. R.; Davies, J. F.; Wilson, K. R.

Accurate predictions of aerosol/cloud interactions require simple, physically accurate parameterizations of the cloud condensation nuclei (CCN) activity of aerosols. Current models assume that organic aerosol species contribute to CCN activity by lowering water activity. We measured droplet diameters at the point of CCN activation for particles composed of dicarboxylic acids or secondary organic aerosol and ammonium sulfate. Droplet activation diameters were 40 to 60% larger than predicted if the organic was assumed to be dissolved within the bulk droplet, suggesting that a new mechanism is needed to explain cloud droplet formation. A compressed film model explains how surface tension depressionmore » by interfacial organic molecules can alter the relationship between water vapor supersaturation and droplet size (i.e., the Köhler curve), leading to the larger diameters observed at activation.« less

An interfacial mechanism for cloud droplet formation on organic aerosols.

PubMed

Ruehl, Christopher R; Davies, James F; Wilson, Kevin R

2016-03-25

Accurate predictions of aerosol/cloud interactions require simple, physically accurate parameterizations of the cloud condensation nuclei (CCN) activity of aerosols. Current models assume that organic aerosol species contribute to CCN activity by lowering water activity. We measured droplet diameters at the point of CCN activation for particles composed of dicarboxylic acids or secondary organic aerosol and ammonium sulfate. Droplet activation diameters were 40 to 60% larger than predicted if the organic was assumed to be dissolved within the bulk droplet, suggesting that a new mechanism is needed to explain cloud droplet formation. A compressed film model explains how surface tension depression by interfacial organic molecules can alter the relationship between water vapor supersaturation and droplet size (i.e., the Köhler curve), leading to the larger diameters observed at activation. Copyright © 2016, American Association for the Advancement of Science.

Is cooperation viable in mobile organisms? Simple Walk Away rule favors the evolution of cooperation in groups

PubMed Central

Aktipis, C. Athena

2011-01-01

The evolution of cooperation through partner choice mechanisms is often thought to involve relatively complex cognitive abilities. Using agent-based simulations I model a simple partner choice rule, the ‘Walk Away’ rule, where individuals stay in groups that provide higher returns (by virtue of having more cooperators), and ‘Walk Away’ from groups providing low returns. Implementing this conditional movement rule in a public goods game leads to a number of interesting findings: 1) cooperators have a selective advantage when thresholds are high, corresponding to low tolerance for defectors, 2) high thresholds lead to high initial rates of movement and low final rates of movement (after selection), and 3) as cooperation is selected, the population undergoes a spatial transition from high migration (and a many small and ephemeral groups) to low migration (and large and stable groups). These results suggest that the very simple ‘Walk Away’ rule of leaving uncooperative groups can favor the evolution of cooperation, and that cooperation can evolve in populations in which individuals are able to move in response to local social conditions. A diverse array of organisms are able to leave degraded physical or social environments. The ubiquitous nature of conditional movement suggests that ‘Walk Away’ dynamics may play an important role in the evolution of social behavior in both cognitively complex and cognitively simple organisms. PMID:21666771

Monolayer organic field effect phototransistors: photophysical characterization and modeling

NASA Astrophysics Data System (ADS)

Trukhanov, Vasily A.; Anisimov, Daniil S.; Bruevich, Vladimir V.; Agina, Elena V.; Borshchev, Oleg V.; Ponomarenko, Sergei; Zhang, Jiangbin; Bakulin, Artem A.; Paraschuk, Dmitri Yu.

2016-09-01

Organic field-effect transistors (OFET) can combine photodetection and light amplification and, for example, work as phototransistors. Such organic phototransistors can be used in light-controlled switches and amplifiers, detection circuits, and sensors of ultrasensitive images. In this work, we present photophysical characterization of well-defined ultrathin organic field-effect devices with a semiconductive channel based on Langmuir-Blodgett monolayer film. We observe clear generation of photocurrent under illumination with a modulated laser at 405 nm. The increase of photocurrent with the optical modulation frequency indicates the presence of defect states serving as traps for photogenerated carriers and/or the saturation of charge concentration in the thin active layer. We also propose a simple one-dimensional numerical model of a photosensitive OFET. The model is based on the Poisson, current continuity and drift-diffusion equations allows future evaluation of the photocurrent generation mechanism in the studied systems.

Agent based model of effects of task allocation strategies in flat organizations

NASA Astrophysics Data System (ADS)

Sobkowicz, Pawel

2016-09-01

A common practice in many organizations is to pile the work on the best performers. It is easy to implement by the management and, despite the apparent injustice, appears to be working in many situations. In our work we present a simple agent based model, constructed to simulate this practice and to analyze conditions under which the overall efficiency of the organization (for example measured by the backlog of unresolved issues) breaks down, due to the cumulative effect of the individual overloads. The model confirms that the strategy mentioned above is, indeed, rational: it leads to better global results than an alternative one, using equal workload distribution among all workers. The presented analyses focus on the behavior of the organizations close to the limit of the maximum total throughput and provide results for the growth of the unprocessed backlog in several situations, as well as suggestions related to avoiding such buildup.

On being the right size: scaling effects in designing a human-on-a-chip

PubMed Central

Moraes, Christopher; Labuz, Joseph M.; Leung, Brendan M.; Inoue, Mayumi; Chun, Tae-Hwa; Takayama, Shuichi

2013-01-01

Developing a human-on-a-chip by connecting multiple model organ systems would provide an intermediate screen for therapeutic efficacy and toxic side effects of drugs prior to conducting expensive clinical trials. However, correctly designing individual organs and scaling them relative to each other to make a functional microscale human analog is challenging, and a generalized approach has yet to be identified. In this work, we demonstrate the importance of rational design of both the individual organ and its relationship with other organs, using a simple two-compartment system simulating insulin-dependent glucose uptake in adipose tissues. We demonstrate that inter-organ scaling laws depend on both the number of cells, and on the spatial arrangement of those cells within the microfabricated construct. We then propose a simple and novel inter-organ ‘metabolically-supported functional scaling’ approach predicated on maintaining in vivo cellular basal metabolic rates, by limiting resources available to cells on the chip. This approach leverages findings from allometric scaling models in mammals that limited resources in vivo prompts cells to behave differently than in resource-rich in vitro cultures. Although applying scaling laws directly to tissues can result in systems that would be quite challenging to implement, engineering workarounds may be used to circumvent these scaling issues. Specific workarounds discussed include the limited oxygen carrying capacity of cell culture media when used as a blood substitute and the ability to engineer non-physiological structures to augment organ function, to create the transport-accessible, yet resource-limited environment necessary for cells to mimic in vivo functionality. Furthermore, designing the structure of individual tissues in each organ compartment may be a useful strategy to bypass scaling concerns at the inter-organ level. PMID:23925524

An Inexpensive 2-D and 3-D Model of the Sarcomere as a Teaching Aid

ERIC Educational Resources Information Center

Rios, Vitor Passos; Bonfim, Vanessa Maria Gomes

2013-01-01

To address a common problem of teaching the sliding filament theory (that is, students have difficulty in visualizing how the component proteins of the sarcomere differ, how they organize themselves into a single working unit, and how they function in relation to each other), we have devised a simple model, with inexpensive materials, to be built…

Cellular Gauge Symmetry and the Li Organization Principle: A Mathematical Addendum. Quantifying energetic dynamics in physical and biological systems through a simple geometric tool and geodetic curves.

PubMed

Yurkin, Alexander; Tozzi, Arturo; Peters, James F; Marijuán, Pedro C

2017-12-01

The present Addendum complements the accompanying paper "Cellular Gauge Symmetry and the Li Organization Principle"; it illustrates a recently-developed geometrical physical model able to assess electronic movements and energetic paths in atomic shells. The model describes a multi-level system of circular, wavy and zigzag paths which can be projected onto a horizontal tape. This model ushers in a visual interpretation of the distribution of atomic electrons' energy levels and the corresponding quantum numbers through rather simple tools, such as compasses, rulers and straightforward calculations. Here we show how this geometrical model, with the due corrections, among them the use of geodetic curves, might be able to describe and quantify the structure and the temporal development of countless physical and biological systems, from Langevin equations for random paths, to symmetry breaks occurring ubiquitously in physical and biological phenomena, to the relationships among different frequencies of EEG electric spikes. Therefore, in our work we explore the possible association of binomial distribution and geodetic curves configuring a uniform approach for the research of natural phenomena, in biology, medicine or the neurosciences. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characteristics of pattern formation and evolution in approximations of Physarum transport networks.

PubMed

Jones, Jeff

2010-01-01

Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation.

Statistical Mechanics of US Supreme Court

NASA Astrophysics Data System (ADS)

Lee, Edward; Broedersz, Chase; Bialek, William; Biophysics Theory Group Team

2014-03-01

We build simple models for the distribution of voting patterns in a group, using the Supreme Court of the United States as an example. The least structured, or maximum entropy, model that is consistent with the observed pairwise correlations among justices' votes is equivalent to an Ising spin glass. While all correlations (perhaps surprisingly) are positive, the effective pairwise interactions in the spin glass model have both signs, recovering some of our intuition that justices on opposite sides of the ideological spectrum should have a negative influence on one another. Despite the competing interactions, a strong tendency toward unanimity emerges from the model, and this agrees quantitatively with the data. The model shows that voting patterns are organized in a relatively simple ``energy landscape,'' correctly predicts the extent to which each justice is correlated with the majority, and gives us a measure of the influence that justices exert on one another. These results suggest that simple models, grounded in statistical physics, can capture essential features of collective decision making quantitatively, even in a complex political context. Funded by National Science Foundation Grants PHY-0957573 and CCF-0939370, WM Keck Foundation, Lewis-Sigler Fellowship, Burroughs Wellcome Fund, and Winston Foundation.

Collective chemotaxis and segregation of active bacterial colonies

NASA Astrophysics Data System (ADS)

Amar, M. Ben

2016-02-01

Still recently, bacterial fluid suspensions have motivated a lot of works, both experimental and theoretical, with the objective to understand their collective dynamics from universal and simple rules. Since some species are active, most of these works concern the strong interactions that these bacteria exert on a forced flow leading to instabilities, chaos and turbulence. Here, we investigate the self-organization of expanding bacterial colonies under chemotaxis, proliferation and eventually active-reaction. We propose a simple model to understand and quantify the physical properties of these living organisms which either give cohesion or on the contrary dispersion to the colony. Taking into account the diffusion and capture of morphogens complicates the model since it induces a bacterial density gradient coupled to bacterial density fluctuations and dynamics. Nevertheless under some specific conditions, it is possible to investigate the pattern formation as a usual viscous fingering instability. This explains the similarity and differences of patterns according to the physical bacterial suspension properties and explain the factors which favor compactness or branching.

Electrochemistry of Simple Organometallic Models of Iron-Iron Hydrogenases in Organic Solvent and Water.

PubMed

Gloaguen, Frederic

2016-01-19

Synthetic models of the active site of iron-iron hydrogenases are currently the subjects of numerous studies aimed at developing H2-production catalysts based on cheap and abundant materials. In this context, the present report offers an electrochemist's view of the catalysis of proton reduction by simple binuclear iron(I) thiolate complexes. Although these complexes probably do not follow a biocatalytic pathway, we analyze and discuss the interplay between the reduction potential and basicity and how these antagonist properties impact the mechanisms of proton-coupled electron transfer to the metal centers. This question is central to any consideration of the activity at the molecular level of hydrogenases and related enzymes. In a second part, special attention is paid to iron thiolate complexes holding rigid and unsaturated bridging ligands. The complexes that enjoy mild reduction potentials and stabilized reduced forms are promising iron-based catalysts for the photodriven evolution of H2 in organic solvents and, more importantly, in water.

Omics Data Complementarity Underlines Functional Cross-Communication in Yeast.

PubMed

Malod-Dognin, Noël; Pržulj, Nataša

2017-06-10

Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational intractability of finding the exact answer. We perform a simple integration of three types of baker's yeast omics data to elucidate the functional organization and lines of cross-functional communication. We examine protein-protein interaction (PPI), co-expression (COEX) and genetic interaction (GI) data, and explore their relationship with the gold standard of functional organization, the Gene Ontology (GO). We utilize a simple framework that identifies functional cross-communication lines in each of the three data types, in GO, and collectively in the integrated model of the three omics data types; we present each of them in our new Functional Organization Map (FOM) model. We compare the FOMs of the three omics datasets with the FOM of GO and find that GI is in best agreement with GO, followed COEX and PPI. We integrate the three FOMs into a unified FOM and find that it is in better agreement with the FOM of GO than those of any omics dataset alone, demonstrating functional complementarity of different omics data.

Fluorescence correlation spectroscopy diffusion laws to probe the submicron cell membrane organization.

PubMed

Wawrezinieck, Laure; Rigneault, Hervé; Marguet, Didier; Lenne, Pierre-François

2005-12-01

To probe the complexity of the cell membrane organization and dynamics, it is important to obtain simple physical observables from experiments on live cells. Here we show that fluorescence correlation spectroscopy (FCS) measurements at different spatial scales enable distinguishing between different submicron confinement models. By plotting the diffusion time versus the transverse area of the confocal volume, we introduce the so-called FCS diffusion law, which is the key concept throughout this article. First, we report experimental FCS diffusion laws for two membrane constituents, which are respectively a putative raft marker and a cytoskeleton-hindered transmembrane protein. We find that these two constituents exhibit very distinct behaviors. To understand these results, we propose different models, which account for the diffusion of molecules either in a membrane comprising isolated microdomains or in a meshwork. By simulating FCS experiments for these two types of organization, we obtain FCS diffusion laws in agreement with our experimental observations. We also demonstrate that simple observables derived from these FCS diffusion laws are strongly related to confinement parameters such as the partition of molecules in microdomains and the average confinement time of molecules in a microdomain or a single mesh of a meshwork.

Origin of Complexity in Multicellular Organisms

NASA Astrophysics Data System (ADS)

Furusawa, Chikara; Kaneko, Kunihiko

2000-06-01

Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems can exhibit complex pattern formation with spontaneous cell differentiation. Such systems employ a ``cooperative'' use of resources and maintain a larger growth speed than simple cell systems, which exist in a homogeneous state and behave ``selfishly.'' The relevance of the diversity of chemicals and reaction dynamics to the growth of a multicellular organism is demonstrated. Chaotic biochemical dynamics are found to provide the multipotency of stem cells.

Extended probit mortality model for zooplankton against transient change of PCO(2).

PubMed

Sato, Toru; Watanabe, Yuji; Toyota, Koji; Ishizaka, Joji

2005-09-01

The direct injection of CO(2) in the deep ocean is a promising way to mitigate global warming. One of the uncertainties in this method, however, is its impact on marine organisms in the near field. Since the concentration of CO(2), which organisms experience in the ocean, changes with time, it is required to develop a biological impact model for the organisms against the unsteady change of CO(2) concentration. In general, the LC(50) concept is widely applied for testing a toxic agent for the acute mortality. Here, we regard the probit-transformed mortality as a linear function not only of the concentration of CO(2) but also of exposure time. A simple mathematical transform of the function gives a damage-accumulation mortality model for zooplankton. In this article, this model was validated by the mortality test of Metamphiascopsis hirsutus against the transient change of CO(2) concentration.

Poverty trap formed by the ecology of infectious diseases

PubMed Central

Bonds, Matthew H.; Keenan, Donald C.; Rohani, Pejman; Sachs, Jeffrey D.

2010-01-01

While most of the world has enjoyed exponential economic growth, more than one-sixth of the world is today roughly as poor as their ancestors were many generations ago. Widely accepted general explanations for the persistence of such poverty have been elusive and are needed by the international development community. Building on a well-established model of human infectious diseases, we show how formally integrating simple economic and disease ecology models can naturally give rise to poverty traps, where initial economic and epidemiological conditions determine the long-term trajectory of the health and economic development of a society. This poverty trap may therefore be broken by improving health conditions of the population. More generally, we demonstrate that simple human ecological models can help explain broad patterns of modern economic organization. PMID:20007179

Dual chamber stent prevents organ malperfusion in a model of donation after cardiac death.

PubMed

Tillman, Bryan W; Chun, Youngjae; Cho, Sung Kwon; Chen, Yanfei; Liang, Nathan; Maul, Timothy; Demetris, Anthony; Gu, Xinzhu; Wagner, William R; Tevar, Amit D

2016-10-01

The paradigm for donation after cardiac death subjects donor organs to ischemic injury. A dual-chamber organ perfusion stent would maintain organ perfusion without affecting natural cardiac death. A center lumen allows uninterrupted cardiac blood flow, while an external chamber delivers oxygenated blood to the visceral vessels. A prototype organ perfusion stent was constructed from commercial stents. In a porcine model, the organ perfusion stent was deployed, followed by a simulated agonal period. Oxygenated blood perfused the external stent chamber. Organ perfusion was compared between controls (n = 3) and organ perfusion stent (n = 6). Finally, a custom, nitinol, dual chamber organ perfusion stent was fabricated using a retrievable "petal and stem" design. Endovascular organ perfusion stent deployment achieved visceral isolation without adverse impact on cardiac parameters. Visceral oxygen delivery was 4.8-fold greater compared with controls. During the agonal period, organs in organ perfusion stent-treated animals appeared well perfused in contrast with the malperfused controls. A custom nitinol and polyurethane organ perfusion stent was recaptured easily with simple sheath advancement. An organ perfusion stent maintained organ perfusion during the agonal phase in a porcine model of donation after cardiac death organ donation without adversely affecting cardiac function. Ultimately, the custom retrievable design of this study may help resolve the critical shortage of donor organs for transplant. Copyright © 2016 Elsevier Inc. All rights reserved.

Modeling the Free Carrier Recombination Kinetics in PTB7:PCBM Organic Photovoltaics

DOE PAGES

Oosterhout, Stefan D.; Ferguson, Andrew J.; Larson, Bryon W.; ...

2016-10-03

Currently the exact recombination mechanism of free carriers in organic photovoltaic (OPV) devices is poorly understood. Often a reduced Langevin model is used to describe the decay behavior of electrons and holes. Here we propose a novel, simple kinetic model that accurately describes the decay behavior of free carriers in the PTB7:PCBM organic photovoltaic blend. In order to accurately describe the recombination behavior of free carriers as measured by time-resolved microwave conductivity (TRMC), this model needs to only take into account free and trapped holes in the polymer, and free electrons in the fullerene. The model is consistent for differentmore » PTB7:PCBM blend ratios and spans a light intensity range of over 3 orders of magnitude. Furthermore, the model demonstrates that dark carriers exist in the polymer and interact with photoinduced charge carriers, and that the trapping and detrapping rates of the holes are of high importance to the overall carrier lifetime.« less

The heliocentric evolution of cometary infrared spectra - Results from an organic grain model

NASA Technical Reports Server (NTRS)

Chyba, Christopher F.; Sagan, Carl; Mumma, Michael J.

1989-01-01

An emission feature peaking near 3.4 microns that is typical of C-H stretching in hydrocarbons and which fits a simple, two-component thermal emission model for dust in the cometary coma, has been noted in observations of Comets Halley and Wilson. A noteworthy consequence of this modeling is that, at about 1 AU, emission features at wavelengths longer than 3.4 microns come to be 'diluted' by continuum emission. A quantitative development of the model shows it to agree with observational data for Comet Halley for certain, plausible values of the optical constants; the observed heliocentric evolution of the 3.4-micron feature thereby furnishes information on the composition of the comet's organic grains.

RELATIONSHIPS BETWEEEN NITROGEN LOADING AND CONCENTRATIONS OF NITROGEN AND CHLOROPHYLL IN COASTAL EMBAYMENTS

EPA Science Inventory

We describe results obtained with a simple model that uses loading rates of total nitrogen (TN), defined as dissolved inorganic nitrogen plus dissolved and particulate organic nitrogen, to calculate annually and spatially averaged concentrations of TN in coastal embayments. We al...

The significance of organ prolapse in gastroschisis.

PubMed

Koehler, Shannon M; Szabo, Aniko; Loichinger, Matt; Peterson, Erika; Christensen, Melissa; Wagner, Amy J

2017-12-01

The aim of this study was to evaluate the incidence and importance of organ prolapse (stomach, bladder, reproductive organs) in gastroschisis. This is a retrospective review of gastroschisis patients from 2000 to 2014 at a single tertiary institution. Statistical analysis was performed using a chi-square test, Student's t test, log-rank test, or Cox regression analysis models. All tests were conducted as two-tailed tests, and p-values <0.05 were considered statistically significant. One hundred seventy-one gastroschisis patients were identified. Sixty-nine (40.6%) had at least one prolapsed organ besides bowel. The most commonly prolapsed organs were stomach (n=45, 26.3%), reproductive organs (n=34, 19.9%), and bladder (n=15, 8.8%). Patients with prolapsed organs were more likely to have simple gastroschisis with significant decreases in the rate of atresia and necrosis/perforation. They progressed to earlier enteral feeds, discontinuation of parenteral nutrition, and discharge. Likewise, these patients were less likely to have complications such as central line infections, sepsis, and short gut syndrome. Gastroschisis is typically described as isolated bowel herniation, but a large portion have prolapse of other organs. Prolapsed organs are associated with simple gastroschisis, and improved outcomes most likely due to a larger fascial defect. This may be useful for prenatal and postnatal counseling of families. Case Control/Retrospective Comparative Study. Level III. Copyright © 2017 Elsevier Inc. All rights reserved.

Prediction of peak shape in hydro-organic and micellar-organic liquid chromatography as a function of mobile phase composition.

PubMed

Baeza-Baeza, J J; Ruiz-Angel, M J; García-Alvarez-Coque, M C

2007-09-07

A simple model is proposed that relates the parameters describing the peak width with the retention time, which can be easily predicted as a function of mobile phase composition. This allows the further prediction of peak shape with global errors below 5%, using a modified Gaussian model with a parabolic variance. The model is useful in the optimisation of chromatographic resolution to assess an eventual overlapping of close peaks. The dependence of peak shape with mobile phase composition was studied for mobile phases containing acetonitrile in the presence and absence of micellised surfactant (micellar-organic and hydro-organic reversed-phase liquid chromatography, RPLC). In micellar RPLC, both modifiers (surfactant and acetonitrile) were observed to decrease or improve the efficiencies in the same percentage, at least in the studied concentration ranges. The study also revealed that the problem of achieving smaller efficiencies in this chromatographic mode, compared to hydro-organic RPLC, is not only related to the presence of surfactant covering the stationary phase, but also to the smaller concentration of organic solvent in the mobile phase.

Self-organized huddles of rat pups modeled by simple rules of individual behavior.

PubMed

Schank, J C; Alberts, J R

1997-11-07

Starting at infancy and continuing throughout adult life, huddling is a major component of the behavioral repertoire of Norway rats (Rattus norvegicus). Huddling behavior maintains the cohesion of litters throughout early life, and in adulthood, it remains a consistent feature of social behavior of R. norvegicus. During infancy, rats have severely limited sensorimotor capabilities, and yet they are capable of aggregating and display a form of group regulatory behavior that conserves metabolic effort and augments body temperature regulation. The functions of huddling are generally understood as group adaptations, which are beyond the capabilities of the individual infant rat. We show, however, that huddling as aggregative or cohesive behavior can emerge as a self-organizing process from autonomous individuals following simple sensorimotor rules. In our model, two sets of sensorimotor parameters characterize the topotaxic responses and the dynamics of contact in 7-day-old rats. The first set of parameters are conditional probabilities of activity and inactivity given prior activity or inactivity and the second set are preferences for objects in the infant rat's environment. We found that the behavior of the model and of actual rat pups compare very favorably, demonstrating that the aggregative feature of huddling can emerge from the local sensorimotor interactions of individuals, and that complex group regulatory behaviors in infant rats may also emerge from self-organizing processes. We discuss the model and the underlying approach as a paradigm for investigating the dynamics of social interactions, group behavior, and developmental change.

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

Seinfeld, John H.

This project addressed the following research need in the Atmospheric System Research (ASR) Science and Program Plan: "Measurements downwind of urban sources of aerosol particles and precursor gases have shown that the mass concentration of secondary organic aerosol (SOA) can be several-fold greater than can be explained on the basis of current model calculations using observed precursor concentrations. ASR will continue conducting laboratory experiments on both gas-phase and aqueous-phase SOA formation to characterize the particle formation and the organic gases that react to form new organic aerosol material on aerosol seeds. ASR will use these experiments to guide the developmentmore » of comprehensive chemical mechanisms... to guide the development of parameterizations that are simple enough to be applied to aerosol life cycle models."« less

Chemistry of decomposition of freshwater wetland sedimentary organic material during ramped pyrolysis

NASA Astrophysics Data System (ADS)

Williams, E. K.; Rosenheim, B. E.

2011-12-01

Ramped pyrolysis methodology, such as that used in the programmed-temperature pyrolysis/combustion system (PTP/CS), improves radiocarbon analysis of geologic materials devoid of authigenic carbonate compounds and with low concentrations of extractable authochthonous organic molecules. The approach has improved sediment chronology in organic-rich sediments proximal to Antarctic ice shelves (Rosenheim et al., 2008) and constrained the carbon sequestration potential of suspended sediments in the lower Mississippi River (Roe et al., in review). Although ramped pyrolysis allows for separation of sedimentary organic material based upon relative reactivity, chemical information (i.e. chemical composition of pyrolysis products) is lost during the in-line combustion of pyrolysis products. A first order approximation of ramped pyrolysis/combustion system CO2 evolution, employing a simple Gaussian decomposition routine, has been useful (Rosenheim et al., 2008), but improvements may be possible. First, without prior compound-specific extractions, the molecular composition of sedimentary organic matter is unknown and/or unidentifiable. Second, even if determined as constituents of sedimentary organic material, many organic compounds have unknown or variable decomposition temperatures. Third, mixtures of organic compounds may result in significant chemistry within the pyrolysis reactor, prior to introduction of oxygen along the flow path. Gaussian decomposition of the reaction rate may be too simple to fully explain the combination of these factors. To relate both the radiocarbon age over different temperature intervals and the pyrolysis reaction thermograph (temperature (°C) vs. CO2 evolved (μmol)) obtained from PTP/CS to chemical composition of sedimentary organic material, we present a modeling framework developed based upon the ramped pyrolysis decomposition of simple mixtures of organic compounds (i.e. cellulose, lignin, plant fatty acids, etc.) often found in sedimentary organic material to account for changes in thermograph shape. The decompositions will be compositionally verified by 13C NMR analysis of pyrolysis residues from interrupted reactions. This will allow for constraint of decomposition temperatures of individual compounds as well as chemical reactions between volatilized moieties in mixtures of these compounds. We will apply this framework with 13C NMR analysis of interrupted pyrolysis residues and radiocarbon data from PTP/CS analysis of sedimentary organic material from a freshwater marsh wetland in Barataria Bay, Louisiana. We expect to characterize the bulk chemical composition during pyrolysis and as well as diagenetic changes with depth. Most importantly, we expect to constrain the potential and the limitations of this modeling framework for application to other depositional environments.

The emergence of extracellular matrix mechanics and cell traction forces as important regulators of cellular self-organization.

PubMed

Checa, Sara; Rausch, Manuel K; Petersen, Ansgar; Kuhl, Ellen; Duda, Georg N

2015-01-01

Physical cues play a fundamental role in a wide range of biological processes, such as embryogenesis, wound healing, tumour invasion and connective tissue morphogenesis. Although it is well known that during these processes, cells continuously interact with the local extracellular matrix (ECM) through cell traction forces, the role of these mechanical interactions on large scale cellular and matrix organization remains largely unknown. In this study, we use a simple theoretical model to investigate cellular and matrix organization as a result of mechanical feedback signals between cells and the surrounding ECM. The model includes bi-directional coupling through cellular traction forces to deform the ECM and through matrix deformation to trigger cellular migration. In addition, we incorporate the mechanical contribution of matrix fibres and their reorganization by the cells. We show that a group of contractile cells will self-polarize at a large scale, even in homogeneous environments. In addition, our simulations mimic the experimentally observed alignment of cells in the direction of maximum stiffness and the building up of tension as a consequence of cell and fibre reorganization. Moreover, we demonstrate that cellular organization is tightly linked to the mechanical feedback loop between cells and matrix. Cells with a preference for stiff environments have a tendency to form chains, while cells with a tendency for soft environments tend to form clusters. The model presented here illustrates the potential of simple physical cues and their impact on cellular self-organization. It can be used in applications where cell-matrix interactions play a key role, such as in the design of tissue engineering scaffolds and to gain a basic understanding of pattern formation in organogenesis or tissue regeneration.

Modeling Personnel Turnover in the Parametric Organization

NASA Technical Reports Server (NTRS)

Dean, Edwin B.

1991-01-01

A primary issue in organizing a new parametric cost analysis function is to determine the skill mix and number of personnel required. The skill mix can be obtained by a functional decomposition of the tasks required within the organization and a matrixed correlation with educational or experience backgrounds. The number of personnel is a function of the skills required to cover all tasks, personnel skill background and cross training, the intensity of the workload for each task, migration through various tasks by personnel along a career path, personnel hiring limitations imposed by management and the applicant marketplace, personnel training limitations imposed by management and personnel capability, and the rate at which personnel leave the organization for whatever reason. Faced with the task of relating all of these organizational facets in order to grow a parametric cost analysis (PCA) organization from scratch, it was decided that a dynamic model was required in order to account for the obvious dynamics of the forming organization. The challenge was to create such a simple model which would be credible during all phases of organizational development. The model development process was broken down into the activities of determining the tasks required for PCA, determining the skills required for each PCA task, determining the skills available in the applicant marketplace, determining the structure of the dynamic model, implementing the dynamic model, and testing the dynamic model.

Complex Autocatalysis in Simple Chemistries.

PubMed

Virgo, Nathaniel; Ikegami, Takashi; McGregor, Simon

2016-01-01

Life on Earth must originally have arisen from abiotic chemistry. Since the details of this chemistry are unknown, we wish to understand, in general, which types of chemistry can lead to complex, lifelike behavior. Here we show that even very simple chemistries in the thermodynamically reversible regime can self-organize to form complex autocatalytic cycles, with the catalytic effects emerging from the network structure. We demonstrate this with a very simple but thermodynamically reasonable artificial chemistry model. By suppressing the direct reaction from reactants to products, we obtain the simplest kind of autocatalytic cycle, resulting in exponential growth. When these simple first-order cycles are prevented from forming, the system achieves superexponential growth through more complex, higher-order autocatalytic cycles. This leads to nonlinear phenomena such as oscillations and bistability, the latter of which is of particular interest regarding the origins of life.

A novel model for estimating organic chemical bioconcentration in agricultural plants

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

Hung, H.; Mackay, D.; Di Guardo, A.

1995-12-31

There is increasing recognition that much human and wildlife exposure to organic contaminants can be traced through the food chain to bioconcentration in vegetation. For risk assessment, there is a need for an accurate model to predict organic chemical concentrations in plants. Existing models range from relatively simple correlations of concentrations using octanol-water or octanol-air partition coefficients, to complex models involving extensive physiological data. To satisfy the need for a relatively accurate model of intermediate complexity, a novel approach has been devised to predict organic chemical concentrations in agricultural plants as a function of soil and air concentrations, without themore » need for extensive plant physiological data. The plant is treated as three compartments, namely, leaves, roots and stems (including fruit and seeds). Data readily available from the literature, including chemical properties, volume, density and composition of each compartment; metabolic and growth rate of plant; and readily obtainable environmental conditions at the site are required as input. Results calculated from the model are compared with observed and experimentally-determined concentrations. It is suggested that the model, which includes a physiological database for agricultural plants, gives acceptably accurate predictions of chemical partitioning between plants, air and soil.« less

Responses of timber rattlesnakes to fire: Lessons from two prescribed burns

Treesearch

Steven J. Beaupre; Lara E. Douglas

2012-01-01

Timber rattlesnakes (Crotalus horridus) are excellent model organisms for understanding the effects of large scale habitat manipulations because of their low-energy lifestyle, rapid response to changes in resource environment, uniform diet (small mammals), and simple behaviors. We present two case studies that illustrate interactions between timber...

Problem-Solving in the Pre-Clinical Curriculum: The Uses of Computer Simulations.

ERIC Educational Resources Information Center

Michael, Joel A.; Rovick, Allen A.

1986-01-01

Promotes the use of computer-based simulations in the pre-clinical medical curriculum as a means of providing students with opportunities for problem solving. Describes simple simulations of skeletal muscle loads, complex simulations of major organ systems and comprehensive simulation models of the entire human body. (TW)

Fractal Hypothesis of the Pelagic Microbial Ecosystem-Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web?

PubMed

Våge, Selina; Thingstad, T Frede

2015-01-01

Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales.

Fractal Hypothesis of the Pelagic Microbial Ecosystem—Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web?

PubMed Central

Våge, Selina; Thingstad, T. Frede

2015-01-01

Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales. PMID:26648929

Culture and Demography: From Reluctant Bedfellows to Committed Partners

PubMed Central

Bachrach, Christine A.

2015-01-01

Demography and culture have had a long but ambivalent relationship. Cultural influences are widely recognized as important for demographic outcomes, but are often “backgrounded” in demographic research. I argue that progress towards a more successful integration is feasible and suggest a network model of culture as a potential tool. The network model bridges both traditional (holistic and institutional) and contemporary (tool kit) models of culture used in the social sciences and offers a simple vocabulary for the diverse set of cultural concepts such as attitudes, beliefs and norms, and quantitative measures of how culture is organized. The proposed model conceptualizes culture as a nested network of meanings which are represented by schemas that range in complexity from simple concepts to multifaceted cultural models. I illustrate the potential value of a model using accounts of the cultural changes underpinning the transformation of marriage in the U.S. and point to developments in the social, cognitive and computational sciences that could facilitate the application of the model in empirical demographic research. PMID:24338643

Culture and demography: from reluctant bedfellows to committed partners.

PubMed

Bachrach, Christine A

2014-02-01

Demography and culture have had a long but ambivalent relationship. Cultural influences are widely recognized as important for demographic outcomes but are often "backgrounded" in demographic research. I argue that progress toward a more successful integration is feasible and suggest a network model of culture as a potential tool. The network model bridges both traditional (holistic and institutional) and contemporary (tool kit) models of culture used in the social sciences and offers a simple vocabulary for a diverse set of cultural concepts, such as attitudes, beliefs, and norms, as well as quantitative measures of how culture is organized. The proposed model conceptualizes culture as a nested network of meanings represented by schemas that range in complexity from simple concepts to multifaceted cultural models. I illustrate the potential value of a model using accounts of the cultural changes underpinning the transformation of marriage in the United States and point to developments in the social, cognitive, and computational sciences that could facilitate the application of the model in empirical demographic research.

Cloud Macroscopic Organization: Order Emerging from Randomness

NASA Technical Reports Server (NTRS)

Yuan, Tianle

2011-01-01

Clouds play a central role in many aspects of the climate system and their forms and shapes are remarkably diverse. Appropriate representation of clouds in climate models is a major challenge because cloud processes span at least eight orders of magnitude in spatial scales. Here we show that there exists order in cloud size distribution of low-level clouds, and that it follows a power-law distribution with exponent gamma close to 2. gamma is insensitive to yearly variations in environmental conditions, but has regional variations and land-ocean contrasts. More importantly, we demonstrate this self-organizing behavior of clouds emerges naturally from a complex network model with simple, physical organizing principles: random clumping and merging. We also demonstrate symmetry between clear and cloudy skies in terms of macroscopic organization because of similar fundamental underlying organizing principles. The order in the apparently complex cloud-clear field thus has its root in random local interactions. Studying cloud organization with complex network models is an attractive new approach that has wide applications in climate science. We also propose a concept of cloud statistic mechanics approach. This approach is fully complementary to deterministic models, and the two approaches provide a powerful framework to meet the challenge of representing clouds in our climate models when working in tandem.

Mechanistic simulation of normal-tissue damage in radiotherapy—implications for dose-volume analyses

NASA Astrophysics Data System (ADS)

Rutkowska, Eva; Baker, Colin; Nahum, Alan

2010-04-01

A radiobiologically based 3D model of normal tissue has been developed in which complications are generated when 'irradiated'. The aim is to provide insight into the connection between dose-distribution characteristics, different organ architectures and complication rates beyond that obtainable with simple DVH-based analytical NTCP models. In this model the organ consists of a large number of functional subunits (FSUs), populated by stem cells which are killed according to the LQ model. A complication is triggered if the density of FSUs in any 'critical functioning volume' (CFV) falls below some threshold. The (fractional) CFV determines the organ architecture and can be varied continuously from small (series-like behaviour) to large (parallel-like). A key feature of the model is its ability to account for the spatial dependence of dose distributions. Simulations were carried out to investigate correlations between dose-volume parameters and the incidence of 'complications' using different pseudo-clinical dose distributions. Correlations between dose-volume parameters and outcome depended on characteristics of the dose distributions and on organ architecture. As anticipated, the mean dose and V20 correlated most strongly with outcome for a parallel organ, and the maximum dose for a serial organ. Interestingly better correlation was obtained between the 3D computer model and the LKB model with dose distributions typical for serial organs than with those typical for parallel organs. This work links the results of dose-volume analyses to dataset characteristics typical for serial and parallel organs and it may help investigators interpret the results from clinical studies.

Mate Finding, Sexual Spore Production, and the Spread of Fungal Plant Parasites.

PubMed

Hamelin, Frédéric M; Castella, François; Doli, Valentin; Marçais, Benoît; Ravigné, Virginie; Lewis, Mark A

2016-04-01

Sexual reproduction and dispersal are often coupled in organisms mixing sexual and asexual reproduction, such as fungi. The aim of this study is to evaluate the impact of mate limitation on the spreading speed of fungal plant parasites. Starting from a simple model with two coupled partial differential equations, we take advantage of the fact that we are interested in the dynamics over large spatial and temporal scales to reduce the model to a single equation. We obtain a simple expression for speed of spread, accounting for both sexual and asexual reproduction. Taking Black Sigatoka disease of banana plants as a case study, the model prediction is in close agreement with the actual spreading speed (100 km per year), whereas a similar model without mate limitation predicts a wave speed one order of magnitude greater. We discuss the implications of these results to control parasites in which sexual reproduction and dispersal are intrinsically coupled.

High-resolution Episcopic Microscopy (HREM) - Simple and Robust Protocols for Processing and Visualizing Organic Materials

PubMed Central

Geyer, Stefan H.; Maurer-Gesek, Barbara; Reissig, Lukas F.; Weninger, Wolfgang J.

2017-01-01

We provide simple protocols for generating digital volume data with the high-resolution episcopic microscopy (HREM) method. HREM is capable of imaging organic materials with volumes up to 5 x 5 x 7 mm3 in typical numeric resolutions between 1 x 1 x 1 and 5 x 5 x 5 µm3. Specimens are embedded in methacrylate resin and sectioned on a microtome. After each section an image of the block surface is captured with a digital video camera that sits on the phototube connected to the compound microscope head. The optical axis passes through a green fluorescent protein (GFP) filter cube and is aligned with a position, at which the bock holder arm comes to rest after each section. In this way, a series of inherently aligned digital images, displaying subsequent block surfaces are produced. Loading such an image series in three-dimensional (3D) visualization software facilitates the immediate conversion to digital volume data, which permit virtual sectioning in various orthogonal and oblique planes and the creation of volume and surface rendered computer models. We present three simple, tissue specific protocols for processing various groups of organic specimens, including mouse, chick, quail, frog and zebra fish embryos, human biopsy material, uncoated paper and skin replacement material. PMID:28715372

High-resolution Episcopic Microscopy (HREM) - Simple and Robust Protocols for Processing and Visualizing Organic Materials.

PubMed

Geyer, Stefan H; Maurer-Gesek, Barbara; Reissig, Lukas F; Weninger, Wolfgang J

2017-07-07

We provide simple protocols for generating digital volume data with the high-resolution episcopic microscopy (HREM) method. HREM is capable of imaging organic materials with volumes up to 5 x 5 x 7 mm 3 in typical numeric resolutions between 1 x 1 x 1 and 5 x 5 x 5 µm 3 . Specimens are embedded in methacrylate resin and sectioned on a microtome. After each section an image of the block surface is captured with a digital video camera that sits on the phototube connected to the compound microscope head. The optical axis passes through a green fluorescent protein (GFP) filter cube and is aligned with a position, at which the bock holder arm comes to rest after each section. In this way, a series of inherently aligned digital images, displaying subsequent block surfaces are produced. Loading such an image series in three-dimensional (3D) visualization software facilitates the immediate conversion to digital volume data, which permit virtual sectioning in various orthogonal and oblique planes and the creation of volume and surface rendered computer models. We present three simple, tissue specific protocols for processing various groups of organic specimens, including mouse, chick, quail, frog and zebra fish embryos, human biopsy material, uncoated paper and skin replacement material.

A simple theory of molecular organization in fullerene-containing liquid crystals

NASA Astrophysics Data System (ADS)

Peroukidis, S. D.; Vanakaras, A. G.; Photinos, D. J.

2005-10-01

Systematic efforts to synthesize fullerene-containing liquid crystals have produced a variety of successful model compounds. We present a simple molecular theory, based on the interconverting shape approach [Vanakaras and Photinos, J. Mater. Chem. 15, 2002 (2005)], that relates the self-organization observed in these systems to their molecular structure. The interactions are modeled by dividing each molecule into a number of submolecular blocks to which specific interactions are assigned. Three types of blocks are introduced, corresponding to fullerene units, mesogenic units, and nonmesogenic linkage units. The blocks are constrained to move on a cubic three-dimensional lattice and molecular flexibility is allowed by retaining a number of representative conformations within the block representation of the molecule. Calculations are presented for a variety of molecular architectures including twin mesogenic branch monoadducts of C60, twin dendromesogenic branch monoadducts, and conical (badminton shuttlecock) multiadducts of C60. The dependence of the phase diagrams on the interaction parameters is explored. In spite of its many simplifications and the minimal molecular modeling used (three types of chemically distinct submolecular blocks with only repulsive interactions), the theory accounts remarkably well for the phase behavior of these systems.

Measurements of PANs during the New England Air Quality Study 2002

NASA Astrophysics Data System (ADS)

Roberts, J. M.; Marchewka, M.; Bertman, S. B.; Sommariva, R.; Warneke, C.; de Gouw, J.; Kuster, W.; Goldan, P.; Williams, E.; Lerner, B. M.; Murphy, P.; Fehsenfeld, F. C.

2007-10-01

Measurements of peroxycarboxylic nitric anhydrides (PANs) were made during the New England Air Quality Study 2002 cruise of the NOAA RV Ronald H Brown. The four compounds observed, PAN, peroxypropionic nitric anhydride (PPN), peroxymethacrylic nitric anhydride (MPAN), and peroxyisobutyric nitric anhydride (PiBN) were compared with results from other continental and Gulf of Maine sites. Systematic changes in PPN/PAN ratio, due to differential thermal decomposition rates, were related quantitatively to air mass aging. At least one early morning period was observed when O3 seemed to have been lost probably due to NO3 and N2O5 chemistry. The highest O3 episode was observed in the combined plume of isoprene sources and anthropogenic volatile organic compounds (VOCs) and NOx sources from the greater Boston area. A simple linear combination model showed that the organic precursors leading to elevated O3 were roughly half from the biogenic and half from anthropogenic VOC regimes. An explicit chemical box model confirmed that the chemistry in the Boston plume is well represented by the simple linear combination model. This degree of biogenic hydrocarbon involvement in the production of photochemical ozone has significant implications for air quality control strategies in this region.

The time series approach to short term load forecasting

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

Hagan, M.T.; Behr, S.M.

The application of time series analysis methods to load forecasting is reviewed. It is shown than Box and Jenkins time series models, in particular, are well suited to this application. The logical and organized procedures for model development using the autocorrelation function make these models particularly attractive. One of the drawbacks of these models is the inability to accurately represent the nonlinear relationship between load and temperature. A simple procedure for overcoming this difficulty is introduced, and several Box and Jenkins models are compared with a forecasting procedure currently used by a utility company.

Simple process of hybrid white quantum dot/organic light-emitting diodes by using quantum dot plate and fluorescence

NASA Astrophysics Data System (ADS)

Lee, Ho Won; Lee, Ki-Heon; Lee, Jae Woo; Kim, Jong-Hoon; Yang, Heesun; Kim, Young Kwan

2015-02-01

In this work, the simple process of hybrid quantum dot (QD)/organic light-emitting diode (OLED) was proposed to apply a white illumination light by using QD plate and organic fluorescence. Conventional blue fluorescent OLEDs were firstly fabricated and then QD plates of various concentrations, which can be controlled of UV-vis absorption and photoluminescence spectrum, were attached under glass substrate of completed blue devices. The suggested process indicates that we could fabricate the white device through very simple process without any deposition of orange or red organic emitters. Therefore, this work would be demonstrated that the potential simple process for white applications can be applied and also can be extended to additional research on light applications.

Optimized ex-ovo culturing of chick embryos to advanced stages of development.

PubMed

Cloney, Kellie; Franz-Odendaal, Tamara Anne

2015-01-24

Research in anatomy, embryology, and developmental biology has largely relied on the use of model organisms. In order to study development in live embryos model organisms, such as the chicken, are often used. The chicken is an excellent model organism due to its low cost and minimal maintenance, however they present observational challenges because they are enclosed in an opaque eggshell. In order to properly view the embryo as it develops, the shell must be windowed or removed. Both windowing and ex ovo techniques have been developed to assist researchers in the study of embryonic development. However, each of the methods has limitations and challenges. Here, we present a simple, optimized ex ovo culture technique for chicken embryos that enables the observation of embryonic development from stage HH 19 into late stages of development (HH 40), when many organs have developed. This technique is easy to adopt in both undergraduate classes and more advanced research laboratories where embryo manipulations are conducted.

[The trial of business data analysis at the Department of Radiology by constructing the auto-regressive integrated moving-average (ARIMA) model].

PubMed

Tani, Yuji; Ogasawara, Katsuhiko

2012-01-01

This study aimed to contribute to the management of a healthcare organization by providing management information using time-series analysis of business data accumulated in the hospital information system, which has not been utilized thus far. In this study, we examined the performance of the prediction method using the auto-regressive integrated moving-average (ARIMA) model, using the business data obtained at the Radiology Department. We made the model using the data used for analysis, which was the number of radiological examinations in the past 9 years, and we predicted the number of radiological examinations in the last 1 year. Then, we compared the actual value with the forecast value. We were able to establish that the performance prediction method was simple and cost-effective by using free software. In addition, we were able to build the simple model by pre-processing the removal of trend components using the data. The difference between predicted values and actual values was 10%; however, it was more important to understand the chronological change rather than the individual time-series values. Furthermore, our method was highly versatile and adaptable compared to the general time-series data. Therefore, different healthcare organizations can use our method for the analysis and forecasting of their business data.

Self-organization of cosmic radiation pressure instability. II - One-dimensional simulations

NASA Technical Reports Server (NTRS)

Hogan, Craig J.; Woods, Jorden

1992-01-01

The clustering of statistically uniform discrete absorbing particles moving solely under the influence of radiation pressure from uniformly distributed emitters is studied in a simple one-dimensional model. Radiation pressure tends to amplify statistical clustering in the absorbers; the absorbing material is swept into empty bubbles, the biggest bubbles grow bigger almost as they would in a uniform medium, and the smaller ones get crushed and disappear. Numerical simulations of a one-dimensional system are used to support the conjecture that the system is self-organizing. Simple statistics indicate that a wide range of initial conditions produce structure approaching the same self-similar statistical distribution, whose scaling properties follow those of the attractor solution for an isolated bubble. The importance of the process for large-scale structuring of the interstellar medium is briefly discussed.

The Kinematics of Plant Nutation Reveals a Simple Relation between Curvature and the Orientation of Differential Growth.

PubMed

Bastien, Renaud; Meroz, Yasmine

2016-12-01

Nutation is an oscillatory movement that plants display during their development. Despite its ubiquity among plants movements, the relation between the observed movement and the underlying biological mechanisms remains unclear. Here we show that the kinematics of the full organ in 3D give a simple picture of plant nutation, where the orientation of the curvature along the main axis of the organ aligns with the direction of maximal differential growth. Within this framework we reexamine the validity of widely used experimental measurements of the apical tip as markers of growth dynamics. We show that though this relation is correct under certain conditions, it does not generally hold, and is not sufficient to uncover the specific role of each mechanism. As an example we re-interpret previously measured experimental observations using our model.

Co-digestion of solid waste: Towards a simple model to predict methane production.

PubMed

Kouas, Mokhles; Torrijos, Michel; Schmitz, Sabine; Sousbie, Philippe; Sayadi, Sami; Harmand, Jérôme

2018-04-01

Modeling methane production is a key issue for solid waste co-digestion. Here, the effect of a step-wise increase in the organic loading rate (OLR) on reactor performance was investigated, and four new models were evaluated to predict methane yields using data acquired in batch mode. Four co-digestion experiments of mixtures of 2 solid substrates were conducted in semi-continuous mode. Experimental methane yields were always higher than the BMP values of mixtures calculated from the BMP of each substrate, highlighting the importance of endogenous production (methane produced from auto-degradation of microbial community and generated solids). The experimental methane productions under increasing OLRs corresponded well to the modeled data using the model with constant endogenous production and kinetics identified at 80% from total batch time. This model provides a simple and useful tool for technical design consultancies and plant operators to optimize the co-digestion and the choice of the OLRs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Maximum efficiency of state-space models of nanoscale energy conversion devices

NASA Astrophysics Data System (ADS)

Einax, Mario; Nitzan, Abraham

2016-07-01

The performance of nano-scale energy conversion devices is studied in the framework of state-space models where a device is described by a graph comprising states and transitions between them represented by nodes and links, respectively. Particular segments of this network represent input (driving) and output processes whose properly chosen flux ratio provides the energy conversion efficiency. Simple cyclical graphs yield Carnot efficiency for the maximum conversion yield. We give general proof that opening a link that separate between the two driving segments always leads to reduced efficiency. We illustrate these general result with simple models of a thermoelectric nanodevice and an organic photovoltaic cell. In the latter an intersecting link of the above type corresponds to non-radiative carriers recombination and the reduced maximum efficiency is manifested as a smaller open-circuit voltage.

Maximum efficiency of state-space models of nanoscale energy conversion devices.

PubMed

Einax, Mario; Nitzan, Abraham

2016-07-07

The performance of nano-scale energy conversion devices is studied in the framework of state-space models where a device is described by a graph comprising states and transitions between them represented by nodes and links, respectively. Particular segments of this network represent input (driving) and output processes whose properly chosen flux ratio provides the energy conversion efficiency. Simple cyclical graphs yield Carnot efficiency for the maximum conversion yield. We give general proof that opening a link that separate between the two driving segments always leads to reduced efficiency. We illustrate these general result with simple models of a thermoelectric nanodevice and an organic photovoltaic cell. In the latter an intersecting link of the above type corresponds to non-radiative carriers recombination and the reduced maximum efficiency is manifested as a smaller open-circuit voltage.

Collaborative Research: failure of RockMasses from Nucleation and Growth of Microscopic Defects and Disorder

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

Klein, William

Over the 21 years of funding we have pursued several projects related to earthquakes, damage and nucleation. We developed simple models of earthquake faults which we studied to understand Gutenburg-Richter scaling, foreshocks and aftershocks, the effect of spatial structure of the faults and its interaction with underlying self organization and phase transitions. In addition we studied the formation of amorphous solids via the glass transition. We have also studied nucleation with a particular concentration on transitions in systems with a spatial symmetry change. In addition we investigated the nucleation process in models that mimic rock masses. We obtained the structuremore » of the droplet in both homogeneous and heterogeneous nucleation. We also investigated the effect of defects or asperities on the nucleation of failure in simple models of earthquake faults.« less

Simulated Carbon Cycling in a Model Microbial Mat.

NASA Astrophysics Data System (ADS)

Decker, K. L.; Potter, C. S.

2006-12-01

We present here the novel addition of detailed organic carbon cycling to our model of a hypersaline microbial mat ecosystem. This ecosystem model, MBGC (Microbial BioGeoChemistry), simulates carbon fixation through oxygenic and anoxygenic photosynthesis, and the release of C and electrons for microbial heterotrophs via cyanobacterial exudates and also via a pool of dead cells. Previously in MBGC, the organic portion of the carbon cycle was simplified into a black-box rate of accumulation of simple and complex organic compounds based on photosynthesis and mortality rates. We will discuss the novel inclusion of fermentation as a source of carbon and electrons for use in methanogenesis and sulfate reduction, and the influence of photorespiration on labile carbon exudation rates in cyanobacteria. We will also discuss the modeling of decomposition of dead cells and the ultimate release of inorganic carbon. The detailed modeling of organic carbon cycling is important to the accurate representation of inorganic carbon flux through the mat, as well as to accurate representation of growth models of the heterotrophs under different environmental conditions. Because the model ecosystem is an analog of ancient microbial mats that had huge impacts on the atmosphere of early earth, this MBGC can be useful as a biological component to either early earth models or models of other planets that potentially harbor life.

How to Catch a Smurf? - Ageing and Beyond… In vivo Assessment of Intestinal Permeability in Multiple Model Organisms.

PubMed

Martins, Raquel R; McCracken, Andrew W; Simons, Mirre J P; Henriques, Catarina M; Rera, Michael

2018-02-05

The Smurf Assay (SA) was initially developed in the model organism Drosophila melanogaster where a dramatic increase of intestinal permeability has been shown to occur during aging (Rera et al. , 2011). We have since validated the protocol in multiple other model organisms (Dambroise et al. , 2016) and have utilized the assay to further our understanding of aging (Tricoire and Rera, 2015; Rera et al. , 2018). The SA has now also been used by other labs to assess intestinal barrier permeability (Clark et al. , 2015; Katzenberger et al. , 2015; Barekat et al. , 2016; Chakrabarti et al. , 2016; Gelino et al. , 2016). The SA in itself is simple; however, numerous small details can have a considerable impact on its experimental validity and subsequent interpretation. Here, we provide a detailed update on the SA technique and explain how to catch a Smurf while avoiding the most common experimental fallacies.

Charophytes: Evolutionary Giants and Emerging Model Organisms

PubMed Central

Domozych, David S.; Popper, Zoë A.; Sørensen, Iben

2016-01-01

Charophytes are the group of green algae whose ancestral lineage gave rise to land plants in what resulted in a profoundly transformative event in the natural history of the planet. Extant charophytes exhibit many features that are similar to those found in land plants and their relatively simple phenotypes make them efficacious organisms for the study of many fundamental biological phenomena. Several taxa including Micrasterias, Penium, Chara, and Coleochaete are valuable model organisms for the study of cell biology, development, physiology and ecology of plants. New and rapidly expanding molecular studies are increasing the use of charophytes that in turn, will dramatically enhance our understanding of the evolution of plants and the adaptations that allowed for survival on land. The Frontiers in Plant Science series on “Charophytes” provides an assortment of new research reports and reviews on charophytes and their emerging significance as model plants. PMID:27777578

Quiet swimming at low Reynolds number

NASA Astrophysics Data System (ADS)

Andersen, Anders; Wadhwa, Navish; Kiørboe, Thomas

2015-04-01

The stresslet provides a simple model of the flow created by a small, freely swimming and neutrally buoyant aquatic organism and shows that the far field fluid disturbance created by such an organism in general decays as one over distance squared. Here we discuss a quieter swimming mode that eliminates the stresslet component of the flow and leads to a faster spatial decay of the fluid disturbance described by a force quadrupole that decays as one over distance cubed. Motivated by recent experimental results on fluid disturbances due to small aquatic organisms, we demonstrate that a three-Stokeslet model of a swimming organism which uses breast stroke type kinematics is an example of such a quiet swimmer. We show that the fluid disturbance in both the near field and the far field is significantly reduced by appropriately arranging the propulsion apparatus, and we find that the far field power laws are valid surprisingly close to the organism. Finally, we discuss point force models as a general framework for hypothesis generation and experimental exploration of fluid mediated predator-prey interactions in the planktonic world.

Quiet swimming at low Reynolds number.

PubMed

Andersen, Anders; Wadhwa, Navish; Kiørboe, Thomas

2015-04-01

The stresslet provides a simple model of the flow created by a small, freely swimming and neutrally buoyant aquatic organism and shows that the far field fluid disturbance created by such an organism in general decays as one over distance squared. Here we discuss a quieter swimming mode that eliminates the stresslet component of the flow and leads to a faster spatial decay of the fluid disturbance described by a force quadrupole that decays as one over distance cubed. Motivated by recent experimental results on fluid disturbances due to small aquatic organisms, we demonstrate that a three-Stokeslet model of a swimming organism which uses breast stroke type kinematics is an example of such a quiet swimmer. We show that the fluid disturbance in both the near field and the far field is significantly reduced by appropriately arranging the propulsion apparatus, and we find that the far field power laws are valid surprisingly close to the organism. Finally, we discuss point force models as a general framework for hypothesis generation and experimental exploration of fluid mediated predator-prey interactions in the planktonic world.

MOPED enables discoveries through consistently processed proteomics data

PubMed Central

Higdon, Roger; Stewart, Elizabeth; Stanberry, Larissa; Haynes, Winston; Choiniere, John; Montague, Elizabeth; Anderson, Nathaniel; Yandl, Gregory; Janko, Imre; Broomall, William; Fishilevich, Simon; Lancet, Doron; Kolker, Natali; Kolker, Eugene

2014-01-01

The Model Organism Protein Expression Database (MOPED, http://moped.proteinspire.org), is an expanding proteomics resource to enable biological and biomedical discoveries. MOPED aggregates simple, standardized and consistently processed summaries of protein expression and metadata from proteomics (mass spectrometry) experiments from human and model organisms (mouse, worm and yeast). The latest version of MOPED adds new estimates of protein abundance and concentration, as well as relative (differential) expression data. MOPED provides a new updated query interface that allows users to explore information by organism, tissue, localization, condition, experiment, or keyword. MOPED supports the Human Proteome Project’s efforts to generate chromosome and diseases specific proteomes by providing links from proteins to chromosome and disease information, as well as many complementary resources. MOPED supports a new omics metadata checklist in order to harmonize data integration, analysis and use. MOPED’s development is driven by the user community, which spans 90 countries guiding future development that will transform MOPED into a multi-omics resource. MOPED encourages users to submit data in a simple format. They can use the metadata a checklist generate a data publication for this submission. As a result, MOPED will provide even greater insights into complex biological processes and systems and enable deeper and more comprehensive biological and biomedical discoveries. PMID:24350770

Influence of pH on Drug Absorption from the Gastrointestinal Tract: A Simple Chemical Model

NASA Astrophysics Data System (ADS)

Hickman, Raymond J. S.; Neill, Jane

1997-07-01

A simple model of the gastrointestinal tract is obtained by placing ethyl acetate in contact with water at pH 2 and pH 8 in separate test tubes. The ethyl acetate corresponds to the lipid material lining the tract while the water corresponds to the aqueous contents of the stomach (pH 2) and intestine (pH 8). The compounds aspirin, paracetamol and 3-aminophenol are used as exemplars of acidic, neutral and basic drugs respectively to illustrate the influence which pH has on the distribution of each class of drug between the aqueous and organic phases of the model. The relative concentration of drug in the ethyl acetate is judged by applying microlitre-sized samples of ethyl acetate to a layer of fluorescent silica which, after evaporation of the ethyl acetate, is viewed under an ultraviolet lamp. Each of the three drugs, if present in the ethyl acetate, becomes visible as a dark spot on the silica layer. The observations made in the model system correspond well to the patterns of drug absorption from the gastrointestinal tract described in pharmacology texts and these observations are convincingly explained in terms of simple acid-base chemistry.

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

Moore, J. A. M.; Jiang, J.; Post, W. M.

Carbon cycle models often lack explicit belowground organism activity, yet belowground organisms regulate carbon storage and release in soil. Ectomycorrhizal fungi are important players in the carbon cycle because they are a conduit into soil for carbon assimilated by the plant. It is hypothesized that ectomycorrhizal fungi can also be active decomposers when plant carbon allocation to fungi is low. Here, we reviewed the literature on ectomycorrhizal decomposition and we developed a simulation model of the plant-mycorrhizae interaction where a reduction in plant productivity stimulates ectomycorrhizal fungi to decompose soil organic matter. Our review highlights evidence demonstrating the potential formore » ectomycorrhizal fungi to decompose soil organic matter. Our model output suggests that ectomycorrhizal activity accounts for a portion of carbon decomposed in soil, but this portion varied with plant productivity and the mycorrhizal carbon uptake strategy simulated. Lower organic matter inputs to soil were largely responsible for reduced soil carbon storage. Using mathematical theory, we demonstrated that biotic interactions affect predictions of ecosystem functions. Specifically, we developed a simple function to model the mycorrhizal switch in function from plant symbiont to decomposer. In conclusion, we show that including mycorrhizal fungi with the flexibility of mutualistic and saprotrophic lifestyles alters predictions of ecosystem function.« less

How self-organization can guide evolution.

PubMed

Glancy, Jonathan; Stone, James V; Wilson, Stuart P

2016-11-01

Self-organization and natural selection are fundamental forces that shape the natural world. Substantial progress in understanding how these forces interact has been made through the study of abstract models. Further progress may be made by identifying a model system in which the interaction between self-organization and selection can be investigated empirically. To this end, we investigate how the self-organizing thermoregulatory huddling behaviours displayed by many species of mammals might influence natural selection of the genetic components of metabolism. By applying a simple evolutionary algorithm to a well-established model of the interactions between environmental, morphological, physiological and behavioural components of thermoregulation, we arrive at a clear, but counterintuitive, prediction: rodents that are able to huddle together in cold environments should evolve a lower thermal conductance at a faster rate than animals reared in isolation. The model therefore explains how evolution can be accelerated as a consequence of relaxed selection , and it predicts how the effect may be exaggerated by an increase in the litter size, i.e. by an increase in the capacity to use huddling behaviours for thermoregulation. Confirmation of these predictions in future experiments with rodents would constitute strong evidence of a mechanism by which self-organization can guide natural selection.

Précis of Simple heuristics that make us smart.

PubMed

Todd, P M; Gigerenzer, G

2000-10-01

How can anyone be rational in a world where knowledge is limited, time is pressing, and deep thought is often an unattainable luxury? Traditional models of unbounded rationality and optimization in cognitive science, economics, and animal behavior have tended to view decision-makers as possessing supernatural powers of reason, limitless knowledge, and endless time. But understanding decisions in the real world requires a more psychologically plausible notion of bounded rationality. In Simple heuristics that make us smart (Gigerenzer et al. 1999), we explore fast and frugal heuristics--simple rules in the mind's adaptive toolbox for making decisions with realistic mental resources. These heuristics can enable both living organisms and artificial systems to make smart choices quickly and with a minimum of information by exploiting the way that information is structured in particular environments. In this précis, we show how simple building blocks that control information search, stop search, and make decisions can be put together to form classes of heuristics, including: ignorance-based and one-reason decision making for choice, elimination models for categorization, and satisficing heuristics for sequential search. These simple heuristics perform comparably to more complex algorithms, particularly when generalizing to new data--that is, simplicity leads to robustness. We present evidence regarding when people use simple heuristics and describe the challenges to be addressed by this research program.

Combining a Standard Fischer Esterification Experiment with Stereochemical and Molecular-Modeling Concepts

ERIC Educational Resources Information Center

Clausen, Thomas P.

2011-01-01

The Fisher esterification reaction is ideally suited for the undergraduate organic laboratory because it is easy to carry out and often involves a suitable introduction to basic laboratory techniques including extraction, distillation, and simple spectroscopic (IR and NMR) analyses. Here, a Fisher esterification reaction is described in which the…

Conceptual Frameworks in Undergraduate Nursing Curricula: Report of a National Survey.

ERIC Educational Resources Information Center

McEwen, Melanie; Brown, Sandra C.

2002-01-01

Responses from 300 accredited nursing schools indicated that they used eclectic conceptual frameworks for curriculum; the most common component was the nursing process. Associate degree programs were more likely to use simple-to-complex organization. Diploma programs were more likely to use the medical model than baccalaureate programs. Frameworks…

The Pea Seedling as a Model of Normal and Abnormal Morphogenesis

ERIC Educational Resources Information Center

Kurkdjian, Armen; And Others

1974-01-01

Describes several simple and inexpensive experiments designed to facilitate the study of normal and abnormal morphogenesis in the biology laboratory. Seedlings of the common garden pea are used in the experiments, and abnormal morphogenesis (tumors) are induced by a virulent strain of the crown-gall organism, Agrobacterium tumefaciens. (JR)

Circularly Polarized Luminescence from Simple Organic Molecules

PubMed Central

Sánchez-Carnerero, Esther M.; Agarrabeitia, Antonia R.; Moreno, Florencio; Maroto, Beatriz L.; Muller, Gilles; Ortiz, María J.

2015-01-01

This article aims to show the identity of “CPL-active simple organic molecules” as a new concept in Organic Chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and nonaggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented. PMID:26136234

Quantitative Proteomics by Metabolic Labeling of Model Organisms*

PubMed Central

Gouw, Joost W.; Krijgsveld, Jeroen; Heck, Albert J. R.

2010-01-01

In the biological sciences, model organisms have been used for many decades and have enabled the gathering of a large proportion of our present day knowledge of basic biological processes and their derailments in disease. Although in many of these studies using model organisms, the focus has primarily been on genetics and genomics approaches, it is important that methods become available to extend this to the relevant protein level. Mass spectrometry-based proteomics is increasingly becoming the standard to comprehensively analyze proteomes. An important transition has been made recently by moving from charting static proteomes to monitoring their dynamics by simultaneously quantifying multiple proteins obtained from differently treated samples. Especially the labeling with stable isotopes has proved an effective means to accurately determine differential expression levels of proteins. Among these, metabolic incorporation of stable isotopes in vivo in whole organisms is one of the favored strategies. In this perspective, we will focus on methodologies to stable isotope label a variety of model organisms in vivo, ranging from relatively simple organisms such as bacteria and yeast to Caenorhabditis elegans, Drosophila, and Arabidopsis up to mammals such as rats and mice. We also summarize how this has opened up ways to investigate biological processes at the protein level in health and disease, revealing conservation and variation across the evolutionary tree of life. PMID:19955089

Simultaneous modeling of habitat suitability, occupancy, and relative abundance: African elephants in Zimbabwe

USGS Publications Warehouse

Martin, Julien; Chamaille-Jammes, Simon; Nichols, James D.; Fritz, Herve; Hines, James E.; Fonnesbeck, Christopher J.; MacKenzie, Darryl I.; Bailey, Larissa L.

2010-01-01

The recent development of statistical models such as dynamic site occupancy models provides the opportunity to address fairly complex management and conservation problems with relatively simple models. However, surprisingly few empirical studies have simultaneously modeled habitat suitability and occupancy status of organisms over large landscapes for management purposes. Joint modeling of these components is particularly important in the context of management of wild populations, as it provides a more coherent framework to investigate the population dynamics of organisms in space and time for the application of management decision tools. We applied such an approach to the study of water hole use by African elephants in Hwange National Park, Zimbabwe. Here we show how such methodology may be implemented and derive estimates of annual transition probabilities among three dry-season states for water holes: (1) unsuitable state (dry water holes with no elephants); (2) suitable state (water hole with water) with low abundance of elephants; and (3) suitable state with high abundance of elephants. We found that annual rainfall and the number of neighboring water holes influenced the transition probabilities among these three states. Because of an increase in elephant densities in the park during the study period, we also found that transition probabilities from low abundance to high abundance states increased over time. The application of the joint habitat–occupancy models provides a coherent framework to examine how habitat suitability and factors that affect habitat suitability influence the distribution and abundance of organisms. We discuss how these simple models can further be used to apply structured decision-making tools in order to derive decisions that are optimal relative to specified management objectives. The modeling framework presented in this paper should be applicable to a wide range of existing data sets and should help to address important ecological, conservation, and management problems that deal with occupancy, relative abundance, and habitat suitability.

The enhanced Software Life Cyle Support Environment (ProSLCSE): Automation for enterprise and process modeling

NASA Technical Reports Server (NTRS)

Milligan, James R.; Dutton, James E.

1993-01-01

In this paper, we have introduced a comprehensive method for enterprise modeling that addresses the three important aspects of how an organization goes about its business. FirstEP includes infrastructure modeling, information modeling, and process modeling notations that are intended to be easy to learn and use. The notations stress the use of straightforward visual languages that are intuitive, syntactically simple, and semantically rich. ProSLCSE will be developed with automated tools and services to facilitate enterprise modeling and process enactment. In the spirit of FirstEP, ProSLCSE tools will also be seductively easy to use. Achieving fully managed, optimized software development and support processes will be long and arduous for most software organizations, and many serious problems will have to be solved along the way. ProSLCSE will provide the ability to document, communicate, and modify existing processes, which is the necessary first step.

Improving Secondary Organic Aerosol (SOA) Models using Global Sensitivity Analysis and by Comparison to Chamber Data.

NASA Astrophysics Data System (ADS)

Miller, D. O.; Brune, W. H.

2017-12-01

Accurate estimates of secondary organic aerosol (SOA) from atmospheric models is a major research challenge due to the complexity of the chemical and physical processes involved in the SOA formation and continuous aging. The primary uncertainties of SOA models include those associated with the formation of gas-phase products, the conversion between gas phase and particle phase, the aging mechanisms of SOA, and other processes related to the heterogeneous and particle-phase reactions. To address this challenge, we us a modular modeling framework that combines both simple and near-explicit gas-phase reactions and a two-dimensional volatility basis set (2D-VBS) to simulate the formation and evolution of SOA. Global sensitivity analysis is used to assess the relative importance of the model input parameters. In addition, the model is compared to the measurements from the Focused Isoprene eXperiment at the California Institute of Technology (FIXCIT).

Self-organized dynamics in local load-sharing fiber bundle models.

PubMed

Biswas, Soumyajyoti; Chakrabarti, Bikas K

2013-10-01

We study the dynamics of a local load-sharing fiber bundle model in two dimensions under an external load (which increases with time at a fixed slow rate) applied at a single point. Due to the local load-sharing nature, the redistributed load remains localized along the boundary of the broken patch. The system then goes to a self-organized state with a stationary average value of load per fiber along the (increasing) boundary of the broken patch (damaged region) and a scale-free distribution of avalanche sizes and other related quantities are observed. In particular, when the load redistribution is only among nearest surviving fiber(s), the numerical estimates of the exponent values are comparable with those of the Manna model. When the load redistribution is uniform along the patch boundary, the model shows a simple mean-field limit of this self-organizing critical behavior, for which we give analytical estimates of the saturation load per fiber values and avalanche size distribution exponent. These are in good agreement with numerical simulation results.

A coarsening model for self-organization of tropical convection

NASA Astrophysics Data System (ADS)

Craig, G. C.; Mack, J. M.

2013-08-01

If the influence of humidity on cumulus convection causes moist regions of the tropical troposphere to become moister and dry regions to become drier, and if horizontal mixing of moisture is not rapid enough to overcome this tendency, then the atmosphere will tend to separate into increasingly large moist and dry regions through a process of coarsening. We present a simple model for the moisture budget of the free troposphere, including subsidence drying, convective moistening, and horizontal mixing, and a constraint on total precipitation representing radiative-convective equilibrium. When initialized with a spatially uncorrelated moisture distribution, the model shows self-organization of precipitation with two main stages: A coarsening stage where the correlation length grows proportional to time to the power 1/2 and a droplet stage where precipitation is confined to a decreasing number of circular moist regions. A potential function is introduced to characterize the tendency for self-organization, which could be a useful diagnostic for analyzing cloud-resolving model simulations.

Analysis of population mortality kinetics with application to the longevity followup of the Navy's '1,000 aviators'

NASA Technical Reports Server (NTRS)

Economos, A. C.; Miquel, J.

1979-01-01

A simple physiological model of mortality kinetics is used to assess the intuitive concept that the aging rates of populations are proportional to their mortality rates. It is assumed that the vitality of an individual can be expressed as a simple summation of the weighted functional capacities of its organs and homeostatic systems that are indispensable for survival. It is shown that the mortality kinetics of a population can be derived by a linear transformation of the frequency distribution of vitality, assuming a uniform constant rate of decline of the physiological functions. A simple comparison of two populations is not possible when they have different vitality frequency distributions. Analysis of the data using the model suggests that the differences in decline of survivorship with age between the military pilot population, a medically insured population, and the control population can be accounted for by the effect of physical selection on the vitality frequency distribution of the screened populations.

Decomposition by ectomycorrhizal fungi alters soil carbon storage in a simulation model

DOE PAGES

Moore, J. A. M.; Jiang, J.; Post, W. M.; ...

2015-03-06

Carbon cycle models often lack explicit belowground organism activity, yet belowground organisms regulate carbon storage and release in soil. Ectomycorrhizal fungi are important players in the carbon cycle because they are a conduit into soil for carbon assimilated by the plant. It is hypothesized that ectomycorrhizal fungi can also be active decomposers when plant carbon allocation to fungi is low. Here, we reviewed the literature on ectomycorrhizal decomposition and we developed a simulation model of the plant-mycorrhizae interaction where a reduction in plant productivity stimulates ectomycorrhizal fungi to decompose soil organic matter. Our review highlights evidence demonstrating the potential formore » ectomycorrhizal fungi to decompose soil organic matter. Our model output suggests that ectomycorrhizal activity accounts for a portion of carbon decomposed in soil, but this portion varied with plant productivity and the mycorrhizal carbon uptake strategy simulated. Lower organic matter inputs to soil were largely responsible for reduced soil carbon storage. Using mathematical theory, we demonstrated that biotic interactions affect predictions of ecosystem functions. Specifically, we developed a simple function to model the mycorrhizal switch in function from plant symbiont to decomposer. In conclusion, we show that including mycorrhizal fungi with the flexibility of mutualistic and saprotrophic lifestyles alters predictions of ecosystem function.« less

Evaluating the multimedia fate of organic chemicals: A level III fugacity model

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

Mackay, D.; Paterson, S.

A multimedia model is developed and applied to selected organic chemicals in evaluative and real regional environments. The model employs the fugacity concept and treats four bulk compartments: air, water, soil, and bottom sediment, which consist of subcompartments of varying proportions of air, water, and mineral and organic matter. Chemical equilibrium is assumed to apply within (but not between) each bulk compartment. Expressions are included for emissions, advective flows, degrading reactions, and interphase transport by diffusive and non-diffusive processes. Input to the model consists of a description of the environment, the physical-chemical and reaction properties of the chemical, and emissionmore » rates. For steady-state conditions the solution is a simple algebraic expression. The model is applied to six chemicals in the region of southern Ontario and the calculated fate and concentrations are compared with observations. The results suggest that the model may be used to determine the processes that control the environmental fate of chemicals in a region and provide approximate estimates of relative media concentrations.« less

Maximum entropy production allows a simple representation of heterogeneity in semiarid ecosystems.

PubMed

Schymanski, Stanislaus J; Kleidon, Axel; Stieglitz, Marc; Narula, Jatin

2010-05-12

Feedbacks between water use, biomass and infiltration capacity in semiarid ecosystems have been shown to lead to the spontaneous formation of vegetation patterns in a simple model. The formation of patterns permits the maintenance of larger overall biomass at low rainfall rates compared with homogeneous vegetation. This results in a bias of models run at larger scales neglecting subgrid-scale variability. In the present study, we investigate the question whether subgrid-scale heterogeneity can be parameterized as the outcome of optimal partitioning between bare soil and vegetated area. We find that a two-box model reproduces the time-averaged biomass of the patterns emerging in a 100 x 100 grid model if the vegetated fraction is optimized for maximum entropy production (MEP). This suggests that the proposed optimality-based representation of subgrid-scale heterogeneity may be generally applicable to different systems and at different scales. The implications for our understanding of self-organized behaviour and its modelling are discussed.

Comparative evaluation of anaerobic digestion for sewage sludge and various organic wastes with simple modeling.

PubMed

Hidaka, Taira; Wang, Feng; Tsumori, Jun

2015-09-01

Anaerobic co-digestion of sewage sludge and other organic wastes, such as kitchen garbage, food waste, and agricultural waste, at a wastewater treatment plant (WWTP) is a promising method for both energy and material recovery. Substrate characteristics and the anaerobic digestion performance of sewage sludge and various organic wastes were compared using experiments and modeling. Co-digestion improved the value of digested sewage sludge as a fertilizer. The relationship between total and soluble elemental concentrations was correlated with the periodic table: most Na and K (alkali metals) were soluble, and around 20-40% of Mg and around 10-20% of Ca (alkaline earth metals) were soluble. The ratio of biodegradable chemical oxygen demand of organic wastes was 65-90%. The methane conversion ratio and methane production rate under mesophilic conditions were evaluated using a simplified mathematical model. There was reasonably close agreement between the model simulations and the experimental results in terms of methane production and nitrogen concentration. These results provide valuable information and indicate that the model can be used as a pre-evaluation tool to facilitate the introduction of co-digestion at WWTPs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bacteria as a new model system for aging studies: investigations using light microscopy.

PubMed

Ackermann, Martin

2008-04-01

Aging-the decline in an individual's condition over time-is at the center of an active research field in medicine and biology. Some very basic questions have, however, remained unresolved, the most fundamental being: do all organisms age? Or are there organisms that would continue to live forever if not killed by external forces? For a long time it was believed that aging only affected organisms such as animals, plants, and fungi. Bacteria, in contrast, were assumed to be potentially immortal and until recently this assertion remained untested. We used phase-contrast microscopy (on an Olympus BX61) to follow individual bacterial cells over many divisions to prove that some bacteria show a distinction between an aging mother cell and a rejuvenated daughter, and that these bacteria thus age. This indicates that aging is a more fundamental property of organisms than was previously assumed. Bacteria can now be used as very simple model system for investigating why and how organisms age.

Heterogeneous distribution of metabolites across plant species

NASA Astrophysics Data System (ADS)

Takemoto, Kazuhiro; Arita, Masanori

2009-07-01

We investigate the distribution of flavonoids, a major category of plant secondary metabolites, across species. Flavonoids are known to show high species specificity, and were once considered as chemical markers for understanding adaptive evolution and characterization of living organisms. We investigate the distribution among species using bipartite networks, and find that two heterogeneous distributions are conserved among several families: the power-law distributions of the number of flavonoids in a species and the number of shared species of a particular flavonoid. In order to explain the possible origin of the heterogeneity, we propose a simple model with, essentially, a single parameter. As a result, we show that two respective power-law statistics emerge from simple evolutionary mechanisms based on a multiplicative process. These findings provide insights into the evolution of metabolite diversity and characterization of living organisms that defy genome sequence analysis for different reasons.

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

Vega-Carrillo, Hector Rene; Manzanares-Acuna, Eduardo; Hernandez-Davila, Victor Martin

The use of 131I is widely used in diagnostic and treatment of patients. If the patient is pregnant the 131I presence in the thyroid it becomes a source of constant exposition to other organs and the fetus. In this study the absorbed dose in the uterus of a 3 months pregnant woman with 131I in her thyroid gland has been calculated. The dose was determined using Monte Carlo methods in which a detailed model of the woman has been developed. The dose was also calculated using a simple procedure that was refined including the photons' attenuation in the woman organsmore » and body. To verify these results an experiment was carried out using a neck phantom with 131I. Comparing the results it was found that the simple calculation tend to overestimate the absorbed dose, by doing the corrections due to body and organs photon attenuation the dose is 0.14 times the Monte Carlo estimation.« less

Biologically inspired information theory: Adaptation through construction of external reality models by living systems.

PubMed

Nakajima, Toshiyuki

2015-12-01

Higher animals act in the world using their external reality models to cope with the uncertain environment. Organisms that have not developed such information-processing organs may also have external reality models built in the form of their biochemical, physiological, and behavioral structures, acquired by natural selection through successful models constructed internally. Organisms subject to illusions would fail to survive in the material universe. How can organisms, or living systems in general, determine the external reality from within? This paper starts with a phenomenological model, in which the self constitutes a reality model developed through the mental processing of phenomena. Then, the it-from-bit concept is formalized using a simple mathematical model. For this formalization, my previous work on an algorithmic process is employed to constitute symbols referring to the external reality, called the inverse causality, with additional improvements to the previous work. Finally, as an extension of this model, the cognizers system model is employed to describe the self as one of many material entities in a world, each of which acts as a subject by responding to the surrounding entities. This model is used to propose a conceptual framework of information theory that can deal with both the qualitative (semantic) and quantitative aspects of the information involved in biological processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

A spin exchange model for singlet fission

NASA Astrophysics Data System (ADS)

Yago, Tomoaki; Wakasa, Masanobu

2018-03-01

Singlet fission has been analyzed with the Dexter model in which electron exchange occurs between chromophores, conserving the spin for each electron. In the present study, we propose a spin exchange model for singlet fission. In the spin exchange model, spins are exchanged by the exchange interaction between two electrons. Our analysis with simple spin functions demonstrates that singlet fission is possible by spin exchange. A necessary condition for spin exchange is a variation in exchange interactions. We also adapt the spin exchange model to triplet fusion and triplet energy transfer, which often occur after singlet fission in organic solids.

Understanding mobility degeneration mechanism in organic thin-film transistors (OTFT)

NASA Astrophysics Data System (ADS)

Wang, Wei; Wang, Long; Xu, Guangwei; Gao, Nan; Wang, Lingfei; Ji, Zhuoyu; Lu, Congyan; Lu, Nianduan; Li, Ling; Liu, Miwng

2017-08-01

Mobility degradation at high gate bias is often observed in organic thin film transistors. We propose a mechanism for this confusing phenomenon, based on the percolation theory with the presence of disordered energy landscape with an exponential density of states. Within a simple model we show how the surface states at insulator/organic interface trap a portion of channel carriers, and result in decrease of mobility as well as source/drain current with gate voltage. Depending on the competition between the carrier accumulation and surface trapping effect, two different carrier density dependences of mobility are obtained, in excellent agreement with experiment data.

Pharmacokinetic study of arctigenin in rat plasma and organ tissue by RP-HPLC method.

PubMed

He, Fan; Dou, De-Qiang; Hou, Qiang; Sun, Yu; Kang, Ting-Guo

2013-01-01

A high-performance liquid chromatography (HPLC) technique was developed for the determination of arctigenin in plasma and various organs of rats after the oral administration of 30, 50 and 70 mgkg(-1) of arctigenin to the Sprague-Dawley rats. Results showed that the validated HPLC method was simple, fast, reproducible and suitable to the determination of arctigenin in rat plasma and organ tissue and one-compartmental model with zero-order absorption process can well describe the changes of arctigenin concentration in the plasma. The concentration of compound was highest in the spleen, less in the liver and the least in the lung.

[Caenorhabditis elegans: a powerful tool for drug discovery].

PubMed

Jia, Xi-Hua; Cao, Cheng

2009-07-01

A simple model organism Caenorhabditis elegans has contributed substantially to the fundamental researches in biology. In an era of functional genomics, nematode worm has been developed into a multi-purpose tool that can be exploited to identify disease-causing or disease-associated genes, validate potential drug targets. This, coupled with its genetic amenability, low cost experimental manipulation and compatibility with high throughput screening in an intact physiological condition, makes the model organism into an effective toolbox for drug discovery. This review shows the unique features of C. elegans, how it can play a valuable role in our understanding of the molecular mechanism of human diseases and finding drug leads in drug development process.

The use of models to predict potential contamination aboard orbital vehicles

NASA Technical Reports Server (NTRS)

Boraas, Martin E.; Seale, Dianne B.

1989-01-01

A model of fungal growth on air-exposed, nonnutritive solid surfaces, developed for utilization aboard orbital vehicles is presented. A unique feature of this testable model is that the development of a fungal mycelium can facilitate its own growth by condensation of water vapor from its environment directly onto fungal hyphae. The fungal growth rate is limited by the rate of supply of volatile nutrients and fungal biomass is limited by either the supply of nonvolatile nutrients or by metabolic loss processes. The model discussed is structurally simple, but its dynamics can be quite complex. Biofilm accumulation can vary from a simple linear increase to sustained exponential growth, depending on the values of the environmental variable and model parameters. The results of the model are consistent with data from aquatic biofilm studies, insofar as the two types of systems are comparable. It is shown that the model presented is experimentally testable and provides a platform for the interpretation of observational data that may be directly relevant to the question of growth of organisms aboard the proposed Space Station.

Hot limpets: predicting body temperature in a conductance-mediated thermal system.

PubMed

Denny, Mark W; Harley, Christopher D G

2006-07-01

Living at the interface between the marine and terrestrial environments, intertidal organisms may serve as a bellwether for environmental change and a test of our ability to predict its biological consequences. However, current models do not allow us to predict the body temperature of intertidal organisms whose heat budgets are strongly affected by conduction to and from the substratum. Here, we propose a simple heat-budget model of one such animal, the limpet Lottia gigantea, and test the model against measurements made in the field. Working solely from easily measured physical and meteorological inputs, the model predicts the daily maximal body temperatures of live limpets within a fraction of a degree, suggesting that it may be a useful tool for exploring the thermal biology of limpets and for predicting effects of climate change. The model can easily be adapted to predict the temperatures of chitons, acorn barnacles, keyhole limpets, and encrusting animals and plants.

In silico method for modelling metabolism and gene product expression at genome scale

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

Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem

2012-07-03

Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome andmore » transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.« less

Mate-finding as an overlooked critical determinant of dispersal variation in sexually-reproducing animals.

PubMed

Gilroy, James J; Lockwood, Julie L

2012-01-01

Dispersal is a critically important process in ecology, but robust predictive models of animal dispersal remain elusive. We identify a potentially ubiquitous component of variation in animal dispersal that has been largely overlooked until now: the influence of mate encounters on settlement probability. We use an individual-based model to simulate dispersal in sexually-reproducing organisms that follow a simple set of movement rules based on conspecific encounters, within an environment lacking spatial habitat heterogeneity. We show that dispersal distances vary dramatically with fluctuations in population density in such a model, even in the absence of variation in dispersive traits between individuals. In a simple random-walk model with promiscuous mating, dispersal distributions become increasingly 'fat-tailed' at low population densities due to the increasing scarcity of mates. Similar variation arises in models incorporating territoriality. In a model with polygynous mating, we show that patterns of sex-biased dispersal can even be reversed across a gradient of population density, despite underlying dispersal mechanisms remaining unchanged. We show that some widespread dispersal patterns found in nature (e.g. fat tailed distributions) can arise as a result of demographic variability in the absence of heterogeneity in dispersive traits across the population. This implies that models in which individual dispersal distances are considered to be fixed traits might be unrealistic, as dispersal distances vary widely under a single dispersal mechanism when settlement is influenced by mate encounters. Mechanistic models offer a promising means of advancing our understanding of dispersal in sexually-reproducing organisms.

77 FR 50741 - Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

... interested persons. \\1\\ 15 U.S.C. 78s(b)(1). \\2\\ 17 CFR 240.19b-4. I. Self-Regulatory Organization's... orders'' as ``simple orders''. Investors generally refer to orders as either ``simple'' or ``complex'' and the terminology ``straight, one-sided orders'' is not as commonly-known. Since simple orders are...

The Polygonal Model: A Simple Representation of Biomolecules as a Tool for Teaching Metabolism

ERIC Educational Resources Information Center

Bonafe, Carlos Francisco Sampaio; Bispo, Jose Ailton Conceição; de Jesus, Marcelo Bispo

2018-01-01

Metabolism involves numerous reactions and organic compounds that the student must master to understand adequately the processes involved. Part of biochemical learning should include some knowledge of the structure of biomolecules, although the acquisition of such knowledge can be time-consuming and may require significant effort from the student.…

Strategic Planning for Smart Leadership: Rethinking Your Organization's Collective Future through a Workbook-Based, Three-Level Model.

ERIC Educational Resources Information Center

Austin, William J.

This book is a simple, user-friendly, and practical guide to strategic planning. Chapter 1 gives an introduction to and overview of strategic planning. Chapters 2 through 4 review strategic-planning theory, the current nature of planning theory, its emergence as organizational practice, organizational structure schemes, and the limitations of…

Why Flies? Inexpensive Public Engagement Exercises to Explain the Value of Basic Biomedical Research on "Drosophila melanogaster"

ERIC Educational Resources Information Center

Pulver, Stefan R.; Cognigni, Paola; Denholm, Barry; Fabre, Caroline; Gu, Wendy X. W.; Linneweber, Gerit; Prieto-Godino, Lucia; Urbancic, Vasja; Zwart, Maarten; Miguel-Aliaga, Irene

2011-01-01

Invertebrate model organisms are powerful systems for uncovering conserved principles of animal biology. Despite widespread use in scientific communities, invertebrate research is often severely undervalued by laypeople. Here, we present a set of simple, inexpensive public outreach exercises aimed at explaining to the public why basic research on…

The Library and Human Memory Simulation Studies. Reports on File Organization Studies.

ERIC Educational Resources Information Center

Reilly, Kevin D.

This report describes digital computer simulation efforts in a study of memory systems for two important cases: that of the individual the brain; and that of society, the library. A neural system model is presented in which a complex system is produced by connecting simple hypothetical neurons whose states change under application of a…

Predicting the response of soil organic matter microbial decomposition to moisture

NASA Astrophysics Data System (ADS)

Chenu, Claire; Garnier, Patricia; Monga, Olivier; Moyano, Fernando; Pot, Valérie; Nunan, Naoise; Coucheney, Elsa; Otten, Wilfred

2014-05-01

Next to temperature, soil moisture is a main driver of soil C and N transformations in soils, because it affects microbial activity and survival. The moisture sensitivity of soil organic matter decay may be a source of uncertainty of similar magnitude to that of the temperature sensitivity and receives much less attention. The basic concepts and mechanisms relating soil water to microorganisms were identified early (i.e. in steady state conditions : direct effects on microbial physiology, diffusion substrates, nutrients, extracellular enzymes, diffusion of oxygen, movement of microorganisms). However, accounting for how moisture controls soil microbial activity remains essentially empirical and poorly accounts for soil characteristics. Soil microorganisms live in a complex 3-D framework of mineral and organic particles defining pores of various sizes, connections with adjacent pores, and with pore walls of contrasted nature, which result in a variety of microhabitats. The water regime to which microorganisms are exposed can be predicted to depend the size and connectivity of pores in which they are located. Furthermore, the spatial distribution of microorganisms as well as that of organic matter is very heterogeneous, determining the diffusion distances between substrates and decomposers. A new generation of pore scale models of C dynamics in soil may challenge the difficulty of modelling such a complex system. These models are based on an explicit representation of soil structure (i.e. soil particles and voids), microorganisms and organic matter localisation. We tested here the ability of such a model to account for changes in microbial respiration with soil moisture. In the model MOSAIC II, soil pore space is described using a sphere network coming from a geometrical modelling algorithm. MicroCT tomography images were used to implement this representation of soil structure. A biological sub-model describes the hydrolysis of insoluble SOM into dissolved organic matter, its assimilation, respiration and microbial mortality. A recent improvement of the model was the description of the diffusion of soluble organic matter. We tested the model using the results from an experiment where a simple substrate (fructose) was decomposed by bacteria within a simple media (sand). Separate incubations in microcosms were carried out using five different bacterial communities at two different moisture conditions corresponding to water potentials of -0.01 and -0.1 bars. We calibrated the biological parameters using the experimental data obtained at high water content and we tested the model without any parameters change at low water content. Both the experiments and simulations showed a decrease in mineralisation with a decrease of water content, of which pattern depended on the bacterial species and its physiological characteristics. The model was able to correctly simulate the decrease of connectivity between substrate and microorganism due the decrease of water content. The potential and required developments of such models in describing how heterotrophic respiration is affected by micro-scale distribution and processes in soils and in testing scenarios regarding water regimes in a changing climate is discussed.

Self-organization, the cascade model, and natural hazards.

PubMed

Turcotte, Donald L; Malamud, Bruce D; Guzzetti, Fausto; Reichenbach, Paola

2002-02-19

We consider the frequency-size statistics of two natural hazards, forest fires and landslides. Both appear to satisfy power-law (fractal) distributions to a good approximation under a wide variety of conditions. Two simple cellular-automata models have been proposed as analogs for this observed behavior, the forest fire model for forest fires and the sand pile model for landslides. The behavior of these models can be understood in terms of a self-similar inverse cascade. For the forest fire model the cascade consists of the coalescence of clusters of trees; for the sand pile model the cascade consists of the coalescence of metastable regions.

Self-organization, the cascade model, and natural hazards

PubMed Central

Turcotte, Donald L.; Malamud, Bruce D.; Guzzetti, Fausto; Reichenbach, Paola

2002-01-01

We consider the frequency-size statistics of two natural hazards, forest fires and landslides. Both appear to satisfy power-law (fractal) distributions to a good approximation under a wide variety of conditions. Two simple cellular-automata models have been proposed as analogs for this observed behavior, the forest fire model for forest fires and the sand pile model for landslides. The behavior of these models can be understood in terms of a self-similar inverse cascade. For the forest fire model the cascade consists of the coalescence of clusters of trees; for the sand pile model the cascade consists of the coalescence of metastable regions. PMID:11875206

Adequate model complexity for scenario analysis of VOC stripping in a trickling filter.

PubMed

Vanhooren, H; Verbrugge, T; Boeije, G; Demey, D; Vanrolleghem, P A

2001-01-01

Two models describing the stripping of volatile organic contaminants (VOCs) in an industrial trickling filter system are developed. The aim of the models is to investigate the effect of different operating conditions (VOC loads and air flow rates) on the efficiency of VOC stripping and the resulting concentrations in the gas and liquid phases. The first model uses the same principles as the steady-state non-equilibrium activated sludge model Simple Treat, in combination with an existing biofilm model. The second model is a simple mass balance based model only incorporating air and liquid and thus neglecting biofilm effects. In a first approach, the first model was incorporated in a five-layer hydrodynamic model of the trickling filter, using the carrier material design specifications for porosity, water hold-up and specific surface area. A tracer test with lithium was used to validate this approach, and the gas mixing in the filters was studied using continuous CO2 and O2 measurements. With the tracer test results, the biodegradation model was adapted, and it became clear that biodegradation and adsorption to solids can be neglected. On this basis, a simple dynamic mass balance model was built. Simulations with this model reveal that changing the air flow rate in the trickling filter system has little effect on the VOC stripping efficiency at steady state. However, immediately after an air flow rate change, quite high flux and concentration peaks of VOCs can be expected. These phenomena are of major importance for the design of an off-gas treatment facility.

Implications of tristability in pattern-forming ecosystems

NASA Astrophysics Data System (ADS)

Zelnik, Yuval R.; Gandhi, Punit; Knobloch, Edgar; Meron, Ehud

2018-03-01

Many ecosystems show both self-organized spatial patterns and multistability of possible states. The combination of these two phenomena in different forms has a significant impact on the behavior of ecosystems in changing environments. One notable case is connected to tristability of two distinct uniform states together with patterned states, which has recently been found in model studies of dryland ecosystems. Using a simple model, we determine the extent of tristability in parameter space, explore its effects on the system dynamics, and consider its implications for state transitions or regime shifts. We analyze the bifurcation structure of model solutions that describe uniform states, periodic patterns, and hybrid states between the former two. We map out the parameter space where these states exist, and note how the different states interact with each other. We further focus on two special implications with ecological significance, breakdown of the snaking range and complex fronts. We find that the organization of the hybrid states within a homoclinic snaking structure breaks down as it meets a Maxwell point where simple fronts are stationary. We also discover a new series of complex fronts between the uniform states, each with its own velocity. We conclude with a brief discussion of the significance of these findings for the dynamics of regime shifts and their potential control.

A general method for radio spectrum efficiency defining

NASA Astrophysics Data System (ADS)

Ramadanovic, Ljubomir M.

1986-08-01

A general method for radio spectrum efficiency defining is proposed. Although simple it can be applied to various radio services. The concept of spectral elements, as information carriers, is introduced to enable the organization of larger spectral spaces - radio network models - characteristic for a particular radio network. The method is applied to some radio network models, concerning cellular radio telephone systems and digital radio relay systems, to verify its unified approach capability. All discussed radio services operate continuously.

Self-Organized Percolation and Critical Sales Fluctuations

NASA Astrophysics Data System (ADS)

Weisbuch, Gérard; Solomon, Sorin

There is a discrepancy between the standard view of equilibrium through price adjustment in economics and the observation of large fluctuations in stock markets. We study here a simple model where agents decisions not only depend upon their individual preferences but also upon information obtained from their neighbors in a social network. The model shows that information diffusion coupled to the adjustment process drives the system to criticality with large fluctuations rather than converging smoothly to equilibrium.

Optimization in the Face of Contradictory Criteria - the Example of Muscle

NASA Astrophysics Data System (ADS)

Davison, M.; Shiner, J. S.

2002-09-01

Biological thought suggests that organisms tend toward optimal design through evolution. This optimization should be evident in the physiology of organs and organ systems. However, a given organ often has multiple roles to play in the optimization of the organism, and sometimes the logical optimization criteria for the different roles may be contradictory. In this paper we consider the case of skeletal muscle. One of its obvious functions is movement of the organism, for which efficiency is clearly a goal. However, muscle is also important for temperature regulation through shivering. In this latter function muscle should produce heat; i.e. it should be maximally inefficient. The thermodynamic optimizations desired for these two roles appear diametrically opposed. We show a way out of this dilemma by constructing a simple, physiologically motivated model of the contraction-relaxation cycle of muscle. This model muscle can be both an efficient mover in a ‘purposeful contraction’ regime, characterized by large movements of low frequency, and a good heat producer in a distinct ‘shivering’ regime characterized by small movements of high frequency.

Real versus Artificial Variation in the Thermal Sensitivity of Biological Traits.

PubMed

Pawar, Samraat; Dell, Anthony I; Savage, Van M; Knies, Jennifer L

2016-02-01

Whether the thermal sensitivity of an organism's traits follows the simple Boltzmann-Arrhenius model remains a contentious issue that centers around consideration of its operational temperature range and whether the sensitivity corresponds to one or a few underlying rate-limiting enzymes. Resolving this issue is crucial, because mechanistic models for temperature dependence of traits are required to predict the biological effects of climate change. Here, by combining theory with data on 1,085 thermal responses from a wide range of traits and organisms, we show that substantial variation in thermal sensitivity (activation energy) estimates can arise simply because of variation in the range of measured temperatures. Furthermore, when thermal responses deviate systematically from the Boltzmann-Arrhenius model, variation in measured temperature ranges across studies can bias estimated activation energy distributions toward higher mean, median, variance, and skewness. Remarkably, this bias alone can yield activation energies that encompass the range expected from biochemical reactions (from ~0.2 to 1.2 eV), making it difficult to establish whether a single activation energy appropriately captures thermal sensitivity. We provide guidelines and a simple equation for partially correcting for such artifacts. Our results have important implications for understanding the mechanistic basis of thermal responses of biological traits and for accurately modeling effects of variation in thermal sensitivity on responses of individuals, populations, and ecological communities to changing climatic temperatures.

Critical space-time networks and geometric phase transitions from frustrated edge antiferromagnetism

NASA Astrophysics Data System (ADS)

Trugenberger, Carlo A.

2015-12-01

Recently I proposed a simple dynamical network model for discrete space-time that self-organizes as a graph with Hausdorff dimension dH=4 . The model has a geometric quantum phase transition with disorder parameter (dH-ds) , where ds is the spectral dimension of the dynamical graph. Self-organization in this network model is based on a competition between a ferromagnetic Ising model for vertices and an antiferromagnetic Ising model for edges. In this paper I solve a toy version of this model defined on a bipartite graph in the mean-field approximation. I show that the geometric phase transition corresponds exactly to the antiferromagnetic transition for edges, the dimensional disorder parameter of the former being mapped to the staggered magnetization order parameter of the latter. The model has a critical point with long-range correlations between edges, where a continuum random geometry can be defined, exactly as in Kazakov's famed 2D random lattice Ising model but now in any number of dimensions.

Health crises and media relations: relationship management-by-fire.

PubMed

Springston, Jeffrey K; Weaver-Lariscy, Ruthann

2007-01-01

Media relations is an important function in the operation of any health organization, yet it is often relegated as a simple task function. Such an orientation can be problematic, particularly in times of crisis. This article provides an overview of some of the inherent internal conflicts within health organizations that may mitigate against the best media relations practices in times of crises. The article surveys some of the predominant theoretical models used for crisis management, and suggests directions for the further development of media relations and crisis communication theory and practice.

Self-organized synthesis of silver dendritic nanostructures via an electroless metal deposition method

NASA Astrophysics Data System (ADS)

Qiu, T.; Wu, X. L.; Mei, Y. F.; Chu, P. K.; Siu, G. G.

2005-09-01

Unique silver dendritic nanostructures, with stems, branches, and leaves, were synthesized with self-organization via a simple electroless metal deposition method in a conventional autoclave containing aqueous HF and AgNO3 solution. Their growth mechanisms are discussed in detail on the basis of a self-assembled localized microscopic electrochemical cell model. A process of diffusion-limited aggregation is suggested for the formation of the silver dendritic nanostructures. This nanostructured material is of great potential to be building blocks for assembling mini-functional devices of the next generation.

Equilibrium and disequilibrium chemistry of adiabatic, solar-composition planetary atmospheres

NASA Technical Reports Server (NTRS)

Lewis, J. S.

1976-01-01

The impact of atmospheric and cloud-structure models on the nonequilibrium chemical behavior of the atmospheres of the Jovian planets is discussed. Quantitative constraints on photochemical, lightning, and charged-particle production of organic matter and chromophores are emphasized whenever available. These considerations imply that inorganic chromophore production is far more important than that of organic chromophores, and that lightning is probably a negligibly significant process relative to photochemistry on Jupiter. Production of complex molecules by gas-phase disequilibrium processes on Saturn, Uranus, and Neptune is severely limited by condensation of even simple intermediates.

Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth System Models

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

Xu, Xiaofeng; Schimel, Joshua; Thornton, Peter E

2014-01-01

Microbial assimilation of soil organic carbon is one of the fundamental processes of global carbon cycling and it determines the magnitude of microbial biomass in soils. Mechanistic understanding of microbial assimilation of soil organic carbon and its controls is important for to improve Earth system models ability to simulate carbon-climate feedbacks. Although microbial assimilation of soil organic carbon is broadly considered to be an important parameter, it really comprises two separate physiological processes: one-time assimilation efficiency and time-dependent microbial maintenance energy. Representing of these two mechanisms is crucial to more accurately simulate carbon cycling in soils. In this study, amore » simple modeling framework was developed to evaluate the substrate and environmental controls on microbial assimilation of soil organic carbon using a new term: microbial annual active period (the length of microbes remaining active in one year). Substrate quality has a positive effect on microbial assimilation of soil organic carbon: higher substrate quality (lower C:N ratio) leads to higher ratio of microbial carbon to soil organic carbon and vice versa. Increases in microbial annual active period from zero stimulate microbial assimilation of soil organic carbon; however, when microbial annual active period is longer than an optimal threshold, increasing this period decreases microbial biomass. The simulated ratios of soil microbial biomass to soil organic carbon are reasonably consistent with a recently compiled global dataset at the biome-level. The modeling framework of microbial assimilation of soil organic carbon and its controls developed in this study offers an applicable ways to incorporate microbial contributions to the carbon cycling into Earth system models for simulating carbon-climate feedbacks and to explain global patterns of microbial biomass.« less

The Caenorhabditis elegans Excretory System: A Model for Tubulogenesis, Cell Fate Specification, and Plasticity

PubMed Central

Sundaram, Meera V.; Buechner, Matthew

2016-01-01

The excretory system of the nematode Caenorhabditis elegans is a superb model of tubular organogenesis involving a minimum of cells. The system consists of just three unicellular tubes (canal, duct, and pore), a secretory gland, and two associated neurons. Just as in more complex organs, cells of the excretory system must first adopt specific identities and then coordinate diverse processes to form tubes of appropriate topology, shape, connectivity, and physiological function. The unicellular topology of excretory tubes, their varied and sometimes complex shapes, and the dynamic reprogramming of cell identity and remodeling of tube connectivity that occur during larval development are particularly fascinating features of this organ. The physiological roles of the excretory system in osmoregulation and other aspects of the animal’s life cycle are only beginning to be explored. The cellular mechanisms and molecular pathways used to build and shape excretory tubes appear similar to those used in both unicellular and multicellular tubes in more complex organs, such as the vertebrate vascular system and kidney, making this simple organ system a useful model for understanding disease processes. PMID:27183565

Exploring simple, transparent, interpretable and predictive QSAR models for classification and quantitative prediction of rat toxicity of ionic liquids using OECD recommended guidelines.

PubMed

Das, Rudra Narayan; Roy, Kunal; Popelier, Paul L A

2015-11-01

The present study explores the chemical attributes of diverse ionic liquids responsible for their cytotoxicity in a rat leukemia cell line (IPC-81) by developing predictive classification as well as regression-based mathematical models. Simple and interpretable descriptors derived from a two-dimensional representation of the chemical structures along with quantum topological molecular similarity indices have been used for model development, employing unambiguous modeling strategies that strictly obey the guidelines of the Organization for Economic Co-operation and Development (OECD) for quantitative structure-activity relationship (QSAR) analysis. The structure-toxicity relationships that emerged from both classification and regression-based models were in accordance with the findings of some previous studies. The models suggested that the cytotoxicity of ionic liquids is dependent on the cationic surfactant action, long alkyl side chains, cationic lipophilicity as well as aromaticity, the presence of a dialkylamino substituent at the 4-position of the pyridinium nucleus and a bulky anionic moiety. The models have been transparently presented in the form of equations, thus allowing their easy transferability in accordance with the OECD guidelines. The models have also been subjected to rigorous validation tests proving their predictive potential and can hence be used for designing novel and "greener" ionic liquids. The major strength of the present study lies in the use of a diverse and large dataset, use of simple reproducible descriptors and compliance with the OECD norms. Copyright © 2015 Elsevier Ltd. All rights reserved.

Diversity within a Birdsong

NASA Astrophysics Data System (ADS)

Laje, Rodrigo; Mindlin, Gabriel B.

2002-12-01

We present a model for the activities of neural circuits in a nucleus found in the brains of songbirds: the robust nucleus of the archistriatum (RA). This is a fore brain song control nucleus responsible for the phasic and precise neural signals driving vocal and respiratory motor neurons during singing. Driving a physical model of the avian vocal organ with the signals generated by the neural model, we produce synthetic songs. This allows us to show that certain connectivity architectures in the RA give rise to a wide range of different vocalizations under simple excitatory instructions.

A Simple Model for the Evolution of Multi-Stranded Coronal Loops

NASA Technical Reports Server (NTRS)

Fuentes, M. C. Lopez; Klimchuk, J. A.

2010-01-01

We develop and analyze a simple cellular automaton (CA) model that reproduces the main properties of the evolution of soft X-ray coronal loops. We are motivated by the observation that these loops evolve in three distinguishable phases that suggest the development, maintainance, and decay of a self-organized system. The model is based on the idea that loops are made of elemental strands that are heated by the relaxation of magnetic stress in the form of nanoflares. In this vision, usually called "the Parker conjecture" (Parker 1988), the origin of stress is the displacement of the strand footpoints due to photospheric convective motions. Modeling the response and evolution of the plasma we obtain synthetic light curves that have the same characteristic properties (intensity, fluctuations, and timescales) as the observed cases. We study the dependence of these properties on the model parameters and find scaling laws that can be used as observational predictions of the model. We discuss the implications of our results for the interpretation of recent loop observations in different wavelengths. Subject headings: Sun: corona - Sun: flares - Sun: magnetic topology - Sun: X-rays, gamma rays

Circularly Polarized Luminescence from Simple Organic Molecules.

PubMed

Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago

2015-09-21

This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theory of periodic swarming of bacteria: Application to Proteus mirabilis

NASA Astrophysics Data System (ADS)

Czirók, A.; Matsushita, M.; Vicsek, T.

2001-03-01

The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common species exhibiting this type of growth), a series of concentric rings are developed as the bacteria multiply and swarm following a scenario that periodically repeats itself. We have developed a theoretical description for this process in order to obtain a deeper insight into some of the typical processes governing the phenomena in systems of many interacting living units. Our approach is based on simple assumptions directly related to the latest experimental observations on colony formation under various conditions. The corresponding one-dimensional model consists of two coupled differential equations investigated here both by numerical integrations and by analyzing the various expressions obtained from these equations using a few natural assumptions about the parameters of the model. We determine the phase diagram corresponding to systems exhibiting periodic swarming, and discuss in detail how the various stages of the colony development can be interpreted in our framework. We point out that all of our theoretical results are in excellent agreement with the complete set of available observations. Thus the present study represents one of the few examples where self-organized biological pattern formation is understood within a relatively simple theoretical approach, leading to results and predictions fully compatible with experiments.

Shift scheduling model considering workload and worker’s preference for security department

NASA Astrophysics Data System (ADS)

Herawati, A.; Yuniartha, D. R.; Purnama, I. L. I.; Dewi, LT

2018-04-01

Security department operates for 24 hours and applies shift scheduling to organize its workers as well as in hotel industry. This research has been conducted to develop shift scheduling model considering the workers physical workload using rating of perceived exertion (RPE) Borg’s Scale and workers’ preference to accommodate schedule flexibility. The mathematic model is developed in integer linear programming and results optimal solution for simple problem. Resulting shift schedule of the developed model has equally distribution shift allocation among workers to balance the physical workload and give flexibility for workers in working hours arrangement.

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

NASA Astrophysics Data System (ADS)

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

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

Stochastic models for plant microtubule self-organization and structure.

PubMed

Eren, Ezgi C; Dixit, Ram; Gautam, Natarajan

2015-12-01

One of the key enablers of shape and growth in plant cells is the cortical microtubule (CMT) system, which is a polymer array that forms an appropriately-structured scaffolding in each cell. Plant biologists have shown that stochastic dynamics and simple rules of interactions between CMTs can lead to a coaligned CMT array structure. However, the mechanisms and conditions that cause CMT arrays to become organized are not well understood. It is prohibitively time-consuming to use actual plants to study the effect of various genetic mutations and environmental conditions on CMT self-organization. In fact, even computer simulations with multiple replications are not fast enough due to the spatio-temporal complexity of the system. To redress this shortcoming, we develop analytical models and methods for expeditiously computing CMT system metrics that are related to self-organization and array structure. In particular, we formulate a mean-field model to derive sufficient conditions for the organization to occur. We show that growth-prone dynamics itself is sufficient to lead to organization in presence of interactions in the system. In addition, for such systems, we develop predictive methods for estimation of system metrics such as expected average length and number of CMTs over time, using a stochastic fluid-flow model, transient analysis, and approximation algorithms tailored to our problem. We illustrate the effectiveness of our approach through numerical test instances and discuss biological insights.

Derivation of rigorous conditions for high cell-type diversity by algebraic approach.

PubMed

Yoshida, Hiroshi; Anai, Hirokazu; Horimoto, Katsuhisa

2007-01-01

The development of a multicellular organism is a dynamic process. Starting with one or a few cells, the organism develops into different types of cells with distinct functions. We have constructed a simple model by considering the cell number increase and the cell-type order conservation, and have assessed conditions for cell-type diversity. This model is based on a stochastic Lindenmayer system with cell-to-cell interactions for three types of cells. In the present model, we have successfully derived complex but rigorous algebraic relations between the proliferation and transition rates for cell-type diversity by using a symbolic method: quantifier elimination (QE). Surprisingly, three modes for the proliferation and transition rates have emerged for large ratios of the initial cells to the developed cells. The three modes have revealed that the equality between the development rates for the highest cell-type diversity is reduced during the development process of multicellular organisms. Furthermore, we have found that the highest cell-type diversity originates from order conservation.

Mycoplasma pneumoniae, an Underutilized Model for Bacterial Cell Biology

PubMed Central

2014-01-01

In recent decades, bacterial cell biology has seen great advances, and numerous model systems have been developed to study a wide variety of cellular processes, including cell division, motility, assembly of macromolecular structures, and biogenesis of cell polarity. Considerable attention has been given to these model organisms, which include Escherichia coli, Bacillus subtilis, Caulobacter crescentus, and Myxococcus xanthus. Studies of these processes in the pathogenic bacterium Mycoplasma pneumoniae and its close relatives have also been carried out on a smaller scale, but this work is often overlooked, in part due to this organism's reputation as minimalistic and simple. In this minireview, I discuss recent work on the role of the M. pneumoniae attachment organelle (AO), a structure required for adherence to host cells, in these processes. The AO is constructed from proteins that generally lack homology to those found in other organisms, and this construction occurs in coordination with cell cycle events. The proteins of the M. pneumoniae AO share compositional features with proteins with related roles in model organisms. Once constructed, the AO becomes activated for its role in a form of gliding motility whose underlying mechanism appears to be distinct from that of other gliding bacteria, including Mycoplasma mobile. Together with the FtsZ cytoskeletal protein, motility participates in the cell division process. My intention is to bring this deceptively complex organism into alignment with the better-known model systems. PMID:25157081

Simple models for studying complex spatiotemporal patterns of animal behavior

NASA Astrophysics Data System (ADS)

Tyutyunov, Yuri V.; Titova, Lyudmila I.

2017-06-01

Minimal mathematical models able to explain complex patterns of animal behavior are essential parts of simulation systems describing large-scale spatiotemporal dynamics of trophic communities, particularly those with wide-ranging species, such as occur in pelagic environments. We present results obtained with three different modelling approaches: (i) an individual-based model of animal spatial behavior; (ii) a continuous taxis-diffusion-reaction system of partial-difference equations; (iii) a 'hybrid' approach combining the individual-based algorithm of organism movements with explicit description of decay and diffusion of the movement stimuli. Though the models are based on extremely simple rules, they all allow description of spatial movements of animals in a predator-prey system within a closed habitat, reproducing some typical patterns of the pursuit-evasion behavior observed in natural populations. In all three models, at each spatial position the animal movements are determined by local conditions only, so the pattern of collective behavior emerges due to self-organization. The movement velocities of animals are proportional to the density gradients of specific cues emitted by individuals of the antagonistic species (pheromones, exometabolites or mechanical waves of the media, e.g., sound). These cues play a role of taxis stimuli: prey attract predators, while predators repel prey. Depending on the nature and the properties of the movement stimulus we propose using either a simplified individual-based model, a continuous taxis pursuit-evasion system, or a little more detailed 'hybrid' approach that combines simulation of the individual movements with the continuous model describing diffusion and decay of the stimuli in an explicit way. These can be used to improve movement models for many species, including large marine predators.

Modeling vocalization with ECoG cortical activity recorded during vocal production in the macaque monkey.

PubMed

Fukushima, Makoto; Saunders, Richard C; Fujii, Naotaka; Averbeck, Bruno B; Mishkin, Mortimer

2014-01-01

Vocal production is an example of controlled motor behavior with high temporal precision. Previous studies have decoded auditory evoked cortical activity while monkeys listened to vocalization sounds. On the other hand, there have been few attempts at decoding motor cortical activity during vocal production. Here we recorded cortical activity during vocal production in the macaque with a chronically implanted electrocorticographic (ECoG) electrode array. The array detected robust activity in motor cortex during vocal production. We used a nonlinear dynamical model of the vocal organ to reduce the dimensionality of `Coo' calls produced by the monkey. We then used linear regression to evaluate the information in motor cortical activity for this reduced representation of calls. This simple linear model accounted for circa 65% of the variance in the reduced sound representations, supporting the feasibility of using the dynamical model of the vocal organ for decoding motor cortical activity during vocal production.

Microscale Organic Laboratory: IV. A Simple and Rapid Procedure for Carrying Out Wittig Reactions.

ERIC Educational Resources Information Center

Pike, R. M.; And Others

1986-01-01

Describes two examples where synthetic salt-base mixtures are used in a microscale organic laboratory program as a simple and quick procedure for carrying out Wittig reactions. Both experimental procedures are outlined and discussed. (TW)

A simple and fast method for extraction and quantification of cryptophyte phycoerythrin.

PubMed

Thoisen, Christina; Hansen, Benni Winding; Nielsen, Søren Laurentius

2017-01-01

The microalgal pigment phycoerythrin (PE) is of commercial interest as natural colorant in food and cosmetics, as well as fluoroprobes for laboratory analysis. Several methods for extraction and quantification of PE are available but they comprise typically various extraction buffers, repetitive freeze-thaw cycles and liquid nitrogen, making extraction procedures more complicated. A simple method for extraction of PE from cryptophytes is described using standard laboratory materials and equipment. The cryptophyte cells on the filters were disrupted at -80 °C and added phosphate buffer for extraction at 4 °C followed by absorbance measurement. The cryptophyte Rhodomonas salina was used as a model organism. •Simple method for extraction and quantification of phycoerythrin from cryptophytes.•Minimal usage of equipment and chemicals, and low labor costs.•Applicable for industrial and biological purposes.

RUNX in Invertebrates.

PubMed

Hughes, S; Woollard, A

2017-01-01

Runx genes have been identified in all metazoans and considerable conservation of function observed across a wide range of phyla. Thus, insight gained from studying simple model organisms is invaluable in understanding RUNX biology in higher animals. Consequently, this chapter will focus on the Runx genes in the diploblasts, which includes sea anemones and sponges, as well as the lower triploblasts, including the sea urchin, nematode, planaria and insect. Due to the high degree of functional redundancy amongst vertebrate Runx genes, simpler model organisms with a solo Runx gene, like C. elegans, are invaluable systems in which to probe the molecular basis of RUNX function within a whole organism. Additionally, comparative analyses of Runx sequence and function allows for the development of novel evolutionary insights. Strikingly, recent data has emerged that reveals the presence of a Runx gene in a protist, demonstrating even more widespread occurrence of Runx genes than was previously thought. This review will summarize recent progress in using invertebrate organisms to investigate RUNX function during development and regeneration, highlighting emerging unifying themes.

Singlet-Oxygen Generation in Alkaline Periodate Solution.

PubMed

Bokare, Alok D; Choi, Wonyong

2015-12-15

A nonphotochemical generation of singlet oxygen ((1)O2) using potassium periodate (KIO4) in alkaline condition (pH > 8) was investigated for selective oxidation of aqueous organic pollutants. The generation of (1)O2 was initiated by the spontaneous reaction between IO4(-) and hydroxyl ions, along with a stoichiometric conversion of IO4(-) to iodate (IO3(-)). The reactivity of in-situ-generated (1)O2 was monitored by using furfuryl alcohol (FFA) as a model substrate. The formation of (1)O2 in the KIO4/KOH system was experimentally confirmed using electron spin resonance (ESR) measurements in corroboration with quenching studies using azide as a selective (1)O2 scavenger. The reaction in the KIO4/KOH solution in both oxic and anoxic conditions initiated the generation of superoxide ion as a precursor of the singlet oxygen (confirmed by using superoxide scavengers), and the presence of molecular oxygen was not required as a precursor of (1)O2. Although hydrogen peroxide had no direct influence on the FFA oxidation process, the presence of natural organic matter, such as humic and fulvic acids, enhanced the oxidation efficiency. Using the oxidation of simple organic diols as model compounds, the enhanced (1)O2 formation is attributed to periodate-mediated oxidation of vicinal hydroxyl groups present in humic and fulvic constituent moieties. The efficient and simple generation of (1)O2 using the KIO4/KOH system without any light irradiation can be employed for the selective oxidation of aqueous organic compounds under neutral and near-alkaline conditions.

HESS Opinions Catchments as meta-organisms - a new blueprint for hydrological modelling

NASA Astrophysics Data System (ADS)

Savenije, Hubert H. G.; Hrachowitz, Markus

2017-02-01

Catchment-scale hydrological models frequently miss essential characteristics of what determines the functioning of catchments. The most important active agent in catchments is the ecosystem. It manipulates and partitions moisture in a way that supports the essential functions of survival and productivity: infiltration of water, retention of moisture, mobilization and retention of nutrients, and drainage. Ecosystems do this in the most efficient way, establishing a continuous, ever-evolving feedback loop with the landscape and climatic drivers. In brief, hydrological systems are alive and have a strong capacity to adjust themselves to prevailing and changing environmental conditions. Although most models take Newtonian theory at heart, as best they can, what they generally miss is Darwinian theory on how an ecosystem evolves and adjusts its environment to maintain crucial hydrological functions. In addition, catchments, such as many other natural systems, do not only evolve over time, but develop features of spatial organization, including surface or sub-surface drainage patterns, as a by-product of this evolution. Models that fail to account for patterns and the associated feedbacks miss a critical element of how systems at the interface of atmosphere, biosphere and pedosphere function. In contrast to what is widely believed, relatively simple, semi-distributed conceptual models have the potential to accommodate organizational features and their temporal evolution in an efficient way, a reason for that being that because their parameters (and their evolution over time) are effective at the modelling scale, and thus integrate natural heterogeneity within the system, they may be directly inferred from observations at the same scale, reducing the need for calibration and related problems. In particular, the emergence of new and more detailed observation systems from space will lead towards a more robust understanding of spatial organization and its evolution. This will further permit the development of relatively simple time-dynamic functional relationships that can meaningfully represent spatial patterns and their evolution over time, even in poorly gauged environments.

Diatom-sedimentation feedback generates a self-organized geomorphic landscape on intertidal mudflats (Invited)

NASA Astrophysics Data System (ADS)

van de Koppel, J.; Weerman, E.; Herman, P.

2010-12-01

During spring, intertidal flats can exhibit strikingly regular spatial patterns of diatom-covered hummocks alternating with almost bare, water-filled hollows. We hypothesize that 1) the formation of this geomorphic landscape is caused by a strong interaction between benthic diatoms and sediment dynamics, inducing spatial self-organization, and 2) that self-organization affects ecosystem functioning by increasing the net average sedimentation on the tidal flat. We present a combined empirical and mathematical study to test the first hypothesis. We determined how the sediment erosion threshold varied with diatom cover and elevation. Our results were incorporated into a mathematical model to investigate whether the proposed mechanism could explain the formation of the observed patterns. Our mathematical model confirmed that the interaction between sedimentation, diatom growth and water redistribution could induce the formation of regular patterns on the intertidal mudflat. The model predicts that areas exhibiting spatially-self-organized patterns have increased sediment accretion and diatom biomass compared with areas lacking spatial patterns. We tested this prediction by following the sediment elevation during the season on both patterned and unpatterned parts of the mudflat. The results of our study confirmed our model prediction, as more sediment was found to accumulate in patterned parts of the mudflat, revealing how self-organization affected the functioning of mudflat ecosystems. Our study on intertidal mudflats provides a simple but clear-cut example of how the interaction between biological and geomorphological processes, through the process of self-organization, induces a self-organized geomorphic landscape.

Growth factors, nutrient signaling, and cardiovascular aging

PubMed Central

Fontana, Luigi; Vinciguerra, Manlio; Longo, Valter D.

2012-01-01

Growth factors regulated by specific macronutrients have been shown to promote aging and accelerate mortality in the great majority of the organisms studied. In particular, the enzymes activated by growth hormone (GH), insulin and insulin-like growth factor 1 (IGF-I) in mammals and their orthologs in simple model organisms represent perhaps the best-understood proteins involved in the aging process. Dietary restriction (DR), which reduces the level of IGF-I and of other growth factors, has been associated with protection from diabetes, cancer, and cardiovascular diseases and deficiencies in GH signaling and IGF-I are strongly associated with protection from cancer and diabetes in both mice and humans, but their role in cardiac function and cardiovascular diseases is controversial. Here we review the link between growth factors, cardiac function and heart disease with focus on the cardioprotective and sensitizing effect of growth factors in both model organisms and humans. PMID:22499903

Critical properties of unlimited gliding: Unexpected flocking behavior driven by the exchange of information

NASA Astrophysics Data System (ADS)

Bigus-Kwiatkowska, Marta; Fronczak, Agata; Fronczak, Piotr

2018-03-01

Inspired by albatrosses that use thermal lifts to fly across oceans we develop a simple model of gliders that serves us to study theoretical limitations of unlimited exploration of the Earth. Our studies, grounded in physical theory of continuous percolation and biased random walks, allow us to identify a variety of percolation transitions, which are understood as providing potentially unlimited movement through a space in a specified direction. We discover an unexpected phenomenon of self-organization of gliders in clusters, which resembles the flock organization of birds. This self-organization is intriguing, as it occurs thanks to exchange of information only and without any particular rules that could favor the clustering of the gliders (in contrast to the causes well known in literature, like, for example, attractive forces used in the Vicsek-type models or fitness functions used in evolutionary computation).

Understanding of Leaf Development-the Science of Complexity.

PubMed

Malinowski, Robert

2013-06-25

The leaf is the major organ involved in light perception and conversion of solar energy into organic carbon. In order to adapt to different natural habitats, plants have developed a variety of leaf forms, ranging from simple to compound, with various forms of dissection. Due to the enormous cellular complexity of leaves, understanding the mechanisms regulating development of these organs is difficult. In recent years there has been a dramatic increase in the use of technically advanced imaging techniques and computational modeling in studies of leaf development. Additionally, molecular tools for manipulation of morphogenesis were successfully used for in planta verification of developmental models. Results of these interdisciplinary studies show that global growth patterns influencing final leaf form are generated by cooperative action of genetic, biochemical, and biomechanical inputs. This review summarizes recent progress in integrative studies on leaf development and illustrates how intrinsic features of leaves (including their cellular complexity) influence the choice of experimental approach.

Understanding of Leaf Development—the Science of Complexity

PubMed Central

Malinowski, Robert

2013-01-01

The leaf is the major organ involved in light perception and conversion of solar energy into organic carbon. In order to adapt to different natural habitats, plants have developed a variety of leaf forms, ranging from simple to compound, with various forms of dissection. Due to the enormous cellular complexity of leaves, understanding the mechanisms regulating development of these organs is difficult. In recent years there has been a dramatic increase in the use of technically advanced imaging techniques and computational modeling in studies of leaf development. Additionally, molecular tools for manipulation of morphogenesis were successfully used for in planta verification of developmental models. Results of these interdisciplinary studies show that global growth patterns influencing final leaf form are generated by cooperative action of genetic, biochemical, and biomechanical inputs. This review summarizes recent progress in integrative studies on leaf development and illustrates how intrinsic features of leaves (including their cellular complexity) influence the choice of experimental approach. PMID:27137383

Growth factors, nutrient signaling, and cardiovascular aging.

PubMed

Fontana, Luigi; Vinciguerra, Manlio; Longo, Valter D

2012-04-13

Growth factors regulated by specific macronutrients have been shown to promote aging and accelerate mortality in the majority of the organisms studied. In particular, the enzymes activated by growth hormone, insulin, and insulin-like growth factor-1 in mammals and their orthologs in simple model organisms represent perhaps the best-understood proteins involved in the aging process. Dietary restriction, which reduces the level of insulin-like growth factor-1 and of other growth factors, has been associated with protection from diabetes, cancer, and cardiovascular diseases, and deficiencies in growth hormone signaling and insulin-like growth factor-1 are strongly associated with protection from cancer and diabetes in both mice and humans; however, their role in cardiac function and cardiovascular diseases is controversial. Here, we review the link between growth factors, cardiac function, and heart disease with focus on the cardioprotective and sensitizing effect of growth factors in both model organisms and humans.

Beneath Our Feet: Strategies for Locomotion in Granular Media

NASA Astrophysics Data System (ADS)

Hosoi, A. E.; Goldman, Daniel I.

2015-01-01

“If you find yourself in a hole, stop digging.” Although Denis Healey's famous adage ( Metcalfe 2007 ) may offer sound advice for politicians, it is less relevant to worms, clams, and other higher organisms that rely on their digging ability for survival. In this article, we review recent work on the development of simple models that elucidate the fundamental principles underlying digging and burrowing strategies employed by biological systems. Four digging regimes are identified based on dimensionless digger size and the dimensionless inertial number. We select biological organisms to represent three of the four regimes: razor clams, sandfish, and nematodes. Models for all three diggers are derived and discussed, and analogies are drawn to low-Reynolds number swimmers.

Molecular mechanisms of floral organ specification by MADS domain proteins.

PubMed

Yan, Wenhao; Chen, Dijun; Kaufmann, Kerstin

2016-02-01

Flower development is a model system to understand organ specification in plants. The identities of different types of floral organs are specified by homeotic MADS transcription factors that interact in a combinatorial fashion. Systematic identification of DNA-binding sites and target genes of these key regulators show that they have shared and unique sets of target genes. DNA binding by MADS proteins is not based on 'simple' recognition of a specific DNA sequence, but depends on DNA structure and combinatorial interactions. Homeotic MADS proteins regulate gene expression via alternative mechanisms, one of which may be to modulate chromatin structure and accessibility in their target gene promoters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Assessing exposure to transformation products of soil-applied organic contaminants in surface water: comparison of model predictions and field data.

PubMed

Kern, Susanne; Singer, Heinz; Hollender, Juliane; Schwarzenbach, René P; Fenner, Kathrin

2011-04-01

Transformation products (TPs) of chemicals released to soil, for example, pesticides, are regularly detected in surface and groundwater with some TPs even dominating observed pesticide levels. Given the large number of TPs potentially formed in the environment, straightforward prioritization methods based on available data and simple, evaluative models are required to identify TPs with a high aquatic exposure potential. While different such methods exist, none of them has so far been systematically evaluated against field data. Using a dynamic multimedia, multispecies model for TP prioritization, we compared the predicted relative surface water exposure potential of pesticides and their TPs with experimental data for 16 pesticides and 46 TPs measured in a small river draining a Swiss agricultural catchment. Twenty TPs were determined quantitatively using solid-phase extraction liquid chromatography mass spectrometry (SPE-LC-MS/MS), whereas the remaining 26 TPs could only be detected qualitatively because of the lack of analytical reference standards. Accordingly, the two sets of TPs were used for quantitative and qualitative model evaluation, respectively. Quantitative comparison of predicted with measured surface water exposure ratios for 20 pairs of TPs and parent pesticides indicated agreement within a factor of 10, except for chloridazon-desphenyl and chloridazon-methyl-desphenyl. The latter two TPs were found to be present in elevated concentrations during baseflow conditions and in groundwater samples across Switzerland, pointing toward high concentrations in exfiltrating groundwater. A simple leaching relationship was shown to qualitatively agree with the observed baseflow concentrations and to thus be useful in identifying TPs for which the simple prioritization model might underestimate actual surface water concentrations. Application of the model to the 26 qualitatively analyzed TPs showed that most of those TPs categorized as exhibiting a high aquatic exposure potential could be confirmed to be present in the majority of water samples investigated. On the basis of these results, we propose a generally applicable, model-based approach to identify those TPs of soil-applied organic contaminants that exhibit a high aquatic exposure potential to prioritize them for higher-tier, experimental investigations.

Selective complexation of K+ and Na+ in simple polarizable ion-ligating systems.

PubMed

Bostick, David L; Brooks, Charles L

2010-09-29

An influx of experimental and theoretical studies of ion transport protein structure has inspired efforts to understand underlying determinants of ionic selectivity. Design principles for selective ion binding can be effectively isolated and interrogated using simplified models composed of a single ion surrounded by a set of ion-ligating molecular species. While quantum mechanical treatments of such systems naturally incorporate electronic degrees of freedom, their computational overhead typically prohibits thorough dynamic sampling of configurational space and, thus, requires approximations when determining ion-selective free energy. As an alternative, we employ dynamical simulations with a polarizable force field to probe the structure and K(+)/Na(+) selectivity in simple models composed of one central K(+)/Na(+) ion surrounded by 0-8 identical model compounds: N-methylacetamide, formamide, or water. In the absence of external restraints, these models represent gas-phase clusters displaying relaxed coordination structures with low coordination number. Such systems display Na(+) selectivity when composed of more than ∼3 organic carbonyl-containing compounds and always display K(+) selectivity when composed of water molecules. Upon imposing restraints that solely enforce specific coordination numbers, we find all models are K(+)-selective when ∼7-8-fold ion coordination is achieved. However, when models composed of the organic compounds provide ∼4-6-fold coordination, they retain their Na(+) selectivity. From these trends, design principles emerge that are of basic importance in the behavior of K(+) channel selectivity filters and suggest a basis not only for K(+) selectivity but also for modulation of block and closure by smaller ions.

Organic geochemistry of sediments from the continental margin off southern New England, U.S.A.--Part I. Amino acids, carbohydrates and lignin

NASA Technical Reports Server (NTRS)

Steinberg, S. M.; Venkatesan, M. I.; Kaplan, I. R.

1987-01-01

Total organic carbon (TOC), lignin, amino acids, sugars and amino sugars were measured in recent sediments for the continental margin off southern New England. The various organic carbon fractions decreased in concentration with increasing distance from shore. The fraction of the TOC that was accounted for by these major components also decreased with increasing distance from shore. The concentration of lignin indicated that only about 3-5% of the organic carbon in the nearshore sediment was of terrestrial origin. The various fractions were highly correlated, which was consistent with a simple linear mixing model of shelf organic matter with material form the slope and rise and indicated a significant transport of sediment from the continental shelf to the continental slope and rise.

Titan's organic chemistry

NASA Technical Reports Server (NTRS)

Sagan, C.; Thompson, W. R.; Khare, B. N.

1985-01-01

Voyager discovered nine simple organic molecules in the atmosphere of Titan. Complex organic solids, called tholins, produced by irradiation of the simulated Titanian atmosphere, are consistent with measured properties of Titan from ultraviolet to microwave frequencies and are the likely main constituents of the observed red aerosols. The tholins contain many of the organic building blocks central to life on earth. At least 100-m, and possibly kms thicknesses of complex organics have been produced on Titan during the age of the solar system, and may exist today as submarine deposits beneath an extensive ocean of simple hydrocarbons.

Capillarity Guided Patterning of Microliquids.

PubMed

Kang, Myeongwoo; Park, Woohyun; Na, Sangcheol; Paik, Sang-Min; Lee, Hyunjae; Park, Jae Woo; Kim, Ho-Young; Jeon, Noo Li

2015-06-01

Soft lithography and other techniques have been developed to investigate biological and chemical phenomena as an alternative to photolithography-based patterning methods that have compatibility problems. Here, a simple approach for nonlithographic patterning of liquids and gels inside microchannels is described. Using a design that incorporates strategically placed microstructures inside the channel, microliquids or gels can be spontaneously trapped and patterned when the channel is drained. The ability to form microscale patterns inside microfluidic channels using simple fluid drain motion offers many advantages. This method is geometrically analyzed based on hydrodynamics and verified with simulation and experiments. Various materials (i.e., water, hydrogels, and other liquids) are successfully patterned with complex shapes that are isolated from each other. Multiple cell types are patterned within the gels. Capillarity guided patterning (CGP) is fast, simple, and robust. It is not limited by pattern shape, size, cell type, and material. In a simple three-step process, a 3D cancer model that mimics cell-cell and cell-extracellular matrix interactions is engineered. The simplicity and robustness of the CGP will be attractive for developing novel in vitro models of organ-on-a-chip and other biological experimental platforms amenable to long-term observation of dynamic events using advanced imaging and analytical techniques. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of conceptual models in a physical therapy curriculum: application of an integrated model of theory, research, and clinical practice.

PubMed

Darrah, Johanna; Loomis, Joan; Manns, Patricia; Norton, Barbara; May, Laura

2006-11-01

The Department of Physical Therapy, University of Alberta, Edmonton, Alberta, Canada, recently implemented a Master of Physical Therapy (MPT) entry-level degree program. As part of the curriculum design, two models were developed, a Model of Best Practice and the Clinical Decision-Making Model. Both models incorporate four key concepts of the new curriculum: 1) the concept that theory, research, and clinical practice are interdependent and inform each other; 2) the importance of client-centered practice; 3) the terminology and philosophical framework of the World Health Organization's International Classification of Functioning, Disability, and Health; and 4) the importance of evidence-based practice. In this article the general purposes of models for learning are described; the two models developed for the MPT program are described; and examples of their use with curriculum design and teaching are provided. Our experiences with both the development and use of models of practice have been positive. The models have provided both faculty and students with a simple, systematic structured framework to organize teaching and learning in the MPT program.

Radiation Chemistry in Organized Assemblies.

ERIC Educational Resources Information Center

Thomas, J. K.; Chen, T. S.

1981-01-01

Expands the basic concepts regarding the radiation chemistry of simple aqueous systems to more complex, but well defined, organized assemblies. Discusses the differences in behavior in comparison to simple systems. Reviews these techniques: pulse radiolysis, laser flash, photolysis, and steady state irradiation by gamma rays or light. (CS)

Application of the IAS theory combining to a three compartments description of natural organic matter to the adsorption of atrazine or diuron on activated carbon.

PubMed

Baudu, M; Raveau, D; Guibaud, G

2004-07-01

The study of natural organic matter (NOM) adsorption on an activated carbon showed that equilibrium cannot be described according to a simple model such as a Freundlich isotherm and confirms the need for a closer description of the organic matter to simulate the competitive adsorption with micropollutants. A representation of the organic matter in three fractions is chosen: non-adsorbable, weak and strong adsorbable. The Ideal Adsorbed Solution Theory (IAST) can, under restrictive conditions, be used to effectively predict the competition between the pesticides and the organic matter. Therefore, it was noted that the model simulated with good precision the competition between atrazine or diuron and natural organic matter in aqueous solution for two activated carbons (A and B). The same parameters for the modeling of organic matter adsorption (Freudlich constants for two absorbable fractions) are used with the two pesticides. However, IAST does not allow correct modeling of pesticide adsorption onto two other (C and D) activated carbons in solution in natural water to be described. IAS theory does not reveal competition between diuron and NOM and pore blockage mechanism by the NOM is proposed as the major effect for the adsorption capacity reduction. However, the difference observed between the two pesticides could be due to in addition to the pore blockage effect, a particular phenomenon with the diuron, especially with D activated carbon. We can suppose specific interactions between the diuron and the adsorbed organic matter and a competition between adsorption sites of NOM and activated carbon surface.

Gaseous VOCs rapidly modify particulate matter and its biological effects – Part 1: Simple VOCs and model PM

PubMed Central

Ebersviller, S.; Lichtveld, K.; Sexton, K. G.; Zavala, J.; Lin, Y-H.; Jaspers, I.; Jeffries, H. E.

2013-01-01

This is the first of a three-part study designed to demonstrate dynamic entanglements among gaseous organic compounds (VOC), particulate matter (PM), and their subsequent potential biological effects. We study these entanglements in increasingly complex VOC and PM mixtures in urban-like conditions in a large outdoor chamber. To the traditional chemical and physical characterizations of gas and PM, we added new measurements of gas-only- and PM-only-biological effects, using cultured human lung cells as model indicators. These biological effects are assessed here as increases in cellular damage or expressed irritation (i.e., cellular toxic effects) from cells exposed to chamber air relative to cells exposed to clean air. The exposure systems permit gas-only- or PM-only-exposures from the same air stream containing both gases and PM in equilibria, i.e., there are no extractive operations prior to cell exposure. Our simple experiments in this part of the study were designed to eliminate many competing atmospheric processes to reduce ambiguity in our results. Simple volatile and semi-volatile organic gases that have inherent cellular toxic properties were tested individually for biological effect in the dark (at constant humidity). Airborne mixtures were then created with each compound and PM that has no inherent cellular toxic properties for another cellular exposure. Acrolein and p-tolualdehyde were used as model VOCs and mineral oil aerosol (MOA) was selected as a surrogate for organic-containing PM. MOA is appropriately complex in composition to represent ambient PM, and it exhibits no inherent cellular toxic effects and thus did not contribute any biological detrimental effects on its own. Chemical measurements, combined with the responses of our biological exposures, clearly demonstrate that gas-phase pollutants can modify the composition of PM (and its resulting detrimental effects on lung cells) – even if the gas-phase pollutants are not considered likely to partition to the condensed phase: the VOC-modified-PM showed significantly more damage and inflammation to lung cells than did the original PM. Because gases and PM are transported and deposited differently within the atmosphere and the lungs, these results have significant consequences. For example, current US policies for research and regulation of PM do not recognize this “effect modification” phenomena (NAS, 2004). These results present an unambiguous demonstration that – even in these simple mixtures – physical and thermal interactions alone can cause a modification of the distribution of species among the phases of airborne pollution mixtures and can result in a non-toxic phase becoming toxic due to atmospheric thermal processes only. Subsequent work extends the simple results reported here to systems with photochemical transformations of complex urban mixtures and to systems with diesel exhaust produced by different fuels. PMID:23457430

Assessing the Performance of Computationally Simple and Complex Representations of Aerosol Processes using a Testbed Methodology

NASA Astrophysics Data System (ADS)

Fast, J. D.; Ma, P.; Easter, R. C.; Liu, X.; Zaveri, R. A.; Rasch, P.

2012-12-01

Predictions of aerosol radiative forcing in climate models still contain large uncertainties, resulting from a poor understanding of certain aerosol processes, the level of complexity of aerosol processes represented in models, and the ability of models to account for sub-grid scale variability of aerosols and processes affecting them. In addition, comparing the performance and computational efficiency of new aerosol process modules used in various studies is problematic because different studies often employ different grid configurations, meteorology, trace gas chemistry, and emissions that affect the temporal and spatial evolution of aerosols. To address this issue, we have developed an Aerosol Modeling Testbed (AMT) to systematically and objectively evaluate aerosol process modules. The AMT consists of the modular Weather Research and Forecasting (WRF) model, a series of testbed cases for which extensive in situ and remote sensing measurements of meteorological, trace gas, and aerosol properties are available, and a suite of tools to evaluate the performance of meteorological, chemical, aerosol process modules. WRF contains various parameterizations of meteorological, chemical, and aerosol processes and includes interactive aerosol-cloud-radiation treatments similar to those employed by climate models. In addition, the physics suite from a global climate model, Community Atmosphere Model version 5 (CAM5), has also been ported to WRF so that these parameterizations can be tested at various spatial scales and compared directly with field campaign data and other parameterizations commonly used by the mesoscale modeling community. In this study, we evaluate simple and complex treatments of the aerosol size distribution and secondary organic aerosols using the AMT and measurements collected during three field campaigns: the Megacities Initiative Local and Global Observations (MILAGRO) campaign conducted in the vicinity of Mexico City during March 2006, the Carbonaceous Aerosol and Radiative Effects Study (CARES) conducted in the vicinity of Sacramento California during June 2010, and the California Nexus (CalNex) campaign conducted in southern California during May and June of 2010. For the aerosol size distribution, we compare the predictions from the GOCART bulk aerosol model, the MADE/SORGAM modal aerosol model, the Modal Aerosol Model (MAM) employed by CAM5, and the Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) which uses a sectional representation. For secondary organic aerosols, we compare simple fixed mass yield approaches with the numerically complex volatility basis set approach. All simulations employ the same emissions, meteorology, trace gas chemistry (except for that involving condensable organic species), and initial and boundary conditions. Performance metrics from the AMT are used to assess performance in terms of simulated mass, composition, size distribution (except for GOCART), and aerosol optical properties in relation to computational expense. In addition to statistical measures, qualitative differences among the different aerosol models over the computational domain are presented to examine variations in how aerosols age among the aerosol models.

Is fracture a bigger problem for smaller animals? Force and fracture scaling for a simple model of cutting, puncture and crushing

PubMed Central

Choi, Seunghee; Coon, Joshua J.; Goggans, Matthew Scott; Kreisman, Thomas F.; Silver, Daniel M.; Nesson, Michael H.

2016-01-01

Many of the materials that are challenging for large animals to cut or puncture are also cut and punctured by much smaller organisms that are limited to much smaller forces. Small organisms can overcome their force limitations by using sharper tools, but one drawback may be an increased susceptibility to fracture. We use simple contact mechanics models to estimate how much smaller the diameter of the tips or edges of tools such as teeth, claws and cutting blades must be in smaller organisms in order for them to puncture or cut the same materials as larger organisms. In order to produce the same maximum stress when maximum force scales as the square of body length, the diameter of the tool region that is in contact with the target material must scale isometrically for punch-like tools (e.g. scorpion stings) on thick targets, and for crushing tools (e.g. molars). For punch-like tools on thin targets, and for cutting blades on thick targets, the tip or edge diameters must be even smaller than expected from isometry in smaller animals. The diameters of a small sample of unworn punch-like tools from a large range of animal sizes are consistent with the model, scaling isometrically or more steeply (positively allometric). In addition, we find that the force required to puncture a thin target using real biological tools scales linearly with tip diameter, as predicted by the model. We argue that, for smaller tools, the minimum energy to fracture the tool will be a greater fraction of the minimum energy required to puncture the target, making fracture more likely. Finally, energy stored in tool bending, relative to the energy to fracture the tool, increases rapidly with the aspect ratio (length/width), and we expect that smaller organisms often have to employ higher aspect ratio tools in order to puncture or cut to the required depth with available force. The extra stored energy in higher aspect ratio tools is likely to increase the probability of fracture. We discuss some of the implications of the suggested scaling rules and possible adaptations to compensate for fracture sensitivity in smaller organisms. PMID:27274804

Zipf's Law in Gene Expression

NASA Astrophysics Data System (ADS)

Furusawa, Chikara; Kaneko, Kunihiko

2003-02-01

Using data from gene expression databases on various organisms and tissues, including yeast, nematodes, human normal and cancer tissues, and embryonic stem cells, we found that the abundances of expressed genes exhibit a power-law distribution with an exponent close to -1; i.e., they obey Zipf’s law. Furthermore, by simulations of a simple model with an intracellular reaction network, we found that Zipf’s law of chemical abundance is a universal feature of cells where such a network optimizes the efficiency and faithfulness of self-reproduction. These findings provide novel insights into the nature of the organization of reaction dynamics in living cells.

Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-random Features of Cortical Synaptic Wiring

PubMed Central

Miner, Daniel; Triesch, Jochen

2016-01-01

Understanding the structure and dynamics of cortical connectivity is vital to understanding cortical function. Experimental data strongly suggest that local recurrent connectivity in the cortex is significantly non-random, exhibiting, for example, above-chance bidirectionality and an overrepresentation of certain triangular motifs. Additional evidence suggests a significant distance dependency to connectivity over a local scale of a few hundred microns, and particular patterns of synaptic turnover dynamics, including a heavy-tailed distribution of synaptic efficacies, a power law distribution of synaptic lifetimes, and a tendency for stronger synapses to be more stable over time. Understanding how many of these non-random features simultaneously arise would provide valuable insights into the development and function of the cortex. While previous work has modeled some of the individual features of local cortical wiring, there is no model that begins to comprehensively account for all of them. We present a spiking network model of a rodent Layer 5 cortical slice which, via the interactions of a few simple biologically motivated intrinsic, synaptic, and structural plasticity mechanisms, qualitatively reproduces these non-random effects when combined with simple topological constraints. Our model suggests that mechanisms of self-organization arising from a small number of plasticity rules provide a parsimonious explanation for numerous experimentally observed non-random features of recurrent cortical wiring. Interestingly, similar mechanisms have been shown to endow recurrent networks with powerful learning abilities, suggesting that these mechanism are central to understanding both structure and function of cortical synaptic wiring. PMID:26866369

A heuristic simulation model of Lake Ontario circulation and mass balance transport

USGS Publications Warehouse

McKenna, J.E.; Chalupnicki, M.A.

2011-01-01

The redistribution of suspended organisms and materials by large-scale currents is part of natural ecological processes in large aquatic systems but can contribute to ecosystem disruption when exotic elements are introduced into the system. Toxic compounds and planktonic organisms spend various lengths of time in suspension before settling to the bottom or otherwise being removed. We constructed a simple physical simulation model, including the influence of major tributaries, to qualitatively examine circulation patterns in Lake Ontario. We used a simple mass balance approach to estimate the relative water input to and export from each of 10 depth regime-specific compartments (nearshore vs. offshore) comprising Lake Ontario. Despite its simplicity, our model produced circulation patterns similar to those reported by more complex studies in the literature. A three-gyre pattern, with the classic large counterclockwise central lake circulation, and a simpler two-gyre system were both observed. These qualitative simulations indicate little offshore transport along the south shore, except near the mouths of the Niagara River and Oswego River. Complex flow structure was evident, particularly near the Niagara River mouth and in offshore waters of the eastern basin. Average Lake Ontario residence time is 8 years, but the fastest model pathway indicated potential transport of plankton through the lake in as little as 60 days. This simulation illustrates potential invasion pathways and provides rough estimates of planktonic larval dispersal or chemical transport among nearshore and offshore areas of Lake Ontario. ?? 2011 Taylor & Francis.

On the dynamics of a human body model.

NASA Technical Reports Server (NTRS)

Huston, R. L.; Passerello, C. E.

1971-01-01

Equations of motion for a model of the human body are developed. Basically, the model consists of an elliptical cylinder representing the torso, together with a system of frustrums of elliptical cones representing the limbs. They are connected to the main body and each other by hinges and ball and socket joints. Vector, tensor, and matrix methods provide a systematic organization of the geometry. The equations of motion are developed from the principles of classical mechanics. The solution of these equations then provide the displacement and rotation of the main body when the external forces and relative limb motions are specified. Three simple example motions are studied to illustrate the method. The first is an analysis and comparison of simple lifting on the earth and the moon. The second is an elementary approach to underwater swimming, including both viscous and inertia effects. The third is an analysis of kicking motion and its effect upon a vertically suspended man such as a parachutist.

The Melting of Aqueous Foams

NASA Technical Reports Server (NTRS)

Durian, Douglas J.; Gopal, Anthony D.; Vera, Moin U.; Langer, Stephen A.

1996-01-01

Diffusing-wave spectroscopy measurements show that ordinarily solid aqueous foams flow by a series of stick-slip avalanche-like rearrangements of neighboring bubbles from one tight packing configuration to another. Contrary to a recent prediction, the distribution of avalanche sizes do not obey a power-law distribution characteristic of self-organized criticality. This can be understood from a simple model of foam mechanics based on bubble-bubble interactions.

Genetic and molecular dosimetry of HZE radiation (7-IML-1)

NASA Technical Reports Server (NTRS)

Nelson, Gregory A.

1992-01-01

The objectives of the study are to determine the kinetics of production and to characterize the unique aspects of genetic and developmental lesion induced in animal cells by radiation present in the space environment. Special attention is given to heavy charged particles. The organism Caenorhabditis elegans, a simple nematode, is used as a model system for a coordinated set of ground-based and flight experiments.

Steady-state photoconductivity and multi-particle interactions in high-mobility organic semiconductors.

PubMed

Irkhin, P; Najafov, H; Podzorov, V

2015-10-19

Fundamental understanding of photocarrier generation, transport and recombination under a steady-state photoexcitation has been an important goal of organic electronics and photonics, since these processes govern such electronic properties of organic semiconductors as, for instance, photoconductivity. Here, we discovered that photoconductivity of a highly ordered organic semiconductor rubrene exhibits several distinct regimes, in which photocurrent as a function of cw (continuous wave) excitation intensity is described by a power law with exponents sequentially taking values 1, 1/3 and ¼. We show that in pristine crystals this photocurrent is generated at the very surface of the crystals, while the bulk photocurrent is drastically smaller and follows a different sequence of exponents, 1 and ½. We describe a simple experimental procedure, based on an application of "gauge effect" in high vacuum, that allows to disentangle the surface and bulk contributions to photoconductivity. A model based on singlet exciton fission, triplet fusion and triplet-charge quenching that can describe these non-trivial effects in photoconductivity of highly ordered organic semiconductors is proposed. Observation of these effects in photoconductivity and modeling of the underlying microscopic mechanisms described in this work represent a significant step forward in our understanding of electronic properties of organic semiconductors.

The pre- and post-accretion irradiation history of cometary ices

NASA Technical Reports Server (NTRS)

Chyba, Christopher; Sagan, Carl

1989-01-01

Comets Halley and Wilson exhibited similar 3.4 micron emission features at approx. 1 AU from the Sun. A simple model of thermal emission from organic grains fits the feature, provides optical depths in good agreement with spacecraft measurements, and explains the absence of longer-wavelength organic features as due to spectral heliocentric evolution (Chyba and Sagan, 1987). The model utilizes transmission spectra of organics synthesized in the laboratory by irradiation of candidate cometary ices; the authors have long noted that related gas-phase syntheses yield polycyclic aromatic hydrocarbons, among other organic residues (Sagan et al., 1967). The authors previously concluded (Chyba and Sagan, 1987) that Halley's loss of several meters' depth with each perihelion passage, combined with the good fit of the Halley 3.4 micron feature to that of comet Wilson (Allen and Wickramasinghe, 1987), argues for the primordial - but not necessarily interstellar - origin of cometary organics. The authors examine the relative importance to the formation of organics of the variety of radiation environments experienced by comets. They conclude that there is at present no compelling reason to choose any of three contributing mechanisms (pre-accretion UV, pre-accretion cosmic ray, and post-accretion radionuclide processing) as the most important.

Light-Driven Reversible Transformation between Self-Organized Simple Cubic Lattice and Helical Superstructure Enabled by a Molecular Switch Functionalized Nanocage.

PubMed

Zhou, Kang; Bisoyi, Hari Krishna; Jin, Jian-Qiu; Yuan, Cong-Long; Liu, Zhen; Shen, Dong; Lu, Yan-Qing; Zheng, Zhi-Gang; Zhang, Weian; Li, Quan

2018-04-23

Self-organized stimuli-responsive smart materials with adjustable attributes are highly desirable for a plethora of device applications. Simple cubic lattice is quite uncommon in soft condensed matter due to its lower packing factor. Achieving a stable simple cubic soft lattice and endowing such a lattice with dynamic reconstruction capability solely by a facile light irradiation are of paramount significance for both fundamental studies and engineering explorations. Herein, an elegant stable self-organized simple cubic soft lattice, i.e., blue phase II, in a chiral liquid crystal (LC) system is disclosed, which is stable down to room temperature and exhibits both reversible lattice deformation and transformation to a helical superstructure, i.e., cholesteric LC, by light stimulation. Such an amazing trait is attained by doping a judiciously designed achiral photoresponsive molecular switch functionalized polyhedral oligomeric silsesquioxane nanocage into a chiral LC host. An unprecedented reversible collapse and reconstruction of such a high symmetric simple cubic blue phase II driven by light has been achieved. Furthermore, a well-defined conglomerate micropattern composed of simple cubic soft lattice and helical superstructure, which is challenging to fabricate in organic and inorganic crystalline materials, is produced using photomasking technology. Moreover, the promising photonic application based on such a micropattern is demonstrated. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Local pH oscillations witness autocatalytic self-organization of biomorphic nanostructures

NASA Astrophysics Data System (ADS)

Montalti, M.; Zhang, G.; Genovese, D.; Morales, J.; Kellermeier, M.; García-Ruiz, J. M.

2017-02-01

Bottom-up self-assembly of simple molecular compounds is a prime pathway to complex materials with interesting structures and functions. Coupled reaction systems are known to spontaneously produce highly ordered patterns, so far observed in soft matter. Here we show that similar phenomena can occur during silica-carbonate crystallization, the emerging order being preserved. The resulting materials, called silica biomorphs, exhibit non-crystallographic curved morphologies and hierarchical textures, much reminiscent of structural principles found in natural biominerals. We have used a fluorescent chemosensor to probe local conditions during the growth of such self-organized nanostructures. We demonstrate that the pH oscillates in the local microenvironment near the growth front due to chemical coupling, which becomes manifest in the final mineralized architectures as intrinsic banding patterns with the same periodicity. A better understanding of dynamic autocatalytic crystallization processes in such simple model systems is key to the rational development of advanced materials and to unravel the mechanisms of biomineralization.

The Unique Propulsive Wake Pattern of the Swimming Sea Slug Aplysia

NASA Astrophysics Data System (ADS)

Zhou, Zhuoyu; Mittal, Rajat

2017-11-01

The Aplysia, also sometimes referred to as the `Sea Hare,' is a sea slug that swims elegantly using large-amplitude flapping of its mantle. The Sea Hare has become a very valuable laboratory animal for investigation into nervous systems and brain behavior due to its simple neural system with large neurons and axons. Recently, attempts have also been made to develop biohybrid robots with both organic actuation and organic motor-pattern control inspired by the locomotion of Aplysia. While extensive works have been done to investigate this animal's neurobiology, relatively little is known about its propulsive mechanisms and swimming energetics. In this study, incompressible flow simulations with a simple kinematical model are used to gain insights into vortex dynamics, thrust generation and energetics of locomotion. The effect of mantle kinematics on the propulsive performance is examined, and simulations indicate a unique vortex wake pattern that is responsible for thrust generation. The research is supported by NSF Grant PLR-1246317 and NSF XSEDE Grant TG-CTS100002.

Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid

NASA Astrophysics Data System (ADS)

Metere, Alfredo; Oleynikov, Peter; Dzugutov, Mikhail; O'Keeffe, Michael

2014-12-01

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process, can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.

A high-resolution conceptual model for diffuse organic micropollutant loads in streams

NASA Astrophysics Data System (ADS)

Stamm, Christian; Honti, Mark; Ghielmetti, Nico

2013-04-01

The ecological state of surface waters has become the dominant aspect in water quality assessments. Toxicity is a key determinant of the ecological state, but organic micropollutants (OMP) are seldom monitored with the same spatial and temporal frequency as for example nutrients, mainly due the demanding analytical methods and costs. However, diffuse transport pathways are at least equally complex for OMPs as for nutrients and there are still significant knowledge gaps. Moreover, concentrations of the different compounds would need to be known with fairly high temporal resolution because acute toxicity can be as important as the chronic one. Fully detailed mechanistic models of diffuse OMP loads require an immense set of site-specific knowledge and are rarely applicable for catchments lacking an exceptional monitoring coverage. Simple empirical methods are less demanding but usually work with more temporal aggregation and that's why they have limited possibilities to support the estimation of the ecological state. This study presents a simple conceptual model that aims to simulate the concentrations of selected organic micropollutants with daily resolution at 11 locations in the stream network of a small catchment (46 km2). The prerequisite is a known hydrological and meteorological background (daily discharge, precipitation and air temperature time series), a land use map and some historic measurements of the desired compounds. The model is conceptual in the sense that all important diffuse transport pathways are simulated separately, but each with a simple empirical process rate. Consequently, some site-specific observations are required to calibrate the model, but afterwards the model can be used for forecasting and scenario analysis as the calibrated process rates typically describe invariant properties of the catchment. We simulated 6 different OMPs from the categories of agricultural and urban pesticides and urban biocides. The application of agricultural pesticides was also simulated with the model using a heat-sum approach. Calibration was carried out with weekly aggregated samples covering the growing season in 2 years. The model could reproduce the observed OMP concentrations with varying success. Compounds that are less persistent in the environment and thus have a dominant temporal dynamics (pesticides with a short half-life) could be simulated in general better than the persistent ones. For the latter group the relatively stable available stock meant that there were no clear seasonal dynamics, which revealed that transport processes are quite uncertain even when daily rainfall is used as the main driver. Nevertheless the daily concentration distribution could still be simulated with higher accuracy than the individual peaks. Thus we can model the concentration-duration relationship for daily resolution in an acceptable way for each compound.

The Barley Phytomer

PubMed Central

Forster, Brian P.; Franckowiak, Jerome D.; Lundqvist, Udda; Lyon, Jackie; Pitkethly, Ian; Thomas, William T. B.

2007-01-01

Background and Aims Morphological mutants have been useful in elucidating the phytomeric structure of plants. Recently described mutants have shed new light on the ontogeny (development of plant structures) and the phytomeric system of barley (Hordeum vulgare). Since the current model for barley phytomers was not adequate to explain the nature of some mutants, a new model is proposed. Methods New phytomer mutants were detected by visual assessment of mutant families in the Optic barley mutation grid population. This was done at various growth stages using laboratory, glasshouse and field screens. Simple explanations were adopted to account for aberrant phytomer phenotypes and a thesis for a new phytomer model was developed. Key Results and Conclusions A barley phytomer model is presented, in which the origins of vegetative and generative structures can be explained by a single repeating phytomer unit. Organs on the barley plant are divided into two classes, single or paired, depending on their origin. Paired structures are often fused together to create specific organs. The model can be applied to wheat (Triticum aestivum) and related grasses. PMID:17901062

Integrity of chromatin and replicating DNA in nuclei released from fission yeast by semi-automated grinding in liquid nitrogen

PubMed Central

2011-01-01

Background Studies of nuclear function in many organisms, especially those with tough cell walls, are limited by lack of availability of simple, economical methods for large-scale preparation of clean, undamaged nuclei. Findings Here we present a useful method for nuclear isolation from the important model organism, the fission yeast, Schizosaccharomyces pombe. To preserve in vivo molecular configurations, we flash-froze the yeast cells in liquid nitrogen. Then we broke their tough cell walls, without damaging their nuclei, by grinding in a precision-controlled motorized mortar-and-pestle apparatus. The cryo-ground cells were resuspended and thawed in a buffer designed to preserve nuclear morphology, and the nuclei were enriched by differential centrifugation. The washed nuclei were free from contaminating nucleases and have proven well-suited as starting material for genome-wide chromatin analysis and for preparation of fragile DNA replication intermediates. Conclusions We have developed a simple, reproducible, economical procedure for large-scale preparation of endogenous-nuclease-free, morphologically intact nuclei from fission yeast. With appropriate modifications, this procedure may well prove useful for isolation of nuclei from other organisms with, or without, tough cell walls. PMID:22088094

Integrity of chromatin and replicating DNA in nuclei released from fission yeast by semi-automated grinding in liquid nitrogen.

PubMed

Givens, Robert M; Mesner, Larry D; Hamlin, Joyce L; Buck, Michael J; Huberman, Joel A

2011-11-16

Studies of nuclear function in many organisms, especially those with tough cell walls, are limited by lack of availability of simple, economical methods for large-scale preparation of clean, undamaged nuclei. Here we present a useful method for nuclear isolation from the important model organism, the fission yeast, Schizosaccharomyces pombe. To preserve in vivo molecular configurations, we flash-froze the yeast cells in liquid nitrogen. Then we broke their tough cell walls, without damaging their nuclei, by grinding in a precision-controlled motorized mortar-and-pestle apparatus. The cryo-ground cells were resuspended and thawed in a buffer designed to preserve nuclear morphology, and the nuclei were enriched by differential centrifugation. The washed nuclei were free from contaminating nucleases and have proven well-suited as starting material for genome-wide chromatin analysis and for preparation of fragile DNA replication intermediates. We have developed a simple, reproducible, economical procedure for large-scale preparation of endogenous-nuclease-free, morphologically intact nuclei from fission yeast. With appropriate modifications, this procedure may well prove useful for isolation of nuclei from other organisms with, or without, tough cell walls.

An honest day's work: pay for performance in a pediatric radiology department.

PubMed

Bisset, George S

2017-06-01

Compensation models in radiology take a variety of forms, but regardless of practice type, successful models must reward productivity, be simple, and epitomize fairness. The ideal model should also be flexible enough to transition, based upon the changing strategic goals of a department. The plan should be constructed around rewarding the behaviors that the organization values. In this minisymposium article the author presents the value of different types of compensation plans and discusses advantages and disadvantages. Finally, the author presents a pay-for-performance model that has had long-term success at a private-turned-academic practice in pediatric radiology.

Methods for quantifying simple gravity sensing in Drosophila melanogaster.

PubMed

Inagaki, Hidehiko K; Kamikouchi, Azusa; Ito, Kei

2010-01-01

Perception of gravity is essential for animals: most animals possess specific sense organs to detect the direction of the gravitational force. Little is known, however, about the molecular and neural mechanisms underlying their behavioral responses to gravity. Drosophila melanogaster, having a rather simple nervous system and a large variety of molecular genetic tools available, serves as an ideal model for analyzing the mechanisms underlying gravity sensing. Here we describe an assay to measure simple gravity responses of flies behaviorally. This method can be applied for screening genetic mutants of gravity perception. Furthermore, in combination with recent genetic techniques to silence or activate selective sets of neurons, it serves as a powerful tool to systematically identify neural substrates required for the proper behavioral responses to gravity. The assay requires 10 min to perform, and two experiments can be performed simultaneously, enabling 12 experiments per hour.

[Quality management in cardiovascular echography].

PubMed

Gullace, Giuseppe

2002-12-01

The quality management of an organization can be defined as the ability to identify, plan and implement programs of measure, analysis, verification and control that allow to monitor management, resources, activities, processes and output/outcome of the same organization, including the satisfaction of the customers. Whatever the model used, it is demonstrated that the management-quality system, either for professional quality or for organization, turns out to be effective even in the health organizations within and to any level of organizational-structural complexity. The present paper concerns the experience of the Italian Society of Cardiovascular Echography (SIEC) on quality certification, both as a scientific society compared to other health organizations and to cardiovascular echo laboratories, and the definition of minimum requirements for the accreditation of the same laboratories. The model most frequently used for quality management is represented by the ISO 9000: Vision 2000, that is a management model with specific reference to the organization and the customer satisfaction. The model applied to the health structure needs a rapid change in mentality that addresses the operators to define, share and achieve objectives to be brought on by means of an active collaboration, group activity and deep sense of belonging necessary to the attainment of expected objectives. When the model is applied by a scientific society, it is necessary to take into account the different structural and functional organization, the constitution and the operators differing on the point of view of origin, experiences, mentality, and roles. The ISO 9000: Vision 2000 model can be applied also to the cardiovascular echo laboratory which may be compared to a simple organization; for its corrected functioning, SIEC has defined minimal requirements for the accreditation, realization and modalities to carry out and manage quality. The quality system represents a new way of operating of an organization that enhances capability and performance of the operators, stimulates their creativity and facilitates the activities of all, to guarantee both the quality of the product and the satisfaction of operators and customers at the same time.

Modelling of The Atmospheric Chemistry of Organic Nitrates

NASA Astrophysics Data System (ADS)

Winsland, N.

Organic nitrates are linked to the formation of tropospheric ozone and the cycling and transport of nitrogen-containing species in the atmosphere. Few laboratory stud- ies have been carried out on the reactions of organic nitrates. Photolysis quantum yield studies and UV absorption spectra have been carried out for the simple alkyl nitrates and PAN. Studies of PAN and ethyl nitrate with other atmospheric components (the hydroxyl radical - OH - and the chlorine atom - Cl) have been carried out to mea- sure their rates of reaction. However, the products and mechanisms of these reactions are poorly understood. We present here the results of modelling the reactions of the C1-C8 alkyl nitrates and PAN with the hydroxyl radical. These models are based on information from current literature and from photochemical reactor studies carried out at the Environment Institute, EU Joint Research Centre, Ispra, Italy. These studies give us a more detailed understanding of the mechanisms and products of the atmospheric loss of organic nitrates due to reaction with the hydroxyl radical. Preliminary studies show that the major products are aldehydes, ketones, nitro-oxy aldehydes, nitro-oxy ketones, NOx and nitric acid.

[Quality assurance of the renal applications software].

PubMed

del Real Núñez, R; Contreras Puertas, P I; Moreno Ortega, E; Mena Bares, L M; Maza Muret, F R; Latre Romero, J M

2007-01-01

The need for quality assurance of all technical aspects of nuclear medicine studies is widely recognised. However, little attention has been paid to the quality assurance of the applications software. Our work reported here aims at verifying the analysis software for processing of renal nuclear medicine studies (renograms). The software tools were used to build a synthetic dynamic model of renal system. The model consists of two phases: perfusion and function. The organs of interest (kidneys, bladder and aortic artery) were simple geometric forms. The uptake of the renal structures was described by mathematic functions. Curves corresponding to normal or pathological conditions were simulated for kidneys, bladder and aortic artery by appropriate selection of parameters. There was no difference between the parameters of the mathematic curves and the quantitative data produced by the renal analysis program. Our test procedure is simple to apply, reliable, reproducible and rapid to verify the renal applications software.

Learning molecular energies using localized graph kernels.

PubMed

Ferré, Grégoire; Haut, Terry; Barros, Kipton

2017-03-21

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.

Learning molecular energies using localized graph kernels

NASA Astrophysics Data System (ADS)

Ferré, Grégoire; Haut, Terry; Barros, Kipton

2017-03-01

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.

Reactive extraction of lactic acid with trioctylamine/methylene chloride/n-hexane

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

Han, D.H.; Hong, W.H.

The trioctylamine (TOA)/methylene chloride (MC)/n-hexane system was used as the extraction agent for the extraction of lactic acid. Curves of equilibrium and hydration were obtained at various temperatures and concentrations of TOA. A modified mass action model was proposed to interpret the equilibrium and the hydration curves. The reaction mechanism and the corresponding parameters which best represent the equilibrium data were estimated, and the concentration of water in the organic phase was predicted by inserting the parameters into the simple mathematical equation of the modified model. The concentration of MC and the change of temperature were important factors for themore » extraction and the stripping process. The stripping was performed by a simple distillation which was a combination of temperature-swing regeneration and diluent-swing regeneration. The type of inactive diluent has no influence on the stripping. The stripping efficiencies were about 70%.« less

Simple, fast, and low-cost camera-based water content measurement with colorimetric fluorescent indicator

NASA Astrophysics Data System (ADS)

Song, Seok-Jeong; Kim, Tae-Il; Kim, Youngmi; Nam, Hyoungsik

2018-05-01

Recently, a simple, sensitive, and low-cost fluorescent indicator has been proposed to determine water contents in organic solvents, drugs, and foodstuffs. The change of water content leads to the change of the indicator's fluorescence color under the ultra-violet (UV) light. Whereas the water content values could be estimated from the spectrum obtained by a bulky and expensive spectrometer in the previous research, this paper demonstrates a simple and low-cost camera-based water content measurement scheme with the same fluorescent water indicator. Water content is calculated over the range of 0-30% by quadratic polynomial regression models with color information extracted from the captured images of samples. Especially, several color spaces such as RGB, xyY, L∗a∗b∗, u‧v‧, HSV, and YCBCR have been investigated to establish the optimal color information features over both linear and nonlinear RGB data given by a camera before and after gamma correction. In the end, a 2nd order polynomial regression model along with HSV in a linear domain achieves the minimum mean square error of 1.06% for a 3-fold cross validation method. Additionally, the resultant water content estimation model is implemented and evaluated in an off-the-shelf Android-based smartphone.

Modelling the fate of organic micropollutants in stormwater ponds.

PubMed

Vezzaro, Luca; Eriksson, Eva; Ledin, Anna; Mikkelsen, Peter S

2011-06-01

Urban water managers need to estimate the potential removal of organic micropollutants (MP) in stormwater treatment systems to support MP pollution control strategies. This study documents how the potential removal of organic MP in stormwater treatment systems can be quantified by using multimedia models. The fate of four different MP in a stormwater retention pond was simulated by applying two steady-state multimedia fate models (EPI Suite and SimpleBox) commonly applied in chemical risk assessment and a dynamic multimedia fate model (Stormwater Treatment Unit Model for Micro Pollutants--STUMP). The four simulated organic stormwater MP (iodopropynyl butylcarbamate--IPBC, benzene, glyphosate and pyrene) were selected according to their different urban sources and environmental fate. This ensures that the results can be extended to other relevant stormwater pollutants. All three models use substance inherent properties to calculate MP fate but differ in their ability to represent the small physical scale and high temporal variability of stormwater treatment systems. Therefore the three models generate different results. A Global Sensitivity Analysis (GSA) highlighted that settling/resuspension of particulate matter was the most sensitive process for the dynamic model. The uncertainty of the estimated MP fluxes can be reduced by calibrating the dynamic model against total suspended solids data. This reduction in uncertainty was more significant for the substances with strong tendency to sorb, i.e. glyphosate and pyrene and less significant for substances with a smaller tendency to sorb, i.e. IPBC and benzene. The results provide support to the elaboration of MP pollution control strategies by limiting the need for extensive and complex monitoring campaigns targeting the wide range of specific organic MP found in stormwater runoff. Copyright © 2011 Elsevier B.V. All rights reserved.

Unifying model of shoot gravitropism reveals proprioception as a central feature of posture control in plants

PubMed Central

Bastien, Renaud; Bohr, Tomas; Moulia, Bruno; Douady, Stéphane

2013-01-01

Gravitropism, the slow reorientation of plant growth in response to gravity, is a key determinant of the form and posture of land plants. Shoot gravitropism is triggered when statocysts sense the local angle of the growing organ relative to the gravitational field. Lateral transport of the hormone auxin to the lower side is then enhanced, resulting in differential gene expression and cell elongation causing the organ to bend. However, little is known about the dynamics, regulation, and diversity of the entire bending and straightening process. Here, we modeled the bending and straightening of a rod-like organ and compared it with the gravitropism kinematics of different organs from 11 angiosperms. We show that gravitropic straightening shares common traits across species, organs, and orders of magnitude. The minimal dynamic model accounting for these traits is not the widely cited gravisensing law but one that also takes into account the sensing of local curvature, what we describe here as a graviproprioceptive law. In our model, the entire dynamics of the bending/straightening response is described by a single dimensionless “bending number” B that reflects the ratio between graviceptive and proprioceptive sensitivities. The parameter B defines both the final shape of the organ at equilibrium and the timing of curving and straightening. B can be estimated from simple experiments, and the model can then explain most of the diversity observed in experiments. Proprioceptive sensing is thus as important as gravisensing in gravitropic control, and the B ratio can be measured as phenotype in genetic studies. PMID:23236182

Unifying model of shoot gravitropism reveals proprioception as a central feature of posture control in plants.

PubMed

Bastien, Renaud; Bohr, Tomas; Moulia, Bruno; Douady, Stéphane

2013-01-08

Gravitropism, the slow reorientation of plant growth in response to gravity, is a key determinant of the form and posture of land plants. Shoot gravitropism is triggered when statocysts sense the local angle of the growing organ relative to the gravitational field. Lateral transport of the hormone auxin to the lower side is then enhanced, resulting in differential gene expression and cell elongation causing the organ to bend. However, little is known about the dynamics, regulation, and diversity of the entire bending and straightening process. Here, we modeled the bending and straightening of a rod-like organ and compared it with the gravitropism kinematics of different organs from 11 angiosperms. We show that gravitropic straightening shares common traits across species, organs, and orders of magnitude. The minimal dynamic model accounting for these traits is not the widely cited gravisensing law but one that also takes into account the sensing of local curvature, what we describe here as a graviproprioceptive law. In our model, the entire dynamics of the bending/straightening response is described by a single dimensionless "bending number" B that reflects the ratio between graviceptive and proprioceptive sensitivities. The parameter B defines both the final shape of the organ at equilibrium and the timing of curving and straightening. B can be estimated from simple experiments, and the model can then explain most of the diversity observed in experiments. Proprioceptive sensing is thus as important as gravisensing in gravitropic control, and the B ratio can be measured as phenotype in genetic studies.

Description and validation of the Simple, Efficient, Dynamic, Global, Ecological Simulator (SEDGES v.1.0)

NASA Astrophysics Data System (ADS)

Paiewonsky, Pablo; Elison Timm, Oliver

2018-03-01

In this paper, we present a simple dynamic global vegetation model whose primary intended use is auxiliary to the land-atmosphere coupling scheme of a climate model, particularly one of intermediate complexity. The model simulates and provides important ecological-only variables but also some hydrological and surface energy variables that are typically either simulated by land surface schemes or else used as boundary data input for these schemes. The model formulations and their derivations are presented here, in detail. The model includes some realistic and useful features for its level of complexity, including a photosynthetic dependency on light, full coupling of photosynthesis and transpiration through an interactive canopy resistance, and a soil organic carbon dependence for bare-soil albedo. We evaluate the model's performance by running it as part of a simple land surface scheme that is driven by reanalysis data. The evaluation against observational data includes net primary productivity, leaf area index, surface albedo, and diagnosed variables relevant for the closure of the hydrological cycle. In this setup, we find that the model gives an adequate to good simulation of basic large-scale ecological and hydrological variables. Of the variables analyzed in this paper, gross primary productivity is particularly well simulated. The results also reveal the current limitations of the model. The most significant deficiency is the excessive simulation of evapotranspiration in mid- to high northern latitudes during their winter to spring transition. The model has a relative advantage in situations that require some combination of computational efficiency, model transparency and tractability, and the simulation of the large-scale vegetation and land surface characteristics under non-present-day conditions.

Predicting spiral wave patterns from cell properties in a model of biological self-organization.

PubMed

Geberth, Daniel; Hütt, Marc-Thorsten

2008-09-01

In many biological systems, biological variability (i.e., systematic differences between the system components) can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In principle, the distribution of single-element properties should thus allow predicting features of such patterns. For a mathematical model of a paradigmatic and well-studied pattern formation process, spiral waves of cAMP signaling in colonies of the slime mold Dictyostelium discoideum, we explore this possibility and observe a pronounced anticorrelation between spiral waves and cell properties (namely, the firing rate) and particularly a clustering of spiral wave tips in regions devoid of spontaneously firing (pacemaker) cells. Furthermore, we observe local inhomogeneities in the distribution of spiral chiralities, again induced by the pacemaker distribution. We show that these findings can be explained by a simple geometrical model of spiral wave generation.

Crossover from Super- to Subdiffusive Motion and Memory Effects in Crystalline Organic Semiconductors

NASA Astrophysics Data System (ADS)

De Filippis, G.; Cataudella, V.; Mishchenko, A. S.; Nagaosa, N.; Fierro, A.; de Candia, A.

2015-02-01

The transport properties at finite temperature of crystalline organic semiconductors are investigated, within the Su-Schrieffer-Heeger model, by combining an exact diagonalization technique, Monte Carlo approaches, and a maximum entropy method. The temperature-dependent mobility data measured in single crystals of rubrene are successfully reproduced: a crossover from super- to subdiffusive motion occurs in the range 150 ≤T ≤200 K , where the mean free path becomes of the order of the lattice parameter and strong memory effects start to appear. We provide an effective model, which can successfully explain features of the absorption spectra at low frequencies. The observed response to slowly varying electric field is interpreted by means of a simple model where the interaction between the charge carrier and lattice polarization modes is simulated by a harmonic interaction between a fictitious particle and an electron embedded in a viscous fluid.

Crossover from super- to subdiffusive motion and memory effects in crystalline organic semiconductors.

PubMed

De Filippis, G; Cataudella, V; Mishchenko, A S; Nagaosa, N; Fierro, A; de Candia, A

2015-02-27

The transport properties at finite temperature of crystalline organic semiconductors are investigated, within the Su-Schrieffer-Heeger model, by combining an exact diagonalization technique, Monte Carlo approaches, and a maximum entropy method. The temperature-dependent mobility data measured in single crystals of rubrene are successfully reproduced: a crossover from super- to subdiffusive motion occurs in the range 150≤T≤200  K, where the mean free path becomes of the order of the lattice parameter and strong memory effects start to appear. We provide an effective model, which can successfully explain features of the absorption spectra at low frequencies. The observed response to slowly varying electric field is interpreted by means of a simple model where the interaction between the charge carrier and lattice polarization modes is simulated by a harmonic interaction between a fictitious particle and an electron embedded in a viscous fluid.

Spatiotemporal pattern in somitogenesis: a non-Turing scenario with wave propagation.

PubMed

Nagahara, Hiroki; Ma, Yue; Takenaka, Yoshiko; Kageyama, Ryoichiro; Yoshikawa, Kenichi

2009-08-01

Living organisms maintain their lives under far-from-equilibrium conditions by creating a rich variety of spatiotemporal structures in a self-organized manner, such as temporal rhythms, switching phenomena, and development of the body. In this paper, we focus on the dynamical process of morphogens in somitogenesis in mice where propagation of the gene expression level plays an essential role in creating the spatially periodic patterns of the vertebral columns. We present a simple discrete reaction-diffusion model which includes neighboring interaction through an activator, but not diffusion of an inhibitor. We can produce stationary periodic patterns by introducing the effect of spatial discreteness to the field. Based on the present model, we discuss the underlying physical principles that are independent of the details of biomolecular reactions. We also discuss the framework of spatial discreteness based on the reaction-diffusion model in relation to a cellular array, by comparison with an actual experimental observation.

Predicting spiral wave patterns from cell properties in a model of biological self-organization

NASA Astrophysics Data System (ADS)

Geberth, Daniel; Hütt, Marc-Thorsten

2008-09-01

In many biological systems, biological variability (i.e., systematic differences between the system components) can be expected to outrank statistical fluctuations in the shaping of self-organized patterns. In principle, the distribution of single-element properties should thus allow predicting features of such patterns. For a mathematical model of a paradigmatic and well-studied pattern formation process, spiral waves of cAMP signaling in colonies of the slime mold Dictyostelium discoideum, we explore this possibility and observe a pronounced anticorrelation between spiral waves and cell properties (namely, the firing rate) and particularly a clustering of spiral wave tips in regions devoid of spontaneously firing (pacemaker) cells. Furthermore, we observe local inhomogeneities in the distribution of spiral chiralities, again induced by the pacemaker distribution. We show that these findings can be explained by a simple geometrical model of spiral wave generation.

S3QL: A distributed domain specific language for controlled semantic integration of life sciences data

PubMed Central

2011-01-01

Background The value and usefulness of data increases when it is explicitly interlinked with related data. This is the core principle of Linked Data. For life sciences researchers, harnessing the power of Linked Data to improve biological discovery is still challenged by a need to keep pace with rapidly evolving domains and requirements for collaboration and control as well as with the reference semantic web ontologies and standards. Knowledge organization systems (KOSs) can provide an abstraction for publishing biological discoveries as Linked Data without complicating transactions with contextual minutia such as provenance and access control. We have previously described the Simple Sloppy Semantic Database (S3DB) as an efficient model for creating knowledge organization systems using Linked Data best practices with explicit distinction between domain and instantiation and support for a permission control mechanism that automatically migrates between the two. In this report we present a domain specific language, the S3DB query language (S3QL), to operate on its underlying core model and facilitate management of Linked Data. Results Reflecting the data driven nature of our approach, S3QL has been implemented as an application programming interface for S3DB systems hosting biomedical data, and its syntax was subsequently generalized beyond the S3DB core model. This achievement is illustrated with the assembly of an S3QL query to manage entities from the Simple Knowledge Organization System. The illustrative use cases include gastrointestinal clinical trials, genomic characterization of cancer by The Cancer Genome Atlas (TCGA) and molecular epidemiology of infectious diseases. Conclusions S3QL was found to provide a convenient mechanism to represent context for interoperation between public and private datasets hosted at biomedical research institutions and linked data formalisms. PMID:21756325

S3QL: a distributed domain specific language for controlled semantic integration of life sciences data.

PubMed

Deus, Helena F; Correa, Miriã C; Stanislaus, Romesh; Miragaia, Maria; Maass, Wolfgang; de Lencastre, Hermínia; Fox, Ronan; Almeida, Jonas S

2011-07-14

The value and usefulness of data increases when it is explicitly interlinked with related data. This is the core principle of Linked Data. For life sciences researchers, harnessing the power of Linked Data to improve biological discovery is still challenged by a need to keep pace with rapidly evolving domains and requirements for collaboration and control as well as with the reference semantic web ontologies and standards. Knowledge organization systems (KOSs) can provide an abstraction for publishing biological discoveries as Linked Data without complicating transactions with contextual minutia such as provenance and access control.We have previously described the Simple Sloppy Semantic Database (S3DB) as an efficient model for creating knowledge organization systems using Linked Data best practices with explicit distinction between domain and instantiation and support for a permission control mechanism that automatically migrates between the two. In this report we present a domain specific language, the S3DB query language (S3QL), to operate on its underlying core model and facilitate management of Linked Data. Reflecting the data driven nature of our approach, S3QL has been implemented as an application programming interface for S3DB systems hosting biomedical data, and its syntax was subsequently generalized beyond the S3DB core model. This achievement is illustrated with the assembly of an S3QL query to manage entities from the Simple Knowledge Organization System. The illustrative use cases include gastrointestinal clinical trials, genomic characterization of cancer by The Cancer Genome Atlas (TCGA) and molecular epidemiology of infectious diseases. S3QL was found to provide a convenient mechanism to represent context for interoperation between public and private datasets hosted at biomedical research institutions and linked data formalisms.

The roles of microclimatic diversity and of behavior in mediating the responses of ectotherms to climate change.

PubMed

Woods, H Arthur; Dillon, Michael E; Pincebourde, Sylvain

2015-12-01

We analyze the effects of changing patterns of thermal availability, in space and time, on the performance of small ectotherms. We approach this problem by breaking it into a series of smaller steps, focusing on: (1) how macroclimates interact with living and nonliving objects in the environment to produce a mosaic of thermal microclimates and (2) how mobile ectotherms filter those microclimates into realized body temperatures by moving around in them. Although the first step (generation of mosaics) is conceptually straightforward, there still exists no general framework for predicting spatial and temporal patterns of microclimatic variation. We organize potential variation along three axes-the nature of the objects producing the microclimates (abiotic versus biotic), how microclimates translate macroclimatic variation (amplify versus buffer), and the temporal and spatial scales over which microclimatic conditions vary (long versus short). From this organization, we propose several general rules about patterns of microclimatic diversity. To examine the second step (behavioral sampling of locally available microclimates), we construct a set of models that simulate ectotherms moving on a thermal landscape according to simple sets of diffusion-based rules. The models explore the effects of both changes in body size (which affect the time scale over which organisms integrate operative body temperatures) and increases in the mean and variance of temperature on the thermal landscape. Collectively, the models indicate that both simple behavioral rules and interactions between body size and spatial patterns of thermal variation can profoundly affect the distribution of realized body temperatures experienced by ectotherms. These analyses emphasize the rich set of problems still to solve before arriving at a general, predictive theory of the biological consequences of climate change. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Transcription activator-like effectors(TALEs)based genome engineering].

PubMed

Zhao, Mei-Wei; Duan, Cheng-Li; Liu, Jiang

2013-10-01

Systematic reverse-engineering of functional genome architecture requires precise modifications of gene sequences and transcription levels. The development and application of transcription activator-like effectors(TALEs) has created a wealth of genome engineering possibilities. TALEs are a class of naturally occurring DNA-binding proteins found in the plant pathogen Xanthomonas species. The DNA-binding domain of each TALE typically consists of tandem 34-amino acid repeat modules rearranged according to a simple cipher to target new DNA sequences. Customized TALEs can be used for a wide variety of genome engineering applications, including transcriptional modulation and genome editing. Such "genome engineering" has now been established in human cells and a number of model organisms, thus opening the door to better understanding gene function in model organisms, improving traits in crop plants and treating human genetic disorders.

Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction.

PubMed

Palmer, David S; Frolov, Andrey I; Ratkova, Ekaterina L; Fedorov, Maxim V

2010-12-15

We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).

An analytical model for in situ extraction of organic vapors

USGS Publications Warehouse

Roy, W.R.; Griffin, R.A.

1991-01-01

This paper introduces a simple convective-flow model that can be used as a screening tool and for conducting sensitivity analyses for in situ vapor extraction of organic compounds from porous media. An assumption basic to this model was that the total mass of volatile organic chemicals (VOC) exists in three forms: as vapors, in the soil solution, and adsorbed to soil particles. The equilibrium partitioning between the vapor-liquid phase was described by Henry's law constants (K(H)) and between the liquid-soil phase by soil adsorption constants (K(d)) derived from soil organic carbon-water partition coefficients (K(oc)). The model was used to assess the extractability of 36 VOCs from a hypothetical site. Most of the VOCs appeared to be removable from soil by this technology, although modeling results suggested that rates for the alcohols and ketones may be very slow. In general, rates for weakly adsorbed compounds (K(oc) < 100 mL/g) were significantly higher when K(H) was greater than 10-4 atm??m3??mol-1. When K(oc) was greater than about 100 mL/g, the rates of extraction were sensitive to the amount of organic carbon present in the soil. The air permeability of the soil material (k) was a critical factor. In situ extraction needs careful evaluation when k is less than 10 millidarcies to determine its applicability. An increase in the vacuum applied to an extraction well accelerated removal rates but the diameter of the well had little effect. However, an increase in the length of the well screen open to the contaminated zone significantly affected removal rates, especially in low-permeability materials.This paper introduces a simple convective-flow model that can be used as a screening tool and for conducting sensitivity analyses for in situ vapor extraction of organic compounds from porous media. An assumption basic to this model was that the total mass of volatile organic chemicals (VOC) exists in three forms: as vapors, in the soil solution, and adsorbed to soil particles. The equilibrium partitioning between the vapor-liquid phase was described by Henry's law constants (KH) and between the liquid-soil phase by soil adsorption constants (Kd) derived from soil organic carbon-water partition coefficients (Koc). The model was used to assess the extractability of 36 VOCs from a hypothetical site. Most of the VOCs appeared to be removable from soil by this technology, although modeling results suggested that rates for the alcohols and ketones may be very slow. In general, rates for weakly adsorbed compounds (Koc < 100 mL/g) were significantly higher when KH was greater than 10-4atm-m3-mol-1. When Koc was greater than about 100 mL/g, the rates of extraction were sensitive to the amount of organic carbon present in the soil. The air permeability of the soil material (k) was a critical factor. In situ extraction needs careful evaluation when k is less than 10 millidarcies to determine its applicability. An increase in the vacuum applied to an extraction well accelerated removal rates but the diameter of the well had little effect. However, an increase in the length of the well screen open to the contaminated zone significantly affected removal rates, especially in low-permeability materials.

A method for generating reliable atomistic models of amorphous polymers based on a random search of energy minima

NASA Astrophysics Data System (ADS)

Curcó, David; Casanovas, Jordi; Roca, Marc; Alemán, Carlos

2005-07-01

A method for generating atomistic models of dense amorphous polymers is presented. The method is organized in a two-steps procedure. First, structures are generated using an algorithm that minimizes the torsional strain. After this, a relaxation algorithm is applied to minimize the non-bonding interactions. Two alternative relaxation methods, which are based simple minimization and Concerted Rotation techniques, have been implemented. The performance of the method has been checked by simulating polyethylene, polypropylene, nylon 6, poly(L,D-lactic acid) and polyglycolic acid.

Modulation of the endogenous production of protoporphyrin IX in a yeast-based model organism

NASA Astrophysics Data System (ADS)

Joniová, Jaroslava; Gerelli, Emmanuel; Wagnières, Georges

2017-02-01

The main aim of this study was to assess conditions at which simple yeast-based model organism produces maximal levels of protoporphyrin IX (PpIX) after an exogenous administration of its precursor, 5-aminolevulinic acid (ALA), and the ferrous-ion chelator 2,2'-bipyridyl. We observed that the fluorescing porphyrin, produced after these administrations, was likely to be PpIX since fluorescence spectroscopy of the porphyrins produced endogenously in yeast cells resembles that of PpIX in DMSO and in vivo in the chick's chorioallantoic membrane model. Also, fluorescence lifetimes of these porphyrins are very similar to that of PpIX in vitro and in vivo. This suggests that PpIX is the main fluorescent compound produced by yeast in our conditions. We found that the conditions at which yeast produces the maximal PpIX were a synchronous administration of 5 μM ALA and 1 mM 2,2'-bipyridyl for yeast incubated in aqueous glucose and 1 mM 2,2'-bipyridyl in the presence of YPD medium. Such a simple model is of high interest to study basic mechanisms involved in the mitochondrial respiration since PpIX, which is produced in this organelle, can be used as an oxygen sensor, or to perform photodynamic therapy and photodiagnosis. Since the absorption and scattering coefficients of this model are much smaller than those of soft tissues over the visible part of the spectrum, a version of this model loaded with appropriated amounts of light absorbing and scattering particles could be designed as a phantom to mimic tumors containing PpIX, a useful tool to optimize certain cancer photodetection set-ups.

Network architectures and circuit function: testing alternative hypotheses in multifunctional networks.

PubMed

Leonard, J L

2000-05-01

Understanding how species-typical movement patterns are organized in the nervous system is a central question in neurobiology. The current explanations involve 'alphabet' models in which an individual neuron may participate in the circuit for several behaviors but each behavior is specified by a specific neural circuit. However, not all of the well-studied model systems fit the 'alphabet' model. The 'equation' model provides an alternative possibility, whereby a system of parallel motor neurons, each with a unique (but overlapping) field of innervation, can account for the production of stereotyped behavior patterns by variable circuits. That is, it is possible for such patterns to arise as emergent properties of a generalized neural network in the absence of feedback, a simple version of a 'self-organizing' behavioral system. Comparison of systems of identified neurons suggest that the 'alphabet' model may account for most observations where CPGs act to organize motor patterns. Other well-known model systems, involving architectures corresponding to feed-forward neural networks with a hidden layer, may organize patterned behavior in a manner consistent with the 'equation' model. Such architectures are found in the Mauthner and reticulospinal circuits, 'escape' locomotion in cockroaches, CNS control of Aplysia gill, and may also be important in the coordination of sensory information and motor systems in insect mushroom bodies and the vertebrate hippocampus. The hidden layer of such networks may serve as an 'internal representation' of the behavioral state and/or body position of the animal, allowing the animal to fine-tune oriented, or particularly context-sensitive, movements to the prevalent conditions. Experiments designed to distinguish between the two models in cases where they make mutually exclusive predictions provide an opportunity to elucidate the neural mechanisms by which behavior is organized in vivo and in vitro. Copyright 2000 S. Karger AG, Basel

Risk management in spatio-temporally varying field by true slime mold

NASA Astrophysics Data System (ADS)

Ito, Kentaro; Sumpter, David; Nakagaki, Toshiyuki

Revealing how lower organisms solve complicated problems is a challenging research area, which could reveal the evolutionary origin of biological information processing. Here we report on the ability of a single-celled organism, true slime mold, to find a smart solution of risk management under spatio-temporally varying conditions. We designed test conditions under which there were three food-locations at vertices of equilateral triangle and a toxic light illuminated the organism on alternating halves of the triangle. We found that the organism behavior depended on the period of the repeated illumination, even though the total exposure time was kept the same . A simple mathematical model for the experimental results is proposed from a dynamical system point of view. We discuss our results in the context of a strategy of risk management by Physarum.

A novel single compartment in vitro model for electrophysiological research using the perfluorocarbon FC-770.

PubMed

Choudhary, M; Clavica, F; van Mastrigt, R; van Asselt, E

2016-06-20

Electrophysiological studies of whole organ systems in vitro often require measurement of nerve activity and/or stimulation of the organ via the associated nerves. Currently two-compartment setups are used for such studies. These setups are complicated and require two fluids in two separate compartments and stretching the nerve across one chamber to the other, which may damage the nerves. We aimed at developing a simple single compartment setup by testing the electrophysiological properties of FC-770 (a perfluorocarbon) for in vitro recording of bladder afferent nerve activity and electrical stimulation of the bladder. Perflurocarbons are especially suitable for such a setup because of their high oxygen carrying capacity and insulating properties. In male Wistar rats, afferent nerve activity was recorded from postganglionic branches of the pelvic nerve in vitro, in situ and in vivo. The bladder was stimulated electrically via the efferent nerves. Organ viability was monitored by recording spontaneous contractions of the bladder. Additionally, histological examinations were done to test the effect of FC-770 on the bladder tissue. Afferent nerve activity was successfully recorded in a total of 11 rats. The bladders were stimulated electrically and high amplitude contractions were evoked. Histological examinations and monitoring of spontaneous contractions showed that FC-770 maintained organ viability and did not cause damage to the tissue. We have shown that FC-770 enables a simple, one compartment in vitro alternative for the generally used two compartment setups for whole organ electrophysiological studies.

Self-assembly and hierarchical patterning of aligned organic nanowire arrays by solvent evaporation on substrates with patterned wettability.

PubMed

Bao, Rong-Rong; Zhang, Cheng-Yi; Zhang, Xiu-Juan; Ou, Xue-Mei; Lee, Chun-Sing; Jie, Jian-Sheng; Zhang, Xiao-Hong

2013-06-26

The controlled growth and alignment of one-dimensional organic nanostructures at well-defined locations considerably hinders the integration of nanostructures for electronic and optoelectronic applications. Here, we demonstrate a simple process to achieve the growth, alignment, and hierarchical patterning of organic nanowires on substrates with controlled patterns of surface wettability. The first-level pattern is confined by the substrate patterns of wettability. Organic nanostructures are preferentially grown on solvent wettable regions. The second-level pattern is the patterning of aligned organic nanowires deposited by controlling the shape and movement of the solution contact lines during evaporation on the wettable regions. This process is controlled by the cover-hat-controlled method or vertical evaportation method. Therefore, various new patterns of organic nanostructures can be obtained by combing these two levels of patterns. This simple method proves to be a general approach that can be applied to other organic nanostructure systems. Using the as-prepared patterned nanowire arrays, an optoelectronic device (photodetector) is easily fabricated. Hence, the proposed simple, large-scale, low-cost method of preparing patterns of highly ordered organic nanostructures has high potential applications in various electronic and optoelectronic devices.

A simple, gravimetric method to quantify inorganic carbon in calcareous soils

USDA-ARS?s Scientific Manuscript database

Total carbon (TC) in calcareous soils has two components: inorganic carbon (IC) as calcite and or dolomite and organic carbon (OC) in the soil organic matter. The IC must be measured and subtracted from TC to obtain OC. Our objective was to develop a simple gravimetric technique to quantify IC. Th...

A Simple Mnemonic for Tautomerization Mechanisms in Organic Chemistry

ERIC Educational Resources Information Center

Stephens, Chad E.

2010-01-01

The familiar word OREO (as in the cookie) is presented as a simple mnemonic for remembering the basic steps of the classical tautomerization mechanisms in organic chemistry. For acid-catalyzed tautomerizations, OREO stands for proton on, resonance, proton off. For base-catalyzed tautomerizations, OREO stands for proton off, resonance, proton on.…

Prospects for Classifying Complex Imagery Using a Self-Organizing Neural Network

DTIC Science & Technology

1989-01-11

complex imagery. In his original re- port, Fukushima demonstrated that this system could discriminate between simple alphabetical characters...on a VAX-8600 minicomputer. Wire frame models of three different vehicles were used to test the properties which Fukushima had demonstrated. The...Table No. Page 3-1 Parameters for Training on Three Input Images 14 3-2 Trained Results 17 vn 1. INTRODUCTION The Neocognitron of Fukushima [2

A New Concept Map Model for E-Learning Environments

NASA Astrophysics Data System (ADS)

Dattolo, Antonina; Luccio, Flaminia L.

Web-based education enables learners and teachers to access a wide quantity of continuously updated educational sources. In order to support the learning process, a system has to provide some fundamental features, such as simple mechanisms for the identification of the collection of “interesting” documents, adequate structures for storing, organizing and visualizing these documents, and appropriate mechanisms for creating personalized adaptive paths and views for learners.

The theoretical current-voltage dependence of a non-degenerate disordered organic material obtained with conductive atomic force microscopy

NASA Astrophysics Data System (ADS)

Woellner, Cristiano F.; Freire, José A.; Guide, Michele; Nguyen, Thuc-Quyen

2011-08-01

We develop a simple continuum model for the current voltage characteristics of a material as measured by the conducting atomic force microscopy, including space charge effects. We address the effect of the point contact on the magnitude of the current and on the transition voltages between the different current regimes by comparing these with the corresponding expressions obtained with planar electrodes.

Lotka-Volterra competition models for sessile organisms.

PubMed

Spencer, Matthew; Tanner, Jason E

2008-04-01

Markov models are widely used to describe the dynamics of communities of sessile organisms, because they are easily fitted to field data and provide a rich set of analytical tools. In typical ecological applications, at any point in time, each point in space is in one of a finite set of states (e.g., species, empty space). The models aim to describe the probabilities of transitions between states. In most Markov models for communities, these transition probabilities are assumed to be independent of state abundances. This assumption is often suspected to be false and is rarely justified explicitly. Here, we start with simple assumptions about the interactions among sessile organisms and derive a model in which transition probabilities depend on the abundance of destination states. This model is formulated in continuous time and is equivalent to a Lotka-Volterra competition model. We fit this model and a variety of alternatives in which transition probabilities do not depend on state abundances to a long-term coral reef data set. The Lotka-Volterra model describes the data much better than all models we consider other than a saturated model (a model with a separate parameter for each transition at each time interval, which by definition fits the data perfectly). Our approach provides a basis for further development of stochastic models of sessile communities, and many of the methods we use are relevant to other types of community. We discuss possible extensions to spatially explicit models.

A Review of Hemolysis Prediction Models for Computational Fluid Dynamics.

PubMed

Yu, Hai; Engel, Sebastian; Janiga, Gábor; Thévenin, Dominique

2017-07-01

Flow-induced hemolysis is a crucial issue for many biomedical applications; in particular, it is an essential issue for the development of blood-transporting devices such as left ventricular assist devices, and other types of blood pumps. In order to estimate red blood cell (RBC) damage in blood flows, many models have been proposed in the past. Most models have been validated by their respective authors. However, the accuracy and the validity range of these models remains unclear. In this work, the most established hemolysis models compatible with computational fluid dynamics of full-scale devices are described and assessed by comparing two selected reference experiments: a simple rheometric flow and a more complex hemodialytic flow through a needle. The quantitative comparisons show very large deviations concerning hemolysis predictions, depending on the model and model parameter. In light of the current results, two simple power-law models deliver the best compromise between computational efficiency and obtained accuracy. Finally, hemolysis has been computed in an axial blood pump. The reconstructed geometry of a HeartMate II shows that hemolysis occurs mainly at the tip and leading edge of the rotor blades, as well as at the leading edge of the diffusor vanes. © 2017 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Volatility of organic aerosol: evaporation of ammonium sulfate/succinic acid aqueous solution droplets.

PubMed

Yli-Juuti, Taina; Zardini, Alessandro A; Eriksson, Axel C; Hansen, Anne Maria K; Pagels, Joakim H; Swietlicki, Erik; Svenningsson, Birgitta; Glasius, Marianne; Worsnop, Douglas R; Riipinen, Ilona; Bilde, Merete

2013-01-01

Condensation and evaporation modify the properties and effects of atmospheric aerosol particles. We studied the evaporation of aqueous succinic acid and succinic acid/ammonium sulfate droplets to obtain insights on the effect of ammonium sulfate on the gas/particle partitioning of atmospheric organic acids. Droplet evaporation in a laminar flow tube was measured in a Tandem Differential Mobility Analyzer setup. A wide range of droplet compositions was investigated, and for some of the experiments the composition was tracked using an Aerosol Mass Spectrometer. The measured evaporation was compared to model predictions where the ammonium sulfate was assumed not to directly affect succinic acid evaporation. The model captured the evaporation rates for droplets with large organic content but overestimated the droplet size change when the molar concentration of succinic acid was similar to or lower than that of ammonium sulfate, suggesting that ammonium sulfate enhances the partitioning of dicarboxylic acids to aqueous particles more than currently expected from simple mixture thermodynamics. If extrapolated to the real atmosphere, these results imply enhanced partitioning of secondary organic compounds to particulate phase in environments dominated by inorganic aerosol.

Volatility of Organic Aerosol: Evaporation of Ammonium Sulfate/Succinic Acid Aqueous Solution Droplets

PubMed Central

2013-01-01

Condensation and evaporation modify the properties and effects of atmospheric aerosol particles. We studied the evaporation of aqueous succinic acid and succinic acid/ammonium sulfate droplets to obtain insights on the effect of ammonium sulfate on the gas/particle partitioning of atmospheric organic acids. Droplet evaporation in a laminar flow tube was measured in a Tandem Differential Mobility Analyzer setup. A wide range of droplet compositions was investigated, and for some of the experiments the composition was tracked using an Aerosol Mass Spectrometer. The measured evaporation was compared to model predictions where the ammonium sulfate was assumed not to directly affect succinic acid evaporation. The model captured the evaporation rates for droplets with large organic content but overestimated the droplet size change when the molar concentration of succinic acid was similar to or lower than that of ammonium sulfate, suggesting that ammonium sulfate enhances the partitioning of dicarboxylic acids to aqueous particles more than currently expected from simple mixture thermodynamics. If extrapolated to the real atmosphere, these results imply enhanced partitioning of secondary organic compounds to particulate phase in environments dominated by inorganic aerosol. PMID:24107221

Resilience of Cyber Systems with Over- and Underregulation.

PubMed

Gisladottir, Viktoria; Ganin, Alexander A; Keisler, Jeffrey M; Kepner, Jeremy; Linkov, Igor

2017-09-01

Recent cyber attacks provide evidence of increased threats to our critical systems and infrastructure. A common reaction to a new threat is to harden the system by adding new rules and regulations. As federal and state governments request new procedures to follow, each of their organizations implements their own cyber defense strategies. This unintentionally increases time and effort that employees spend on training and policy implementation and decreases the time and latitude to perform critical job functions, thus raising overall levels of stress. People's performance under stress, coupled with an overabundance of information, results in even more vulnerabilities for adversaries to exploit. In this article, we embed a simple regulatory model that accounts for cybersecurity human factors and an organization's regulatory environment in a model of a corporate cyber network under attack. The resulting model demonstrates the effect of under- and overregulation on an organization's resilience with respect to insider threats. Currently, there is a tendency to use ad-hoc approaches to account for human factors rather than to incorporate them into cyber resilience modeling. It is clear that using a systematic approach utilizing behavioral science, which already exists in cyber resilience assessment, would provide a more holistic view for decisionmakers. © 2016 Society for Risk Analysis.

The French Health Care System; What can We Learn?

PubMed

El Taguri, A; Nasef, A

2008-12-01

All public systems look for the best organizational structure to funnel part of their national income into healthcare services. Appropriate policies may differ widely across country settings. Most healthcare systems fall under one of two broad categories, either Bismark or Beveridge systems. There is no simple ideal model for the organization of health services, but most healthcare systems that follow the Beveridge healthcare model are poor performers. The Libyan Health system is a low responsive, inefficient and underperforming system that lacks goals and/or SMART. (Specific, Measurable, Achievable, Realistic, Time specific) objectives. A look at different organization models in the world would reinforce efforts to reorganize and improve the performance of the Libyan National Healthcare services. The French Health Care System (FHCS) ranked first according to the WHO and the European Health Consumer Powerhouse. The FHCS was described to have a technically efficient, generous healthcare system that provides the best overall health care. This makes the FHCS a practical model of organization having many of the essential aspects of a modern national health service. In this review, we describe the main features of the FHCS, current challenges and future trends with particular attention paid to aspects that could be of importance to the Libyan Healthcare System.

Self-Organized Criticality, Plasticity and Sensorimotor Coupling. Explorations with a Neurorobotic Model in a Behavioural Preference Task

PubMed Central

Aguilera, Miguel; Barandiaran, Xabier E.; Bedia, Manuel G.; Seron, Francisco

2015-01-01

During the last two decades, analysis of 1/ƒ noise in cognitive science has led to a considerable progress in the way we understand the organization of our mental life. However, there is still a lack of specific models providing explanations of how 1/ƒ noise is generated in coupled brain-body-environment systems, since existing models and experiments typically target either externally observable behaviour or isolated neuronal systems but do not address the interplay between neuronal mechanisms and sensorimotor dynamics. We present a conceptual model of a minimal neurorobotic agent solving a behavioural task that makes it possible to relate mechanistic (neurodynamic) and behavioural levels of description. The model consists of a simulated robot controlled by a network of Kuramoto oscillators with homeostatic plasticity and the ability to develop behavioural preferences mediated by sensorimotor patterns. With only three oscillators, this simple model displays self-organized criticality in the form of robust 1/ƒ noise and a wide multifractal spectrum. We show that the emergence of self-organized criticality and 1/ƒ noise in our model is the result of three simultaneous conditions: a) non-linear interaction dynamics capable of generating stable collective patterns, b) internal plastic mechanisms modulating the sensorimotor flows, and c) strong sensorimotor coupling with the environment that induces transient metastable neurodynamic regimes. We carry out a number of experiments to show that both synaptic plasticity and strong sensorimotor coupling play a necessary role, as constituents of self-organized criticality, in the generation of 1/ƒ noise. The experiments also shown to be useful to test the robustness of 1/ƒ scaling comparing the results of different techniques. We finally discuss the role of conceptual models as mediators between nomothetic and mechanistic models and how they can inform future experimental research where self-organized critically includes sensorimotor coupling among the essential interaction-dominant process giving rise to 1/ƒ noise. PMID:25706744

Assessment of Simple Models for Molecular Simulation of Ethylene Carbonate and Propylene Carbonate as Solvents for Electrolyte Solutions.

PubMed

Chaudhari, Mangesh I; Muralidharan, Ajay; Pratt, Lawrence R; Rempe, Susan B

2018-02-12

Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples. The basic results discussed suggest that an empirically parameterized, non-polarizable force field can reproduce experimental structural, thermodynamic, and dielectric properties of EC and PC liquids with acceptable accuracy. More sophisticated force fields might include molecular polarizability and Buckingham-model description of inter-atomic overlap repulsions as extensions to Lennard-Jones models of van der Waals interactions. Simple approaches should be similarly successful also for applications to organic molecular ions in EC/PC solutions, but the important case of Li[Formula: see text] deserves special attention because of the particularly strong interactions of that small ion with neighboring solvent molecules. To treat the Li[Formula: see text] ions in liquid EC/PC solutions, we identify interaction models defined by empirically scaled partial charges for ion-solvent interactions. The empirical adjustments use more basic inputs, electronic structure calculations and ab initio molecular dynamics simulations, and also experimental results on Li[Formula: see text] thermodynamics and transport in EC/PC solutions. Application of such models to the mechanism of Li[Formula: see text] transport in glassy SEI models emphasizes the advantage of long time-scale molecular dynamics studies of these non-equilibrium materials.

Chaos and unpredictability in evolution.

PubMed

Doebeli, Michael; Ispolatov, Iaroslav

2014-05-01

The possibility of complicated dynamic behavior driven by nonlinear feedbacks in dynamical systems has revolutionized science in the latter part of the last century. Yet despite examples of complicated frequency dynamics, the possibility of long-term evolutionary chaos is rarely considered. The concept of "survival of the fittest" is central to much evolutionary thinking and embodies a perspective of evolution as a directional optimization process exhibiting simple, predictable dynamics. This perspective is adequate for simple scenarios, when frequency-independent selection acts on scalar phenotypes. However, in most organisms many phenotypic properties combine in complicated ways to determine ecological interactions, and hence frequency-dependent selection. Therefore, it is natural to consider models for evolutionary dynamics generated by frequency-dependent selection acting simultaneously on many different phenotypes. Here we show that complicated, chaotic dynamics of long-term evolutionary trajectories in phenotype space is very common in a large class of such models when the dimension of phenotype space is large, and when there are selective interactions between the phenotypic components. Our results suggest that the perspective of evolution as a process with simple, predictable dynamics covers only a small fragment of long-term evolution. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

The Pathway for Oxygen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion: The Pathway for Oxygen.

PubMed

Bassingthwaighte, James B; Raymond, Gary M; Dash, Ranjan K; Beard, Daniel A; Nolan, Margaret

2016-01-01

The 'Pathway for Oxygen' is captured in a set of models describing quantitative relationships between fluxes and driving forces for the flux of oxygen from the external air source to the mitochondrial sink at cytochrome oxidase. The intervening processes involve convection, membrane permeation, diffusion of free and heme-bound O2 and enzymatic reactions. While this system's basic elements are simple: ventilation, alveolar gas exchange with blood, circulation of the blood, perfusion of an organ, uptake by tissue, and consumption by chemical reaction, integration of these pieces quickly becomes complex. This complexity led us to construct a tutorial on the ideas and principles; these first PathwayO2 models are simple but quantitative and cover: (1) a 'one-alveolus lung' with airway resistance, lung volume compliance, (2) bidirectional transport of solute gasses like O2 and CO2, (3) gas exchange between alveolar air and lung capillary blood, (4) gas solubility in blood, and circulation of blood through the capillary syncytium and back to the lung, and (5) blood-tissue gas exchange in capillaries. These open-source models are at Physiome.org and provide background for the many respiratory models there.

The Pathway for Oxygen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion

PubMed Central

Bassingthwaighte, James B.; Raymond, Gary M.; Dash, Ranjan K.; Beard, Daniel A.; Nolan, Margaret

2016-01-01

The ‘Pathway for Oxygen’ is captured in a set of models describing quantitative relationships between fluxes and driving forces for the flux of oxygen from the external air source to the mitochondrial sink at cytochrome oxidase. The intervening processes involve convection, membrane permeation, diffusion of free and heme-bound O2 and enzymatic reactions. While this system’s basic elements are simple: ventilation, alveolar gas exchange with blood, circulation of the blood, perfusion of an organ, uptake by tissue, and consumption by chemical reaction, integration of these pieces quickly becomes complex. This complexity led us to construct a tutorial on the ideas and principles; these first PathwayO2 models are simple but quantitative and cover: 1) a ‘one-alveolus lung’ with airway resistance, lung volume compliance, 2) bidirectional transport of solute gasses like O2 and CO2, 3) gas exchange between alveolar air and lung capillary blood, 4) gas solubility in blood, and circulation of blood through the capillary syncytium and back to the lung, and 5) blood-tissue gas exchange in capillaries. These open-source models are at Physiome.org and provide background for the many respiratory models there. PMID:26782201

Grid cell hexagonal patterns formed by fast self-organized learning within entorhinal cortex.

PubMed

Mhatre, Himanshu; Gorchetchnikov, Anatoli; Grossberg, Stephen

2012-02-01

Grid cells in the dorsal segment of the medial entorhinal cortex (dMEC) show remarkable hexagonal activity patterns, at multiple spatial scales, during spatial navigation. It has previously been shown how a self-organizing map can convert firing patterns across entorhinal grid cells into hippocampal place cells that are capable of representing much larger spatial scales. Can grid cell firing fields also arise during navigation through learning within a self-organizing map? This article describes a simple and general mathematical property of the trigonometry of spatial navigation which favors hexagonal patterns. The article also develops a neural model that can learn to exploit this trigonometric relationship. This GRIDSmap self-organizing map model converts path integration signals into hexagonal grid cell patterns of multiple scales. GRIDSmap creates only grid cell firing patterns with the observed hexagonal structure, predicts how these hexagonal patterns can be learned from experience, and can process biologically plausible neural input and output signals during navigation. These results support an emerging unified computational framework based on a hierarchy of self-organizing maps for explaining how entorhinal-hippocampal interactions support spatial navigation. Copyright © 2010 Wiley Periodicals, Inc.

Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

PubMed

Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

2016-02-01

Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Prosthetic avian vocal organ controlled by a freely behaving bird based on a low dimensional model of the biomechanical periphery.

PubMed

Arneodo, Ezequiel M; Perl, Yonatan Sanz; Goller, Franz; Mindlin, Gabriel B

2012-01-01

Because of the parallels found with human language production and acquisition, birdsong is an ideal animal model to study general mechanisms underlying complex, learned motor behavior. The rich and diverse vocalizations of songbirds emerge as a result of the interaction between a pattern generator in the brain and a highly nontrivial nonlinear periphery. Much of the complexity of this vocal behavior has been understood by studying the physics of the avian vocal organ, particularly the syrinx. A mathematical model describing the complex periphery as a nonlinear dynamical system leads to the conclusion that nontrivial behavior emerges even when the organ is commanded by simple motor instructions: smooth paths in a low dimensional parameter space. An analysis of the model provides insight into which parameters are responsible for generating a rich variety of diverse vocalizations, and what the physiological meaning of these parameters is. By recording the physiological motor instructions elicited by a spontaneously singing muted bird and computing the model on a Digital Signal Processor in real-time, we produce realistic synthetic vocalizations that replace the bird's own auditory feedback. In this way, we build a bio-prosthetic avian vocal organ driven by a freely behaving bird via its physiologically coded motor commands. Since it is based on a low-dimensional nonlinear mathematical model of the peripheral effector, the emulation of the motor behavior requires light computation, in such a way that our bio-prosthetic device can be implemented on a portable platform.

Universality in the Self Organized Critical behavior of a cellular model of superconducting vortex dynamics

NASA Astrophysics Data System (ADS)

Sun, Yudong; Vadakkan, Tegy; Bassler, Kevin

2007-03-01

We study the universality and robustness of variants of the simple model of superconducting vortex dynamics first introduced by Bassler and Paczuski in Phys. Rev. Lett. 81, 3761 (1998). The model is a coarse-grained model that captures the essential features of the plastic vortex motion. It accounts for the repulsive interaction between vortices, the pining of vortices at quenched disordered locations in the material, and the over-damped dynamics of the vortices that leads to tearing of the flux line lattice. We report the results of extensive simulations of the critical ``Bean state" dynamics of the model. We find a phase diagram containing four distinct phases of dynamical behavior, including two phases with distinct Self Organized Critical (SOC) behavior. Exponents describing the avalanche scaling behavior in the two SOC phases are determined using finite-size scaling. The exponents are found to be robust within each phase and for different variants of the model. The difference of the scaling behavior in the two phases is also observed in the morphology of the avalanches.

Some Physical Principles Governing Spatial and Temporal Organization in Living Systems

NASA Astrophysics Data System (ADS)

Ali, Md Zulfikar

Spatial and temporal organization in living organisms are crucial for a variety of biological functions and arise from the interplay of large number of interacting molecules. One of the central questions in systems biology is to understand how such an intricate organization emerges from the molecular biochemistry of the cell. In this dissertation we explore two projects. The first project relates to pattern formation in a cell membrane as an example of spatial organization, and the second project relates to the evolution of oscillatory networks as a simple example of temporal organization. For the first project, we introduce a model for pattern formation in a two-component lipid bilayer and study the interplay between membrane composition and membrane geometry, demonstrating the existence of a rich phase diagram. Pattern formation is governed by the interplay between phase separation driven by lipid-lipid interactions and tendency of lipid domains with high intrinsic curvature to deform the membrane away from its preferred position. Depending on membrane parameters, we find the formation of compact lipid micro-clusters or of striped domains. We calculate the stripe width analytically and find good agreement with stripe widths obtained from the simulations. For the second project, we introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm and apply it to study the following problems. Using the model, we study robustness and designabilty of a 2-component network that generate oscillations. We completely enumerate the sequence space and the phenotypic space, and discuss the relationship between designabilty, robustness and evolvability. We further apply the model to studies of neutral drift in networks that yield oscillatory dynamics, e.g. starting with a relatively simple network and allowing it to evolve by adding nodes and connections while requiring that oscillatory dynamics be preserved. Our studies demonstrate both the importance of employing a sequence-based evolutionary scheme and the relative rapidity (in evolutionary time) for the redistribution of function over new nodes via neutral drift. In addition we discovered another much slower timescale for network evolution, reflecting hidden order in sequence space that we interpret in terms of sparsely connected domains. Finally, we use the model to study the evolution of an oscillator from a non-oscillatory network under the influence of external periodic forcing as a model for evolution of circadian rhythm in living systems. We use a greedy algorithm based on optimizing biologically motivated fitness functions and find that the algorithm successfully produces oscillators. However, the distribution of free-period of evolved oscillators depends on the choice of fitness functions and the nature of forcing.

Examining the volume efficiency of the cortical architecture in a multi-processor network model.

PubMed

Ruppin, E; Schwartz, E L; Yeshurun, Y

1993-01-01

The convoluted form of the sheet-like mammalian cortex naturally raises the question whether there is a simple geometrical reason for the prevalence of cortical architecture in the brains of higher vertebrates. Addressing this question, we present a formal analysis of the volume occupied by a massively connected network or processors (neurons) and then consider the pertaining cortical data. Three gross macroscopic features of cortical organization are examined: the segregation of white and gray matter, the circumferential organization of the gray matter around the white matter, and the folded cortical structure. Our results testify to the efficiency of cortical architecture.

Voltage Amplifier Based on Organic Electrochemical Transistor.

PubMed

Braendlein, Marcel; Lonjaret, Thomas; Leleux, Pierre; Badier, Jean-Michel; Malliaras, George G

2017-01-01

Organic electrochemical transistors (OECTs) are receiving a great deal of attention as amplifying transducers for electrophysiology. A key limitation of this type of transistors, however, lies in the fact that their output is a current, while most electrophysiology equipment requires a voltage input. A simple circuit is built and modeled that uses a drain resistor to produce a voltage output. It is shown that operating the OECT in the saturation regime provides increased sensitivity while maintaining a linear signal transduction. It is demonstrated that this circuit provides high quality recordings of the human heart using readily available electrophysiology equipment, paving the way for the use of OECTs in the clinic.

A Global Assessment of Dissolved Organic Carbon in Precipitation

NASA Astrophysics Data System (ADS)

Safieddine, Sarah A.; Heald, Colette L.

2017-11-01

Precipitation is the largest physical removal pathway of atmospheric reactive organic carbon in the form of dissolved organic carbon (DOC). We present the first global DOC distribution simulated with a global model. A total of 85 and 188 Tg C yr-1 are deposited to the ocean and the land, respectively, with DOC ranging between 0.1 and 10 mg C L-1 in this GEOS-Chem simulation. We compare the 2010 simulated DOC to a 30 year synthesis of measurements. Despite limited measurements and imperfect temporal matching, the model is able to reproduce much of the spatial variability of DOC (r = 0.63), with a low bias of 35%. We present the global average carbon oxidation state (OSc>¯) as a simple metric for describing the chemical composition. In the atmosphere, -1.8≤OSc>¯≤-0.6, and the increase in solubility upon oxidation leads to a global increase in OSc>¯ in precipitation with -0.6≤OSc>¯DOC≤0.

Unraveling the mechanisms of synapse formation and axon regeneration: the awesome power of C. elegans genetics.

PubMed

Jin, YiShi

2015-11-01

Since Caenorhabditis elegans was chosen as a model organism by Sydney Brenner in 1960's, genetic studies in this organism have been instrumental in discovering the function of genes and in deciphering molecular signaling network. The small size of the organism and the simple nervous system enable the complete reconstruction of the first connectome. The stereotypic developmental program and the anatomical reproducibility of synaptic connections provide a blueprint to dissect the mechanisms underlying synapse formation. Recent technological innovation using laser surgery of single axons and in vivo imaging has also made C. elegans a new model for axon regeneration. Importantly, genes regulating synaptogenesis and axon regeneration are highly conserved in function across animal phyla. This mini-review will summarize the main approaches and the key findings in understanding the mechanisms underlying the development and maintenance of the nervous system. The impact of such findings underscores the awesome power of C. elegans genetics.

SOA formation by biogenic and carbonyl compounds: data evaluation and application.

PubMed

Ervens, Barbara; Kreidenweis, Sonia M

2007-06-01

The organic fraction of atmospheric aerosols affects the physical and chemical properties of the particles and their role in the climate system. Current models greatly underpredict secondary organic aerosol (SOA) mass. Based on a compilation of literature studies that address SOA formation, we discuss different parameters that affect the SOA formation efficiency of biogenic compounds (alpha-pinene, isoprene) and aliphatic aldehydes (glyoxal, hexanal, octanal, hexadienal). Applying a simple model, we find that the estimated SOA mass after one week of aerosol processing under typical atmospheric conditions is increased by a few microg m(-3) (low NO(x) conditions). Acid-catalyzed reactions can create > 50% more SOA mass than processes under neutral conditions; however, other parameters such as the concentration ratio of organics/NO(x), relative humidity, and absorbing mass are more significant. The assumption of irreversible SOA formation not limited by equilibrium in the particle phase or by depletion of the precursor leads to unrealistically high SOA masses for some of the assumptions we made (surface vs volume controlled processes).

Advantages of Thesaurus Representation Using the Simple Knowledge Organization System (SKOS) Compared with Proposed Alternatives

ERIC Educational Resources Information Center

Pastor-Sanchez, Juan-Antonio; Martinez Mendez, Francisco Javier; Rodriguez-Munoz, Jose Vicente

2009-01-01

Introduction: This paper presents an analysis of the Simple Knowledge Organization System (SKOS) compared with other alternatives for thesaurus representation in the Semantic Web. Method: Based on functional and structural changes of thesauri, provides an overview of the current context in which lexical paradigm is abandoned in favour of the…

Toward a mechanistic understanding of patterns in biomineralization and new insights for old dogmas in geological settings (Invited)

NASA Astrophysics Data System (ADS)

Dove, P. M.; Hamm, L.; Giuffre, A. J.; Han, N.; De Yoreo, J. J.

2013-12-01

The ability of organisms to mineralize tissues into skeletons and other functional structures is a remarkable achievement of biology. Yet, the physical basis for how macromolecules regulate the placement and onset of mineral formation is not well established. Efforts to understand nucleation onto organic substrates have produced two, seemingly contradictory, lines of thought: The biomineralization community widely assumes the organic matrix promotes nucleation through stereochemical matching to guide the organization of solute ions, while materials synthesis groups use simple binding assays to correlate high binding strength with good promoters of nucleation. This study reconciles the two views and provides a mechanistic explanation for template-directed nucleation by correlating heterogeneous nucleation barriers with crystal-substrate binding free energies. Using surface assembled monolayers (SAM) as simple model systems, we first measure the kinetics of calcite nucleation onto model substrates that present different functional group chemistries (carboxyl, thiol, phosphate, hydroxyl) and conformations (C11, C16 chain lengths). We find rates are substrate-specific and obey predictions of classical nucleation theory at supersaturations that extend above the solubility of amorphous calcium carbonate (ACC). Analysis of the kinetic data shows the thermodynamic barrier to nucleation is reduced by minimizing the interfacial free energy of the system, γ. We then use dynamic force spectroscopy to independently measure calcite-substrate binding free energies, ΔGb. Moreover, we show that within the classical theory of nucleation, γ and ΔGb should be linearly related. The results bear out this prediction and demonstrate that low energy barriers to nucleation correlate with strong crystal-substrate binding. This relationship is general to all functional group chemistries and conformations. These findings reconcile the long-standing concept of templated nucleation through stereochemical matching with the conventional wisdom that ';good binders are good nucleators'. Alternative perspectives become internally consistent when viewed through the lens of crystal-substrate binding and provide a physical basis for how organic chemistry can direct temporal and spatial patterns of carbonate nucleation.

Further Development of Verification Check-Cases for Six- Degree-of-Freedom Flight Vehicle Simulations

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Madden, Michael M.; Shelton, Robert; Jackson, A. A.; Castro, Manuel P.; Noble, Deleena M.; Zimmerman, Curtis J.; Shidner, Jeremy D.; White, Joseph P.; Dutta, Doumyo;

Disease induction by human microbial pathogens in plant-model systems: potential, problems and prospects.

PubMed

van Baarlen, Peter; van Belkum, Alex; Thomma, Bart P H J

2007-02-01

Relatively simple eukaryotic model organisms such as the genetic model weed plant Arabidopsis thaliana possess an innate immune system that shares important similarities with its mammalian counterpart. In fact, some human pathogens infect Arabidopsis and cause overt disease with human symptomology. In such cases, decisive elements of the plant's immune system are likely to be targeted by the same microbial factors that are necessary for causing disease in humans. These similarities can be exploited to identify elementary microbial pathogenicity factors and their corresponding targets in a green host. This circumvents important cost aspects that often frustrate studies in humans or animal models and, in addition, results in facile ethical clearance.

Development of vehicle model test-bending of a simple structural surfaces model for automotive vehicle sedan

NASA Astrophysics Data System (ADS)

Nor, M. K. Mohd; Noordin, A.; Ruzali, M. F. S.; Hussen, M. H.; Mustapa@Othman, N.

2017-04-01

Simple Structural Surfaces (SSS) method is offered as a means of organizing the process for rationalizing the basic vehicle body structure load paths. The application of this simplified approach is highly beneficial in the development of modern passenger car structure design. In Malaysia, the SSS topic has been widely adopted and seems compulsory in various automotive programs related to automotive vehicle structures in many higher education institutions. However, there is no real physical model of SSS available to gain considerable insight and understanding into the function of each major subassembly in the whole vehicle structures. Based on this motivation, a real physical SSS of sedan model and the corresponding model vehicle tests of bending is proposed in this work. The proposed approach is relatively easy to understand as compared to Finite Element Method (FEM). The results prove that the proposed vehicle model test is useful to physically demonstrate the importance of providing continuous load path using the necessary structural components within the vehicle structures. It is clearly observed that the global bending stiffness reduce significantly when more panels are removed from the complete SSS model. The analysis shows the front parcel shelf is an important subassembly to sustain bending load.

Variable C : N : P stoichiometry of dissolved organic matter cycling in the Community Earth System Model

DOE PAGES

Letscher, R. T.; Moore, J. K.; Teng, Y. -C.; ...

2015-01-12

Dissolved organic matter (DOM) plays an important role in the ocean's biological carbon pump by providing an advective/mixing pathway for ~ 20% of export production. DOM is known to have a stoichiometry depleted in nitrogen (N) and phosphorus (P) compared to the particulate organic matter pool, a fact that is often omitted from biogeochemical ocean general circulation models. However the variable C : N : P stoichiometry of DOM becomes important when quantifying carbon export from the upper ocean and linking the nutrient cycles of N and P with that of carbon. Here we utilize recent advances in DOM observationalmore » data coverage and offline tracer-modeling techniques to objectively constrain the variable production and remineralization rates of the DOM C : N : P pools in a simple biogeochemical-ocean model of DOM cycling. The optimized DOM cycling parameters are then incorporated within the Biogeochemical Elemental Cycling (BEC) component of the Community Earth System Model (CESM) and validated against the compilation of marine DOM observations. The optimized BEC simulation including variable DOM C : N : P cycling was found to better reproduce the observed DOM spatial gradients than simulations that used the canonical Redfield ratio. Global annual average export of dissolved organic C, N, and P below 100 m was found to be 2.28 Pg C yr -1 (143 Tmol C yr -1, 16.4 Tmol N yr -1, and 1 Tmol P yr -1, respectively, with an average export C : N : P stoichiometry of 225 : 19 : 1 for the semilabile (degradable) DOM pool. Dissolved organic carbon (DOC) export contributed ~ 25% of the combined organic C export to depths greater than 100 m.« less

Organelle Size Scaling of the Budding Yeast Vacuole by Relative Growth and Inheritance.

PubMed

Chan, Yee-Hung M; Reyes, Lorena; Sohail, Saba M; Tran, Nancy K; Marshall, Wallace F

2016-05-09

It has long been noted that larger animals have larger organs compared to smaller animals of the same species, a phenomenon termed scaling [1]. Julian Huxley proposed an appealingly simple model of "relative growth"-in which an organ and the whole body grow with their own intrinsic rates [2]-that was invoked to explain scaling in organs from fiddler crab claws to human brains. Because organ size is regulated by complex, unpredictable pathways [3], it remains unclear whether scaling requires feedback mechanisms to regulate organ growth in response to organ or body size. The molecular pathways governing organelle biogenesis are simpler than organogenesis, and therefore organelle size scaling in the cell provides a more tractable case for testing Huxley's model. We ask the question: is it possible for organelle size scaling to arise if organelle growth is independent of organelle or cell size? Using the yeast vacuole as a model, we tested whether mutants defective in vacuole inheritance, vac8Δ and vac17Δ, tune vacuole biogenesis in response to perturbations in vacuole size. In vac8Δ/vac17Δ, vacuole scaling increases with the replicative age of the cell. Furthermore, vac8Δ/vac17Δ cells continued generating vacuole at roughly constant rates even when they had significantly larger vacuoles compared to wild-type. With support from computational modeling, these results suggest there is no feedback between vacuole biogenesis rates and vacuole or cell size. Rather, size scaling is determined by the relative growth rates of the vacuole and the cell, thus representing a cellular version of Huxley's model. Copyright © 2016 Elsevier Ltd. All rights reserved.

Degradation of organic pollutants by Vacuum-Ultraviolet (VUV): Kinetic model and efficiency.

PubMed

Xie, Pengchao; Yue, Siyang; Ding, Jiaqi; Wan, Ying; Li, Xuchun; Ma, Jun; Wang, Zongping

2018-04-15

Vacuum-Ultraviolet (VUV), an efficient and green method to produce hydroxyl radical (•OH), is effective in degrading numerous organic contaminants in aqueous solution. Here, we proposed an effective and simple kinetic model to describe the degradation of organic pollutants in VUV system, by taking the •OH scavenging effects of formed organic intermediates as co-existing organic matter in whole. Using benzoic acid (BA) as a •OH probe, •OH was regarded vital for pollutant degradation in VUV system, and the thus developed model successfully predicted its degradation kinetics under different conditions. Effects of typical influencing factors such as BA concentrations and UV intensity were investigated quantitatively by the model. Temperature was found to be an important influencing factor in the VUV system, and the quantum yield of •OH showed a positive linear dependence on temperature. Impacts of humic acid (HA), alkalinity, chloride, and water matrices (realistic waters) on the oxidation efficiency were also examined. BA degradation was significantly inhibited by HA due to its scavenging of •OH, but was influenced much less by the alkalinity and chloride; high oxidation efficiency was still obtained in the realistic water. The degradation kinetics of three other typical micropollutants including bisphenol A (BPA), nitrobenzene (NB) and dimethyl phthalate (DMP), and the mixture of co-existing BA, BPA and DMP were further studied, and the developed model predicted the experimental data well, especially in realistic water. It is expected that this study will provide an effective approach to predict the degradation of organic micropollutants by the promising VUV system, and broaden the application of VUV system in water treatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Semantic representation of CDC-PHIN vocabulary using Simple Knowledge Organization System.

PubMed

Zhu, Min; Mirhaji, Parsa

2008-11-06

PHIN Vocabulary Access and Distribution System (VADS) promotes the use of standards based vocabulary within CDC information systems. However, the current PHIN vocabulary representation hinders its wide adoption. Simple Knowledge Organization System (SKOS) is a W3C draft specification to support the formal representation of Knowledge Organization Systems (KOS) within the framework of the Semantic Web. We present a method of adopting SKOS to represent PHIN vocabulary in order to enable automated information sharing and integration.

Two-way Coupling of a Process-Based Crop Growth Model (BioCro) and a Biogeochemistry Model (DayCent) and its Application to an Energy Crop Site in the mid-west USA

NASA Astrophysics Data System (ADS)

Jaiswal, D.; Long, S.; Parton, W. J.; Hartman, M.

2012-12-01

A coupled modeling system of crop growth model (BioCro) and biogeochemical model (DayCent) has been developed to assess the two-way interactions between plant growth and biogeochemistry. Crop growth in BioCro is simulated using a detailed mechanistic biochemical and biophysical multi-layer canopy model and partitioning of dry biomass into different plant organs according to phenological stages. Using hourly weather records, the model partitions light between dynamically changing sunlit and shaded portions of the canopy and computes carbon and water exchange with the atmosphere and through the canopy for each hour of the day, each day of the year. The model has been parameterized for the bioenergy crops sugarcane, Miscanthus and switchgrass, and validation has shown it to predict growth cycles and partitioning of biomass to a high degree of accuracy. As such it provides an ideal input for a soil biogeochemical model. DayCent is an established model for predicting long-term changes in soil C & N and soil-atmosphere exchanges of greenhouse gases. At present, DayCent uses a relatively simple productivity model. In this project BioCro has replaced this simple model to provide DayCent with a productivity and growth model equal in detail to its biogeochemistry. Dynamic coupling of these two models to produce CroCent allows for differential C: N ratios of litter fall (based on rates of senescence of different plant organs) and calibration of the model for realistic plant productivity in a mechanistic way. A process-based approach to modeling plant growth is needed for bioenergy crops because research on these crops (especially second generation feedstocks) has started only recently, and detailed agronomic information for growth, yield and management is too limited for effective empirical models. The coupled model provides means to test and improve the model against high resolution data, such as that obtained by eddy covariance and explore yield implications of different crop and soil management.

The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models

PubMed Central

Pires, Mathias M.; Cantor, Maurício; Guimarães, Paulo R.; de Aguiar, Marcus A. M.; dos Reis, Sérgio F.; Coltri, Patricia P.

2015-01-01

The network structure of biological systems provides information on the underlying processes shaping their organization and dynamics. Here we examined the structure of the network depicting protein interactions within the spliceosome, the macromolecular complex responsible for splicing in eukaryotic cells. We show the interactions of less connected spliceosome proteins are nested subsets of the connections of the highly connected proteins. At the same time, the network has a modular structure with groups of proteins sharing similar interaction patterns. We then investigated the role of affinity and specificity in shaping the spliceosome network by adapting a probabilistic model originally designed to reproduce food webs. This food-web model was as successful in reproducing the structure of protein interactions as it is in reproducing interactions among species. The good performance of the model suggests affinity and specificity, partially determined by protein size and the timing of association to the complex, may be determining network structure. Moreover, because network models allow building ensembles of realistic networks while encompassing uncertainty they can be useful to examine the dynamics and vulnerability of intracelullar processes. Unraveling the mechanisms organizing the spliceosome interactions is important to characterize the role of individual proteins on splicing catalysis and regulation. PMID:26443080

Speciations and Extinctions in a Self-Organizing Critical Model of Tree-Like Evolution

NASA Astrophysics Data System (ADS)

Kramer, M.; Vandewalle, N.; Ausloos, M.

1996-04-01

We study analytically a simple model of a self-organized critical evolution. The model considers both extinction and speciation events leading to the growth of phylogenetic-like trees. Through a mean-field like theory, we study the evolution of the local configurations for the tree leaves. The fitness threshold, below which life activity takes place through avalanches of all sizes is calculated. The transition between speciating (evolving) and dead trees is obtained and is in agreement with numerical simulations. Moreover, this theoretical work suggests that the structure of the tree is strongly dependent on the extinction strength. Nous étudions analytiquement un modèle simple d'évolution auto-organisée critique. Le modèle considère des extinctions et des spéciations conduisant à une croissance d'arbre phylogénétiques. Nous étudions ici par une théorie de champ moyen l'évolution des configurations des extrémités de l'arbre. Le seuil critique de “fitness” en-dessous duquel des explosions d'activité biologique de toutes tailles se produisent est calculé. La transition entre arbres croissants et arbres éteints est également obtenue en accord avec les simulations. En outre, ce travail théorique suggère que la structure des arbres générés dépend fortement du paramètre d'extinctions.

Steady-state photoconductivity and multi-particle interactions in high-mobility organic semiconductors

PubMed Central

Irkhin, P.; Najafov, H.; Podzorov, V.

2015-01-01

Fundamental understanding of photocarrier generation, transport and recombination under a steady-state photoexcitation has been an important goal of organic electronics and photonics, since these processes govern such electronic properties of organic semiconductors as, for instance, photoconductivity. Here, we discovered that photoconductivity of a highly ordered organic semiconductor rubrene exhibits several distinct regimes, in which photocurrent as a function of cw (continuous wave) excitation intensity is described by a power law with exponents sequentially taking values 1, 1/3 and ¼. We show that in pristine crystals this photocurrent is generated at the very surface of the crystals, while the bulk photocurrent is drastically smaller and follows a different sequence of exponents, 1 and ½. We describe a simple experimental procedure, based on an application of “gauge effect” in high vacuum, that allows to disentangle the surface and bulk contributions to photoconductivity. A model based on singlet exciton fission, triplet fusion and triplet-charge quenching that can describe these non-trivial effects in photoconductivity of highly ordered organic semiconductors is proposed. Observation of these effects in photoconductivity and modeling of the underlying microscopic mechanisms described in this work represent a significant step forward in our understanding of electronic properties of organic semiconductors. PMID:26478121

Differential solvation of intrinsically disordered linkers drives the formation of spatially organized droplets in ternary systems of linear multivalent proteins

NASA Astrophysics Data System (ADS)

Harmon, Tyler S.; Holehouse, Alex S.; Pappu, Rohit V.

2018-04-01

Intracellular biomolecular condensates are membraneless organelles that encompass large numbers of multivalent protein and nucleic acid molecules. The bodies assemble via a combination of liquid–liquid phase separation and gelation. A majority of condensates included multiple components and show multilayered organization as opposed to being well-mixed unitary liquids. Here, we put forward a simple thermodynamic framework to describe the emergence of spatially organized droplets in multicomponent systems comprising of linear multivalent polymers also known as associative polymers. These polymers, which mimic proteins and/or RNA have the architecture of domains or motifs known as stickers that are interspersed by flexible spacers known as linkers. Using a minimalist numerical model for a four-component system, we have identified features of linear multivalent molecules that are necessary and sufficient for generating spatially organized droplets. We show that differences in sequence-specific effective solvation volumes of disordered linkers between interaction domains enable the formation of spatially organized droplets. Molecules with linkers that are preferentially solvated are driven to the interface with the bulk solvent, whereas molecules that have linkers with negligible effective solvation volumes form cores in the core–shell architectures that emerge in the minimalist four-component systems. Our modeling has relevance for understanding the physical determinants of spatially organized membraneless organelles.

A bio-inspired kinematic controller for obstacle avoidance during reaching tasks with real robots.

PubMed

Srinivasa, Narayan; Bhattacharyya, Rajan; Sundareswara, Rashmi; Lee, Craig; Grossberg, Stephen

2012-11-01

This paper describes a redundant robot arm that is capable of learning to reach for targets in space in a self-organized fashion while avoiding obstacles. Self-generated movement commands that activate correlated visual, spatial and motor information are used to learn forward and inverse kinematic control models while moving in obstacle-free space using the Direction-to-Rotation Transform (DIRECT). Unlike prior DIRECT models, the learning process in this work was realized using an online Fuzzy ARTMAP learning algorithm. The DIRECT-based kinematic controller is fault tolerant and can handle a wide range of perturbations such as joint locking and the use of tools despite not having experienced them during learning. The DIRECT model was extended based on a novel reactive obstacle avoidance direction (DIRECT-ROAD) model to enable redundant robots to avoid obstacles in environments with simple obstacle configurations. However, certain configurations of obstacles in the environment prevented the robot from reaching the target with purely reactive obstacle avoidance. To address this complexity, a self-organized process of mental rehearsals of movements was modeled, inspired by human and animal experiments on reaching, to generate plans for movement execution using DIRECT-ROAD in complex environments. These mental rehearsals or plans are self-generated by using the Fuzzy ARTMAP algorithm to retrieve multiple solutions for reaching each target while accounting for all the obstacles in its environment. The key aspects of the proposed novel controller were illustrated first using simple examples. Experiments were then performed on real robot platforms to demonstrate successful obstacle avoidance during reaching tasks in real-world environments. Copyright © 2012 Elsevier Ltd. All rights reserved.

Simulating Streamflow and Dissolved Organic Matter Export from small Forested Watersheds

NASA Astrophysics Data System (ADS)

Xu, N.; Wilson, H.; Saiers, J. E.

2010-12-01

Coupling the rainfall-runoff process and solute transport in catchment models is important for understanding the dynamics of water-quality-relevant constituents in a watershed. To simulate the hydrologic and biogeochemical processes in a parametrically parsimonious way remains challenging. The purpose of this study is to quantify the export of water and dissolved organic matter (DOM) from a forested catchment by developing and testing a coupled model for rainfall-runoff and soil-water flushing of DOM. Natural DOM plays an important role in terrestrial and aquatic systems by affecting nutrient cycling, contaminant mobility and toxicity, and drinking water quality. Stream-water discharge and DOM concentrations were measured in a first-order stream in Harvard Forest, Massachusetts. These measurements show that stream water DOM concentrations are greatest during hydrologic events induced by rainfall or snowmelt and decline to low, steady levels during periods of baseflow. Comparison of the stream-discharge data to calculations of a simple rainfall-runoff model reveals a hysteretic relationship between stream-flow rates and the storage of water within the catchment. A modified version of the rainfall-runoff model that accounts for hysteresis in the storage-discharge relationship in a parametrically simple way is capable of describing much, but not all, of the variation in the time-series data on stream discharge. Our ongoing research is aimed at linking the new rainfall-runoff formulation with coupled equations that predict soil-flushing and stream-water concentrations of DOM as functions of the temporal change in catchment water storage. This model will provide a predictive tool for examining how changes in climatic variables would affect the runoff generation and DOM fluxes from terrestrial landscape.

Mechanochemical Symmetry Breaking in Hydra Aggregates

PubMed Central

Mercker, Moritz; Köthe, Alexandra; Marciniak-Czochra, Anna

2015-01-01

Tissue morphogenesis comprises the self-organized creation of various patterns and shapes. Although detailed underlying mechanisms are still elusive in many cases, an increasing amount of experimental data suggests that chemical morphogen and mechanical processes are strongly coupled. Here, we develop and test a minimal model of the axis-defining step (i.e., symmetry breaking) in aggregates of the Hydra polyp. Based on previous findings, we combine osmotically driven shape oscillations with tissue mechanics and morphogen dynamics. We show that the model incorporating a simple feedback loop between morphogen patterning and tissue stretch reproduces a wide range of experimental data. Finally, we compare different hypothetical morphogen patterning mechanisms (Turing, tissue-curvature, and self-organized criticality). Our results suggest the experimental investigation of bigger (i.e., multiple head) aggregates as a key step for a deeper understanding of mechanochemical symmetry breaking in Hydra. PMID:25954896

Caenorhabditis elegans in regenerative medicine: a simple model for a complex discipline.

PubMed

Aitlhadj, Layla; Stürzenbaum, Stephen R

2014-06-01

Stem cell research is a major focus of regenerative medicine, which amalgamates diverse disciplines ranging from developmental cell biology to chemical and genetic therapy. Although embryonic stem cells have provided the foundation of stem cell therapy, they offer an in vitro study system that might not provide the best insight into mechanisms and behaviour of cells within living organisms. Caenorhabditis elegans is a well defined model organism with highly conserved cell development and signalling processes that specify cell fate. Its genetic amenability coupled with its chemical screening applicability make the nematode well suited as an in vivo system in which regenerative therapy and stem cell processes can be explored. Here, we describe some of the major advances in stem cell research from the worm's perspective. Copyright © 2014 Elsevier Ltd. All rights reserved.

The yeast replicative aging model.

PubMed

He, Chong; Zhou, Chuankai; Kennedy, Brian K

2018-03-08

It has been nearly three decades since the budding yeast Saccharomyces cerevisiae became a significant model organism for aging research and it has emerged as both simple and powerful. The replicative aging assay, which interrogates the number of times a "mother" cell can divide and produce "daughters", has been a stalwart in these studies, and genetic approaches have led to the identification of hundreds of genes impacting lifespan. More recently, cell biological and biochemical approaches have been developed to determine how cellular processes become altered with age. Together, the tools are in place to develop a holistic view of aging in this single-celled organism. Here, we summarize the current state of understanding of yeast replicative aging with a focus on the recent studies that shed new light on how aging pathways interact to modulate lifespan in yeast. Copyright © 2018. Published by Elsevier B.V.

Distinct polymer physics principles govern chromatin dynamics in mouse and Drosophila topological domains.

PubMed

Ea, Vuthy; Sexton, Tom; Gostan, Thierry; Herviou, Laurie; Baudement, Marie-Odile; Zhang, Yunzhe; Berlivet, Soizik; Le Lay-Taha, Marie-Noëlle; Cathala, Guy; Lesne, Annick; Victor, Jean-Marc; Fan, Yuhong; Cavalli, Giacomo; Forné, Thierry

2015-08-15

In higher eukaryotes, the genome is partitioned into large "Topologically Associating Domains" (TADs) in which the chromatin displays favoured long-range contacts. While a crumpled/fractal globule organization has received experimental supports at higher-order levels, the organization principles that govern chromatin dynamics within these TADs remain unclear. Using simple polymer models, we previously showed that, in mouse liver cells, gene-rich domains tend to adopt a statistical helix shape when no significant locus-specific interaction takes place. Here, we use data from diverse 3C-derived methods to explore chromatin dynamics within mouse and Drosophila TADs. In mouse Embryonic Stem Cells (mESC), that possess large TADs (median size of 840 kb), we show that the statistical helix model, but not globule models, is relevant not only in gene-rich TADs, but also in gene-poor and gene-desert TADs. Interestingly, this statistical helix organization is considerably relaxed in mESC compared to liver cells, indicating that the impact of the constraints responsible for this organization is weaker in pluripotent cells. Finally, depletion of histone H1 in mESC alters local chromatin flexibility but not the statistical helix organization. In Drosophila, which possesses TADs of smaller sizes (median size of 70 kb), we show that, while chromatin compaction and flexibility are finely tuned according to the epigenetic landscape, chromatin dynamics within TADs is generally compatible with an unconstrained polymer configuration. Models issued from polymer physics can accurately describe the organization principles governing chromatin dynamics in both mouse and Drosophila TADs. However, constraints applied on this dynamics within mammalian TADs have a peculiar impact resulting in a statistical helix organization.

Topological structure dynamics revealing collective evolution in active nematics

PubMed Central

Shi, Xia-qing; Ma, Yu-qiang

2013-01-01

Topological defects frequently emerge in active matter like bacterial colonies, cytoskeleton extracts on substrates, self-propelled granular or colloidal layers and so on, but their dynamical properties and the relations to large-scale organization and fluctuations in these active systems are seldom touched. Here we reveal, through a simple model for active nematics using self-driven hard elliptic rods, that the excitation, annihilation and transportation of topological defects differ markedly from those in non-active media. These dynamical processes exhibit strong irreversibility in active nematics in the absence of detailed balance. Moreover, topological defects are the key factors in organizing large-scale dynamic structures and collective flows, resulting in multi-spatial temporal effects. These findings allow us to control the self-organization of active matter through topological structures. PMID:24346733

Collaboratively Conceived, Designed and Implemented: Matching Visualization Tools with Geoscience Data Collections and Geoscience Data Collections with Visualization Tools via the ToolMatch Service.

NASA Astrophysics Data System (ADS)

Hoebelheinrich, N. J.; Lynnes, C.; West, P.; Ferritto, M.

2014-12-01

Two problems common to many geoscience domains are the difficulties in finding tools to work with a given dataset collection, and conversely, the difficulties in finding data for a known tool. A collaborative team from the Earth Science Information Partnership (ESIP) has gotten together to design and create a web service, called ToolMatch, to address these problems. The team began their efforts by defining an initial, relatively simple conceptual model that addressed the two uses cases briefly described above. The conceptual model is expressed as an ontology using OWL (Web Ontology Language) and DCterms (Dublin Core Terms), and utilizing standard ontologies such as DOAP (Description of a Project), FOAF (Friend of a Friend), SKOS (Simple Knowledge Organization System) and DCAT (Data Catalog Vocabulary). The ToolMatch service will be taking advantage of various Semantic Web and Web standards, such as OpenSearch, RESTful web services, SWRL (Semantic Web Rule Language) and SPARQL (Simple Protocol and RDF Query Language). The first version of the ToolMatch service was deployed in early fall 2014. While more complete testing is required, a number of communities besides ESIP member organizations have expressed interest in collaborating to create, test and use the service and incorporate it into their own web pages, tools and / or services including the USGS Data Catalog service, DataONE, the Deep Carbon Observatory, Virtual Solar Terrestrial Observatory (VSTO), and the U.S. Global Change Research Program. In this session, presenters will discuss the inception and development of the ToolMatch service, the collaborative process used to design, refine, and test the service, and future plans for the service.

Self-organization in a simple model of adaptive agents playing 2×2 games with arbitrary payoff matrices

NASA Astrophysics Data System (ADS)

Fort, H.; Viola, S.

2004-03-01

We analyze, both analytically and numerically, the self-organization of a system of “selfish” adaptive agents playing an arbitrary iterated pairwise game (defined by a 2×2 payoff matrix). Examples of possible games to play are the prisoner’s dilemma (PD) game, the chicken game, the hero game, etc. The agents have no memory, use strategies not based on direct reciprocity nor “tags” and are chosen at random, i.e., geographical vicinity is neglected. They can play two possible strategies: cooperate (C) or defect (D). The players measure their success by comparing their utilities with an estimate for the expected benefits and update their strategy following a simple rule. Two versions of the model are studied: (1) the deterministic version (the agents are either in definite states C or D) and (2) the stochastic version (the agents have a probability c of playing C). Using a general master equation we compute the equilibrium states into which the system self-organizes, characterized by their average probability of cooperation ceq. Depending on the payoff matrix, we show that ceq can take five different values. We also consider the mixing of agents using two different payoff matrices and show that any value of ceq can be reached by tuning the proportions of agents using each payoff matrix. In particular, this can be used as a way to simulate the effect of a fraction d of “antisocial” individuals—incapable of realizing any value to cooperation—on the cooperative regime hold by a population of neutral or “normal” agents.

Self-organization in a simple model of adaptive agents playing 2 x 2 games with arbitrary payoff matrices.

PubMed

Fort, H; Viola, S

2004-03-01

We analyze, both analytically and numerically, the self-organization of a system of "selfish" adaptive agents playing an arbitrary iterated pairwise game (defined by a 2 x 2 payoff matrix). Examples of possible games to play are the prisoner's dilemma (PD) game, the chicken game, the hero game, etc. The agents have no memory, use strategies not based on direct reciprocity nor "tags" and are chosen at random, i.e., geographical vicinity is neglected. They can play two possible strategies: cooperate (C) or defect (D). The players measure their success by comparing their utilities with an estimate for the expected benefits and update their strategy following a simple rule. Two versions of the model are studied: (1) the deterministic version (the agents are either in definite states C or D) and (2) the stochastic version (the agents have a probability c of playing C). Using a general master equation we compute the equilibrium states into which the system self-organizes, characterized by their average probability of cooperation c(eq). Depending on the payoff matrix, we show that c(eq) can take five different values. We also consider the mixing of agents using two different payoff matrices and show that any value of c(eq) can be reached by tuning the proportions of agents using each payoff matrix. In particular, this can be used as a way to simulate the effect of a fraction d of "antisocial" individuals--incapable of realizing any value to cooperation--on the cooperative regime hold by a population of neutral or "normal" agents.

Point process models for localization and interdependence of punctate cellular structures.

PubMed

Li, Ying; Majarian, Timothy D; Naik, Armaghan W; Johnson, Gregory R; Murphy, Robert F

2016-07-01

Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.

Refiners Switch to RFG Complex Model

EIA Publications

1998-01-01

On January 1, 1998, domestic and foreign refineries and importers must stop using the "simple" model and begin using the "complex" model to calculate emissions of volatile organic compounds (VOC), toxic air pollutants (TAP), and nitrogen oxides (NOx) from motor gasoline. The primary differences between application of the two models is that some refineries may have to meet stricter standards for the sulfur and olefin content of the reformulated gasoline (RFG) they produce and all refineries will now be held accountable for NOx emissions. Requirements for calculating emissions from conventional gasoline under the anti-dumping rule similarly change for exhaust TAP and NOx. However, the change to the complex model is not expected to result in an increase in the price premium for RFG or constrain supplies.

Hydrodynamic Contributions to Amoeboid Cell Motility

NASA Astrophysics Data System (ADS)

Lewis, Owen; Guy, Robert

2011-11-01

Understanding the methods by which cells move is a fundamental problem in modern biology. Recent evidence has shown that the fluid dynamics of cytoplasm can play a vital role in cellular motility. The slime mold Physarum polycephalum provides an excellent model organism for the study of amoeboid motion. In this research, we use both analytic and computational models to investigate intracellular fluid flow in a simple model of Physarum. In both models, of we are specifically interested in stresses generated by cytoplasmic flow which act in the direction of cellular motility. In our numerical model, the Immersed Boundary Method is used to account for such stresses. We investigate the relationship between contraction waves, low waves and locomotive forces, and attempt characterize conditions necessary to generate directed motion.

Sensitivity of Aerosol Mass and Microphysics to varying treatments of Condensational Growth of Secondary Organic Compounds in a regional model

NASA Astrophysics Data System (ADS)

Lowe, Douglas; Topping, David; McFiggans, Gordon

2017-04-01

Gas to particle partitioning of atmospheric compounds occurs through disequilibrium mass transfer rather than through instantaneous equilibrium. However, it is common to treat only the inorganic compounds as partitioning dynamically whilst organic compounds, represented by the Volatility Basis Set (VBS), are partitioned instantaneously. In this study we implement a more realistic dynamic partitioning of organic compounds in a regional framework and assess impact on aerosol mass and microphysics. It is also common to assume condensed phase water is only associated with inorganic components. We thus also assess sensitivity to assuming all organics are hygroscopic according to their prescribed molecular weight. For this study we use WRF-Chem v3.4.1, focusing on anthropogenic dominated North-Western Europe. Gas-phase chemistry is represented using CBM-Z whilst aerosol dynamics are simulated using the 8-section MOSAIC scheme, including a 9-bin VBS treatment of organic aerosol. Results indicate that predicted mass loadings can vary significantly. Without gas phase ageing of higher volatility compounds, dynamic partitioning always results in lower mass loadings downwind of emission sources. The inclusion of condensed phase water in both partitioning models increases the predicted PM mass, resulting from a larger contribution from higher volatility organics, if present. If gas phase ageing of VBS compounds is allowed to occur in a dynamic model, this can often lead to higher predicted mass loadings, contrary to expected behaviour from a simple non-reactive gas phase box model. As descriptions of aerosol phase processes improve within regional models, the baseline descriptions of partitioning should retain the ability to treat dynamic partitioning of organics compounds. Using our simulations, we discuss whether derived sensitivities to aerosol processes in existing models may be inherently biased. This work was supported by the Natural Environment Research Council within the RONOCO (NE/F004656/1) and CCN-Vol (NE/L007827/1) projects.

Sensitivity of Aerosol Mass and Microphysics to Treatments of Condensational Growth of Secondary Organic Compounds in a Regional Model

NASA Astrophysics Data System (ADS)

Topping, D. O.; Lowe, D.; McFiggans, G.; Zaveri, R. A.

2016-12-01

Gas to particle partitioning of atmospheric compounds occurs through disequilibrium mass transfer rather than through instantaneous equilibrium. However, it is common to treat only the inorganic compounds as partitioning dynamically whilst organic compounds, represented by the Volatility Basis Set (VBS), are partitioned instantaneously. In this study we implement a more realistic dynamic partitioning of organic compounds in a regional framework and assess impact on aerosol mass and microphysics. It is also common to assume condensed phase water is only associated with inorganic components. We thus also assess sensitivity to assuming all organics are hygroscopic according to their prescribed molecular weight.For this study we use WRF-Chem v3.4.1, focusing on anthropogenic dominated North-Western Europe. Gas-phase chemistry is represented using CBM-Z whilst aerosol dynamics are simulated using the 8-section MOSAIC scheme, including a 9-bin volatility basis set (VBS) treatment of organic aerosol. Results indicate that predicted mass loadings can vary significantly. Without gas phase ageing of higher volatility compounds, dynamic partitioning always results in lower mass loadings downwind of emission sources. The inclusion of condensed phase water in both partitioning models increases the predicted PM mass, resulting from a larger contribution from higher volatility organics, if present. If gas phase ageing of VBS compounds is allowed to occur in a dynamic model, this can often lead to higher predicted mass loadings, contrary to expected behaviour from a simple non-reactive gas phase box model. As descriptions of aerosol phase processes improve within regional models, the baseline descriptions of partitioning should retain the ability to treat dynamic partitioning of organic compounds. Using our simulations, we discuss whether derived sensitivities to aerosol processes in existing models may be inherently biased.This work was supported by the Nature Environment Research Council within the RONOCO (NE/F004656/1) and CCN-Vol (NE/L007827/1) projects.

A simple teaching tool for training the pelvic organ prolapse quantification system.

PubMed

Geiss, Ingrid M; Riss, Paul A; Hanzal, Engelbert; Dungl, Andrea

2007-09-01

The pelvic organ prolapse quantification (POPQ) system is currently the most common and specific system describing different prolapse stages. Nevertheless, its use is not yet accepted worldwide in routine care. Our aim was to develop a simple teaching tool for the POPQ system capable of simulating different stages of uterovaginal prolapse for use in medical education with hands on training. We constructed a moveable and flexible tool with an inverted Santa Claus' cap, which simulated the vaginal cuff and the tassel at the end representing the cervix. A wooden embroidery frame fixed the cap and served as the hymen, the reference point for all measurements. Inside the cap, we sewed buttons to define the anatomic landmark points Aa and Ap located 3 cm distal from the frame. After explaining the device to the students, we used the three-by-three grid for recording the quantitative description of the pelvic organ support. First, each student had to demonstrate a specific prolapse with his cap device. Then, a prolapse was simulated on the cap, and the student had to take the relevant measurements and record them in the POPQ grid. The main training effect to understand the POPQ system seems to be the possibility for each trainee to simulate a three-dimensional prolapse with this flexible vagina model.

The emergence of overlapping scale-free genetic architecture in digital organisms.

PubMed

Gerlee, P; Lundh, T

2008-01-01

We have studied the evolution of genetic architecture in digital organisms and found that the gene overlap follows a scale-free distribution, which is commonly found in metabolic networks of many organisms. Our results show that the slope of the scale-free distribution depends on the mutation rate and that the gene development is driven by expansion of already existing genes, which is in direct correspondence to the preferential growth algorithm that gives rise to scale-free networks. To further validate our results we have constructed a simple model of gene development, which recapitulates the results from the evolutionary process and shows that the mutation rate affects the tendency of genes to cluster. In addition we could relate the slope of the scale-free distribution to the genetic complexity of the organisms and show that a high mutation rate gives rise to a more complex genetic architecture.

Gamification - Environmental and Sustainable Development Organizations Could Do More

NASA Astrophysics Data System (ADS)

Ziegler, C. R.; Miller, C. A.; Kilaru, V.; French, R. A.; Costanza, R.; Brookes, A.

2013-12-01

The use of digital games to foster sustainable development and environmental goals has grown over the last 10 years. Innovative thinking and the origins of 'serious games,' 'games for change' and 'gamification' are partly rooted in movies and science fiction. Existing games illustrate a spectrum of approaches: for example, World Food Programme's FoodForce and University of Washington's Foldit. Environmental organizations globally (e.g. US EPA) have dabbled with game development and gamification, but have only touched the tip of the iceberg, particularly when compared to the success of the commercial gaming industry. We explore: 1) the intersection of environmental organization mission statements in the context of gamification efforts , 2) some examples of existing games, from simple to complex, 3) business model approaches (e.g. game development partnerships with academia, private industry, NGOs, etc.), 4) barriers, and 5) benefits of a more concerted and technologically-advanced approach to gamification for environmental organizations.

A kinetic model to explain the grain size and organic matter content dependence of magnetic susceptibility in transitional marine environments: A case study in Ria de Muros (NW Iberia)

NASA Astrophysics Data System (ADS)

Mohamed, Kais J.; Andrade, Alba; Rey, Daniel; Rubio, Belén.; Bernabeu, Ana María.

2017-06-01

Magnetic minerals in marine sediments are sensitive indicators of processes such as provenance changes, climatic controls, pollution, and postdepositional geochemical changes. Magnetic susceptibility is the bulk property of the sediments most commonly used to understand the magnetic characteristics of sediments. Before conclusions can be drawn from changes in this parameter, it is important to understand what factors and to what extent control changes in magnetic susceptibility. The magnetic susceptibility of surficial sediments in the Galician Rias Baixas, in NW Spain, has been shown to covary with sediment texture and organic matter content. Downcore, the magnetic properties of these sediments experience drastic changes as a result of strong dissolution caused by early diagenesis. In this paper, we further explore the relationship between these factors and formalize the observed covariations as the result of a simple second-order kinetic model dependent on the content of organic matter in surficial sediments in the Ria de Muros. The reanalysis of previously reported data from the Rias de Vigo and Pontevedra confirmed the validity of this model and suggested further controls such as wave climate and water depth in the rates at which magnetic susceptibility changes are controlled by organic matter content.

Bacteria, Yeast, Worms, and Flies: Exploiting simple model organisms to investigate human mitochondrial diseases

PubMed Central

Rea, Shane L.; Graham, Brett H.; Nakamaru-Ogiso, Eiko; Kar, Adwitiya; Falk, Marni J.

2013-01-01

The extensive conservation of mitochondrial structure, composition, and function across evolution offers a unique opportunity to expand our understanding of human mitochondrial biology and disease. By investigating the biology of much simpler model organisms, it is often possible to answer questions that are unreachable at the clinical level. Here, we review the relative utility of four different model organisms, namely the bacteria Escherichia coli, the yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, in studying the role of mitochondrial proteins relevant to human disease. E. coli are single cell, prokaryotic bacteria that have proven to be a useful model system in which to investigate mitochondrial respiratory chain protein structure and function. S. cerevisiae is a single-celled eukaryote that can grow equally well by mitochondrial-dependent respiration or by ethanol fermentation, a property that has proven to be a veritable boon for investigating mitochondrial functionality. C. elegans is a multi-cellular, microscopic worm that is organized into five major tissues and has proven to be a robust model animal for in vitro and in vivo studies of primary respiratory chain dysfunction and its potential therapies in humans. Studied for over a century, D. melanogaster is a classic metazoan model system offering an abundance of genetic tools and reagents that facilitates investigations of mitochondrial biology using both forward and reverse genetics. The respective strengths and limitations of each species relative to mitochondrial studies are explored. In addition, an overview is provided of major discoveries made in mitochondrial biology in each of these four model systems. PMID:20818735

Single organic microtwist with tunable pitch.

PubMed

Chen, Hai-Bo; Zhou, Yan; Yin, Jie; Yan, Jing; Ma, Yuguo; Wang, Lei; Cao, Yong; Wang, Jian; Pei, Jian

2009-05-19

A facile synthesis of previously unknown, well-separated, uniform chiral microstructures from achiral pi-conjugated organic molecules was developed by simple solution process. Detailed characterization and formation mechanism were presented. By simple structure modification or temperature change, the pitch of the chiral structure can be fine tuned. Our result opens new possibilities for novel materials in which structure chirality is coupled to device performance.

Introduction of a Simple Experiment for the Undergraduate Organic Chemistry Laboratory Demonstrating the Lewis Acid and Shape-Selective Properties of Zeolite Na-Y

ERIC Educational Resources Information Center

Maloney, Vincent; Szczepanski, Zach

2017-01-01

A simple, inexpensive, discovery-based experiment for undergraduate organic laboratories has been developed that demonstrates the Lewis acid and shape-selective properties of zeolites. Calcined zeolite Na-Y promotes the electrophilic aromatic bromination of toluene with a significantly higher para/ortho ratio than observed under conventional…

A three-dimensional spatiotemporal receptive field model explains responses of area MT neurons to naturalistic movies

PubMed Central

Nishimoto, Shinji; Gallant, Jack L.

2012-01-01

Area MT has been an important target for studies of motion processing. However, previous neurophysiological studies of MT have used simple stimuli that do not contain many of the motion signals that occur during natural vision. In this study we sought to determine whether views of area MT neurons developed using simple stimuli can account for MT responses under more naturalistic conditions. We recorded responses from macaque area MT neurons during stimulation with naturalistic movies. We then used a quantitative modeling framework to discover which specific mechanisms best predict neuronal responses under these challenging conditions. We find that the simplest model that accurately predicts responses of MT neurons consists of a bank of V1-like filters, each followed by a compressive nonlinearity, a divisive nonlinearity and linear pooling. Inspection of the fit models shows that the excitatory receptive fields of MT neurons tend to lie on a single plane within the three-dimensional spatiotemporal frequency domain, and suppressive receptive fields lie off this plane. However, most excitatory receptive fields form a partial ring in the plane and avoid low temporal frequencies. This receptive field organization ensures that most MT neurons are tuned for velocity but do not tend to respond to ambiguous static textures that are aligned with the direction of motion. In sum, MT responses to naturalistic movies are largely consistent with predictions based on simple stimuli. However, models fit using naturalistic stimuli reveal several novel properties of MT receptive fields that had not been shown in prior experiments. PMID:21994372

The dependence of the strength and thickness of field-aligned currents on solar wind and ionospheric parameters

PubMed Central

Johnson, Jay R.; Wing, Simon

2017-01-01

Sheared plasma flows at the low-latitude boundary layer (LLBL) correlate well with early afternoon auroral arcs and upward field-aligned currents. We present a simple analytic model that relates solar wind and ionospheric parameters to the strength and thickness of field-aligned currents (Λ) in a region of sheared velocity, such as the LLBL. We compare the predictions of the model with DMSP observations and find remarkably good scaling of the upward region 1 currents with solar wind and ionospheric parameters in region located at the boundary layer or open field lines at 1100–1700 magnetic local time. We demonstrate that Λ~nsw−0.5 and Λ ~ L when Λ/L < 5 where L is the auroral electrostatic scale length. The sheared boundary layer thickness (Δm) is inferred to be around 3000 km, which appears to have weak dependence on Vsw. J‖ has dependencies on Δm, Σp, nsw, and Vsw. The analytic model provides a simple way to organize data and to infer boundary layer structures from ionospheric data. PMID:29057194

Self-organizing biopsychosocial dynamics and the patient-healer relationship.

PubMed

Pincus, David

2012-01-01

The patient-healer relationship has an increasing area of interest for complementary and alternative medicine (CAM) researchers. This focus on the interpersonal context of treatment is not surprising as dismantling studies, clinical trials and other linear research designs continually point toward the critical role of context and the broadband biopsychosocial nature of therapeutic responses to CAM. Unfortunately, the same traditional research models and methods that fail to find simple and specific treatment-outcome relations are similarly failing to find simple and specific mechanisms to explain how interpersonal processes influence patient outcomes. This paper presents an overview of some of the key models and methods from nonlinear dynamical systems that are better equipped for empirical testing of CAM outcomes on broadband biopsychosocial processes. Suggestions are made for CAM researchers to assist in modeling the interactions among key process dynamics interacting across biopsychosocial scales: empathy, intra-psychic conflict, physiological arousal, and leukocyte telomerase activity. Finally, some speculations are made regarding the possibility for deeper cross-scale information exchange involving quantum temporal nonlocality. Copyright © 2012 S. Karger AG, Basel.

Accurate Behavioral Simulator of All-Digital Time-Domain Smart Temperature Sensors by Using SIMULINK

PubMed Central

Chen, Chun-Chi; Chen, Chao-Lieh; Lin, You-Ting

2016-01-01

This study proposes a new behavioral simulator that uses SIMULINK for all-digital CMOS time-domain smart temperature sensors (TDSTSs) for performing rapid and accurate simulations. Inverter-based TDSTSs offer the benefits of low cost and simple structure for temperature-to-digital conversion and have been developed. Typically, electronic design automation tools, such as HSPICE, are used to simulate TDSTSs for performance evaluations. However, such tools require extremely long simulation time and complex procedures to analyze the results and generate figures. In this paper, we organize simple but accurate equations into a temperature-dependent model (TDM) by which the TDSTSs evaluate temperature behavior. Furthermore, temperature-sensing models of a single CMOS NOT gate were devised using HSPICE simulations. Using the TDM and these temperature-sensing models, a novel simulator in SIMULINK environment was developed to substantially accelerate the simulation and simplify the evaluation procedures. Experiments demonstrated that the simulation results of the proposed simulator have favorable agreement with those obtained from HSPICE simulations, showing that the proposed simulator functions successfully. This is the first behavioral simulator addressing the rapid simulation of TDSTSs. PMID:27509507

Resource-Competing Oscillator Network as a Model of Amoeba-Based Neurocomputer

NASA Astrophysics Data System (ADS)

Aono, Masashi; Hirata, Yoshito; Hara, Masahiko; Aihara, Kazuyuki

An amoeboid organism, Physarum, exhibits rich spatiotemporal oscillatory behavior and various computational capabilities. Previously, the authors created a recurrent neurocomputer incorporating the amoeba as a computing substrate to solve optimization problems. In this paper, considering the amoeba to be a network of oscillators coupled such that they compete for constant amounts of resources, we present a model of the amoeba-based neurocomputer. The model generates a number of oscillation modes and produces not only simple behavior to stabilize a single mode but also complex behavior to spontaneously switch among different modes, which reproduces well the experimentally observed behavior of the amoeba. To explore the significance of the complex behavior, we set a test problem used to compare computational performances of the oscillation modes. The problem is a kind of optimization problem of how to allocate a limited amount of resource to oscillators such that conflicts among them can be minimized. We show that the complex behavior enables to attain a wider variety of solutions to the problem and produces better performances compared with the simple behavior.

A Global Assessment of Rain-Dissolved Organic Carbon

NASA Astrophysics Data System (ADS)

Safieddine, S.; Heald, C. L.

2017-12-01

Precipitation is the largest physical removal pathway of atmospheric organic carbon from the atmosphere. The removed carbon is transferred to the land and ocean in the form of dissolved organic carbon (DOC). Limited measurements have hindered efforts to characterize global DOC. In this poster presentation, we show the first simulated global DOC distribution based on a GEOS-Chem model simulation of the atmospheric reactive carbon budget. Over the ocean, simulated DOC concentrations are between 0.1 to 1 mgCL-1 with a total of 85 TgCyr-1 deposited. DOC concentrations are higher inland, ranging between 1 and 10 mgCL-1, producing a total of 188 TgCyr-1 terrestrial organic wet deposition. We compare the 2010 simulated DOC to a 30-year synthesis of available DOC measurements over different environments. Despite imperfect matching of observational and simulated time intervals, the model is able to reproduce much of the spatial variability of DOC (r= 0.63), with a low bias of 35%. We compare the global average carbon oxidation state (OSc) of both atmospheric and dissolved organic carbon, as a simple metric for describing the chemical composition of organics. In the global atmosphere reactive organic carbon (ROC) is dominated by hydrocarbons and ketones, and OSc, ranges from -1.8 to -0.6. In the dissolved form, formaldehyde, formic acid, primary and secondary semi-volatiles organic aerosol dominate the DOC concentrations. The increase in solubility upon oxidation leads to a global increase in OSc in rainwater with -0.6<=OSc <=0. This simulation provides new insight into the current model representation of the flow of atmospheric and rain-dissolved organic carbon, and new opportunities to use observations and simulations to understand the DOC reaching land and ocean.

Simulation of soil organic carbon in different soil size fractions using 13Carbon measurement data

NASA Astrophysics Data System (ADS)

Gottschalk, P.; Bellarby, J.; Chenu, C.; Foereid, B.; Wattenbach, M.; Zingore, S.; Smith, J.

2009-04-01

We simulate the soil organic carbon (SOC) dynamics at a chronoseqeunce site in France, using the Rothamsted Carbon model. The site exhibits a transition from C3 plants, dominated by pine forest, to a conventional C4 maize rotation. The different 13C signatures of the forest plants and maize are used to distinguish between the woodland derived carbon (C) and the maize derived C. The model is evaluated against total SOC and C derived from forest and maize, respectively. The SOC dynamics of the five SOC pools of the model, decomposable plant material (DPM), resistant plant material (RPM), biomass, humus and inert C, are also compared to the SOC dynamics measured in different soil size fractions. These fractions are > 50 μm (particulate organic matter), 2-50 μm (silt associated SOC) and <2 μm (clay associated SOC). Other authors had shown that the RPM pool of the model corresponds well to SOC measured in the soil size fraction > 50 μm and the sum of the other pools corresponds well to the SOC measured in the soil size fraction < 50 μm. Default model applications show that the model underestimates the fast drop in forest C stocks in the first 20 years after land-use change and overestimates the C accumulation of maize C. Several hypotheses were tested to evaluate the simulations. Input data and internal model parameter uncertainties had minor effects on the simulations results. Accounting for erosion and implementing a simple tillage routine did not improve the simulation fit to the data. We therefore hypothesize that a generic process that is not yet explicitly accounted for in the ROTHC model could explain the loss in soil C after land use change. Such a process could be the loss of the physical protection of soil organic matter as would be observed following cultivation of a previously uncultivated soil. Under native conditions a fraction of organic matter is protected in stable soil aggregates. These aggregates are physically disrupted by continuous and repeated cultivation of the soil. The underestimation of SOC loss by the model can be mainly attributed to the slow turnover of the humus pool. This pool was shown to represent mainly the SOC associated with the silt and clay soil fraction. Here, the clay associated SOC shows as similar turnover time as the humus pool in the model. We split the humus pool into a clay and a silt associated pool. The clay pool now corresponds to the clay associated SOC with the turnover time of the humus pool. The silt pool now corresponds to the silt associated SOC. From the measurements, the latter has a turnover time similar to the turnover time of the particulate organic matter. We therefore use the turnover time of the RPM pool for the silt pool. These modifications improve the simulations of the forest derived C significantly and improve the simulations of the maize derived C. Future work will further evaluate and refine this approach to eventually capture the SOC dynamics associated with physical protection, including the effect of tillage/no-tillage, in a simple approach.

Development of a simple and rapid method for the specific identification of organism causing anthrax by slide latex agglutination.

PubMed

Sumithra, T G; Chaturvedi, V K; Gupta, P K; Sunita, S C; Rai, A K; Kutty, M V H; Laxmi, U; Murugan, M S

2014-05-01

A specific latex agglutination test (LAT) based on anti-PA (protective antigen) antibodies having detection limit of 5 × 10(4) formalin treated Bacillus anthracis cells or 110 ng of PA was optimized in this study. The optimized LAT could detect anthrax toxin in whole blood as well as in serum from the animal models of anthrax infection. The protocol is a simple and promising method for the specific detection of bacteria causing anthrax under routine laboratory, as well as in field, conditions without any special equipments or expertise. The article presents the first report of a latex agglutination test for the specific identification of the cultures of bacteria causing anthrax. As the test is targeting one of anthrax toxic protein (PA), this can also be used to determine virulence of suspected organisms. At the same time, the same LAT can be used directly on whole blood or sera samples under field conditions for the specific diagnosis of anthrax. © 2013 The Society for Applied Microbiology.

Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid

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

Metere, Alfredo, E-mail: alfredo.metere@mmk.su.se; Oleynikov, Peter; Dzugutov, Mikhail

2014-12-21

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process,more » can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.« less

Proton flux and radiation dose from galactic cosmic rays in the lunar regolith and implications for organic synthesis at the poles of the Moon and Mercury

NASA Astrophysics Data System (ADS)

Crites, S. T.; Lucey, P. G.; Lawrence, D. J.

2013-11-01

Galactic cosmic rays are a potential energy source to stimulate organic synthesis from simple ices. The recent detection of organic molecules at the polar regions of the Moon by LCROSS (Colaprete, A. et al. [2010]. Science 330, 463-468, http://dx.doi.org/10.1126/science.1186986), and possibly at the poles of Mercury (Paige, D.A. et al. [2013]. Science 339, 300-303, http://dx.doi.org/10.1126/science.1231106), introduces the question of whether the organics were delivered by impact or formed in situ. Laboratory experiments show that high energy particles can cause organic production from simple ices. We use a Monte Carlo particle scattering code (MCNPX) to model and report the flux of GCR protons at the surface of the Moon and report radiation dose rates and absorbed doses at the Moon’s surface and with depth as a result of GCR protons and secondary particles, and apply scaling factors to account for contributions to dose from heavier ions. We compare our results with dose rate measurements by the Cosmic Ray Telescope for the Effects of Radiation (CRaTER) experiment on Lunar Reconnaissance Orbiter (Schwadron, N.A. et al. [2012]. J. Geophys. Res. 117, E00H13, http://dx.doi.org/10.1029/2011JE003978) and find them in good agreement, indicating that MCNPX can be confidently applied to studies of radiation dose at and within the surface of the Moon. We use our dose rate calculations to conclude that organic synthesis is plausible well within the age of the lunar polar cold traps, and that organics detected at the poles of the Moon may have been produced in situ. Our dose rate calculations also indicate that galactic cosmic rays can induce organic synthesis within the estimated age of the dark deposits at the pole of Mercury that may contain organics.

Extended sorption partitioning models for pesticide leaching risk assessments: Can we improve upon the koc concept?

PubMed

Jarvis, Nicholas

2016-01-01

Models used to assess leaching of pesticides to groundwater still rely on the sorption koc value, even though its limitations have been known for several decades, especially for soils of low organic carbon content (i.e. subsoils). This is mainly because the general applicability of any improved model approach that is also simple enough to use for regulatory purposes has not been demonstrated. The objective of this study was to test and compare alternative models of sorption that could be useful in pesticide risk assessment and management. To this end, a database containing the results of batch sorption experiments for pesticides was compiled from published studies in the literature, which placed at least as much emphasis on measurements in subsoil horizons as in topsoil. The database includes 785 data entries from 34 different published studies and for 21 different active substances. Overall, the apparent koc value, koc(app), roughly doubled as the soil organic carbon content decreased by a factor of ten. Nevertheless, in nearly half of the individual datasets, a constant koc value proved to be an adequate model. Further analysis showed that significant increases in koc(app) in subsoil were found primarily for the more weakly adsorbing compounds (koc values

Building a Database for a Quantitative Model

NASA Technical Reports Server (NTRS)

Kahn, C. Joseph; Kleinhammer, Roger

2014-01-01

A database can greatly benefit a quantitative analysis. The defining characteristic of a quantitative risk, or reliability, model is the use of failure estimate data. Models can easily contain a thousand Basic Events, relying on hundreds of individual data sources. Obviously, entering so much data by hand will eventually lead to errors. Not so obviously entering data this way does not aid linking the Basic Events to the data sources. The best way to organize large amounts of data on a computer is with a database. But a model does not require a large, enterprise-level database with dedicated developers and administrators. A database built in Excel can be quite sufficient. A simple spreadsheet database can link every Basic Event to the individual data source selected for them. This database can also contain the manipulations appropriate for how the data is used in the model. These manipulations include stressing factors based on use and maintenance cycles, dormancy, unique failure modes, the modeling of multiple items as a single "Super component" Basic Event, and Bayesian Updating based on flight and testing experience. A simple, unique metadata field in both the model and database provides a link from any Basic Event in the model to its data source and all relevant calculations. The credibility for the entire model often rests on the credibility and traceability of the data.

Analysis of Nitrogen Cycling in a Forest Stream During Autumn Using a 15N Tracer Addition

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

Tank, J.L.

2000-01-01

We added {sup 15}NH{sub 4}Cl over 6 weeks to Upper Ball Creek, a second-order deciduous forest stream in the Appalachian Mountains, to follow the uptake, spiraling, and fate of nitrogen in a stream food web during autumn. A priori predictions of N flow and retention were made using a simple food web mass balance model. Values of d{sup 15}N were determined for stream water ammonium, nitrate, dissolved organic nitrogen, and various compartments of the food web over time and distance and then compared to model predictions.

An overview of C. elegans biology.

PubMed

Strange, Kevin

2006-01-01

The establishment of Caenorhabditis elegans as a "model organism" began with the efforts of Sydney Brenner in the early 1960s. Brenner's focus was to find a suitable animal model in which the tools of genetic analysis could be used to define molecular mechanisms of development and nervous system function. C. elegans provides numerous experimental advantages for such studies. These advantages include a short life cycle, production of large numbers of offspring, easy and inexpensive laboratory culture, forward and reverse genetic tractability, and a relatively simple anatomy. This chapter will provide a brief overview of C. elegans biology.

A Monte Carlo model for the internal dosimetry of choroid plexuses in nuclear medicine procedures.

PubMed

Amato, Ernesto; Cicone, Francesco; Auditore, Lucrezia; Baldari, Sergio; Prior, John O; Gnesin, Silvano

2018-05-01

Choroid plexuses are vascular structures located in the brain ventricles, showing specific uptake of some diagnostic and therapeutic radiopharmaceuticals currently under clinical investigation, such as integrin-binding arginine-glycine-aspartic acid (RGD) peptides. No specific geometry for choroid plexuses has been implemented in commercially available software for internal dosimetry. The aims of the present study were to assess the dependence of absorbed dose to the choroid plexuses on the organ geometry implemented in Monte Carlo simulations, and to propose an analytical model for the internal dosimetry of these structures for 18 F, 64 Cu, 67 Cu, 68 Ga, 90 Y, 131 I and 177 Lu nuclides. A GAMOS Monte Carlo simulation based on direct organ segmentation was taken as the gold standard to validate a second simulation based on a simplified geometrical model of the choroid plexuses. Both simulations were compared with the OLINDA/EXM sphere model. The gold standard and the simplified geometrical model gave similar dosimetry results (dose difference < 3.5%), indicating that the latter can be considered as a satisfactory approximation of the real geometry. In contrast, the sphere model systematically overestimated the absorbed dose compared to both Monte Carlo models (range: 4-50% dose difference), depending on the isotope energy and organ mass. Therefore, the simplified geometric model was adopted to introduce an analytical approach for choroid plexuses dosimetry in the mass range 2-16 g. The proposed model enables the estimation of the choroid plexuses dose by a simple bi-parametric function, once the organ mass and the residence time of the radiopharmaceutical under investigation are provided. Copyright © 2018 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Persistence of Soil Organic Carbon can be Explained as an Emergent Property of Microbial Ecology and Population Dynamics

NASA Astrophysics Data System (ADS)

Woolf, D.; Lehmann, J.

2016-12-01

The exchange of carbon between soils and the atmosphere represents an important uncertainty in climate predictions. Current Earth system models apply soil organic matter (SOM) models based on independent carbon pools with 1st order decomposition dynamics. It has been widely argued over the last decade that such models do not accurately describe soil processes and mechanisms. For example, the long term persistence of soil organic carbon (SOC) is only adequately described by such models by the post hoc assumption of passive or inert carbon pools. Further, such 1st order models also fail to account for microbially-mediated dynamics such as priming interactions. These shortcomings may limit their applicability to long term predictions under conditions of global environmental change. In addition to incorporating recent conceptual advances in the mechanisms of SOM decomposition and protection, next-generation SOM models intended for use in Earth system models need to meet further quality criteria. Namely, that they should (a) accurately describe historical data from long term trials and the current global distribution of soil organic carbon, (b) be computationally efficient for large number of iterations involved in climate modeling, and (c) have sufficiently simple parameterization that they can be run on spatially-explicit data available at global scale under varying conditions of global change over long time scales. Here we show that linking fundamental ecological principles and microbial population dynamics to SOC turnover rates results in a dynamic model that meets all of these quality criteria. This approach simultaneously eliminates the need to postulate biogeochemically-implausible passive or inert pools, instead showing how SOM persistence emerges from ecological principles, while also reproducing observed priming interactions.

Comparison and correlation of Simple Sequence Repeats distribution in genomes of Brucella species

PubMed Central

Kiran, Jangampalli Adi Pradeep; Chakravarthi, Veeraraghavulu Praveen; Kumar, Yellapu Nanda; Rekha, Somesula Swapna; Kruti, Srinivasan Shanthi; Bhaskar, Matcha

2011-01-01

Computational genomics is one of the important tools to understand the distribution of closely related genomes including simple sequence repeats (SSRs) in an organism, which gives valuable information regarding genetic variations. The central objective of the present study was to screen the SSRs distributed in coding and non-coding regions among different human Brucella species which are involved in a range of pathological disorders. Computational analysis of the SSRs in the Brucella indicates few deviations from expected random models. Statistical analysis also reveals that tri-nucleotide SSRs are overrepresented and tetranucleotide SSRs underrepresented in Brucella genomes. From the data, it can be suggested that over expressed tri-nucleotide SSRs in genomic and coding regions might be responsible in the generation of functional variation of proteins expressed which in turn may lead to different pathogenicity, virulence determinants, stress response genes, transcription regulators and host adaptation proteins of Brucella genomes. Abbreviations SSRs - Simple Sequence Repeats, ORFs - Open Reading Frames. PMID:21738309

People adopt optimal policies in simple decision-making, after practice and guidance.

PubMed

Evans, Nathan J; Brown, Scott D

2017-04-01

Organisms making repeated simple decisions are faced with a tradeoff between urgent and cautious strategies. While animals can adopt a statistically optimal policy for this tradeoff, findings about human decision-makers have been mixed. Some studies have shown that people can optimize this "speed-accuracy tradeoff", while others have identified a systematic bias towards excessive caution. These issues have driven theoretical development and spurred debate about the nature of human decision-making. We investigated a potential resolution to the debate, based on two factors that routinely differ between human and animal studies of decision-making: the effects of practice, and of longer-term feedback. Our study replicated the finding that most people, by default, are overly cautious. When given both practice and detailed feedback, people moved rapidly towards the optimal policy, with many participants reaching optimality with less than 1 h of practice. Our findings have theoretical implications for cognitive and neural models of simple decision-making, as well as methodological implications.

Cross-cultural differences in meter perception.

PubMed

Kalender, Beste; Trehub, Sandra E; Schellenberg, E Glenn

2013-03-01

We examined the influence of incidental exposure to varied metrical patterns from different musical cultures on the perception of complex metrical structures from an unfamiliar musical culture. Adults who were familiar with Western music only (i.e., simple meters) and those who also had limited familiarity with non-Western music were tested on their perception of metrical organization in unfamiliar (Turkish) music with simple and complex meters. Adults who were familiar with Western music detected meter-violating changes in Turkish music with simple meter but not in Turkish music with complex meter. Adults with some exposure to non-Western music that was unmetered or metrically complex detected meter-violating changes in Turkish music with both simple and complex meters, but they performed better on patterns with a simple meter. The implication is that familiarity with varied metrical structures, including those with a non-isochronous tactus, enhances sensitivity to the metrical organization of unfamiliar music.

A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM

PubMed Central

Tyson, JJ; Hong, CI; Thron, CD; Novak, B

1999-01-01

Many organisms display rhythms of physiology and behavior that are entrained to the 24-h cycle of light and darkness prevailing on Earth. Under constant conditions of illumination and temperature, these internal biological rhythms persist with a period close to 1 day ("circadian"), but it is usually not exactly 24 h. Recent discoveries have uncovered stunning similarities among the molecular circuitries of circadian clocks in mice, fruit flies, and bread molds. A consensus picture is coming into focus around two proteins (called PER and TIM in fruit flies), which dimerize and then inhibit transcription of their own genes. Although this picture seems to confirm a venerable model of circadian rhythms based on time-delayed negative feedback, we suggest that just as crucial to the circadian oscillator is a positive feedback loop based on stabilization of PER upon dimerization. These ideas can be expressed in simple mathematical form (phase plane portraits), and the model accounts naturally for several hallmarks of circadian rhythms, including temperature compensation and the per(L) mutant phenotype. In addition, the model suggests how an endogenous circadian oscillator could have evolved from a more primitive, light-activated switch. PMID:20540926

Using energy budgets to combine ecology and toxicology in a mammalian sentinel species

NASA Astrophysics Data System (ADS)

Desforges, Jean-Pierre W.; Sonne, Christian; Dietz, Rune

2017-04-01

Process-driven modelling approaches can resolve many of the shortcomings of traditional descriptive and non-mechanistic toxicology. We developed a simple dynamic energy budget (DEB) model for the mink (Mustela vison), a sentinel species in mammalian toxicology, which coupled animal physiology, ecology and toxicology, in order to mechanistically investigate the accumulation and adverse effects of lifelong dietary exposure to persistent environmental toxicants, most notably polychlorinated biphenyls (PCBs). Our novel mammalian DEB model accurately predicted, based on energy allocations to the interconnected metabolic processes of growth, development, maintenance and reproduction, lifelong patterns in mink growth, reproductive performance and dietary accumulation of PCBs as reported in the literature. Our model results were consistent with empirical data from captive and free-ranging studies in mink and other wildlife and suggest that PCB exposure can have significant population-level impacts resulting from targeted effects on fetal toxicity, kit mortality and growth and development. Our approach provides a simple and cross-species framework to explore the mechanistic interactions of physiological processes and ecotoxicology, thus allowing for a deeper understanding and interpretation of stressor-induced adverse effects at all levels of biological organization.

The energetics of organic synthesis inside and outside the cell

PubMed Central

Amend, Jan P.; LaRowe, Douglas E.; McCollom, Thomas M.; Shock, Everett L.

2013-01-01

Thermodynamic modelling of organic synthesis has largely been focused on deep-sea hydrothermal systems. When seawater mixes with hydrothermal fluids, redox gradients are established that serve as potential energy sources for the formation of organic compounds and biomolecules from inorganic starting materials. This energetic drive, which varies substantially depending on the type of host rock, is present and available both for abiotic (outside the cell) and biotic (inside the cell) processes. Here, we review and interpret a library of theoretical studies that target organic synthesis energetics. The biogeochemical scenarios evaluated include those in present-day hydrothermal systems and in putative early Earth environments. It is consistently and repeatedly shown in these studies that the formation of relatively simple organic compounds and biomolecules can be energy-yielding (exergonic) at conditions that occur in hydrothermal systems. Expanding on our ability to calculate biomass synthesis energetics, we also present here a new approach for estimating the energetics of polymerization reactions, specifically those associated with polypeptide formation from the requisite amino acids. PMID:23754809

Coordination-supported organic polymers: mesoporous inorganic–organic materials with preferred stability

DOE PAGES

Chen, Dong; Zhang, Pengfei; Fang, Qianrong; ...

2018-01-01

A simple and versatile strategy is developed for the synthesis of coordination-supported organic polymers(COPs) via coordination between Al 3+ and 5-amino-8-hydroxyquinoline together with organic imine- or imide-based polycondensation.

Coordination-supported organic polymers: mesoporous inorganic–organic materials with preferred stability

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

Chen, Dong; Zhang, Pengfei; Fang, Qianrong

A simple and versatile strategy is developed for the synthesis of coordination-supported organic polymers(COPs) via coordination between Al 3+ and 5-amino-8-hydroxyquinoline together with organic imine- or imide-based polycondensation.

Learning molecular energies using localized graph kernels

DOE PAGES

Ferré, Grégoire; Haut, Terry Scot; Barros, Kipton Marcos

2017-03-21

We report that recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturallymore » incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. Finally, we benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.« less

Structure and atomic correlations in molecular systems probed by XAS reverse Monte Carlo refinement

NASA Astrophysics Data System (ADS)

Di Cicco, Andrea; Iesari, Fabio; Trapananti, Angela; D'Angelo, Paola; Filipponi, Adriano

2018-03-01

The Reverse Monte Carlo (RMC) algorithm for structure refinement has been applied to x-ray absorption spectroscopy (XAS) multiple-edge data sets for six gas phase molecular systems (SnI2, CdI2, BBr3, GaI3, GeBr4, GeI4). Sets of thousands of molecular replicas were involved in the refinement process, driven by the XAS data and constrained by available electron diffraction results. The equilibrated configurations were analysed to determine the average tridimensional structure and obtain reliable bond and bond-angle distributions. Detectable deviations from Gaussian models were found in some cases. This work shows that a RMC refinement of XAS data is able to provide geometrical models for molecular structures compatible with present experimental evidence. The validation of this approach on simple molecular systems is particularly important in view of its possible simple extension to more complex and extended systems including metal-organic complexes, biomolecules, or nanocrystalline systems.

Learning molecular energies using localized graph kernels

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

Ferré, Grégoire; Haut, Terry Scot; Barros, Kipton Marcos

We report that recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturallymore » incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. Finally, we benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.« less

Emergent of Burden Sharing of Robots with Emotion Model

NASA Astrophysics Data System (ADS)

Kusano, Takuya; Nozawa, Akio; Ide, Hideto

Cooperated multi robots system has much dominance in comparison with single robot system. Multi robots system is able to adapt to various circumstances and has a flexibility for variation of tasks. Robots are necessary that build a cooperative relations and acts as an organization to attain a purpose in multi robots system. Then, group behavior of insects which doesn't have advanced ability is observed. For example, ants called a sociality insect emerge systematic activities by the interaction with using a very simple way. Though ants make a communication with chemical matter, a human plans a communication by words and gestures. In this paper, we paid attention to the interaction based on psychological viewpoint. And a human's emotion model was used for the parameter which became a base of the motion planning of robots. These robots were made to do both-way action in test field with obstacle. As a result, a burden sharing like guide or carrier was seen even though those had a simple setup.

Behavior of silica aerogel networks as highly porous solid solvent media for lipases in a model transesterification reaction.

PubMed

El Rassy, H; Perrard, A; Pierre, A C

2003-03-03

Highly porous silica aerogels with differing balances of hydrophobic and hydrophilic functionalities were studied as a new immobilization medium for enzymes. Two types of lipases from Candida rugosa and Burkholderia cepacia were homogeneously dispersed in wet gel precursors before gelation. The materials obtained were compared in a simple model reaction: transesterification of vinyl laurate by 1-octanol. To allow a better comparison of the hydrophobic/hydrophilic action of the solid, very open aerogel networks with traditional organic hydrophobic/hydrophilic liquid solvents, this reaction was studied in mixtures containing different proportions of 2-methyl-2-butanol, isooctane, and water. The results are discussed in relation to the porous and hydrophobic nature of aerogels, characterized by nitrogen adsorption. It was found that silica aerogels can be considered as "solid" solvents for the enzymes, able to provide hydrophobic/hydrophilic characteristics different from those prevailing in the liquid surrounding the aerogels. A simple mechanism of action for these aerogel networks is proposed.

78 FR 18655 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-27

... from interested persons. \\1\\ 15 U.S.C. 78s(b)(1). \\2\\ 17 CFR 240.19b-4. I. Self-Regulatory Organization... simple, non-complex orders only. The Exchange now proposes to establish the Complex Order Router Subsidy... simple, non-complex orders under the ORS Program. The Participants would have to agree that they are not...

Simple, field portable colorimetric detection device for organic peroxides and hydrogen peroxide

DOEpatents

Pagoria, Philip F.; Mitchell, Alexander R.; Whipple, Richard E.; Carman, M. Leslie; Reynolds, John G.; Nunes, Peter; Shields, Sharon J.

2010-11-09

A simple and effective system for the colorimetric determination of organic peroxides and hydrogen peroxide. A peroxide pen utilizing a swipe material attached to a polyethylene tube contains two crushable vials. The two crushable vials contain a colorimetric reagent separated into dry ingredients and liquid ingredients. After swiping a suspected substance or surface the vials are broken, the reagent is mixed thoroughly and the reagent is allowed to wick into the swipe material. The presence of organic peroxides or hydrogen peroxide is confirmed by a deep blue color.

Prosthetic Avian Vocal Organ Controlled by a Freely Behaving Bird Based on a Low Dimensional Model of the Biomechanical Periphery

PubMed Central

Arneodo, Ezequiel M.; Perl, Yonatan Sanz; Goller, Franz; Mindlin, Gabriel B.

2012-01-01

Because of the parallels found with human language production and acquisition, birdsong is an ideal animal model to study general mechanisms underlying complex, learned motor behavior. The rich and diverse vocalizations of songbirds emerge as a result of the interaction between a pattern generator in the brain and a highly nontrivial nonlinear periphery. Much of the complexity of this vocal behavior has been understood by studying the physics of the avian vocal organ, particularly the syrinx. A mathematical model describing the complex periphery as a nonlinear dynamical system leads to the conclusion that nontrivial behavior emerges even when the organ is commanded by simple motor instructions: smooth paths in a low dimensional parameter space. An analysis of the model provides insight into which parameters are responsible for generating a rich variety of diverse vocalizations, and what the physiological meaning of these parameters is. By recording the physiological motor instructions elicited by a spontaneously singing muted bird and computing the model on a Digital Signal Processor in real-time, we produce realistic synthetic vocalizations that replace the bird's own auditory feedback. In this way, we build a bio-prosthetic avian vocal organ driven by a freely behaving bird via its physiologically coded motor commands. Since it is based on a low-dimensional nonlinear mathematical model of the peripheral effector, the emulation of the motor behavior requires light computation, in such a way that our bio-prosthetic device can be implemented on a portable platform. PMID:22761555

Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons

PubMed Central

Pecevski, Dejan; Buesing, Lars; Maass, Wolfgang

2011-01-01

An important open problem of computational neuroscience is the generic organization of computations in networks of neurons in the brain. We show here through rigorous theoretical analysis that inherent stochastic features of spiking neurons, in combination with simple nonlinear computational operations in specific network motifs and dendritic arbors, enable networks of spiking neurons to carry out probabilistic inference through sampling in general graphical models. In particular, it enables them to carry out probabilistic inference in Bayesian networks with converging arrows (“explaining away”) and with undirected loops, that occur in many real-world tasks. Ubiquitous stochastic features of networks of spiking neurons, such as trial-to-trial variability and spontaneous activity, are necessary ingredients of the underlying computational organization. We demonstrate through computer simulations that this approach can be scaled up to neural emulations of probabilistic inference in fairly large graphical models, yielding some of the most complex computations that have been carried out so far in networks of spiking neurons. PMID:22219717

A unified model of Grignard reagent formation.

PubMed

Shao, Yunqi; Liu, Zhen; Huang, Pan; Liu, Boping

2018-04-25

Grignard reagents are among the most fundamental reagents in organic synthesis, yet studies have hitherto failed to fully explain the selectivity and kinetics of Grignard reagent formation (GRF). The present study provides new insights into the intermediates and pathways of GRF using density functional theory (DFT) calculations. Potential energy surfaces of RX dissociation along different directions reveal the origin of configuration retention of alkenyl and aromatic halides. Radical intermediates participate solely in the dissociation stage, and depend on the geometry of the reactant halide. Dissociation of organic halides yields stabilized surface anions, and the rest of the reaction is ionic in nature. MgX+/RMg+ were proposed as the key intermediates of Mg leaving from the surface in the self-activation of GRF, which explains the accelerated kinetics upon addition of RMgX or MgX2. The intermediacy of the cations was supported by a simple electrochemical experiment. To the best of our knowledge, this is the first unified ionic model (I-model) developed for resolving the controversial issues of GRF.

Experiments and theory of undulatory locomotion in a simple structured medium

PubMed Central

Majmudar, Trushant; Keaveny, Eric E.; Zhang, Jun; Shelley, Michael J.

2012-01-01

Undulatory locomotion of micro-organisms through geometrically complex, fluidic environments is ubiquitous in nature and requires the organism to negotiate both hydrodynamic effects and geometrical constraints. To understand locomotion through such media, we experimentally investigate swimming of the nematode Caenorhabditis elegans through fluid-filled arrays of micro-pillars and conduct numerical simulations based on a mechanical model of the worm that incorporates hydrodynamic and contact interactions with the lattice. We show that the nematode's path, speed and gait are significantly altered by the presence of the obstacles and depend strongly on lattice spacing. These changes and their dependence on lattice spacing are captured, both qualitatively and quantitatively, by our purely mechanical model. Using the model, we demonstrate that purely mechanical interactions between the swimmer and obstacles can produce complex trajectories, gait changes and velocity fluctuations, yielding some of the life-like dynamics exhibited by the real nematode. Our results show that mechanics, rather than biological sensing and behaviour, can explain some of the observed changes in the worm's locomotory dynamics. PMID:22319110

A model for the emergence of cooperation, interdependence, and structure in evolving networks.

PubMed

Jain, S; Krishna, S

2001-01-16

Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of cooperative molecular species arises and evolves to become more complex and structured. The network is modeled by a directed weighted graph whose positive and negative links represent "catalytic" and "inhibitory" interactions among the molecular species, and which evolves as the least populated species (typically those that go extinct) are replaced by new ones. A small autocatalytic set, appearing by chance, provides the seed for the spontaneous growth of connectivity and cooperation in the graph. A highly structured chemical organization arises inevitably as the autocatalytic set enlarges and percolates through the network in a short analytically determined timescale. This self organization does not require the presence of self-replicating species. The network also exhibits catastrophes over long timescales triggered by the chance elimination of "keystone" species, followed by recoveries.

Impact of the glass transition on exciton dynamics in polymer thin films

NASA Astrophysics Data System (ADS)

Ehrenreich, Philipp; Proepper, Daniel; Graf, Alexander; Jores, Stefan; Boris, Alexander V.; Schmidt-Mende, Lukas

2017-11-01

In the development of organic electronics, unlimited design possibilities of conjugated polymers offer a wide variety of mechanical and electronic properties. Thereby, it is crucially important to reveal universal physical characteristics that allow efficient and forward developments of new chemical compounds. In particular for organic solar cells, a deeper understanding of exciton dynamics in polymer films can help to improve the charge generation process further. For this purpose, poly(3-hexylthiophene) (P3HT) is commonly used as a model system, although exciton decay kinetics have found different interpretations. Using temperature-dependent time-resolved photoluminescence spectroscopy in combination with low-temperature spectroscopic ellipsometry, we can show that P3HT is indeed a model system in which excitons follow a simple diffusion/hopping model. Based on our results we can exclude the relevance of hot-exciton emission as well as a dynamic torsional relaxation upon photoexcitation on a ps time scale. Instead, we depict the glass transition temperature of polymers to strongly affect exciton dynamics.

Environment-dependent morphology in plasmodium of true slime mold Physarum polycephalum and a network growth model.

PubMed

Takamatsu, Atsuko; Takaba, Eri; Takizawa, Ginjiro

2009-01-07

Branching network growth patterns, depending on environmental conditions, in plasmodium of true slime mold Physarum polycephalum were investigated. Surprisingly, the patterns resemble those in bacterial colonies even though the biological mechanisms differ greatly. Bacterial colonies are collectives of microorganisms in which individual organisms have motility and interact through nutritious and chemical fields. In contrast, the plasmodium is a giant amoeba-like multinucleated unicellular organism that forms a network of tubular structures through which protoplasm streams. The cell motility of the plasmodium is generated by oscillation phenomena observed in the partial bodies, which interact through the tubular structures. First, we analyze characteristics of the morphology quantitatively, then we abstract local rules governing the growing process to construct a simple network growth model. This model is independent of specific systems, in which only two rules are applied. Finally, we discuss the mechanism of commonly observed biological pattern formations through comparison with the system of bacterial colonies.

Environmental fate and biodegradability of benzene derivatives as studied in a model aquatic ecosystem.

PubMed Central

Lu, P Y; Metcalf, R L

1975-01-01

A model aquatic ecosystem is devised for studying relatively volatile organic compounds and simulating direct discharge of chemical wastes into aquatic ecosystems. Six simple benzene derivatives (aniline, anisole, benzoic acid, chlorobenzene, nitrobenzene, and phthalic anhydride) and other important specialty chemicals: hexachlorobenzene, pentachlorophenol, 2,6-diethylaniline, and 3,5,6-trichloro-2-pyridinol were also chosen for study of environmental behavior and fate in the model aquatic ecosystem. Quantitative relationships of the intrinsic molecular properties of the environmental micropollutants with biological responses are established, e.g., water solubility, partition coefficient, pi constant, sigma constant, ecological magnification, biodegradability index, and comparative detoxication mechanisms, respectively. Water solubility, pi constant, and sigma constant are the most significant factors and control the biological responses of the food chain members. Water solubility and pi constant control the degree of bioaccumulation, and sigma constant limits the metabolism of the xenobiotics via microsomal detoxication enzymes. These highly significant correlations should be useful for predicting environmental fate of organic chemicals. PMID:1157796

A model for the emergence of cooperation, interdependence, and structure in evolving networks

NASA Astrophysics Data System (ADS)

Jain, Sanjay; Krishna, Sandeep

2001-01-01

Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of cooperative molecular species arises and evolves to become more complex and structured. The network is modeled by a directed weighted graph whose positive and negative links represent "catalytic" and "inhibitory" interactions among the molecular species, and which evolves as the least populated species (typically those that go extinct) are replaced by new ones. A small autocatalytic set, appearing by chance, provides the seed for the spontaneous growth of connectivity and cooperation in the graph. A highly structured chemical organization arises inevitably as the autocatalytic set enlarges and percolates through the network in a short analytically determined timescale. This self organization does not require the presence of self-replicating species. The network also exhibits catastrophes over long timescales triggered by the chance elimination of "keystone" species, followed by recoveries.

Simple Epoxide Formation for the Organic Laboratory Using Oxone

ERIC Educational Resources Information Center

Broshears, Williams C.; Esteb, John J.; Richter, Jeremy; Wilson, Anne M.

2004-01-01

Epoxide chemistry is widely used in organic synthesis and regularly discussed in organic chemistry textbooks. An experiment to generate dimethyldioxirane in situ from acetone using Oxone is explained.

Linear modeling of the soil-water partition coefficient normalized to organic carbon content by reversed-phase thin-layer chromatography.

PubMed

Andrić, Filip; Šegan, Sandra; Dramićanin, Aleksandra; Majstorović, Helena; Milojković-Opsenica, Dušanka

2016-08-05

Soil-water partition coefficient normalized to the organic carbon content (KOC) is one of the crucial properties influencing the fate of organic compounds in the environment. Chromatographic methods are well established alternative for direct sorption techniques used for KOC determination. The present work proposes reversed-phase thin-layer chromatography (RP-TLC) as a simpler, yet equally accurate method as officially recommended HPLC technique. Several TLC systems were studied including octadecyl-(RP18) and cyano-(CN) modified silica layers in combination with methanol-water and acetonitrile-water mixtures as mobile phases. In total 50 compounds of different molecular shape, size, and various ability to establish specific interactions were selected (phenols, beznodiazepines, triazine herbicides, and polyaromatic hydrocarbons). Calibration set of 29 compounds with known logKOC values determined by sorption experiments was used to build simple univariate calibrations, Principal Component Regression (PCR) and Partial Least Squares (PLS) models between logKOC and TLC retention parameters. Models exhibit good statistical performance, indicating that CN-layers contribute better to logKOC modeling than RP18-silica. The most promising TLC methods, officially recommended HPLC method, and four in silico estimation approaches have been compared by non-parametric Sum of Ranking Differences approach (SRD). The best estimations of logKOC values were achieved by simple univariate calibration of TLC retention data involving CN-silica layers and moderate content of methanol (40-50%v/v). They were ranked far well compared to the officially recommended HPLC method which was ranked in the middle. The worst estimates have been obtained from in silico computations based on octanol-water partition coefficient. Linear Solvation Energy Relationship study revealed that increased polarity of CN-layers over RP18 in combination with methanol-water mixtures is the key to better modeling of logKOC through significant diminishing of dipolar and proton accepting influence of the mobile phase as well as enhancing molar refractivity in excess of the chromatographic systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular simulations of self-assembly processes in metal-organic frameworks: Model dependence

NASA Astrophysics Data System (ADS)

Biswal, Debasmita; Kusalik, Peter G.

2017-07-01

Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.

Bi-SOC-states in one-dimensional random cellular automaton

NASA Astrophysics Data System (ADS)

Czechowski, Zbigniew; Budek, Agnieszka; Białecki, Mariusz

2017-10-01

Two statistically stationary states with power-law scaling of avalanches are found in a simple 1 D cellular automaton. Features of the fixed points, the spiral saddle and the saddle with index 1, are investigated. The migration of states of the automaton between these two self-organized criticality states is demonstrated during evolution of the system in computer simulations. The automaton, being a slowly driven system, can be applied as a toy model of earthquake supercycles.

Cohesion-decohesion asymmetry in geckos

NASA Astrophysics Data System (ADS)

Puglisi, G.; Truskinovsky, L.

2013-03-01

Lizards and insects can strongly attach to walls and then detach applying negligible additional forces. We propose a simple mechanical model of this phenomenon which implies active muscle control. We show that the detachment force may depend not only on the properties of the adhesive units, but also on the elastic interaction among these units. By regulating the scale of such cooperative interaction, the organism can actively switch between two modes of adhesion: delocalized (pull off) and localized (peeling).

Comparative analysis of model behaviour for flood prediction purposes using Self-Organizing Maps

NASA Astrophysics Data System (ADS)

Herbst, M.; Casper, M. C.; Grundmann, J.; Buchholz, O.

2009-03-01

Distributed watershed models constitute a key component in flood forecasting systems. It is widely recognized that models because of their structural differences have varying capabilities of capturing different aspects of the system behaviour equally well. Of course, this also applies to the reproduction of peak discharges by a simulation model which is of particular interest regarding the flood forecasting problem. In our study we use a Self-Organizing Map (SOM) in combination with index measures which are derived from the flow duration curve in order to examine the conditions under which three different distributed watershed models are capable of reproducing flood events present in the calibration data. These indices are specifically conceptualized to extract data on the peak discharge characteristics of model output time series which are obtained from Monte-Carlo simulations with the distributed watershed models NASIM, LARSIM and WaSIM-ETH. The SOM helps to analyze this data by producing a discretized mapping of their distribution in the index space onto a two dimensional plane such that their pattern and consequently the patterns of model behaviour can be conveyed in a comprehensive manner. It is demonstrated how the SOM provides useful information about details of model behaviour and also helps identifying the model parameters that are relevant for the reproduction of peak discharges and thus for flood prediction problems. It is further shown how the SOM can be used to identify those parameter sets from among the Monte-Carlo data that most closely approximate the peak discharges of a measured time series. The results represent the characteristics of the observed time series with partially superior accuracy than the reference simulation obtained by implementing a simple calibration strategy using the global optimization algorithm SCE-UA. The most prominent advantage of using SOM in the context of model analysis is that it allows to comparatively evaluating the data from two or more models. Our results highlight the individuality of the model realizations in terms of the index measures and shed a critical light on the use and implementation of simple and yet too rigorous calibration strategies.

Human mammary epithelial cells exhibit a bimodal correlated random walk pattern.

PubMed

Potdar, Alka A; Jeon, Junhwan; Weaver, Alissa M; Quaranta, Vito; Cummings, Peter T

2010-03-10

Organisms, at scales ranging from unicellular to mammals, have been known to exhibit foraging behavior described by random walks whose segments confirm to Lévy or exponential distributions. For the first time, we present evidence that single cells (mammary epithelial cells) that exist in multi-cellular organisms (humans) follow a bimodal correlated random walk (BCRW). Cellular tracks of MCF-10A pBabe, neuN and neuT random migration on 2-D plastic substrates, analyzed using bimodal analysis, were found to reveal the BCRW pattern. We find two types of exponentially distributed correlated flights (corresponding to what we refer to as the directional and re-orientation phases) each having its own correlation between move step-lengths within flights. The exponential distribution of flight lengths was confirmed using different analysis methods (logarithmic binning with normalization, survival frequency plots and maximum likelihood estimation). Because of the presence of non-uniform turn angle distribution of move step-lengths within a flight and two different types of flights, we propose that the epithelial random walk is a BCRW comprising of two alternating modes with varying degree of correlations, rather than a simple persistent random walk. A BCRW model rather than a simple persistent random walk correctly matches the super-diffusivity in the cell migration paths as indicated by simulations based on the BCRW model.

A Simple and Low-Cost Procedure for Growing Geobacter sulfurreducens Cell Cultures and Biofilms in Bioelectrochemical Systems

PubMed Central

O’Brien, J. Patrick; Malvankar, Nikhil S.

2017-01-01

Anaerobic microorganisms play a central role in several environmental processes and regulate global biogeochemical cycling of nutrients and minerals. Many anaerobic microorganisms are important for the production of bioenergy and biofuels. However, the major hurdle in studying anaerobic microorganisms in the laboratory is the requirement for sophisticated and expensive gassing stations and glove boxes to create and maintain the anaerobic environment. This appendix presents a simple design for a gassing station that can be used readily by an inexperienced investigator for cultivation of anaerobic microorganisms. In addition, this appendix also details the low-cost assembly of bioelectrochemical systems and outlines a simplified procedure for cultivating and analyzing bacterial cell cultures and biofilms that produce electric current, using Geobacter sulfurreducens as a model organism. PMID:27858972

Why a fly? Using Drosophila to understand the genetics of circadian rhythms and sleep.

PubMed

Hendricks, Joan C; Sehgal, Amita

2004-03-15

Among simple model systems, Drosophila has specific advantages for neurobehavioral investigations. It has been particularly useful for understanding the molecular basis of circadian rhythms. In addition, the genetics of fruit-fly sleep are beginning to develop. This review summarizes the current state of understanding of circadian rhythms and sleep in the fruit fly for the readers of Sleep. We note where information is available in mammals, for comparison with findings in fruit flies, to provide an evolutionary perspective, and we focus on recent findings and new questions. We propose that sleep-specific neural activity may alter cellular function and thus accomplish the restorative function or functions of sleep. In conclusion, we sound some cautionary notes about some of the complexities of working with this "simple" organism.

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

DOE PAGES

McCluskey, Kevin; Baker, Scott E.

2017-02-17

As model organisms filamentous fungi have been important since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycetemore » filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Likewise, shared data has contributed to the success of model systems. Furthermore, the scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.« less

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

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

McCluskey, Kevin; Baker, Scott E.

As model organisms filamentous fungi have been important since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycetemore » filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Likewise, shared data has contributed to the success of model systems. Furthermore, the scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.« less

TAD-free analysis of architectural proteins and insulators.

PubMed

Mourad, Raphaël; Cuvier, Olivier

2018-03-16

The three-dimensional (3D) organization of the genome is intimately related to numerous key biological functions including gene expression and DNA replication regulations. The mechanisms by which molecular drivers functionally organize the 3D genome, such as topologically associating domains (TADs), remain to be explored. Current approaches consist in assessing the enrichments or influences of proteins at TAD borders. Here, we propose a TAD-free model to directly estimate the blocking effects of architectural proteins, insulators and DNA motifs on long-range contacts, making the model intuitive and biologically meaningful. In addition, the model allows analyzing the whole Hi-C information content (2D information) instead of only focusing on TAD borders (1D information). The model outperforms multiple logistic regression at TAD borders in terms of parameter estimation accuracy and is validated by enhancer-blocking assays. In Drosophila, the results support the insulating role of simple sequence repeats and suggest that the blocking effects depend on the number of repeats. Motif analysis uncovered the roles of the transcriptional factors pannier and tramtrack in blocking long-range contacts. In human, the results suggest that the blocking effects of the well-known architectural proteins CTCF, cohesin and ZNF143 depend on the distance between loci, where each protein may participate at different scales of the 3D chromatin organization.

Threshold for extinction and survival in stochastic tumor immune system

NASA Astrophysics Data System (ADS)

Li, Dongxi; Cheng, Fangjuan

2017-10-01

This paper mainly investigates the stochastic character of tumor growth and extinction in the presence of immune response of a host organism. Firstly, the mathematical model describing the interaction and competition between the tumor cells and immune system is established based on the Michaelis-Menten enzyme kinetics. Then, the threshold conditions for extinction, weak persistence and stochastic persistence of tumor cells are derived by the rigorous theoretical proofs. Finally, stochastic simulation are taken to substantiate and illustrate the conclusion we have derived. The modeling results will be beneficial to understand to concept of immunoediting, and develop the cancer immunotherapy. Besides, our simple theoretical model can help to obtain new insight into the complexity of tumor growth.

An electronic implementation of amoeba anticipation

NASA Astrophysics Data System (ADS)

Ziegler, Martin; Ochs, Karlheinz; Hansen, Mirko; Kohlstedt, Hermann

2014-02-01

In nature, the capability of memorizing environmental changes and recalling past events can be observed in unicellular organisms like amoebas. Pershin and Di Ventra have shown that such learning behavior can be mimicked in a simple memristive circuit model consisting of an LC (inductance capacitance) contour and a memristive device. Here, we implement this model experimentally by using an Ag/TiO2- x /Al memristive device. A theoretical analysis of the circuit is used to gain insight into the functionality of this model and to give advice for the circuit implementation. In this respect, the transfer function, resonant frequency, and damping behavior for a varying resistance of the memristive device are discussed in detail.

Detection of Alkylating Agents using Electrical and Mechanical Means

NASA Astrophysics Data System (ADS)

Gerchikov, Yulia; Borzin, Elena; Gannot, Yair; Shemesh, Ariel; Meltzman, Shai; Hertzog-Ronen, Carmit; Tal, Shay; Stolyarova, Sara; Nemirovsky, Yael; Tessler, Nir; Eichen, Yoav

2011-08-01

Alkylating agents are reactive molecules having at least one polar bond between a carbon atom and a good leaving group. These often simple molecules are frequently used in organic synthesis, as sterilizing agents in agriculture and even as anticancer agents in medicine. Unfortunately, for over a century, some of the highly reactive alkylating agents are also being used as blister chemical warfare agents. Being relatively simple to make, the risk is that these will be applied by terrorists as poor people warfare agents. The detection and identification of such alkylating agents is not a simple task because of their high reactivity and simple structure of the reactive site. Here we report on new approaches to the detection and identification of such alkylating agents using electrical (organic field effect transistors) and mechanical (microcantilevers) means.

CLEPS 1.0: A new protocol for cloud aqueous phase oxidation of VOC mechanisms

NASA Astrophysics Data System (ADS)

Mouchel-Vallon, Camille; Deguillaume, Laurent; Monod, Anne; Perroux, Hélène; Rose, Clémence; Ghigo, Giovanni; Long, Yoann; Leriche, Maud; Aumont, Bernard; Patryl, Luc; Armand, Patrick; Chaumerliac, Nadine

2017-03-01

A new detailed aqueous phase mechanism named the Cloud Explicit Physico-chemical Scheme (CLEPS 1.0) is proposed to describe the oxidation of water soluble organic compounds resulting from isoprene oxidation. It is based on structure activity relationships (SARs) which provide global rate constants together with branching ratios for HOṡ abstraction and addition on atmospheric organic compounds. The GROMHE SAR allows the evaluation of Henry's law constants for undocumented organic compounds. This new aqueous phase mechanism is coupled with the MCM v3.3.1 gas phase mechanism through a mass transfer scheme between gas phase and aqueous phase. The resulting multiphase mechanism has then been implemented in a model based on the Dynamically Simple Model for Atmospheric Chemical Complexity (DSMACC) using the Kinetic PreProcessor (KPP) that can serve to analyze data from cloud chamber experiments and field campaigns. The simulation of permanent cloud under low-NOx conditions describes the formation of oxidized monoacids and diacids in the aqueous phase as well as a significant influence on the gas phase chemistry and composition and shows that the aqueous phase reactivity leads to an efficient fragmentation and functionalization of organic compounds.

Tilt angle dependence of backscattering enhancements from organ pipe modes of open water-filled cylinders: Measurements and models

NASA Astrophysics Data System (ADS)

Osterhoudt, Curtis F.; Marston, Philip L.

2003-04-01

A simple target for simulating narrow low-frequency resonances of cylinders is an open metal pipe completely filled with water. We have previously described how the high-Q organ-pipe modes having a pressure node near each end are easily observed in backscattering experiments with small cylinders [C. F. Osterhoudt and P. L. Marston, J. Acoust. Soc. Am. 110, 2773 (2001)]. The resonance occurs because of the strong reflection of internal acoustic waves from the open ends of the pipe [H. Levine and J. Schwinger, Phys. Rev. 73, 383-406 (1948)]. In the present research, the dependence of the backscattering amplitude on the orientation of the cylinder is measured and modeled. The tilt angle dependence is affected by the symmetry of the organ pipe mode. An approximation was also developed for the backscattering amplitude at high Q resonances based on energy conservation, reciprocity, and the optical theorem. While this analysis applies to cylinders suspended in water away from boundaries, the organ-pipe modes studied may be useful for investigating scattering processes for buried or partially buried cylinders. [Research supported in part by ONR.

Spatiotemporal analysis of black spruce forest soils and implications for the fate of C

USGS Publications Warehouse

Harden, Jennifer W.; Manies, Kristen L.; O'Donnell, Jonathan; Johnson, Kristofer; Frolking, Steve; Fan, Zhaosheng

2012-01-01

Post-fire storage of carbon (C) in organic-soil horizons was measured in one Canadian and three Alaskan chronosequences in black spruce forests, together spanning stand ages of nearly 200 yrs. We used a simple mass balance model to derive estimates of inputs, losses, and accumulation rates of C on timescales of years to centuries. The model performed well for the surface and total organic soil layers and presented questions for resolving the dynamics of deeper organic soils. C accumulation in all study areas is on the order of 20–40 gC/m2/yr for stand ages up to ∼200 yrs. Much larger fluxes, both positive and negative, are detected using incremental changes in soil C stocks and by other studies using eddy covariance methods for CO2. This difference suggests that over the course of stand replacement, about 80% of all net primary production (NPP) is returned to the atmosphere within a fire cycle, while about 20% of NPP enters the organic soil layers and becomes available for stabilization or loss via decomposition, leaching, or combustion. Shifts toward more frequent and more severe burning and degradation of deep organic horizons would likely result in an acceleration of the carbon cycle, with greater CO2 emissions from these systems overall.

Can Simple Biophysical Principles Yield Complicated Biological Functions?

NASA Astrophysics Data System (ADS)

Liphardt, Jan

2011-03-01

About once a year, a new regulatory paradigm is discovered in cell biology. As of last count, eukaryotic cells have more than 40 distinct ways of regulating protein concentration and function. Regulatory possibilities include site-specific phosphorylation, epigenetics, alternative splicing, mRNA (re)localization, and modulation of nucleo-cytoplasmic transport. This raises a simple question. Do all the remarkable things cells do, require an intricately choreographed supporting cast of hundreds of molecular machines and associated signaling networks? Alternatively, are there a few simple biophysical principles that can generate apparently very complicated cellular behaviors and functions? I'll discuss two problems, spatial organization of the bacterial chemotaxis system and nucleo-cytoplasmic transport, where the latter might be true. In both cases, the ability to precisely quantify biological organization and function, at the single-molecule level, helped to find signatures of basic biological organizing principles.

Construction of flexible metal-organic framework (MOF) papers through MOF growth on filter paper and their selective dye capture.

PubMed

Park, Jeehyun; Oh, Moonhyun

2017-09-14

The conjugation of metal-organic frameworks (MOFs) with other materials is an excellent strategy for the production of advanced materials having desired properties and so appropriate applicability. In particular, the integration of MOFs with a flexible paper is expected to form valuable materials in separation technology. Here we report a simple method for the generation of MOF papers through the compact and uniform growth of MOF nanoparticles on the cellulose surface of a carboxymethylated filter paper. The resulting MOF papers show a selective capture ability for negatively charged organic dyes and they can be used for dye separation through simple filtration of a dye solution on the MOF papers. In addition, MOF papers can be reused after a simple washing process without losing their effective dye capture ability.

RM-SORN: a reward-modulated self-organizing recurrent neural network.

PubMed

Aswolinskiy, Witali; Pipa, Gordon

2015-01-01

Neural plasticity plays an important role in learning and memory. Reward-modulation of plasticity offers an explanation for the ability of the brain to adapt its neural activity to achieve a rewarded goal. Here, we define a neural network model that learns through the interaction of Intrinsic Plasticity (IP) and reward-modulated Spike-Timing-Dependent Plasticity (STDP). IP enables the network to explore possible output sequences and STDP, modulated by reward, reinforces the creation of the rewarded output sequences. The model is tested on tasks for prediction, recall, non-linear computation, pattern recognition, and sequence generation. It achieves performance comparable to networks trained with supervised learning, while using simple, biologically motivated plasticity rules, and rewarding strategies. The results confirm the importance of investigating the interaction of several plasticity rules in the context of reward-modulated learning and whether reward-modulated self-organization can explain the amazing capabilities of the brain.

Adsorption of humic acids and trace metals in natural waters

NASA Technical Reports Server (NTRS)

Leung, W. H.

1982-01-01

Studies concerning the interactions between suspended hydrous iron oxide and dissolved humic acids and trace metals are reported. As a major component of dissolved organic matters and its readiness for adsorption at the solid/water interface, humic acids may play a very important role in the organometallic geochemistry of suspended sediments and in determining the fate and distribution of trace metals, pesticides and anions in natural water systems. Most of the solid phases in natural waters contain oxides and hydroxides. The most simple promising theory to describe the interactions of hydrous iron oxide interface is the surface complex formation model. In this model, the adsorptions of humic acids on hydrous iron oxide may be interpreted as complex formation of the organic bases (humic acid oxyanions) with surface Fe ions. Measurements on adsorptions were made in both fresh water and seawater. Attempts have been made to fit our data to Langmuir adsorption isotherm. Adsorption equilibrium constants were determined.

Comparing and modelling land use organization in cities

PubMed Central

Lenormand, Maxime; Picornell, Miguel; Cantú-Ros, Oliva G.; Louail, Thomas; Herranz, Ricardo; Barthelemy, Marc; Frías-Martínez, Enrique; San Miguel, Maxi; Ramasco, José J.

2015-01-01

The advent of geolocated information and communication technologies opens the possibility of exploring how people use space in cities, bringing an important new tool for urban scientists and planners, especially for regions where data are scarce or not available. Here we apply a functional network approach to determine land use patterns from mobile phone records. The versatility of the method allows us to run a systematic comparison between Spanish cities of various sizes. The method detects four major land use types that correspond to different temporal patterns. The proportion of these types, their spatial organization and scaling show a strong similarity between all cities that breaks down at a very local scale, where land use mixing is specific to each urban area. Finally, we introduce a model inspired by Schelling's segregation, able to explain and reproduce these results with simple interaction rules between different land uses. PMID:27019730

A complex speciation–richness relationship in a simple neutral model

PubMed Central

Desjardins-Proulx, Philippe; Gravel, Dominique

2012-01-01

Speciation is the “elephant in the room” of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities. We focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. We use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations. PMID:22957181

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web

USGS Publications Warehouse

Jost, Christian; Lawrence, Cathryn A.; Campolongo, Francesca; Wouter, van de Bund; Hill, Sheryl; DeAngelis, Donald L.

2004-01-01

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs—organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients–autotrophs–herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.

Endogenous versus Exogenous Origins of Crises

NASA Astrophysics Data System (ADS)

Sornette, Didier

Are large biological extinctions such as the Cretaceous/Tertiary KT boundary due to a meteorite, extreme volcanic activity or self-organized critical extinction cascades? Are commercial successes due to a progressive reputation cascade or the result of a well orchestrated advertisement? Determining the chain of causality for Xevents in complex systems requires disentangling interwoven exogenous and endogenous contributions with either no clear signature or too many signatures. Here, I review several efforts carried out with collaborators which suggest a general strategy for understanding the organizations of several complex systems under the dual effect of endogenous and exogenous fluctuations. The studied examples are: internet download shocks, book sale shocks, social shocks, financial volatility shocks, and financial crashes. Simple models are offered to quantitatively relate the endogenous organization to the exogenous response of the system. Suggestions for applications of these ideas to many other systems are offered.

Modelling atmospheric transport of persistent organic pollutants in the Northern Hemisphere with a 3-D dynamical model: DEHM-POP

NASA Astrophysics Data System (ADS)

Hansen, K. M.; Christensen, J. H.; Brandt, J.; Frohn, L. M.; Geels, C.

2004-03-01

The Danish Eulerian Hemispheric Model (DEHM) is a 3-D dynamical atmospheric transport model originally developed to describe the atmospheric transport of sulphur into the Arctic. A new version of the model, DEHM-POP, developed to study the atmospheric transport and environmental fate of persistent organic pollutants (POPs) is presented. During environmental cycling, POPs can be deposited and re-emitted several times before reaching a final destination. A description of the exchange processes between the land/ocean surfaces and the atmosphere is included in the model to account for this multi-hop transport. The α-isomer of the pesticide hexachlorocyclohexane (α-HCH) is used as tracer in the model development. The structure of the model and processes included are described in detail. The results from a model simulation showing the atmospheric transport for the years 1991 to 1998 are presented and evaluated against measurements. The annual averaged atmospheric concentration of α-HCH for the 1990s is well described by the model; however, the shorter-term average concentration for most of the stations is not well captured. This indicates that the present simple surface description needs to be refined to get a better description of the air-surface exchange proceses of POPs.

Variable C : N : P stoichiometry of dissolved organic matter cycling in the Community Earth System Model

DOE PAGES

Letscher, R. T.; Moore, J. K.; Teng, Y. -C.; ...

2014-06-16

Dissolved organic matter (DOM) plays an important role in the ocean's biological carbon pump by providing an advective/mixing pathway for ~ 20% of export production. DOM is known to have a stoichiometry depleted in nitrogen (N) and phosphorus (P) compared to the particulate organic matter pool, a~fact that is often omitted from biogeochemical-ocean general circulation models. However the variable C : N : P stoichiometry of DOM becomes important when quantifying carbon export from the upper ocean and linking the nutrient cycles of N and P with that of carbon. Here we utilize recent advances in DOM observational data coveragemore » and offline tracer-modeling techniques to objectively constrain the variable production and remineralization rates of the DOM C / N / P pools in a simple biogeochemical-ocean model of DOM cycling. The optimized DOM cycling parameters are then incorporated within the Biogeochemical Elemental Cycling (BEC) component of the Community Earth System Model and validated against the compilation of marine DOM observations. The optimized BEC simulation including variable DOM C : N : P cycling was found to better reproduce the observed DOM spatial gradients than simulations that used the canonical Redfield ratio. Global annual average export of dissolved organic C, N, and P below 100 m was found to be 2.28 Pg C yr -1 (143 Tmol C yr -1), 16.4 Tmol N yr -1, and 1 Tmol P yr -1, respectively with an average export C : N : P stoichiometry of 225 : 19 : 1 for the semilabile (degradable) DOM pool. DOC export contributed ~ 25% of the combined organic C export to depths greater than 100 m.« less

Microbiology of primary acquired nasolacrimal duct obstruction: simple epiphora, acute dacryocystitis, and chronic dacryocystitis

PubMed Central

Pornpanich, Kanograt; Luemsamran, Panitee; Leelaporn, Amornrut; Santisuk, Jiraporn; Tesavibul, Nattaporn; Lertsuwanroj, Buntitar; Vangveeravong, Sumalee

2016-01-01

Purpose The aim of this study was to determine the microbiology of primary acquired nasolacrimal duct obstruction (PANDO) and its antimicrobial susceptibilities. Methods Ninety-three patients (100 eyes) diagnosed with PANDO, categorized as acute, chronic dacryocystitis, or simple epiphora, were prospectively enrolled. Lacrimal sac contents were cultured for aerobic and anaerobic bacteria and fungi. Cultured organisms were identified, and antimicrobial susceptibility testing was performed for aerobic bacteria. Results Seventy-nine of the 100 samples were culture positive. One hundred twenty-seven organisms were isolated, and 29 different species were identified. Most microorganisms were Gram-positive bacteria (45 samples or 57.0% of all positive culture samples), whereas Gram-negative bacteria, anaerobic bacteria, and fungi were found in 39 (49.4%), 24 (30.4%), and four samples (5.1%), respectively. The most frequently isolated group was coagulase-negative staphylococci (27.8%), followed by nonspore-forming Gram-positive rods (anaerobe) (17.7%) and Pseudomonas aeruginosa (15.2%). Of the 100 samples, five, 45, and 50 samples were obtained from patients with acute dacryocystitis, chronic dacryocystitis, and simple epiphora, respectively. Subgroup analysis showed that Gram-negative organisms were isolated more frequently from the chronic dacryocystitis subgroup than from the simple epiphora subgroup (P=0.012). Antimicrobial susceptibility testing demonstrated that ciprofloxacin was the most effective drug against all Gram-positive and Gram-negative organisms. Conclusion Patients with PANDO, with or without clinical signs of lacrimal infection, were culture positive. Gram-negative organisms were frequently isolated, which were different from previous studies. Ciprofloxacin was the most effective agent against all Gram-positive and Gram-negative organisms. PMID:26955261

Incorporating water table dynamics in climate modeling: 1. Water table observations and equilibrium water table simulations

NASA Astrophysics Data System (ADS)

Fan, Ying; Miguez-Macho, Gonzalo; Weaver, Christopher P.; Walko, Robert; Robock, Alan

2007-05-01

Soil moisture is a key participant in land-atmosphere interactions and an important determinant of terrestrial climate. In regions where the water table is shallow, soil moisture is coupled to the water table. This paper is the first of a two-part study to quantify this coupling and explore its implications in the context of climate modeling. We examine the observed water table depth in the lower 48 states of the United States in search of salient spatial and temporal features that are relevant to climate dynamics. As a means to interpolate and synthesize the scattered observations, we use a simple two-dimensional groundwater flow model to construct an equilibrium water table as a result of long-term climatic and geologic forcing. Model simulations suggest that the water table depth exhibits spatial organization at watershed, regional, and continental scales, which may have implications for the spatial organization of soil moisture at similar scales. The observations suggest that water table depth varies at diurnal, event, seasonal, and interannual scales, which may have implications for soil moisture memory at these scales.

Centimetre-scale electron diffusion in photoactive organic heterostructures

NASA Astrophysics Data System (ADS)

Burlingame, Quinn; Coburn, Caleb; Che, Xiaozhou; Panda, Anurag; Qu, Yue; Forrest, Stephen R.

2018-02-01

The unique properties of organic semiconductors, such as flexibility and lightness, are increasingly important for information displays, lighting and energy generation. But organics suffer from both static and dynamic disorder, and this can lead to variable-range carrier hopping, which results in notoriously poor electrical properties, with low electron and hole mobilities and correspondingly short charge-diffusion lengths of less than a micrometre. Here we demonstrate a photoactive (light-responsive) organic heterostructure comprising a thin fullerene channel sandwiched between an electron-blocking layer and a blended donor:C70 fullerene heterojunction that generates charges by dissociating excitons. Centimetre-scale diffusion of electrons is observed in the fullerene channel, and this can be fitted with a simple electron diffusion model. Our experiments enable the direct measurement of charge diffusivity in organic semiconductors, which is as high as 0.83 ± 0.07 square centimetres per second in a C60 channel at room temperature. The high diffusivity of the fullerene combined with the extraordinarily long charge-recombination time yields diffusion lengths of more than 3.5 centimetres, orders of magnitude larger than expected for an organic system.

Fusomorphogenesis: cell fusion in organ formation.

PubMed

Shemer, G; Podbilewicz, B

2000-05-01

Cell fusion is a universal process that occurs during fertilization and in the formation of organs such as muscles, placenta, and bones. Very little is known about the molecular and cellular mechanisms of cell fusion during pattern formation. Here we review the dynamic anatomy of all cell fusions during embryonic and postembryonic development in an organism. Nearly all the cell fates and cell lineages are invariant in the nematode C. elegans and one third of the cells that are born fuse to form 44 syncytia in a reproducible and stereotyped way. To explain the function of cell fusion in organ formation we propose the fusomorphogenetic model as a simple cellular mechanism to efficiently redistribute membranes using a combination of cell fusion and polarized membrane recycling during morphogenesis. Thus, regulated intercellular and intracellular membrane fusion processes may drive elongation of the embryo as well as postembryonic organ formation in C. elegans. Finally, we use the fusomorphogenetic hypothesis to explain the role of cell fusion in the formation of organs like muscles, bones, and placenta in mammals and other species and to speculate on how the intracellular machinery that drive fusomorphogenesis may have evolved.

Efficient hybrid white organic light-emitting diodes for application of triplet harvesting with simple structure

NASA Astrophysics Data System (ADS)

Hwang, Kyo Min; Lee, Song Eun; Lee, Sungkyu; Yoo, Han Kyu; Baek, Hyun Jung; Kim, Young Kwan; Kim, Jwajin; Yoon, Seung Soo

2016-08-01

In this study, we fabricated hybrid white organic light-emitting diodes (WOLEDs) based on triplet harvesting with a simple structure. All the hole transporting material and host in the emitting layer (EML) of devices utilized the same material N,N'-di-1-naphthalenyl-N,N'-diphenyl [1,1':4',1″:4″,1‴-quaterphenyl]-4,4‴-diamine (4P-NPD), which is known to be blue fluorescent material. Simple hybrid WOLEDs were fabricated with blue fluorescent, green and red phosphorescent materials. We investigated the effect of triplet harvesting (TH) by an exciton generation zone on simple hybrid WOLEDs. The simple hybrid WOLEDs characteristically had a dominant hole mobility, so an exciton generation zone was expected in the EML. Additionally, the optimal the thickness of the hole transporting layer and electron transporting layer was fabricated a simple hybrid WOLEDs. The simple hybrid WOLED exhibits a maximum luminous efficiency of 29.3 cd/A and a maximum external quantum efficiency of 11.2%. The Commission Internationale de l'Éclairage (International Commission on Illumination) coordinates were (0.45, 0.43) at about 10,000 cd/m2.

Simulating statistics of lightning-induced and man made fires

NASA Astrophysics Data System (ADS)

Krenn, R.; Hergarten, S.

2009-04-01

The frequency-area distributions of forest fires show power-law behavior with scaling exponents α in a quite narrow range, relating wildfire research to the theoretical framework of self-organized criticality. Examples of self-organized critical behavior can be found in computer simulations of simple cellular automata. The established self-organized critical Drossel-Schwabl forest fire model (DS-FFM) is one of the most widespread models in this context. Despite its qualitative agreement with event-size statistics from nature, its applicability is still questioned. Apart from general concerns that the DS-FFM apparently oversimplifies the complex nature of forest dynamics, it significantly overestimates the frequency of large fires. We present a straightforward modification of the model rules that increases the scaling exponent α by approximately 1•3 and brings the simulated event-size statistics close to those observed in nature. In addition, combined simulations of both the original and the modified model predict a dependence of the overall distribution on the ratio of lightning induced and man made fires as well as a difference between their respective event-size statistics. The increase of the scaling exponent with decreasing lightning probability as well as the splitting of the partial distributions are confirmed by the analysis of the Canadian Large Fire Database. As a consequence, lightning induced and man made forest fires cannot be treated separately in wildfire modeling, hazard assessment and forest management.

Multi-Scale Models for the Scale Interaction of Organized Tropical Convection

NASA Astrophysics Data System (ADS)

Yang, Qiu

Assessing the upscale impact of organized tropical convection from small spatial and temporal scales is a research imperative, not only for having a better understanding of the multi-scale structures of dynamical and convective fields in the tropics, but also for eventually helping in the design of new parameterization strategies to improve the next-generation global climate models. Here self-consistent multi-scale models are derived systematically by following the multi-scale asymptotic methods and used to describe the hierarchical structures of tropical atmospheric flows. The advantages of using these multi-scale models lie in isolating the essential components of multi-scale interaction and providing assessment of the upscale impact of the small-scale fluctuations onto the large-scale mean flow through eddy flux divergences of momentum and temperature in a transparent fashion. Specifically, this thesis includes three research projects about multi-scale interaction of organized tropical convection, involving tropical flows at different scaling regimes and utilizing different multi-scale models correspondingly. Inspired by the observed variability of tropical convection on multiple temporal scales, including daily and intraseasonal time scales, the goal of the first project is to assess the intraseasonal impact of the diurnal cycle on the planetary-scale circulation such as the Hadley cell. As an extension of the first project, the goal of the second project is to assess the intraseasonal impact of the diurnal cycle over the Maritime Continent on the Madden-Julian Oscillation. In the third project, the goals are to simulate the baroclinic aspects of the ITCZ breakdown and assess its upscale impact on the planetary-scale circulation over the eastern Pacific. These simple multi-scale models should be useful to understand the scale interaction of organized tropical convection and help improve the parameterization of unresolved processes in global climate models.

The polygonal model: A simple representation of biomolecules as a tool for teaching metabolism.

PubMed

Bonafe, Carlos Francisco Sampaio; Bispo, Jose Ailton Conceição; de Jesus, Marcelo Bispo

2018-01-01

Metabolism involves numerous reactions and organic compounds that the student must master to understand adequately the processes involved. Part of biochemical learning should include some knowledge of the structure of biomolecules, although the acquisition of such knowledge can be time-consuming and may require significant effort from the student. In this report, we describe the "polygonal model" as a new means of graphically representing biomolecules. This model is based on the use of geometric figures such as open triangles, squares, and circles to represent hydroxyl, carbonyl, and carboxyl groups, respectively. The usefulness of the polygonal model was assessed by undergraduate students in a classroom activity that consisted of "transforming" molecules from Fischer models to polygonal models and vice and versa. The survey was applied to 135 undergraduate Biology and Nursing students. Students found the model easy to use and we noted that it allowed identification of students' misconceptions in basic concepts of organic chemistry, such as in stereochemistry and organic groups that could then be corrected. The students considered the polygonal model easier and faster for representing molecules than Fischer representations, without loss of information. These findings indicate that the polygonal model can facilitate the teaching of metabolism when the structures of biomolecules are discussed. Overall, the polygonal model promoted contact with chemical structures, e.g. through drawing activities, and encouraged student-student dialog, thereby facilitating biochemical learning. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):66-75, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

Role of special cross-links in structure formation of bacterial DNA polymer

NASA Astrophysics Data System (ADS)

Agarwal, Tejal; Manjunath, G. P.; Habib, Farhat; Lakshmi Vaddavalli, Pavana; Chatterji, Apratim

2018-01-01

Using data from contact maps of the DNA-polymer of Escherichia coli (E. Coli) (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain. Via suitable Monte Carlo simulations, we show that the presence of these cross-links leads to a particular organization of the chain at large (micron) length scales of the DNA. We also investigate the structure of a ring polymer with an equal number of cross-links at random positions along the chain. We find that though the polymer does get organized at the large length scales, the nature of the organization is quite different from the organization observed with cross-links at specific biologically determined positions. We used the contact map of E. Coli bacteria which has around 4.6 million base pairs in a single circular chromosome. In our coarse-grained flexible ring polymer model, we used 4642 monomer beads and observed that around 80 cross-links are enough to induce the large-scale organization of the molecule accounting for statistical fluctuations caused by thermal energy. The length of a DNA chain even of a simple bacterial cell such as E. Coli is much longer than typical proteins, hence we avoided methods used to tackle protein folding problems. We define new suitable quantities to identify the large scale structure of a polymer chain with a few cross-links.

Derivation of the stress-strain behavior of the constituents of bio-inspired layered TiO2/PE-nanocomposites by inverse modeling based on FE-simulations of nanoindentation test.

PubMed

Lasko, G; Schäfer, I; Burghard, Z; Bill, J; Schmauder, S; Weber, U; Galler, D

2013-03-01

Owing to the apparent simple morphology and peculiar properties, nacre, an iridescent layer, coating of the inner part of mollusk shells, has attracted considerable attention of biologists, material scientists and engineers. The basic structural motif in nacre is the assembly of oriented plate-like aragonite crystals with a 'brick' (CaCO3 crystals) and 'mortar' (macromolecular components like proteins) organization. Many scientific researchers recognize that such structures are associated with the excellent mechanical properties of nacre and biomimetic strategies have been proposed to produce new layered nanocomposites. During the past years, increasing efforts have been devoted towards exploiting nacre's structural design principle in the synthesis of novel nanocomposites. However, the direct transfer of nacre's architecture to an artificial inorganic material has not been achieved yet. In the present contribution we report on laminated architecture, composed of the inorganic oxide (TiO2) and organic polyelectrolyte (PE) layers which fulfill this task. To get a better insight and understanding concerning the mechanical behaviour of bio-inspired layered materials consisting of oxide ceramics and organic layers, the elastic-plastic properties of titanium dioxide and organic polyelectrolyte phase are determined via FE-modelling of the nanoindentation process. With the use of inverse modeling and based on numerical models which are applied on the microscopic scale, the material properties of the constituents are derived.

Magnetorotational dynamo chimeras. The missing link to turbulent accretion disk dynamo models?

NASA Astrophysics Data System (ADS)

Riols, A.; Rincon, F.; Cossu, C.; Lesur, G.; Ogilvie, G. I.; Longaretti, P.-Y.

2017-02-01

In Keplerian accretion disks, turbulence and magnetic fields may be jointly excited through a subcritical dynamo mechanisminvolving magnetorotational instability (MRI). This dynamo may notably contribute to explaining the time-variability of various accreting systems, as high-resolution simulations of MRI dynamo turbulence exhibit statistical self-organization into large-scale cyclic dynamics. However, understanding the physics underlying these statistical states and assessing their exact astrophysical relevance is theoretically challenging. The study of simple periodic nonlinear MRI dynamo solutions has recently proven useful in this respect, and has highlighted the role of turbulent magnetic diffusion in the seeming impossibility of a dynamo at low magnetic Prandtl number (Pm), a common regime in disks. Arguably though, these simple laminar structures may not be fully representative of the complex, statistically self-organized states expected in astrophysical regimes. Here, we aim at closing this seeming discrepancy by reporting the numerical discovery of exactly periodic, yet semi-statistical "chimeral MRI dynamo states" which are the organized outcome of a succession of MRI-unstable, non-axisymmetric dynamical stages of different forms and amplitudes. Interestingly, these states, while reminiscent of the statistical complexity of turbulent simulations, involve the same physical principles as simpler laminar cycles, and their analysis further confirms the theory that subcritical turbulent magnetic diffusion impedes the sustainment of an MRI dynamo at low Pm. Overall, chimera dynamo cycles therefore offer an unprecedented dual physical and statistical perspective on dynamos in rotating shear flows, which may prove useful in devising more accurate, yet intuitive mean-field models of time-dependent turbulent disk dynamos. Movies associated to Fig. 1 are available at http://www.aanda.org

Motor and sensory neuropathy due to myelin infolding and paranodal damage in a transgenic mouse model of Charcot–Marie–Tooth disease type 1C

PubMed Central

Lee, Samuel M.; Sha, Di; Mohammed, Anum A.; Asress, Seneshaw; Glass, Jonathan D.; Chin, Lih-Shen; Li, Lian

2013-01-01

Charcot–Marie–Tooth disease type 1C (CMT1C) is a dominantly inherited motor and sensory neuropathy. Despite human genetic evidence linking missense mutations in SIMPLE to CMT1C, the in vivo role of CMT1C-linked SIMPLE mutations remains undetermined. To investigate the molecular mechanism underlying CMT1C pathogenesis, we generated transgenic mice expressing either wild-type or CMT1C-linked W116G human SIMPLE. Mice expressing mutant, but not wild type, SIMPLE develop a late-onset motor and sensory neuropathy that recapitulates key clinical features of CMT1C disease. SIMPLE mutant mice exhibit motor and sensory behavioral impairments accompanied by decreased motor and sensory nerve conduction velocity and reduced compound muscle action potential amplitude. This neuropathy phenotype is associated with focally infolded myelin loops that protrude into the axons at paranodal regions and near Schmidt–Lanterman incisures of peripheral nerves. We find that myelin infolding is often linked to constricted axons with signs of impaired axonal transport and to paranodal defects and abnormal organization of the node of Ranvier. Our findings support that SIMPLE mutation disrupts myelin homeostasis and causes peripheral neuropathy via a combination of toxic gain-of-function and dominant-negative mechanisms. The results from this study suggest that myelin infolding and paranodal damage may represent pathogenic precursors preceding demyelination and axonal degeneration in CMT1C patients. PMID:23359569

A simple method for the extraction and identification of light density microplastics from soil.

PubMed

Zhang, Shaoliang; Yang, Xiaomei; Gertsen, Hennie; Peters, Piet; Salánki, Tamás; Geissen, Violette

2018-03-01

This article introduces a simple and cost-saving method developed to extract, distinguish and quantify light density microplastics of polyethylene (PE) and polypropylene (PP) in soil. A floatation method using distilled water was used to extract the light density microplastics from soil samples. Microplastics and impurities were identified using a heating method (3-5s at 130°C). The number and size of particles were determined using a camera (Leica DFC 425) connected to a microscope (Leica wild M3C, Type S, simple light, 6.4×). Quantification of the microplastics was conducted using a developed model. Results showed that the floatation method was effective in extracting microplastics from soils, with recovery rates of approximately 90%. After being exposed to heat, the microplastics in the soil samples melted and were transformed into circular transparent particles while other impurities, such as organic matter and silicates were not changed by the heat. Regression analysis of microplastics weight and particle volume (a calculation based on image J software analysis) after heating showed the best fit (y=1.14x+0.46, R 2 =99%, p<0.001). Recovery rates based on the empirical model method were >80%. Results from field samples collected from North-western China prove that our method of repetitive floatation and heating can be used to extract, distinguish and quantify light density polyethylene microplastics in soils. Microplastics mass can be evaluated using the empirical model. Copyright © 2017 Elsevier B.V. All rights reserved.

Synaptic Basis for Differential Orientation Selectivity between Complex and Simple Cells in Mouse Visual Cortex

PubMed Central

Li, Ya-tang; Liu, Bao-hua; Chou, Xiao-lin; Zhang, Li I.

2015-01-01

In the primary visual cortex (V1), orientation-selective neurons can be categorized into simple and complex cells primarily based on their receptive field (RF) structures. In mouse V1, although previous studies have examined the excitatory/inhibitory interplay underlying orientation selectivity (OS) of simple cells, the synaptic bases for that of complex cells have remained obscure. Here, by combining in vivo loose-patch and whole-cell recordings, we found that complex cells, identified by their overlapping on/off subfields, had significantly weaker OS than simple cells at both spiking and subthreshold membrane potential response levels. Voltage-clamp recordings further revealed that although excitatory inputs to complex and simple cells exhibited a similar degree of OS, inhibition in complex cells was more narrowly tuned than excitation, whereas in simple cells inhibition was more broadly tuned than excitation. The differential inhibitory tuning can primarily account for the difference in OS between complex and simple cells. Interestingly, the differential synaptic tuning correlated well with the spatial organization of synaptic input: the inhibitory visual RF in complex cells was more elongated in shape than its excitatory counterpart and also was more elongated than that in simple cells. Together, our results demonstrate that OS of complex and simple cells is differentially shaped by cortical inhibition based on its orientation tuning profile relative to excitation, which is contributed at least partially by the spatial organization of RFs of presynaptic inhibitory neurons. SIGNIFICANCE STATEMENT Simple and complex cells, two classes of principal neurons in the primary visual cortex (V1), are generally thought to be equally selective for orientation. In mouse V1, we report that complex cells, identified by their overlapping on/off subfields, has significantly weaker orientation selectivity (OS) than simple cells. This can be primarily attributed to the differential tuning selectivity of inhibitory synaptic input: inhibition in complex cells is more narrowly tuned than excitation, whereas in simple cells inhibition is more broadly tuned than excitation. In addition, there is a good correlation between inhibitory tuning selectivity and the spatial organization of inhibitory inputs. These complex and simple cells with differential degree of OS may provide functionally distinct signals to different downstream targets. PMID:26245969

Synaptic Basis for Differential Orientation Selectivity between Complex and Simple Cells in Mouse Visual Cortex.

PubMed

Li, Ya-tang; Liu, Bao-hua; Chou, Xiao-lin; Zhang, Li I; Tao, Huizhong W

2015-08-05

In the primary visual cortex (V1), orientation-selective neurons can be categorized into simple and complex cells primarily based on their receptive field (RF) structures. In mouse V1, although previous studies have examined the excitatory/inhibitory interplay underlying orientation selectivity (OS) of simple cells, the synaptic bases for that of complex cells have remained obscure. Here, by combining in vivo loose-patch and whole-cell recordings, we found that complex cells, identified by their overlapping on/off subfields, had significantly weaker OS than simple cells at both spiking and subthreshold membrane potential response levels. Voltage-clamp recordings further revealed that although excitatory inputs to complex and simple cells exhibited a similar degree of OS, inhibition in complex cells was more narrowly tuned than excitation, whereas in simple cells inhibition was more broadly tuned than excitation. The differential inhibitory tuning can primarily account for the difference in OS between complex and simple cells. Interestingly, the differential synaptic tuning correlated well with the spatial organization of synaptic input: the inhibitory visual RF in complex cells was more elongated in shape than its excitatory counterpart and also was more elongated than that in simple cells. Together, our results demonstrate that OS of complex and simple cells is differentially shaped by cortical inhibition based on its orientation tuning profile relative to excitation, which is contributed at least partially by the spatial organization of RFs of presynaptic inhibitory neurons. Simple and complex cells, two classes of principal neurons in the primary visual cortex (V1), are generally thought to be equally selective for orientation. In mouse V1, we report that complex cells, identified by their overlapping on/off subfields, has significantly weaker orientation selectivity (OS) than simple cells. This can be primarily attributed to the differential tuning selectivity of inhibitory synaptic input: inhibition in complex cells is more narrowly tuned than excitation, whereas in simple cells inhibition is more broadly tuned than excitation. In addition, there is a good correlation between inhibitory tuning selectivity and the spatial organization of inhibitory inputs. These complex and simple cells with differential degree of OS may provide functionally distinct signals to different downstream targets. Copyright © 2015 the authors 0270-6474/15/3511081-13$15.00/0.

Crowd of individuals walking in opposite directions. A toy model to study the segregation of the group into lanes of individuals moving in the same direction

NASA Astrophysics Data System (ADS)

Goldsztein, Guillermo H.

2017-08-01

Consider a corridor, street or bridge crowded with pedestrians walking in both directions. The individuals do not walk in a completely straight line. They adjust their path to avoid colliding with incoming pedestrians. As a result of these adjustments, the whole group sometimes end up split into lanes of individuals moving in the same direction. While this formation of lanes facilitates the flow and benefits the whole group, it is believed that results from the actions of the individuals acting only on their behalf, without considering others. This phenomenon is an example of self-organization. We analyze a simple model. We assume that individuals move around a two-lane circular track. All of them at the same speed. Half of them in one direction and the rest in the opposite direction. Each time two individuals collide, one of them moves to the other lane. The individual changing lanes is selected randomly. The system self-organizes. Eventually each lane is occupied with individuals moving in only one direction. We show that the time required for the system to self-organize is bounded by a linear function on the number of individuals. This toy model provides an example where global self-organization occurs even though each member of the group acts without considering the rest.

The Role of Logic Modeling in a Collaborative and Iterative Research Process: Lessons from Research and Analysis Conducted with the Federal Voting Assistance Program

DTIC Science & Technology

2016-01-01

outputs, customers , and outcomes (see Figure 2.1). In the Taylor-Powell and Henert simple three-part example, the food would constitute an input, finding... Customer Activities etaidemretnI Goals Strategic Goals Annual Goals Management Objectives Operations M ission External factors Annual...Partners are the individuals or organizations that work with programs to conduct activities or enable outputs. • Customers (intermediate and final

Multilayer network modeling of integrated biological systems. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

NASA Astrophysics Data System (ADS)

De Domenico, Manlio

2018-03-01

Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are highlighting how simple networks - obtained by aggregating or neglecting temporal or categorical description of biological data - are not able to account for the richness of information characterizing biological systems. More complex models, namely multilayer networks, are needed to account for interdependencies, often varying across time, of biological interacting units within a cell, a tissue or parts of an organism.

A new statistical method for transfer coefficient calculations in the framework of the general multiple-compartment model of transport for radionuclides in biological systems.

PubMed

Garcia, F; Arruda-Neto, J D; Manso, M V; Helene, O M; Vanin, V R; Rodriguez, O; Mesa, J; Likhachev, V P; Filho, J W; Deppman, A; Perez, G; Guzman, F; de Camargo, S P

1999-10-01

A new and simple statistical procedure (STATFLUX) for the calculation of transfer coefficients of radionuclide transport to animals and plants is proposed. The method is based on the general multiple-compartment model, which uses a system of linear equations involving geometrical volume considerations. By using experimentally available curves of radionuclide concentrations versus time, for each animal compartment (organs), flow parameters were estimated by employing a least-squares procedure, whose consistency is tested. Some numerical results are presented in order to compare the STATFLUX transfer coefficients with those from other works and experimental data.

Application of Peterson's stray light model to complex optical instruments

NASA Astrophysics Data System (ADS)

Fray, S.; Goepel, M.; Kroneberger, M.

2016-07-01

Gary L. Peterson (Breault Research Organization) presented a simple analytical model for in- field stray light evaluation of axial optical systems. We exploited this idea for more complex optical instruments of the Meteosat Third Generation (MTG) mission. For the Flexible Combined Imager (FCI) we evaluated the in-field stray light of its three-mirroranastigmat telescope, while for the Infrared Sounder (IRS) we performed an end-to-end analysis including the front telescope, interferometer and back telescope assembly and the cold optics. A comparison to simulations will be presented. The authors acknowledge the support by ESA and Thales Alenia Space through the MTG satellites program.

Macro- and micro-chaotic structures in the Hindmarsh-Rose model of bursting neurons

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

Barrio, Roberto, E-mail: rbarrio@unizar.es; Serrano, Sergio; Angeles Martínez, M.

2014-06-01

We study a plethora of chaotic phenomena in the Hindmarsh-Rose neuron model with the use of several computational techniques including the bifurcation parameter continuation, spike-quantification, and evaluation of Lyapunov exponents in bi-parameter diagrams. Such an aggregated approach allows for detecting regions of simple and chaotic dynamics, and demarcating borderlines—exact bifurcation curves. We demonstrate how the organizing centers—points corresponding to codimension-two homoclinic bifurcations—along with fold and period-doubling bifurcation curves structure the biparametric plane, thus forming macro-chaotic regions of onion bulb shapes and revealing spike-adding cascades that generate micro-chaotic structures due to the hysteresis.

Twelve tips for applying change models to curriculum design, development and delivery.

PubMed

McKimm, Judy; Jones, Paul Kneath

2017-10-25

Drawing primarily from business and management literature and the authors' experience, these 12 tips provide guidance to organizations, teams, and individuals involved in curriculum or program development at undergraduate, postgraduate, and continuing education levels. The tips are based around change models and approaches and can help underpin successful curriculum review, development, and delivery, as well as fostering appropriate educational innovation. A range of tools exist to support systematic program development and review, but even relatively simple changes need to take account of many factors, including the complexity of the environment, stakeholder engagement, cultural and psychological aspects, and the importance of followers.

Screening-level models to estimate partition ratios of organic chemicals between polymeric materials, air and water.

PubMed

Reppas-Chrysovitsinos, Efstathios; Sobek, Anna; MacLeod, Matthew

2016-06-15

Polymeric materials flowing through the technosphere are repositories of organic chemicals throughout their life cycle. Equilibrium partition ratios of organic chemicals between these materials and air (KMA) or water (KMW) are required for models of fate and transport, high-throughput exposure assessment and passive sampling. KMA and KMW have been measured for a growing number of chemical/material combinations, but significant data gaps still exist. We assembled a database of 363 KMA and 910 KMW measurements for 446 individual compounds and nearly 40 individual polymers and biopolymers, collected from 29 studies. We used the EPI Suite and ABSOLV software packages to estimate physicochemical properties of the compounds and we employed an empirical correlation based on Trouton's rule to adjust the measured KMA and KMW values to a standard reference temperature of 298 K. Then, we used a thermodynamic triangle with Henry's law constant to calculate a complete set of 1273 KMA and KMW values. Using simple linear regression, we developed a suite of single parameter linear free energy relationship (spLFER) models to estimate KMA from the EPI Suite-estimated octanol-air partition ratio (KOA) and KMW from the EPI Suite-estimated octanol-water (KOW) partition ratio. Similarly, using multiple linear regression, we developed a set of polyparameter linear free energy relationship (ppLFER) models to estimate KMA and KMW from ABSOLV-estimated Abraham solvation parameters. We explored the two LFER approaches to investigate (1) their performance in estimating partition ratios, and (2) uncertainties associated with treating all different polymers as a single "bulk" polymeric material compartment. The models we have developed are suitable for screening assessments of the tendency for organic chemicals to be emitted from materials, and for use in multimedia models of the fate of organic chemicals in the indoor environment. In screening applications we recommend that KMA and KMW be modeled as 0.06 ×KOA and 0.06 ×KOW respectively, with an uncertainty range of a factor of 15.

Modeling soil parameters using hyperspectral image reflectance in subtropical coastal wetlands

NASA Astrophysics Data System (ADS)

Anne, Naveen J. P.; Abd-Elrahman, Amr H.; Lewis, David B.; Hewitt, Nicole A.

2014-12-01

Developing spectral models of soil properties is an important frontier in remote sensing and soil science. Several studies have focused on modeling soil properties such as total pools of soil organic matter and carbon in bare soils. We extended this effort to model soil parameters in areas densely covered with coastal vegetation. Moreover, we investigated soil properties indicative of soil functions such as nutrient and organic matter turnover and storage. These properties include the partitioning of mineral and organic soil between particulate (>53 μm) and fine size classes, and the partitioning of soil carbon and nitrogen pools between stable and labile fractions. Soil samples were obtained from Avicennia germinans mangrove forest and Juncus roemerianus salt marsh plots on the west coast of central Florida. Spectra corresponding to field plot locations from Hyperion hyperspectral image were extracted and analyzed. The spectral information was regressed against the soil variables to determine the best single bands and optimal band combinations for the simple ratio (SR) and normalized difference index (NDI) indices. The regression analysis yielded levels of correlation for soil variables with R2 values ranging from 0.21 to 0.47 for best individual bands, 0.28 to 0.81 for two-band indices, and 0.53 to 0.96 for partial least-squares (PLS) regressions for the Hyperion image data. Spectral models using Hyperion data adequately (RPD > 1.4) predicted particulate organic matter (POM), silt + clay, labile carbon (C), and labile nitrogen (N) (where RPD = ratio of standard deviation to root mean square error of cross-validation [RMSECV]). The SR (0.53 μm, 2.11 μm) model of labile N with R2 = 0.81, RMSECV= 0.28, and RPD = 1.94 produced the best results in this study. Our results provide optimism that remote-sensing spectral models can successfully predict soil properties indicative of ecosystem nutrient and organic matter turnover and storage, and do so in areas with dense canopy cover.

Developmental models for estimating ecological responses to environmental variability: structural, parametric, and experimental issues.

PubMed

Moore, Julia L; Remais, Justin V

2014-03-01

Developmental models that account for the metabolic effect of temperature variability on poikilotherms, such as degree-day models, have been widely used to study organism emergence, range and development, particularly in agricultural and vector-borne disease contexts. Though simple and easy to use, structural and parametric issues can influence the outputs of such models, often substantially. Because the underlying assumptions and limitations of these models have rarely been considered, this paper reviews the structural, parametric, and experimental issues that arise when using degree-day models, including the implications of particular structural or parametric choices, as well as assumptions that underlie commonly used models. Linear and non-linear developmental functions are compared, as are common methods used to incorporate temperature thresholds and calculate daily degree-days. Substantial differences in predicted emergence time arose when using linear versus non-linear developmental functions to model the emergence time in a model organism. The optimal method for calculating degree-days depends upon where key temperature threshold parameters fall relative to the daily minimum and maximum temperatures, as well as the shape of the daily temperature curve. No method is shown to be universally superior, though one commonly used method, the daily average method, consistently provides accurate results. The sensitivity of model projections to these methodological issues highlights the need to make structural and parametric selections based on a careful consideration of the specific biological response of the organism under study, and the specific temperature conditions of the geographic regions of interest. When degree-day model limitations are considered and model assumptions met, the models can be a powerful tool for studying temperature-dependent development.

Genome complexity, robustness and genetic interactions in digital organisms

NASA Astrophysics Data System (ADS)

Lenski, Richard E.; Ofria, Charles; Collier, Travis C.; Adami, Christoph

1999-08-01

Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined `metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

Genome complexity, robustness and genetic interactions in digital organisms.

PubMed

Lenski, R E; Ofria, C; Collier, T C; Adami, C

1999-08-12

Digital organisms are computer programs that self-replicate, mutate and adapt by natural selection. They offer an opportunity to test generalizations about living systems that may extend beyond the organic life that biologists usually study. Here we have generated two classes of digital organism: simple programs selected solely for rapid replication, and complex programs selected to perform mathematical operations that accelerate replication through a set of defined 'metabolic' rewards. To examine the differences in their genetic architecture, we introduced millions of single and multiple mutations into each organism and measured the effects on the organism's fitness. The complex organisms are more robust than the simple ones with respect to the average effects of single mutations. Interactions among mutations are common and usually yield higher fitness than predicted from the component mutations assuming multiplicative effects; such interactions are especially important in the complex organisms. Frequent interactions among mutations have also been seen in bacteria, fungi and fruitflies. Our findings support the view that interactions are a general feature of genetic systems.

Emission of intermediate, semi and low volatile organic compounds from traffic and their impact on secondary organic aerosol concentrations over Greater Paris

NASA Astrophysics Data System (ADS)

Sartelet, K.; Zhu, S.; Moukhtar, S.; André, M.; André, J. M.; Gros, V.; Favez, O.; Brasseur, A.; Redaelli, M.

2018-05-01

Exhaust particle emissions are mostly made of black carbon and/or organic compounds, with some of these organic compounds existing in both the gas and particle phases. Although emissions of volatile organic compounds (VOC) are usually measured at the exhaust, emissions in the gas phase of lower volatility compounds (POAvapor) are not. However, these gas-phase emissions may be oxidised after emission and enhance the formation of secondary organic aerosols (SOA). They are shown here to contribute to most of the SOA formation in Central Paris. POAvapor emissions are usually estimated from primary organic aerosol emissions in the particle phase (POA). However, they could also be estimated from VOC emissions for both gasoline and diesel vehicles using previously published measurements from chamber measurements. Estimating POAvapor from VOC emissions and ageing exhaust emissions with a simple model included in the Polyphemus air-quality platform compare well to measurements of SOA formation performed in chamber experiments. Over Greater Paris, POAvapor emissions estimated using POA and VOC emissions are compared using the HEAVEN bottom-up traffic emissions model. The impact on the simulated atmospheric concentrations is then assessed using the Polyphemus/Polair3D chemistry-transport model. Estimating POAvapor emissions from VOC emissions rather than POA emissions lead to lower emissions along motorway axes (between -50% and -70%) and larger emissions in urban areas (up to between +120% and +140% in Central Paris). The impact on total organic aerosol concentrations (gas plus particle) is lower than the impact on emissions: between -8% and 25% along motorway axes and in urban areas respectively. Particle-phase organic concentrations are lower when POAvapor emissions are estimated from VOC than POA emissions, even in Central Paris where the total organic aerosol concentration is higher, because of different assumptions on the emission volatility distribution, stressing the importance of characterizing not only the emission strength, but also the emission volatility distribution.

The "ick" factor, anticipated regret, and willingness to become an organ donor.

PubMed

O'Carroll, Ronan E; Foster, Catherine; McGeechan, Grant; Sandford, Kayleigh; Ferguson, Eamonn

2011-03-01

This research tested the role of traditional rational-cognitive factors and emotional barriers to posthumous organ donation. An example of an emotional barrier is the "ick" factor, a basic disgust reaction to the idea of organ donation. We also tested the potential role of manipulating anticipated regret to increase intention to donate in people who are not yet registered organ donors. In three experiments involving 621 members of the United Kingdom general public, participants were invited to complete questionnaire measures tapping potential emotional affective attitude barriers such as the "ick" factor, the desire to retain bodily integrity after death, and medical mistrust. Registered posthumous organ donors were compared with nondonors. In Experiments 2 and 3, nondonors were then allocated to a simple anticipated regret manipulation versus a control condition, and the impact on intention to donate was tested. Self-reported emotional barriers and intention to donate in the future. Traditional rational-cognitive factors such as knowledge, attitude, and subjective norm failed to distinguish donors from nondonors. However, in all three experiments, nondonors scored significantly higher than donors on the emotional "ick" factor and bodily integrity scales. A simple anticipated regret manipulation led to a significant increase in intention to register as an organ donor in future. Negative affective attitudes are thus crucial barriers to people registering as organ donors. A simple anticipated regret manipulation has the potential to significantly increase organ donation rates. (c) 2011 APA, all rights reserved

Reconfigurable Complementary Logic Circuits with Ambipolar Organic Transistors

PubMed Central

Yoo, Hocheon; Ghittorelli, Matteo; Smits, Edsger C. P.; Gelinck, Gerwin H.; Lee, Han-Koo; Torricelli, Fabrizio; Kim, Jae-Joon

2016-01-01

Ambipolar organic electronics offer great potential for simple and low-cost fabrication of complementary logic circuits on large-area and mechanically flexible substrates. Ambipolar transistors are ideal candidates for the simple and low-cost development of complementary logic circuits since they can operate as n-type and p-type transistors. Nevertheless, the experimental demonstration of ambipolar organic complementary circuits is limited to inverters. The control of the transistor polarity is crucial for proper circuit operation. Novel gating techniques enable to control the transistor polarity but result in dramatically reduced performances. Here we show high-performance non-planar ambipolar organic transistors with electrical control of the polarity and orders of magnitude higher performances with respect to state-of-art split-gate ambipolar transistors. Electrically reconfigurable complementary logic gates based on ambipolar organic transistors are experimentally demonstrated, thus opening up new opportunities for ambipolar organic complementary electronics. PMID:27762321

Reconfigurable Complementary Logic Circuits with Ambipolar Organic Transistors.

PubMed

Yoo, Hocheon; Ghittorelli, Matteo; Smits, Edsger C P; Gelinck, Gerwin H; Lee, Han-Koo; Torricelli, Fabrizio; Kim, Jae-Joon

2016-10-20

Ambipolar organic electronics offer great potential for simple and low-cost fabrication of complementary logic circuits on large-area and mechanically flexible substrates. Ambipolar transistors are ideal candidates for the simple and low-cost development of complementary logic circuits since they can operate as n-type and p-type transistors. Nevertheless, the experimental demonstration of ambipolar organic complementary circuits is limited to inverters. The control of the transistor polarity is crucial for proper circuit operation. Novel gating techniques enable to control the transistor polarity but result in dramatically reduced performances. Here we show high-performance non-planar ambipolar organic transistors with electrical control of the polarity and orders of magnitude higher performances with respect to state-of-art split-gate ambipolar transistors. Electrically reconfigurable complementary logic gates based on ambipolar organic transistors are experimentally demonstrated, thus opening up new opportunities for ambipolar organic complementary electronics.

On a Possible Unified Scaling Law for Volcanic Eruption Durations

PubMed Central

Cannavò, Flavio; Nunnari, Giuseppe

2016-01-01

Volcanoes constitute dissipative systems with many degrees of freedom. Their eruptions are the result of complex processes that involve interacting chemical-physical systems. At present, due to the complexity of involved phenomena and to the lack of precise measurements, both analytical and numerical models are unable to simultaneously include the main processes involved in eruptions thus making forecasts of volcanic dynamics rather unreliable. On the other hand, accurate forecasts of some eruption parameters, such as the duration, could be a key factor in natural hazard estimation and mitigation. Analyzing a large database with most of all the known volcanic eruptions, we have determined that the duration of eruptions seems to be described by a universal distribution which characterizes eruption duration dynamics. In particular, this paper presents a plausible global power-law distribution of durations of volcanic eruptions that holds worldwide for different volcanic environments. We also introduce a new, simple and realistic pipe model that can follow the same found empirical distribution. Since the proposed model belongs to the family of the self-organized systems it may support the hypothesis that simple mechanisms can lead naturally to the emergent complexity in volcanic behaviour. PMID:26926425

On a Possible Unified Scaling Law for Volcanic Eruption Durations.

PubMed

Cannavò, Flavio; Nunnari, Giuseppe

2016-03-01

Volcanoes constitute dissipative systems with many degrees of freedom. Their eruptions are the result of complex processes that involve interacting chemical-physical systems. At present, due to the complexity of involved phenomena and to the lack of precise measurements, both analytical and numerical models are unable to simultaneously include the main processes involved in eruptions thus making forecasts of volcanic dynamics rather unreliable. On the other hand, accurate forecasts of some eruption parameters, such as the duration, could be a key factor in natural hazard estimation and mitigation. Analyzing a large database with most of all the known volcanic eruptions, we have determined that the duration of eruptions seems to be described by a universal distribution which characterizes eruption duration dynamics. In particular, this paper presents a plausible global power-law distribution of durations of volcanic eruptions that holds worldwide for different volcanic environments. We also introduce a new, simple and realistic pipe model that can follow the same found empirical distribution. Since the proposed model belongs to the family of the self-organized systems it may support the hypothesis that simple mechanisms can lead naturally to the emergent complexity in volcanic behaviour.

Modeling the energetic and exergetic self-sustainability of societies with different structures

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

Sciubba, E.

1995-06-01

The paper examines global energy and exergy flows in various models of organized human societies: from primitive tribal organizations to teocratic/aristocratic societies, to the present industrial (and post-industrial) society, to possible future highly robotized or central control social organizations. The analysis focuses on the very general chain of technological processes connected to the extraction, conversion, distribution and final use of the real energetic content of natural resources (i.e., their exergy): the biological food chain is also considered, albeit in a very simplified and humankind sense. It is argued that, to sustain this chain of processes, it is necessary to usemore » a substantial portion of the final-use energy flow, and to employ a large portion of the total work force sustained by this end-use energy. It is shown that if these quantities can be related to the total exergy flow rate (from the source) and to the total available work force, then this functional relationship takes different forms in different types of society. The procedure is very general: each type of societal organization is reduced to a simple model for which energy and exergy flow diagrams are calculated, under certain well-defined assumptions, which restrain both the exchanges among the functional groups which constitute the model, and the exchanges with the environment. The results can be quantified using some assumptions/projections about energy consumption levels for different stages of technological development which are available in the literature; the procedure is applied to some models of primitive and pre-industrial societies, to the present industrial/post-industrial society, and to a hypothetical model of a future, high-technology society.« less

Ophiuroid robot that self-organizes periodic and non-periodic arm movements.

PubMed

Kano, Takeshi; Suzuki, Shota; Watanabe, Wataru; Ishiguro, Akio

2012-09-01

Autonomous decentralized control is a key concept for understanding the mechanism underlying adaptive and versatile locomotion of animals. Although the design of an autonomous decentralized control system that ensures adaptability by using coupled oscillators has been proposed previously, it cannot comprehensively reproduce the versatility of animal behaviour. To tackle this problem, we focus on using ophiuroids as a simple model that exhibits versatile locomotion including periodic and non-periodic arm movements. Our existing model for ophiuroid locomotion uses an active rotator model that describes both oscillatory and excitatory properties. In this communication, we develop an ophiuroid robot to confirm the validity of this proposed model in the real world. We show that the robot travels by successfully coordinating periodic and non-periodic arm movements in response to external stimuli.

Detailed emission profiles for on-road vehicles derived from ambient measurements during a windless traffic episode in Baltimore using a multi-model approach

NASA Astrophysics Data System (ADS)

Ke, Haohao; Ondov, John M.; Rogge, Wolfgang F.

2013-12-01

Composite chemical profiles of motor vehicle emissions were extracted from ambient measurements at a near-road site in Baltimore during a windless traffic episode in November, 2002, using four independent approaches, i.e., simple peak analysis, windless model-based linear regression, PMF, and UNMIX. Although the profiles are in general agreement, the windless-model-based profile treatment more effectively removes interference from non-traffic sources and is deemed to be more accurate for many species. In addition to abundances of routine pollutants (e.g., NOx, CO, PM2.5, EC, OC, sulfate, and nitrate), 11 particle-bound metals and 51 individual traffic-related organic compounds (including n-alkanes, PAHs, oxy-PAHs, hopanes, alkylcyclohexanes, and others) were included in the modeling.

Hydrodynamic Contributions to Amoeboid Cell Motility

NASA Astrophysics Data System (ADS)

Lewis, Owen; Guy, Robert

2012-11-01

Understanding the methods by which cells move is a fundamental problem in modern biology. Recent evidence has shown that the fluid dynamics of cytoplasm can play a vital role in cellular motility. The slime mold Physarum polycephalum provides an excellent model organism for the study of amoeboid motion. In this research, we use a simply analytic model in conjuction with computational experiments to investigate intracellular fluid flow in a simple model of Physarum. Of particlar interest are stresses generated by cytoplasmic flow which may be used to aid in cellular motility. In our numerical model, the Immersed Boundary Method is used to account for such stresses. We investigate the relationship between contraction waves, flow waves, adhesion, and locomotive forces in an attempt to characterize conditions necessary to generate directed motion.

Effect of sample preparation on the measurement of sugars, organic acids, and polyphenols in apple fruit by mid-infrared spectroscopy.

PubMed

Bureau, Sylvie; Scibisz, Iwona; Le Bourvellec, Carine; Renard, Catherine M G C

2012-04-11

The objectives of this study were (i) to test different conditions of freezing, thawing, and grinding during sample preparation and (ii) to evaluate the possibility of using mid-infrared spectroscopy for analyzing the composition of sugars, organic acids, and polyphenols in apples. Seven commercial apple cultivars were chosen for their large variability in composition (total polyphenols from 406 to 1033 mg kg(-1) fresh weight). The different conditions of sample preparation affected only the phenolic compounds and not sugars or organic acids. The regression models of the mid-infrared spectra showed a good ability to estimate sugar and organic acid contents (R(2) ≥ 0.96), except for citric acid. Good predictions were obtained for total phenolic, flavan-3-ols, and procyanidins (R(2) ≥ 0.94) provided oxidation was avoided during sample preparation. A rapid and simple procedure was then proposed for phenolic compounds using sodium fluoride during sample homogenization at ambient temperature and freeze-drying before spectra acquisition.

Direct X-ray photoconversion in flexible organic thin film devices operated below 1 V

PubMed Central

Basiricò, Laura; Ciavatti, Andrea; Cramer, Tobias; Cosseddu, Piero; Bonfiglio, Annalisa; Fraboni, Beatrice

2016-01-01

The application of organic electronic materials for the detection of ionizing radiations is very appealing thanks to their mechanical flexibility, low-cost and simple processing in comparison to their inorganic counterpart. In this work we investigate the direct X-ray photoconversion process in organic thin film photoconductors. The devices are realized by drop casting solution-processed bis-(triisopropylsilylethynyl)pentacene (TIPS-pentacene) onto flexible plastic substrates patterned with metal electrodes; they exhibit a strong sensitivity to X-rays despite the low X-ray photon absorption typical of low-Z organic materials. We propose a model, based on the accumulation of photogenerated charges and photoconductive gain, able to describe the magnitude as well as the dynamics of the X-ray-induced photocurrent. This finding allows us to fabricate and test a flexible 2 × 2 pixelated X-ray detector operating at 0.2 V, with gain and sensitivity up to 4.7 × 104 and 77,000 nC mGy−1 cm−3, respectively. PMID:27708274

Why the apparent order of bimolecular recombination in blend organic solar cells can be larger than two: A topological consideration

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

Nenashev, A. V.; Dvurechenskii, A. V.; Novosibirsk State University, 630090 Novosibirsk

2016-07-18

The apparent order δ of non-geminate recombination higher than δ = 2 has been evidenced in numerous experiments on organic bulk heterojunction (BHJ) structures intensively studied for photovoltaic applications. This feature is claimed puzzling, since the rate of the bimolecular recombination in organic BHJ systems is proportional to the product of the concentrations of recombining electrons and holes and therefore the reaction order δ = 2 is expected. In organic BHJ structures, electrons and holes are confined to two different material phases: electrons to the acceptor material (usually a fullerene derivative) while holes to the donor phase (usually a polymer). The non-geminatemore » recombination of charge carriers can therefore happen only at the interfaces between the two phases. Considering a simple geometrical model of the BHJ system, we show that the apparent order of recombination can deviate from δ = 2 due solely to the topological structure of the system.« less

Photosynthetically Driven Cycles Produce Extreme pCO2Variability in a Large Eelgrass Meadow and Readily Measured Proxies Can Be Used to Estimate These Changes

NASA Astrophysics Data System (ADS)

Love, B. A.; O'Brien, C.; Bohlmann, H.

2016-02-01

Declining ocean pH has spurred research into the effects of marine carbonate chemistry on a variety of organisms, but less work has focused on the potential role of organisms in changing local carbonate chemistry. It has been suggested that photosynthetic activity of macrophytes in coastal areas can decrease pCO2, increase pH, and may provide areas of refuge for organisms sensitive to ocean acidification. To assess the effect of a large eelgrass meadow on water chemistry, discreet samples were collected hourly over several 24 hour cycles in Padilla Bay, Washington. Calculated pCO2 ranged from less than 100 ppm to greater than 700 ppm, often over the course of only a few hours. Aragonite saturation, DIC and pH were also highly variable. In -situ sensors, including a YSI glass electrode, a custom built DuraFET sensor and a SeaFET sensor were co-deployed to provide a high frequency record of water chemistry over several months. These data, (discrete samples and sensors) were used to develop a model that estimates pCO2 for the summer season based on readily measured parameters. Tidal height, photosynthetically active radiation and pH can predict pCO2 reasonably well in this environment. We compare the data from the 3 pH sensors and analyze the quality of data and predictions based on each one. A simple theoretical model shows that the large observed and modeled changes in pCO2 and pH (up to 800 ppm CO2 or 1 pH unit per day) match the magnitude of changes expected based on experimentally derived photosynthetic rates, measured light and water depth and that CO2 fluxes from gas exchange are expected to be small compared to photosynthetic fluxes in this environment. This study illustrates how eelgrass meadows do have the potential to create favorable carbonate chemistry, and demonstrates both the temporally variable nature of that effect and the possibility of better understanding when and how long it occurs through relatively simple modeling of the system.

Effect of confinements: Bending in Paramecium

NASA Astrophysics Data System (ADS)

Eddins, Aja; Yang, Sung; Spoon, Corrie; Jung, Sunghwan

2012-02-01

Paramecium is a unicellular eukaryote which by coordinated beating of cilia, generates metachronal waves which causes it to execute a helical trajectory. We investigate the swimming parameters of the organism in rectangular PDMS channels and try to quantify its behavior. Surprisingly a swimming Paramecium in certain width of channels executes a bend of its flexible body (and changes its direction of swimming) by generating forces using the cilia. Considering a simple model of beam constrained between two walls, we predict the bent shapes of the organism and the forces it exerts on the walls. Finally we try to explain how bending (by sensing) can occur in channels by conducting experiments in thin film of fluid and drawing analogy to swimming behavior observed in different cases.

A Simple Method for High Throughput Chemical Screening in Caenorhabditis Elegans

PubMed Central

Lucanic, Mark; Garrett, Theo; Gill, Matthew S.; Lithgow, Gordon J.

2018-01-01

Caenorhabditis elegans is a useful organism for testing chemical effects on physiology. Whole organism small molecule screens offer significant advantages for identifying biologically active chemical structures that can modify complex phenotypes such as lifespan. Described here is a simple protocol for producing hundreds of 96-well culture plates with fairly consistent numbers of C. elegans in each well. Next, we specified how to use these cultures to screen thousands of chemicals for effects on the lifespan of the nematode C. elegans. This protocol makes use of temperature sensitive sterile strains, agar plate conditions, and simple animal handling to facilitate the rapid and high throughput production of synchronized animal cultures for screening. PMID:29630057

Enhanced sensitivity for optical loss measurement in planar thin-films (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yuan, Hua-Kang

2016-09-01

An organic-inorganic hybrid material benefits from processing advantages of organics and high refractive indices of inorganics. We focus on a titanium oxide hydrate system combined with common bulk polymers. In particular, we target thin-film structures of a few microns in thickness. Traditional Beer-Lambert approaches for measuring optical losses can only provide an upper limit estimate. This sensitivity is highly limited when considering the low-losses required for mid-range optical applications, on the order of 0.1 cm-1. For intensity based measurements, improving the sensitivity requires an increase in the optical path length. Instead, a new sensitive technique suitable for simple planar thin films is required. A number of systems were modelled to measure optical losses in films of 1 micron thick. The presented techniques utilise evanescent waves and total internal reflection to increase optical path length through the material. It was found that a new way of using prism coupling provides the greatest improvement in sensitivity. In keeping the requirements on the material simple, this method for measuring loss is well suited to any future developments of new materials in thin-film structures.

What Hydra can teach us about chemical ecology -how a simple, soft organism survives in a hostile aqueous environment.

PubMed

Rachamim, Tamar; Sher, Daniel

2012-01-01

Hydra and its fellow cnidarians - sea anemones, corals and jellyfish - are simple, mostly sessile animals that depend on bioactive chemicals for survival. In this review, we briefly describe what is known about the chemical armament of Hydra, and detail future research directions where Hydra can help illuminate major questions in chemical ecology, pharmacology, developmental biology and evolution. Focusing on two groups of putative toxins from Hydra - phospholipase A2s and proteins containing ShK and zinc metalloprotease domains, we ask: how do different venom components act together during prey paralysis? How is a venom arsenal created and how does it evolve? How is the chemical arsenal delivered to its target? To what extent does a chemical and biotic coupling exist between an organism and its environment? We propose a model whereby in Hydra and other cnidarians, bioactive compounds are secreted both as localized point sources (nematocyte discharges) and across extensive body surfaces, likely combining to create complex "chemical landscapes". We speculate that these cnidarian-derived chemical landscapes may affect the surrounding community on scales from microns to, in the case of coral reefs, hundreds of kilometers.

Testing environmental pollutants on soil organisms: A simple assay to investigate the toxicity of environmental pollutants on soil organisms, using CdCl2 and nematodes

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

van Kessel, W.H.; Brocades Zaalberg, R.W.; Seinen, W.

1989-10-01

Juvenile stages of Caenorhabditis elegans (nematoda) were isolated and grown in an axenic medium containing various concentrations of CdCl2. Growth of the organisms was significantly reduced from a level of 1 microM CdCl2. Reproduction of the nematodes was also reduced from that 1 microM exposure level. At levels of 160 and 320 microM, growth was retarded at the early juvenile stages and the organisms did not reach the adult stage and could therefore not reproduce. The test system turned out to be simple and reproducible and is therefore suitable for the investigation of the toxicity of compounds to soil nematodes.

Tympanic membrane organ culture using cell culture well inserts engrafted with tympanic membrane tissue explants.

PubMed

Liew, Lawrence J; Day, Richard M; Dilley, Rodney J

2017-03-01

Tissue engineering approaches using growth factors and various materials for repairing chronic perforations of the tympanic membrane are being developed, but there are surprisingly few relevant tissue culture models available to test new treatments. Here, we present a simple three-dimensional model system based on micro-dissecting the rat tympanic membrane umbo and grafting it into the membrane of a cell culture well insert. Cell outgrowth from the graft produced sufficient cells to populate a membrane of similar surface area to the human tympanic membrane within 2 weeks. Tissue grafts from the annulus region also showed cell outgrowth but were not as productive. The umbo organoid supported substantial cell proliferation and migration under the influence of keratinocyte growth medium. Cells from umbo grafts were enzymatically harvested from the polyethylene terephthalate (PET) membrane for expansion in routine culture and cells could be harvested consecutively from the same graft over multiple cycles. We used harvested cells to test cell migration properties and to engraft a porous silk scaffold material as proof-of-principle for tissue engineering applications. This model is simple enough to be widely adopted for tympanic membrane regeneration studies and has promise as a tissue-equivalent model alternative to animal testing.

On the front and back side quantum efficiency differences in semi-transparent organic solar cells and photodiodes

NASA Astrophysics Data System (ADS)

Bouthinon, B.; Clerc, R.; Verilhac, J. M.; Racine, B.; De Girolamo, J.; Jacob, S.; Lienhard, P.; Joimel, J.; Dhez, O.; Revaux, A.

2018-03-01

The External Quantum Efficiency (EQE) of semi-transparent Bulk Hetero-Junction (BHJ) organic photodiodes processed in air shows significant differences when measured from the front or back side contacts. This difference was found significantly reduced when decreasing the active layer thickness or by applying a negative bias. This work brings new elements to help understanding this effect, providing a large set of experiments featuring different applied voltages, active layers, process conditions, and electron and hole layers. By means of detailed electrical simulations, all these measurements have been found consistent with the mechanisms of irreversible photo-oxidation, modeled as deep trap states (and not as p-type doping). The EQE measurement from front and back sides is thus a simple and efficient way of monitoring the presence and amplitude of oxygen contamination in BHJ organic solar cells and photodiodes.

Environmentally relevant concentrations of tramadol and citalopram alter behaviour of an aquatic invertebrate.

PubMed

Buřič, M; Grabicová, K; Kubec, J; Kouba, A; Kuklina, I; Kozák, P; Grabic, R; Randák, T

2018-05-14

Environmental pollution by pharmaceutically active compounds, used in quantities similar to those of pesticides and other organic micropollutants, is increasingly recognized as a major threat to the aquatic environment. These compounds are only partly removed from wastewaters and, despite their low concentrations, directly and indirectly affect behaviour of freshwater organisms in natural habitats. The aim of this study was to behaviourally assess the effects of an opioid painkiller (tramadol) and antidepressant drug (citalopram) on behaviour patterns of a clonal model species, marbled crayfish. Animals exposed to environmentally relevant concentrations of both tested compounds (∼1 μg l -1 ) exhibited significantly lower velocity and shorter distance moved than controls. Crayfish exposed to tramadol spent more time in shelters. Results were obtained by a simple and rapid method recommended as suitable for assessment of behaviour in aquatic organisms exposed to single pollutants and combinations. Copyright © 2018 Elsevier B.V. All rights reserved.

A Simple Approach to the Visible-Light Photoactivation of Molecular Metal Oxides.

PubMed

Fujimoto, Satomi; Cameron, Jamie M; Wei, Rong-Jia; Kastner, Katharina; Robinson, David; Sans, Victor; Newton, Graham N; Oshio, Hiroki

2017-10-16

This study explores a new method to maximize the visible-light-driven photocatalytic performance of organic-inorganic hybrid polyoxometalates (POMs). Experimental and theoretical investigations of a family of phosphonate-substituted POMs show that modification of grafted organic moieties can be used to tune the electronic structure and photoactivity of the metal oxide component. Unlike fully inorganic polyoxotungstates, these organic-inorganic hybrid species are responsive to visible light and function as photocatalysts (λ > 420 nm) in the decomposition of a model environmental pollutant. The degree of photoactivation is shown to be dependent on the nature of the inductive effect exerted by the covalently grafted substituent groups. This study emphasizes the untapped potential that lies in an orbital engineering approach to hybrid-POM design and helps to underpin the next generation of bespoke, robust, and cost-effective molecular metal oxide photoactive materials and catalysts.

Computational consciousness: building a self-preserving organism.

PubMed

Barros, Allan Kardec

2010-01-01

Consciousness has been a subject of crescent interest among the neuroscience community. However, building machine models of it is quite challenging, as it involves many characteristics and properties of the human brain which are poorly defined or are very abstract. Here I propose to use information theory (IT) to give a mathematical framework to understand consciousness. For this reason, I used the term "computational". This work is grounded on some recent results on the use of IT to understand how the cortex codes information, where redundancy reduction plays a fundamental role. Basically, I propose a system, here called "organism", whose strategy is to extract the maximal amount of information from the environment in order to survive. To highlight the proposed framework, I show a simple organism composed of a single neuron which adapts itself to the outside dynamics by taking into account its internal state, whose perception is understood here to be related to "feelings".

Plastic lab-on-a-chip for fluorescence excitation with integrated organic semiconductor lasers.

PubMed

Vannahme, Christoph; Klinkhammer, Sönke; Lemmer, Uli; Mappes, Timo

2011-04-25

Laser light excitation of fluorescent markers offers highly sensitive and specific analysis for bio-medical or chemical analysis. To profit from these advantages for applications in the field or at the point-of-care, a plastic lab-on-a-chip with integrated organic semiconductor lasers is presented here. First order distributed feedback lasers based on the organic semiconductor tris(8-hydroxyquinoline) aluminum (Alq3) doped with the laser dye 4-dicyanomethylene-2-methyl-6-(p-dimethylaminostyril)-4H-pyrane (DCM), deep ultraviolet induced waveguides, and a nanostructured microfluidic channel are integrated into a poly(methyl methacrylate) (PMMA) substrate. A simple and parallel fabrication process is used comprising thermal imprint, DUV exposure, evaporation of the laser material, and sealing by thermal bonding. The excitation of two fluorescent marker model systems including labeled antibodies with light emitted by integrated lasers is demonstrated.

A stochastic model for the normal tissue complication probability (NTCP) and applicationss.

PubMed

Stocks, Theresa; Hillen, Thomas; Gong, Jiafen; Burger, Martin

2017-12-11

The normal tissue complication probability (NTCP) is a measure for the estimated side effects of a given radiation treatment schedule. Here we use a stochastic logistic birth-death process to define an organ-specific and patient-specific NTCP. We emphasize an asymptotic simplification which relates the NTCP to the solution of a logistic differential equation. This framework is based on simple modelling assumptions and it prepares a framework for the use of the NTCP model in clinical practice. As example, we consider side effects of prostate cancer brachytherapy such as increase in urinal frequency, urinal retention and acute rectal dysfunction. © The authors 2016. Published by Oxford University Press on behalf of the Institute of Mathematics and its Applications. All rights reserved.

The effect of fire and permafrost interactions on soil carbon accumulation in an upland black spruce ecosystem of interior Alaska: Implications for post-thaw carbon loss

USGS Publications Warehouse

O'Donnell, J. A.; Harden, J.W.; McGuire, A.D.; Kanevskiy, M.Z.; Jorgenson, M.T.; Xu, X.

2011-01-01

High-latitude regions store large amounts of organic carbon (OC) in active-layer soils and permafrost, accounting for nearly half of the global belowground OC pool. In the boreal region, recent warming has promoted changes in the fire regime, which may exacerbate rates of permafrost thaw and alter soil OC dynamics in both organic and mineral soil. We examined how interactions between fire and permafrost govern rates of soil OC accumulation in organic horizons, mineral soil of the active layer, and near-surface permafrost in a black spruce ecosystem of interior Alaska. To estimate OC accumulation rates, we used chronosequence, radiocarbon, and modeling approaches. We also developed a simple model to track long-term changes in soil OC stocks over past fire cycles and to evaluate the response of OC stocks to future changes in the fire regime. Our chronosequence and radiocarbon data indicate that OC turnover varies with soil depth, with fastest turnover occurring in shallow organic horizons (~60 years) and slowest turnover in near-surface permafrost (>3000 years). Modeling analysis indicates that OC accumulation in organic horizons was strongly governed by carbon losses via combustion and burial of charred remains in deep organic horizons. OC accumulation in mineral soil was influenced by active layer depth, which determined the proportion of mineral OC in a thawed or frozen state and thus, determined loss rates via decomposition. Our model results suggest that future changes in fire regime will result in substantial reductions in OC stocks, largely from the deep organic horizon. Additional OC losses will result from fire-induced thawing of near-surface permafrost. From these findings, we conclude that the vulnerability of deep OC stocks to future warming is closely linked to the sensitivity of permafrost to wildfire disturbance. ?? 2010 Blackwell Publishing Ltd.

Stem Cell Models: A Guide to Understand and Mitigate Aging?

PubMed

Brunauer, Regina; Alavez, Silvestre; Kennedy, Brian K

2017-01-01

Aging is studied either on a systemic level using life span and health span of animal models, or on the cellular level using replicative life span of yeast or mammalian cells. While useful in identifying general and conserved pathways of aging, both approaches provide only limited information about cell-type specific causes and mechanisms of aging. Stem cells are the regenerative units of multicellular life, and stem cell aging might be a major cause for organismal aging. Using the examples of hematopoietic stem cell aging and human pluripotent stem cell models, we propose that stem cell models of aging are valuable for studying tissue-specific causes and mechanisms of aging and can provide unique insights into the mammalian aging process that may be inaccessible in simple model organisms. © 2016 S. Karger AG, Basel.

Comparison of rigorous and simple vibrational models for the CO2 gasdynamic laser

NASA Technical Reports Server (NTRS)

Monson, D. J.

1977-01-01

The accuracy of a simple vibrational model for computing the gain in a CO2 gasdynamic laser is assessed by comparing results computed from it with results computed from a rigorous vibrational model. The simple model is that of Anderson et al. (1971), in which the vibrational kinetics are modeled by grouping the nonequilibrium vibrational degrees of freedom into two modes, to each of which there corresponds an equation describing vibrational relaxation. The two models agree fairly well in the computed gain at low temperatures, but the simple model predicts too high a gain at the higher temperatures of current interest. The sources of error contributing to the overestimation given by the simple model are determined by examining the simplified relaxation equations.

Analysis of Business Connections Utilizing Theory of Topology of Random Graphs

NASA Astrophysics Data System (ADS)

Trelewicz, Jennifer Q.; Volovich, Igor V.

2006-03-01

A business ecosystem is a system that describes interactions between organizations. In this paper, we build a theoretical framework that defines a model which can be used to analyze the business ecosystem. The basic concepts within the framework are organizations, business connections, and market, that are all defined in the paper. Many researchers analyze the performance and structure of business using the workflow of the business. Our work in business connections answers a different set of questions, concerning the monetary value in the business ecosystem, rather than the task-interaction view that is provided by workflow analysis. We apply methods for analysis of the topology of complex networks, characterized by the concepts of small path length, clustering, and scale-free degree distributions. To model the dynamics of the business ecosystem we analyze the notion of the state of an organization at a given instant of time. We point out that the notion of state in this case is fundamentally different from the concept of state of the system which is used in classical or quantum physics. To describe the state of the organization at a given time one has to know the probability of payments to contracts which in fact depend on the future behavior of the agents on the market. Therefore methods of p-adic analysis are appropriate to explore such a behavior. Microeconomic and macroeconomic factors are indivisible and moreover the actual state of the organization depends on the future. In this framework some simple models are analyzed in detail. Company strategy can be influenced by analysis of models, which can provide a probabilistic understanding of the market, giving degrees of predictability.

Brain Modularity Mediates the Relation between Task Complexity and Performance

NASA Astrophysics Data System (ADS)

Ye, Fengdan; Yue, Qiuhai; Martin, Randi; Fischer-Baum, Simon; Ramos-Nuã+/-Ez, Aurora; Deem, Michael

Recent work in cognitive neuroscience has focused on analyzing the brain as a network, rather than a collection of independent regions. Prior studies taking this approach have found that individual differences in the degree of modularity of the brain network relate to performance on cognitive tasks. However, inconsistent results concerning the direction of this relationship have been obtained, with some tasks showing better performance as modularity increases, and other tasks showing worse performance. A recent theoretical model suggests that these inconsistencies may be explained on the grounds that high-modularity networks favor performance on simple tasks whereas low-modularity networks favor performance on complex tasks. The current study tests these predictions by relating modularity from resting-state fMRI to performance on a set of behavioral tasks. Complex and simple tasks were defined on the basis of whether they drew on executive attention. Consistent with predictions, we found a negative correlation between individuals' modularity and their performance on the complex tasks but a positive correlation with performance on the simple tasks. The results presented here provide a framework for linking measures of whole brain organization to cognitive processing.

Endoperoxide polyketides from a Chinese Plakortis simplex: further evidence of the impact of stereochemistry on antimalarial activity of simple 1,2-dioxanes.

PubMed

Chianese, Giuseppina; Persico, Marco; Yang, Fan; Lin, Hou-Wen; Guo, Yue-Wei; Basilico, Nicoletta; Parapini, Silvia; Taramelli, Donatella; Taglialatela-Scafati, Orazio; Fattorusso, Caterina

2014-09-01

Chemical investigation of the organic extract obtained from the sponge Plakortis simplex collected in the South China Sea afforded five new polyketide endoperoxides (2 and 4-7), along with two known analogues (1 and 3). The stereostructures of these metabolites have been deduced on the basis of spectroscopic analysis and chemical conversion. The isolated endoperoxide derivatives have been tested for their in vitro antimalarial activity against Plasmodium falciparum strains, showing IC50 values in the low micromolar range. The structure-activity relationships were analyzed by means of a detailed computational investigation and rationalized in the light of the mechanism of action proposed for this class of simple antimalarials. The relative orientation of the atoms involved in the putative radical generation and transfer reaction was demonstrated to have a great impact on the antimalarial activity. The resulting 3D pharmacophoric model can be a useful guide to design simple and effective antimalarial lead compounds belonging to the class of 1,2-dioxanes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ultrathin nondoped emissive layers for efficient and simple monochrome and white organic light-emitting diodes.

PubMed

Zhao, Yongbiao; Chen, Jiangshan; Ma, Dongge

2013-02-01

In this paper, highly efficient and simple monochrome blue, green, orange, and red organic light emitting diodes (OLEDs) based on ultrathin nondoped emissive layers (EMLs) have been reported. The ultrathin nondoped EML was constructed by introducing a 0.1 nm thin layer of pure phosphorescent dyes between a hole transporting layer and an electron transporting layer. The maximum external quantum efficiencies (EQEs) reached 17.1%, 20.9%, 17.3%, and 19.2% for blue, green, orange, and red monochrome OLEDs, respectively, indicating the universality of the ultrathin nondoped EML for most phosphorescent dyes. On the basis of this, simple white OLED structures are also demonstrated. The demonstrated complementary blue/orange, three primary blue/green/red, and four color blue/green/orange/red white OLEDs show high efficiency and good white emission, indicating the advantage of ultrathin nondoped EMLs on constructing simple and efficient white OLEDs.

The relative importance of decomposition and transport mechanisms in accounting for soil organic carbon profiles

NASA Astrophysics Data System (ADS)

Guenet, B.; Eglin, T.; Vasilyeva, N.; Peylin, P.; Ciais, P.; Chenu, C.

2013-04-01

Soil is the major terrestrial reservoir of carbon and a substantial part of this carbon is stored in deep layers, typically deeper than 50 cm below the surface. Several studies underlined the quantitative importance of this deep soil organic carbon (SOC) pool and models are needed to better understand this stock and its evolution under climate and land-uses changes. In this study, we tested and compared three simple theoretical models of vertical transport for SOC against SOC profiles measurements from a long-term bare fallow experiment carried out by the Central-Chernozem State Natural Biosphere Reserve in the Kursk Region of Russia. The transport schemes tested are diffusion, advection and both diffusion and advection. They are coupled to three different formulations of soil carbon decomposition kinetics. The first formulation is a first order kinetics widely used in global SOC decomposition models; the second one, so-called "priming" model, links SOC decomposition rate to the amount of fresh organic matter, representing the substrate interactions. The last one is also a first order kinetics, but SOC is split into two pools. Field data are from a set of three bare fallow plots where soil received no input during the past 20, 26 and 58 yr, respectively. Parameters of the models were optimised using a Bayesian method. The best results are obtained when SOC decomposition is assumed to be controlled by fresh organic matter (i.e., the priming model). In comparison to the first-order kinetic model, the priming model reduces the overestimation in the deep layers. We also observed that the transport scheme that improved the fit with the data depended on the soil carbon mineralisation formulation chosen. When soil carbon decomposition was modelled to depend on the fresh organic matter amount, the transport mechanism which improved best the fit to the SOC profile data was the model representing both advection and diffusion. Interestingly, the older the bare fallow is, the lesser the need for diffusion is, suggesting that stabilised carbon may not be transported within the profile by the same mechanisms than more labile carbon.

Towards an improved soil moisture retrieval for organic-rich soils from SMOS passive microwave L-band observations

NASA Astrophysics Data System (ADS)

Bircher, Simone; Richaume, Philippe; Mahmoodi, Ali; Mialon, Arnaud; Fernandez-Moran, Roberto; Wigneron, Jean-Pierre; Demontoux, François; Jonard, François; Weihermüller, Lutz; Andreasen, Mie; Rautiainen, Kimmo; Ikonen, Jaakko; Schwank, Mike; Drusch, Mattias; Kerr, Yann H.

2017-04-01

From the passive L-band microwave radiometer onboard the Soil Moisture and Ocean Salinity (SMOS) space mission global surface soil moisture data is retrieved every 2 - 3 days. Thus far, the empirical L-band Microwave Emission of the Biosphere (L-MEB) radiative transfer model applied in the SMOS soil moisture retrieval algorithm is exclusively calibrated over test sites in dry and temperate climate zones. Furthermore, the included dielectric mixing model relating soil moisture to relative permittivity accounts only for mineral soils. However, soil moisture monitoring over the higher Northern latitudes is crucial since these regions are especially sensitive to climate change. A considerable positive feedback is expected if thawing of these extremely organic soils supports carbon decomposition and release to the atmosphere. Due to differing structural characteristics and thus varying bound water fractions, the relative permittivity of organic material is lower than that of the most mineral soils at a given water content. This assumption was verified by means of L-band relative permittivity laboratory measurements of organic and mineral substrates from various sites in Denmark, Finland, Scotland and Siberia using a resonant cavity. Based on these data, a simple empirical dielectric model for organic soils was derived and implemented in the SMOS Soil Moisture Level 2 Prototype Processor (SML2PP). Unfortunately, the current SMOS retrieved soil moisture product seems to show unrealistically low values compared to in situ soil moisture data collected from organic surface layers in North America, Europe and the Tibetan Plateau so that the impact of the dielectric model for organic soils cannot really be tested. A simplified SMOS processing scheme yielding higher soil moisture levels has recently been proposed and is presently under investigation. Furthermore, recalibration of the model parameters accounting for vegetation and roughness effects that were thus far only evaluated using the default dielectric model for mineral soils is ongoing for the "organic" L-MEB version. Additionally, in order to decide where a soil moisture retrieval using the "organic" dielectric model should be triggered, information on soil organic matter content in the soil surface layer has to be considered in the retrieval algorithm. For this purpose, SoilGrids (www.soilgrids.org) providing soil organic carbon content (SOCC) in g/kg is under study. A SOCC threshold based on the relation between the SoilGrids' SOCC and the presence of organic soil surface layers (relevant to alter the microwave L-band emissions from the land surface) in the SoilGrids' source soil profile information has to be established. In this communication, we present the current status of the above outlined studies with the objective to advance towards an improved soil moisture retrieval for organic-rich soils from SMOS passive microwave L-band observations.

Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.

PubMed

Galperin, Michael Y; Higdon, Roger; Kolker, Eugene

2010-04-01

Comparative analysis of the complete genome sequences from a variety of poorly studied organisms aims at predicting ecological and behavioral properties of these organisms and helping in characterizing their habitats. This task requires finding appropriate descriptors that could be correlated with the core traits of each system and would allow meaningful comparisons. Using the relatively simple bacterial models, first attempts have been made to introduce suitable metrics to describe the complexity of organism's signaling machinery, which included introducing the "bacterial IQ" score. Here, we use an updated census of prokaryotic signal transduction systems to improve this parameter and evaluate its consistency within selected bacterial phyla. We also introduce a more elaborate descriptor, a set of profiles of relative abundance of members of each family of signal transduction proteins encoded in each genome. We show that these family profiles are well conserved within each genus and are often consistent within families of bacteria. Thus, they reflect evolutionary relationships between organisms as well as individual adaptations of each organism to its specific ecological niche.

Biodegradation of coal-related model compounds

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

Campbell, J.A.; Stewart, D.L.; McCulloch, M.

1988-06-01

We have studied the reactions of model compounds having coal-related functionalities (ester linkages, ether linkages, PAH) with the intact organism, cell-free filtrate, and cell-free enzyme of C. versicolor to better understand the process of biosolubilization. Many of the degradation products have been identified by gas chromatography/mass spectroscopy (GC/MS). Results indicate that the two compounds tested with the intact fungal organism were completely degraded. Complete degradation refers to no recovery of model compound. We can probably assume that the other two would also be totally degraded, since we have not yet found a simple compound that will survive long-term exposure tomore » the intact fungus. The ease of degradation with the cell-free filtrate appears to be in the order: phenylbenzoate > benzylbenzoate > benzyl ether > methoxybenzophenone. Esters and ethers that are activated by aromatic rings appear to be susceptible to the fungal extract; however, aromatic ketones are not affected by the extract. From the limited results we have obtained from the isolated enzyme, it appears that the activity may parallel the cell-free filtrate. When the cell-free extract was tested with the model compounds indole, dibenzothiophene, and bibenzyl, no degradation with the enzyme was noted: however, exposure of these compounds to the intact organism resulted in complete degradation. Analysis of the controls indicated no degradation. 8 refs., 1 fig., 1 tab.« less

Terrestrial and marine perspectives on modeling organic matter degradation pathways.

PubMed

Burd, Adrian B; Frey, Serita; Cabre, Anna; Ito, Takamitsu; Levine, Naomi M; Lønborg, Christian; Long, Matthew; Mauritz, Marguerite; Thomas, R Quinn; Stephens, Brandon M; Vanwalleghem, Tom; Zeng, Ning

2016-01-01

Organic matter (OM) plays a major role in both terrestrial and oceanic biogeochemical cycles. The amount of carbon stored in these systems is far greater than that of carbon dioxide (CO2 ) in the atmosphere, and annual fluxes of CO2 from these pools to the atmosphere exceed those from fossil fuel combustion. Understanding the processes that determine the fate of detrital material is important for predicting the effects that climate change will have on feedbacks to the global carbon cycle. However, Earth System Models (ESMs) typically utilize very simple formulations of processes affecting the mineralization and storage of detrital OM. Recent changes in our view of the nature of this material and the factors controlling its transformation have yet to find their way into models. In this review, we highlight the current understanding of the role and cycling of detrital OM in terrestrial and marine systems and examine how this pool of material is represented in ESMs. We include a discussion of the different mineralization pathways available as organic matter moves from soils, through inland waters to coastal systems and ultimately into open ocean environments. We argue that there is strong commonality between aspects of OM transformation in both terrestrial and marine systems and that our respective scientific communities would benefit from closer collaboration. © 2015 John Wiley & Sons Ltd.

Stability analysis of a model gene network links aging, stress resistance, and negligible senescence.

PubMed

Kogan, Valeria; Molodtsov, Ivan; Menshikov, Leonid I; Shmookler Reis, Robert J; Fedichev, Peter

2015-08-28

Several animal species are considered to exhibit what is called negligible senescence, i.e. they do not show signs of functional decline or any increase of mortality with age. Recent studies in naked mole rat and long-lived sea urchins showed that these species do not alter their gene-expression profiles with age as much as other organisms do. This is consistent with exceptional endurance of naked mole rat tissues to various genotoxic stresses. We conjectured, therefore, that the lifelong transcriptional stability of an organism may be a key determinant of longevity. We analyzed the stability of a simple genetic-network model and found that under most common circumstances, such a gene network is inherently unstable. Over a time it undergoes an exponential accumulation of gene-regulation deviations leading to death. However, should the repair systems be sufficiently effective, the gene network can stabilize so that gene damage remains constrained along with mortality of the organism. We investigate the relationship between stress-resistance and aging and suggest that the unstable regime may provide a mathematical basis for the Gompertz "law" of aging in many species. At the same time, this model accounts for the apparently age-independent mortality observed in some exceptionally long-lived animals.

Acoustic signatures of sound source-tract coupling.

PubMed

Arneodo, Ezequiel M; Perl, Yonatan Sanz; Mindlin, Gabriel B

2011-04-01

Birdsong is a complex behavior, which results from the interaction between a nervous system and a biomechanical peripheral device. While much has been learned about how complex sounds are generated in the vocal organ, little has been learned about the signature on the vocalizations of the nonlinear effects introduced by the acoustic interactions between a sound source and the vocal tract. The variety of morphologies among bird species makes birdsong a most suitable model to study phenomena associated to the production of complex vocalizations. Inspired by the sound production mechanisms of songbirds, in this work we study a mathematical model of a vocal organ, in which a simple sound source interacts with a tract, leading to a delay differential equation. We explore the system numerically, and by taking it to the weakly nonlinear limit, we are able to examine its periodic solutions analytically. By these means we are able to explore the dynamics of oscillatory solutions of a sound source-tract coupled system, which are qualitatively different from those of a sound source-filter model of a vocal organ. Nonlinear features of the solutions are proposed as the underlying mechanisms of observed phenomena in birdsong, such as unilaterally produced "frequency jumps," enhancement of resonances, and the shift of the fundamental frequency observed in heliox experiments. ©2011 American Physical Society

Acoustic signatures of sound source-tract coupling

PubMed Central

Arneodo, Ezequiel M.; Perl, Yonatan Sanz; Mindlin, Gabriel B.

2014-01-01

Birdsong is a complex behavior, which results from the interaction between a nervous system and a biomechanical peripheral device. While much has been learned about how complex sounds are generated in the vocal organ, little has been learned about the signature on the vocalizations of the nonlinear effects introduced by the acoustic interactions between a sound source and the vocal tract. The variety of morphologies among bird species makes birdsong a most suitable model to study phenomena associated to the production of complex vocalizations. Inspired by the sound production mechanisms of songbirds, in this work we study a mathematical model of a vocal organ, in which a simple sound source interacts with a tract, leading to a delay differential equation. We explore the system numerically, and by taking it to the weakly nonlinear limit, we are able to examine its periodic solutions analytically. By these means we are able to explore the dynamics of oscillatory solutions of a sound source-tract coupled system, which are qualitatively different from those of a sound source-filter model of a vocal organ. Nonlinear features of the solutions are proposed as the underlying mechanisms of observed phenomena in birdsong, such as unilaterally produced “frequency jumps,” enhancement of resonances, and the shift of the fundamental frequency observed in heliox experiments. PMID:21599213

Electronic Structure and Magnetic Interactions in the Radical Salt [BEDT-TTF]2[CuCl4].

PubMed

Calzado, Carmen J; Rodríguez-García, Bárbara; Galán Mascarós, José Ramón; Hernández, Norge Cruz

2018-06-07

The magnetic behavior and electric properties of the hybrid radical salt [BEDT-TTF] 2 [CuCl 4 ] have been revisited through extended experimental analyses and DDCI and periodic DFT plane waves calculations. Single crystal X-ray diffraction data have been collected at different temperatures, discovering a phase transition occurring in the 250-300 K range. The calculations indicate the presence of intradimer, interdimer, and organic-inorganic π-d interactions in the crystal, a magnetic pattern much more complex than the Bleaney-Bowers model initially assigned to this material. Although this simple model was good enough to reproduce the magnetic susceptibility data, our calculations demonstrate that the actual magnetic structure is significantly more intricate, with alternating antiferromagnetic 1D chains of the organic BEDT-TTF + radical, connected through weak antiferromagnetic interactions with the CuCl 4 2- ions. Combination of experiment and theory allowed us to unambiguously determine and quantify the leading magnetic interactions in the system. The density-of-states curves confirm the semiconductor nature of the system and the dominant organic contribution of the valence and conduction band edges. This general and combined approach appears to be fundamental in order to properly understand the magnetic structure of these complex materials, where experimental data can actually be fitted from a variety of models and parameters.

Calculation of organ doses in x-ray examinations of premature babies

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

Smans, Kristien; Tapiovaara, Markku; Cannie, Mieke

Lung disease represents one of the most life-threatening conditions in prematurely born children. In the evaluation of the neonatal chest, the primary and most important diagnostic study is the chest radiograph. Since prematurely born children are very sensitive to radiation, those radiographs may lead to a significant radiation detriment. Knowledge of the radiation dose is therefore necessary to justify the exposures. To calculate doses in the entire body and in specific organs, computational models of the human anatomy are needed. Using medical imaging techniques, voxel phantoms have been developed to achieve a representation as close as possible to the anatomicalmore » properties. In this study two voxel phantoms, representing prematurely born babies, were created from computed tomography- and magnetic resonance images: Phantom 1 (1910 g) and Phantom 2 (590 g). The two voxel phantoms were used in Monte Carlo calculations (MCNPX) to assess organ doses. The results were compared with the commercially available software package PCXMC in which the available mathematical phantoms can be downsized toward the prematurely born baby. The simple phantom-scaling method used in PCXMC seems to be sufficient to calculate doses for organs within the radiation field. However, one should be careful in specifying the irradiation geometry. Doses in organs that are wholly or partially outside the primary radiation field depend critically on the irradiation conditions and the phantom model.« less

Cloud condensation nucleus activity of internally mixed ammonium sulfate/organic acid aerosol particles

NASA Astrophysics Data System (ADS)

Abbatt, J. P. D.; Broekhuizen, K.; Pradeep Kumar, P.

The ability of mixed ammonium sulfate/organic acid particles to act as cloud condensation nuclei (CCN) has been studied in the laboratory using a continuous flow, thermal-gradient diffusion chamber operated at supersaturations between 0.3% and 0.6%. The organic acids studied were malonic acid, azelaic acid, hexanoic acid, cis-pinonic acid, oleic acid and stearic acid, and the particles were largely prepared by condensation of the organic vapor onto a dry ammonium sulfate core. For malonic acid and hexanoic acid, the mixed particles activated as predicted by a simple Köhler theory model where both species are assumed to be fully soluble and the droplet has the surface tension of water. Three low-solubility species, cis-pinonic acid, azelaic acid and oleic acid, are well modeled where the acid was assumed to be either partially or fully insoluble. Interestingly, although thin coats of stearic acid behaved in a manner similar to that displayed by oleic and cis-pinonic acid, we observed that thick coats led to a complete deactivation of the ammonium sulfate, presumably because the water vapor could not diffuse through the solid stearic acid. We observed no CCN behavior that could be clearly attributed to a lowering of the surface tension of the growing droplet by the presence of the organic constituents, some of which are highly surface active.

Physiologically grounded metrics of model skill: a case study estimating heat stress in intertidal populations

PubMed Central

Kish, Nicole E.; Helmuth, Brian; Wethey, David S.

2016-01-01

Models of ecological responses to climate change fundamentally assume that predictor variables, which are often measured at large scales, are to some degree diagnostic of the smaller-scale biological processes that ultimately drive patterns of abundance and distribution. Given that organisms respond physiologically to stressors, such as temperature, in highly non-linear ways, small modelling errors in predictor variables can potentially result in failures to predict mortality or severe stress, especially if an organism exists near its physiological limits. As a result, a central challenge facing ecologists, particularly those attempting to forecast future responses to environmental change, is how to develop metrics of forecast model skill (the ability of a model to predict defined events) that are biologically meaningful and reflective of underlying processes. We quantified the skill of four simple models of body temperature (a primary determinant of physiological stress) of an intertidal mussel, Mytilus californianus, using common metrics of model performance, such as root mean square error, as well as forecast verification skill scores developed by the meteorological community. We used a physiologically grounded framework to assess each model's ability to predict optimal, sub-optimal, sub-lethal and lethal physiological responses. Models diverged in their ability to predict different levels of physiological stress when evaluated using skill scores, even though common metrics, such as root mean square error, indicated similar accuracy overall. Results from this study emphasize the importance of grounding assessments of model skill in the context of an organism's physiology and, especially, of considering the implications of false-positive and false-negative errors when forecasting the ecological effects of environmental change. PMID:27729979