Plant subcellular proteomics: Application for exploring optimal cell function in soybean.

Science.gov (United States)

Wang, Xin; Komatsu, Setsuko

2016-06-30

Plants have evolved complicated responses to developmental changes and stressful environmental conditions. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular compartments during plant development and in response to biotic and abiotic stresses. Soybean, which is a valuable legume crop rich in protein and vegetable oil, can grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. To date, numerous proteomic studies have been performed in soybean to examine the specific protein profiles of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum. In this review, methods for the purification and purity assessment of subcellular organelles from soybean are summarized. In addition, the findings from subcellular proteomic analyses of soybean during development and under stresses, particularly flooding stress, are presented and the proteins regulated among subcellular compartments are discussed. Continued advances in subcellular proteomics are expected to greatly contribute to the understanding of the responses and interactions that occur within and among subcellular compartments during development and under stressful environmental conditions. Subcellular proteomics has the potential to investigate the cellular events and interactions among subcellular compartments in response to development and stresses in plants. Soybean could grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. Numerous proteomics of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum was carried out to investigate the respecting proteins and their functions in soybean during development or under stresses. In this review, methods of subcellular-organelle enrichment and purity assessment are summarized. In addition, previous findings of

Spatiotemporal visualization of subcellular dynamics of carbon nanotubes

KAUST Repository

Serag, Maged F.

2012-12-12

To date, there is no consensus on the relationship between the physicochemical characteristics of carbon nanotubes (CNTs) and their biological behavior; however, there is growing evidence that the versatile characteristics make their biological fate largely unpredictable and remain an issue of limited knowledge. Here we introduce an experimental methodology for tracking and visualization of postuptake behavior and the intracellular fate of CNTs based on the spatial distribution of diffusion values throughout the plant cell. By using raster scan image correlation spectroscopy (RICS), we were able to generate highly quantitative spatial maps of CNTs diffusion in different cell compartments. The spatial map of diffusion values revealed that the uptake of CNTs is associated with important subcellular events such as carrier-mediated vacuolar transport and autophagy. These results show that RICS is a useful methodology to elucidate the intracellular behavior mechanisms of carbon nanotubes and potentially other fluorescently labeled nanoparticles, which is of relevance for the important issues related to the environmental impact and health hazards. © 2012 American Chemical Society.

Differential subcellular distribution of ion channels and the diversity of neuronal function.

Science.gov (United States)

Nusser, Zoltan

2012-06-01

Following the astonishing molecular diversity of voltage-gated ion channels that was revealed in the past few decades, the ion channel repertoire expressed by neurons has been implicated as the major factor governing their functional heterogeneity. Although the molecular structure of ion channels is a key determinant of their biophysical properties, their subcellular distribution and densities on the surface of nerve cells are just as important for fulfilling functional requirements. Recent results obtained with high resolution quantitative localization techniques revealed complex, subcellular compartment-specific distribution patterns of distinct ion channels. Here I suggest that within a given neuron type every ion channel has a unique cell surface distribution pattern, with the functional consequence that this dramatically increases the computational power of nerve cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

Optogenetic Tools for Subcellular Applications in Neuroscience.

Science.gov (United States)

Rost, Benjamin R; Schneider-Warme, Franziska; Schmitz, Dietmar; Hegemann, Peter

2017-11-01

The ability to study cellular physiology using photosensitive, genetically encoded molecules has profoundly transformed neuroscience. The modern optogenetic toolbox includes fluorescent sensors to visualize signaling events in living cells and optogenetic actuators enabling manipulation of numerous cellular activities. Most optogenetic tools are not targeted to specific subcellular compartments but are localized with limited discrimination throughout the cell. Therefore, optogenetic activation often does not reflect context-dependent effects of highly localized intracellular signaling events. Subcellular targeting is required to achieve more specific optogenetic readouts and photomanipulation. Here we first provide a detailed overview of the available optogenetic tools with a focus on optogenetic actuators. Second, we review established strategies for targeting these tools to specific subcellular compartments. Finally, we discuss useful tools and targeting strategies that are currently missing from the optogenetics repertoire and provide suggestions for novel subcellular optogenetic applications. Copyright © 2017 Elsevier Inc. All rights reserved.

Computational Fluid Dynamics

International Nuclear Information System (INIS)

Myeong, Hyeon Guk

1999-06-01

This book deals with computational fluid dynamics with basic and history of numerical fluid dynamics, introduction of finite volume method using one-dimensional heat conduction equation, solution of two-dimensional heat conduction equation, solution of Navier-Stokes equation, fluid with heat transport, turbulent flow and turbulent model, Navier-Stokes solution by generalized coordinate system such as coordinate conversion, conversion of basic equation, program and example of calculation, application of abnormal problem and high speed solution of numerical fluid dynamics.

Evaluation and comparison of mammalian subcellular localization prediction methods

Directory of Open Access Journals (Sweden)

Fink J Lynn

2006-12-01

Full Text Available Abstract Background Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These data are difficult to obtain experimentally but have become especially important since many whole genome sequencing projects have been finished and many resulting protein sequences are still lacking detailed functional information. In order to address this paucity of data, many computational prediction methods have been developed. However, these methods have varying levels of accuracy and perform differently based on the sequences that are presented to the underlying algorithm. It is therefore useful to compare these methods and monitor their performance. Results In order to perform a comprehensive survey of prediction methods, we selected only methods that accepted large batches of protein sequences, were publicly available, and were able to predict localization to at least nine of the major subcellular locations (nucleus, cytosol, mitochondrion, extracellular region, plasma membrane, Golgi apparatus, endoplasmic reticulum (ER, peroxisome, and lysosome. The selected methods were CELLO, MultiLoc, Proteome Analyst, pTarget and WoLF PSORT. These methods were evaluated using 3763 mouse proteins from SwissProt that represent the source of the training sets used in development of the individual methods. In addition, an independent evaluation set of 2145 mouse proteins from LOCATE with a bias towards the subcellular localization underrepresented in SwissProt was used. The sensitivity and specificity were calculated for each method and compared to a theoretical value based on what might be observed by random chance. Conclusion No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins. All methods showed lower performance on the LOCATE

Nonlinear dynamics as an engine of computation.

Science.gov (United States)

Kia, Behnam; Lindner, John F; Ditto, William L

2017-03-06

Control of chaos teaches that control theory can tame the complex, random-like behaviour of chaotic systems. This alliance between control methods and physics-cybernetical physics-opens the door to many applications, including dynamics-based computing. In this article, we introduce nonlinear dynamics and its rich, sometimes chaotic behaviour as an engine of computation. We review our work that has demonstrated how to compute using nonlinear dynamics. Furthermore, we investigate the interrelationship between invariant measures of a dynamical system and its computing power to strengthen the bridge between physics and computation.This article is part of the themed issue 'Horizons of cybernetical physics'. © 2017 The Author(s).

A Computational Fluid Dynamics Algorithm on a Massively Parallel Computer

Science.gov (United States)

Jespersen, Dennis C.; Levit, Creon

1989-01-01

The discipline of computational fluid dynamics is demanding ever-increasing computational power to deal with complex fluid flow problems. We investigate the performance of a finite-difference computational fluid dynamics algorithm on a massively parallel computer, the Connection Machine. Of special interest is an implicit time-stepping algorithm; to obtain maximum performance from the Connection Machine, it is necessary to use a nonstandard algorithm to solve the linear systems that arise in the implicit algorithm. We find that the Connection Machine ran achieve very high computation rates on both explicit and implicit algorithms. The performance of the Connection Machine puts it in the same class as today's most powerful conventional supercomputers.

MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction

Directory of Open Access Journals (Sweden)

Kohlbacher Oliver

2009-09-01

Full Text Available Abstract Background Knowledge of subcellular localization of proteins is crucial to proteomics, drug target discovery and systems biology since localization and biological function are highly correlated. In recent years, numerous computational prediction methods have been developed. Nevertheless, there is still a need for prediction methods that show more robustness and higher accuracy. Results We extended our previous MultiLoc predictor by incorporating phylogenetic profiles and Gene Ontology terms. Two different datasets were used for training the system, resulting in two versions of this high-accuracy prediction method. One version is specialized for globular proteins and predicts up to five localizations, whereas a second version covers all eleven main eukaryotic subcellular localizations. In a benchmark study with five localizations, MultiLoc2 performs considerably better than other methods for animal and plant proteins and comparably for fungal proteins. Furthermore, MultiLoc2 performs clearly better when using a second dataset that extends the benchmark study to all eleven main eukaryotic subcellular localizations. Conclusion MultiLoc2 is an extensive high-performance subcellular protein localization prediction system. By incorporating phylogenetic profiles and Gene Ontology terms MultiLoc2 yields higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. MultiLoc2 is available as user-friendly and free web-service, available at: http://www-bs.informatik.uni-tuebingen.de/Services/MultiLoc2.

Prediction of protein subcellular localization using support vector machine with the choice of proper kernel

Directory of Open Access Journals (Sweden)

Al Mehedi Hasan

2017-07-01

Full Text Available The prediction of subcellular locations of proteins can provide useful hints for revealing their functions as well as for understanding the mechanisms of some diseases and, finally, for developing novel drugs. As the number of newly discovered proteins has been growing exponentially, laboratory-based experiments to determine the location of an uncharacterized protein in a living cell have become both expensive and time-consuming. Consequently, to tackle these challenges, computational methods are being developed as an alternative to help biologists in selecting target proteins and designing related experiments. However, the success of protein subcellular localization prediction is still a complicated and challenging problem, particularly when query proteins may have multi-label characteristics, i.e. their simultaneous existence in more than one subcellular location, or if they move between two or more different subcellular locations as well. At this point, to get rid of this problem, several types of subcellular localization prediction methods with different levels of accuracy have been proposed. The support vector machine (SVM has been employed to provide potential solutions for problems connected with the prediction of protein subcellular localization. However, the practicability of SVM is affected by difficulties in selecting its appropriate kernel as well as in selecting the parameters of that selected kernel. The literature survey has shown that most researchers apply the radial basis function (RBF kernel to build a SVM based subcellular localization prediction system. Surprisingly, there are still many other kernel functions which have not yet been applied in the prediction of protein subcellular localization. However, the nature of this classification problem requires the application of different kernels for SVM to ensure an optimal result. From this viewpoint, this paper presents the work to apply different kernels for SVM in protein

Understanding the sub-cellular dynamics of silicon transportation and synthesis in diatoms using population-level data and computational optimization.

Directory of Open Access Journals (Sweden)

Narjes Javaheri

2014-06-01

Full Text Available Controlled synthesis of silicon is a major challenge in nanotechnology and material science. Diatoms, the unicellular algae, are an inspiring example of silica biosynthesis, producing complex and delicate nano-structures. This happens in several cell compartments, including cytoplasm and silica deposition vesicle (SDV. Considering the low concentration of silicic acid in oceans, cells have developed silicon transporter proteins (SIT. Moreover, cells change the level of active SITs during one cell cycle, likely as a response to the level of external nutrients and internal deposition rates. Despite this topic being of fundamental interest, the intracellular dynamics of nutrients and cell regulation strategies remain poorly understood. One reason is the difficulties in measurements and manipulation of these mechanisms at such small scales, and even when possible, data often contain large errors. Therefore, using computational techniques seems inevitable. We have constructed a mathematical model for silicon dynamics in the diatom Thalassiosira pseudonana in four compartments: external environment, cytoplasm, SDV and deposited silica. The model builds on mass conservation and Michaelis-Menten kinetics as mass transport equations. In order to find the free parameters of the model from sparse, noisy experimental data, an optimization technique (global and local search, together with enzyme related penalty terms, has been applied. We have connected population-level data to individual-cell-level quantities including the effect of early division of non-synchronized cells. Our model is robust, proven by sensitivity and perturbation analysis, and predicts dynamics of intracellular nutrients and enzymes in different compartments. The model produces different uptake regimes, previously recognized as surge, externally-controlled and internally-controlled uptakes. Finally, we imposed a flux of SITs to the model and compared it with previous classical kinetics

Fluid Dynamics Theory, Computation, and Numerical Simulation

CERN Document Server

Pozrikidis, Constantine

2009-01-01

Fluid Dynamics: Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner. The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming. This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice. There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes. Two distinguishing features of the discourse are: solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty. Matlab codes are presented and discussed for ...

An improved procedure for subcellular spatial alignment during live-cell CLEM.

Directory of Open Access Journals (Sweden)

Benjamin S Padman

Full Text Available Live-cell correlative light and electron microscopy (CLEM offers unique insights into the ultrastructure of dynamic cellular processes. A critical and technically challenging part of CLEM is the 3-dimensional relocation of the intracellular region of interest during sample processing. We have developed a simple CLEM procedure that uses toner particles from a laser printer as orientation marks. This facilitates easy tracking of a region of interest even by eye throughout the whole procedure. Combined with subcellular fluorescence markers for the plasma membrane and nucleus, the toner particles allow for precise subcellular spatial alignment of the optical and electron microscopy data sets. The toner-based reference grid is printed and transferred onto a polymer film using a standard office printer and laminator. We have also designed a polymer film holder that is compatible with most inverted microscopes, and have validated our strategy by following the ultrastructure of mitochondria that were selectively photo-irradiated during live-cell microscopy. In summary, our inexpensive and robust CLEM procedure simplifies optical imaging, without limiting the choice of optical microscope.

Multi-label learning with fuzzy hypergraph regularization for protein subcellular location prediction.

Science.gov (United States)

Chen, Jing; Tang, Yuan Yan; Chen, C L Philip; Fang, Bin; Lin, Yuewei; Shang, Zhaowei

2014-12-01

Protein subcellular location prediction aims to predict the location where a protein resides within a cell using computational methods. Considering the main limitations of the existing methods, we propose a hierarchical multi-label learning model FHML for both single-location proteins and multi-location proteins. The latent concepts are extracted through feature space decomposition and label space decomposition under the nonnegative data factorization framework. The extracted latent concepts are used as the codebook to indirectly connect the protein features to their annotations. We construct dual fuzzy hypergraphs to capture the intrinsic high-order relations embedded in not only feature space, but also label space. Finally, the subcellular location annotation information is propagated from the labeled proteins to the unlabeled proteins by performing dual fuzzy hypergraph Laplacian regularization. The experimental results on the six protein benchmark datasets demonstrate the superiority of our proposed method by comparing it with the state-of-the-art methods, and illustrate the benefit of exploiting both feature correlations and label correlations.

Subcellular Iron Localization Mechanisms in Plants

Directory of Open Access Journals (Sweden)

Emre Aksoy

2017-12-01

Full Text Available The basic micro-nutrient element iron (Fe is present as a cofactor in the active sites of many metalloproteins with important roles in the plant. On the other hand, since it is excessively reactive, excess accumulation in the cell triggers the production of reactive oxygen species, leading to cell death. Therefore, iron homeostasis in the cell is very important for plant growth. Once uptake into the roots, iron is distributed to the subcellular compartments. Subcellular iron transport and hence cellular iron homeostasis is carried out through synchronous control of different membrane protein families. It has been discovered that expression levels of these membrane proteins increase under iron deficiency. Examination of the tasks and regulations of these carriers is very important in terms of understanding the iron intake and distribution mechanisms in plants. Therefore, in this review, the transporters responsible for the uptake of iron into the cell and its subcellular distribution between organelles will be discussed with an emphasis on the current developments about these transporters.

Fluid dynamics theory, computation, and numerical simulation

CERN Document Server

Pozrikidis, C

2001-01-01

Fluid Dynamics Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes Two distinguishing features of the discourse are solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty Matlab codes are presented and discussed for a broad...

Subcellular controls of mercury trophic transfer to a marine fish

Energy Technology Data Exchange (ETDEWEB)

Dang Fei [Department of Biology, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong); Wang Wenxiong, E-mail: wwang@ust.hk [Department of Biology, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong)

2010-09-15

Different behaviors of inorganic mercury [Hg(II)] and methylmercury (MeHg) during trophic transfer along the marine food chain have been widely reported, but the mechanisms are not fully understood. The bioavailability of ingested mercury, quantified by assimilation efficiency (AE), was investigated in a marine fish, the grunt Terapon jarbua, based on mercury subcellular partitioning in prey and purified subcellular fractions of prey tissues. The subcellular distribution of Hg(II) differed substantially among prey types, with cellular debris being a major (49-57% in bivalves) or secondary (14-19% in other prey) binding pool. However, MeHg distribution varied little among prey types, with most MeHg (43-79%) in heat-stable protein (HSP) fraction. The greater AEs measured for MeHg (90-94%) than for Hg(II) (23-43%) confirmed the findings of previous studies. Bioavailability of each purified subcellular fraction rather than the proposed trophically available metal (TAM) fraction could better elucidate mercury assimilation difference. Hg(II) associated with insoluble fraction (e.g. cellular debris) was less bioavailable than that in soluble fraction (e.g. HSP). However, subcellular distribution was shown to be less important for MeHg, with each fraction having comparable MeHg bioavailability. Subcellular distribution in prey should be an important consideration in mercury trophic transfer studies.

Subcellular controls of mercury trophic transfer to a marine fish

International Nuclear Information System (INIS)

Dang Fei; Wang Wenxiong

2010-01-01

Different behaviors of inorganic mercury [Hg(II)] and methylmercury (MeHg) during trophic transfer along the marine food chain have been widely reported, but the mechanisms are not fully understood. The bioavailability of ingested mercury, quantified by assimilation efficiency (AE), was investigated in a marine fish, the grunt Terapon jarbua, based on mercury subcellular partitioning in prey and purified subcellular fractions of prey tissues. The subcellular distribution of Hg(II) differed substantially among prey types, with cellular debris being a major (49-57% in bivalves) or secondary (14-19% in other prey) binding pool. However, MeHg distribution varied little among prey types, with most MeHg (43-79%) in heat-stable protein (HSP) fraction. The greater AEs measured for MeHg (90-94%) than for Hg(II) (23-43%) confirmed the findings of previous studies. Bioavailability of each purified subcellular fraction rather than the proposed trophically available metal (TAM) fraction could better elucidate mercury assimilation difference. Hg(II) associated with insoluble fraction (e.g. cellular debris) was less bioavailable than that in soluble fraction (e.g. HSP). However, subcellular distribution was shown to be less important for MeHg, with each fraction having comparable MeHg bioavailability. Subcellular distribution in prey should be an important consideration in mercury trophic transfer studies.

Gene ontology based transfer learning for protein subcellular localization

Directory of Open Access Journals (Sweden)

Zhou Shuigeng

2011-02-01

Full Text Available Abstract Background Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting multi-aspect protein feature information. Gene ontology, hereinafter referred to as GO, uses a controlled vocabulary to depict biological molecules or gene products in terms of biological process, molecular function and cellular component. With the rapid expansion of annotated protein sequences, gene ontology has become a general protein feature that can be used to construct predictive models in computational biology. Existing models generally either concatenated the GO terms into a flat binary vector or applied majority-vote based ensemble learning for protein subcellular localization, both of which can not estimate the individual discriminative abilities of the three aspects of gene ontology. Results In this paper, we propose a Gene Ontology Based Transfer Learning Model (GO-TLM for large-scale protein subcellular localization. The model transfers the signature-based homologous GO terms to the target proteins, and further constructs a reliable learning system to reduce the adverse affect of the potential false GO terms that are resulted from evolutionary divergence. We derive three GO kernels from the three aspects of gene ontology to measure the GO similarity of two proteins, and derive two other spectrum kernels to measure the similarity of two protein sequences. We use simple non-parametric cross validation to explicitly weigh the discriminative abilities of the five kernels, such that the time & space computational complexities are greatly reduced when compared to the complicated semi-definite programming and semi-indefinite linear programming. The five kernels are then linearly merged into one single kernel for

Dynamics and computation in functional shifts

Science.gov (United States)

Namikawa, Jun; Hashimoto, Takashi

2004-07-01

We introduce a new type of shift dynamics as an extended model of symbolic dynamics, and investigate the characteristics of shift spaces from the viewpoints of both dynamics and computation. This shift dynamics is called a functional shift, which is defined by a set of bi-infinite sequences of some functions on a set of symbols. To analyse the complexity of functional shifts, we measure them in terms of topological entropy, and locate their languages in the Chomsky hierarchy. Through this study, we argue that considering functional shifts from the viewpoints of both dynamics and computation gives us opposite results about the complexity of systems. We also describe a new class of shift spaces whose languages are not recursively enumerable.

The use of computers for instruction in fluid dynamics

Science.gov (United States)

Watson, Val

1987-01-01

Applications for computers which improve instruction in fluid dynamics are examined. Computers can be used to illustrate three-dimensional flow fields and simple fluid dynamics mechanisms, to solve fluid dynamics problems, and for electronic sketching. The usefulness of computer applications is limited by computer speed, memory, and software and the clarity and field of view of the projected display. Proposed advances in personal computers which will address these limitations are discussed. Long range applications for computers in education are considered.

Computational neuropharmacology: dynamical approaches in drug discovery.

Science.gov (United States)

Aradi, Ildiko; Erdi, Péter

2006-05-01

Computational approaches that adopt dynamical models are widely accepted in basic and clinical neuroscience research as indispensable tools with which to understand normal and pathological neuronal mechanisms. Although computer-aided techniques have been used in pharmaceutical research (e.g. in structure- and ligand-based drug design), the power of dynamical models has not yet been exploited in drug discovery. We suggest that dynamical system theory and computational neuroscience--integrated with well-established, conventional molecular and electrophysiological methods--offer a broad perspective in drug discovery and in the search for novel targets and strategies for the treatment of neurological and psychiatric diseases.

Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL).

Science.gov (United States)

Hooper, Cornelia M; Castleden, Ian R; Aryamanesh, Nader; Jacoby, Richard P; Millar, A Harvey

2016-01-01

Barley, wheat, rice and maize provide the bulk of human nutrition and have extensive industrial use as agricultural products. The genomes of these crops each contains >40,000 genes encoding proteins; however, the major genome databases for these species lack annotation information of protein subcellular location for >80% of these gene products. We address this gap, by constructing the compendium of crop protein subcellular locations called crop Proteins with Annotated Locations (cropPAL). Subcellular location is most commonly determined by fluorescent protein tagging of live cells or mass spectrometry detection in subcellular purifications, but can also be predicted from amino acid sequence or protein expression patterns. The cropPAL database collates 556 published studies, from >300 research institutes in >30 countries that have been previously published, as well as compiling eight pre-computed subcellular predictions for all Hordeum vulgare, Triticum aestivum, Oryza sativa and Zea mays protein sequences. The data collection including metadata for proteins and published studies can be accessed through a search portal http://crop-PAL.org. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Subcellular site and nature of intracellular cadmium in plants

International Nuclear Information System (INIS)

Wagner, G.J.

1979-01-01

The mechanisms underlying heavy metal accumulation, toxicity, and tolerance in higher plants are poorly understood. Since subcellular processes are undoubtedly involved in all these phenomena, it is of interest to study the extent, subcellular site and nature of intracellularly accumulated cadmium in higher plants. Whole plants supplied 109 CdCl 2 or 112 CdSO 4 accumulated Cd into roots and aerial tissues. Preparation of protoplasts from aerial tissues followed by subcellular fractionation of the protoplasts to obtain intact vacuoles, chloroplasts and cytosol revealed the presence of Cd in the cytosol but not in vacuoles or chloroplasts. No evidence was obtained for the production of volatile Cd complexes in tobacco

Multi-location gram-positive and gram-negative bacterial protein subcellular localization using gene ontology and multi-label classifier ensemble.

Science.gov (United States)

Wang, Xiao; Zhang, Jun; Li, Guo-Zheng

2015-01-01

It has become a very important and full of challenge task to predict bacterial protein subcellular locations using computational methods. Although there exist a lot of prediction methods for bacterial proteins, the majority of these methods can only deal with single-location proteins. But unfortunately many multi-location proteins are located in the bacterial cells. Moreover, multi-location proteins have special biological functions capable of helping the development of new drugs. So it is necessary to develop new computational methods for accurately predicting subcellular locations of multi-location bacterial proteins. In this article, two efficient multi-label predictors, Gpos-ECC-mPLoc and Gneg-ECC-mPLoc, are developed to predict the subcellular locations of multi-label gram-positive and gram-negative bacterial proteins respectively. The two multi-label predictors construct the GO vectors by using the GO terms of homologous proteins of query proteins and then adopt a powerful multi-label ensemble classifier to make the final multi-label prediction. The two multi-label predictors have the following advantages: (1) they improve the prediction performance of multi-label proteins by taking the correlations among different labels into account; (2) they ensemble multiple CC classifiers and further generate better prediction results by ensemble learning; and (3) they construct the GO vectors by using the frequency of occurrences of GO terms in the typical homologous set instead of using 0/1 values. Experimental results show that Gpos-ECC-mPLoc and Gneg-ECC-mPLoc can efficiently predict the subcellular locations of multi-label gram-positive and gram-negative bacterial proteins respectively. Gpos-ECC-mPLoc and Gneg-ECC-mPLoc can efficiently improve prediction accuracy of subcellular localization of multi-location gram-positive and gram-negative bacterial proteins respectively. The online web servers for Gpos-ECC-mPLoc and Gneg-ECC-mPLoc predictors are freely accessible

Fluid dynamics theory, computation, and numerical simulation

CERN Document Server

Pozrikidis, C

2017-01-01

This book provides an accessible introduction to the basic theory of fluid mechanics and computational fluid dynamics (CFD) from a modern perspective that unifies theory and numerical computation. Methods of scientific computing are introduced alongside with theoretical analysis and MATLAB® codes are presented and discussed for a broad range of topics: from interfacial shapes in hydrostatics, to vortex dynamics, to viscous flow, to turbulent flow, to panel methods for flow past airfoils. The third edition includes new topics, additional examples, solved and unsolved problems, and revised images. It adds more computational algorithms and MATLAB programs. It also incorporates discussion of the latest version of the fluid dynamics software library FDLIB, which is freely available online. FDLIB offers an extensive range of computer codes that demonstrate the implementation of elementary and advanced algorithms and provide an invaluable resource for research, teaching, classroom instruction, and self-study. This ...

Sub-cellular force microscopy in single normal and cancer cells.

Science.gov (United States)

Babahosseini, H; Carmichael, B; Strobl, J S; Mahmoodi, S N; Agah, M

2015-08-07

This work investigates the biomechanical properties of sub-cellular structures of breast cells using atomic force microscopy (AFM). The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity, and the relaxation time of sub-cellular structures. The triple-layered modeling results allow for determination and comparison of the biomechanical properties of the three major sub-cellular structures between normal and cancerous cells: the up plasma membrane/actin cortex, the mid cytoplasm/nucleus, and the low nuclear/integrin sub-domains. The results reveal that the sub-domains become stiffer and significantly more viscous with depth, regardless of cell type. In addition, there is a decreasing trend in the average elastic modulus and apparent viscosity of the all corresponding sub-cellular structures from normal to cancerous cells, which becomes most remarkable in the deeper sub-domain. The presented modeling in this work constitutes a unique AFM-based experimental framework to study the biomechanics of sub-cellular structures. Copyright © 2015 Elsevier Inc. All rights reserved.

HTTR plant dynamic simulation using a hybrid computer

International Nuclear Information System (INIS)

Shimazaki, Junya; Suzuki, Katsuo; Nabeshima, Kunihiko; Watanabe, Koichi; Shinohara, Yoshikuni; Nakagawa, Shigeaki.

1990-01-01

A plant dynamic simulation of High-Temperature Engineering Test Reactor has been made using a new-type hybrid computer. This report describes a dynamic simulation model of HTTR, a hybrid simulation method for SIMSTAR and some results obtained from dynamics analysis of HTTR simulation. It concludes that the hybrid plant simulation is useful for on-line simulation on account of its capability of computation at high speed, compared with that of all digital computer simulation. With sufficient accuracy, 40 times faster computation than real time was reached only by changing an analog time scale for HTTR simulation. (author)

Computable Types for Dynamic Systems

NARCIS (Netherlands)

P.J. Collins (Pieter); K. Ambos-Spies; B. Loewe; W. Merkle

2009-01-01

textabstractIn this paper, we develop a theory of computable types suitable for the study of dynamic systems in discrete and continuous time. The theory uses type-two effectivity as the underlying computational model, but we quickly develop a type system which can be manipulated abstractly, but for

ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes

Directory of Open Access Journals (Sweden)

King Brian R

2012-07-01

Full Text Available Abstract Background Understanding protein subcellular localization is a necessary component toward understanding the overall function of a protein. Numerous computational methods have been published over the past decade, with varying degrees of success. Despite the large number of published methods in this area, only a small fraction of them are available for researchers to use in their own studies. Of those that are available, many are limited by predicting only a small number of organelles in the cell. Additionally, the majority of methods predict only a single location for a sequence, even though it is known that a large fraction of the proteins in eukaryotic species shuttle between locations to carry out their function. Findings We present a software package and a web server for predicting the subcellular localization of protein sequences based on the ngLOC method. ngLOC is an n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The overall prediction accuracy varies from 89.8% to 91.4% across species. This program can predict 11 distinct locations each in plant and animal species. ngLOC also predicts 4 and 5 distinct locations on gram-positive and gram-negative bacterial datasets, respectively. Conclusions ngLOC is a generic method that can be trained by data from a variety of species or classes for predicting protein subcellular localization. The standalone software is freely available for academic use under GNU GPL, and the ngLOC web server is also accessible at http://ngloc.unmc.edu.

Protein subcellular localization assays using split fluorescent proteins

Science.gov (United States)

Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

2009-09-08

The invention provides protein subcellular localization assays using split fluorescent protein systems. The assays are conducted in living cells, do not require fixation and washing steps inherent in existing immunostaining and related techniques, and permit rapid, non-invasive, direct visualization of protein localization in living cells. The split fluorescent protein systems used in the practice of the invention generally comprise two or more self-complementing fragments of a fluorescent protein, such as GFP, wherein one or more of the fragments correspond to one or more beta-strand microdomains and are used to "tag" proteins of interest, and a complementary "assay" fragment of the fluorescent protein. Either or both of the fragments may be functionalized with a subcellular targeting sequence enabling it to be expressed in or directed to a particular subcellular compartment (i.e., the nucleus).

Subcellular localization of class I histone deacetylases in the developing Xenopus tectum

Directory of Open Access Journals (Sweden)

Xia eGuo

2016-01-01

Full Text Available Histone deacetylases (HDACs are thought to localize in the nucleus to regulate gene transcription and play pivotal roles in neurogenesis, apoptosis and plasticity. However, the subcellular distribution of class I HDACs in the developing brain remains unclear. Here, we show that HDAC1 and HDAC2 are located in both the mitochondria and the nucleus in the Xenopus laevis stage 34 tectum and are mainly restricted to the nucleus following further brain development. HDAC3 is widely present in the mitochondria, nucleus and cytoplasm during early tectal development and is mainly distributed in the nucleus in stage 45 tectum. In contrast, HDAC8 is broadly located in the mitochondria, nucleus and cytoplasm during tectal development. These data demonstrate that HDAC1, HDAC2 and HDAC3 are transiently localized in the mitochondria and that the subcellular distribution of class I HDACs in the Xenopus tectum is heterogeneous. Furthermore, we observed that spherical mitochondria accumulate in the cytoplasm at earlier stages, whereas elongated mitochondria are evenly distributed in the tectum at later stages. The activity of histone acetylation (H4K12 remains low in mitochondria during tectal development. Pharmacological blockades of HDACs using a broad spectrum HDAC inhibitor of Trichostatin A (TSA or specific class I HDAC inhibitors of MS-275 and MGCD0103 decrease the number of mitochondria in the tectum at stage 34. These findings highlight a link between the subcellular distribution of class I HDACs and mitochondrial dynamics in the developing optic tectum of Xenopus laevis.

Three-Dimensional Computational Fluid Dynamics

Energy Technology Data Exchange (ETDEWEB)

Haworth, D.C.; O' Rourke, P.J.; Ranganathan, R.

1998-09-01

Computational fluid dynamics (CFD) is one discipline falling under the broad heading of computer-aided engineering (CAE). CAE, together with computer-aided design (CAD) and computer-aided manufacturing (CAM), comprise a mathematical-based approach to engineering product and process design, analysis and fabrication. In this overview of CFD for the design engineer, our purposes are three-fold: (1) to define the scope of CFD and motivate its utility for engineering, (2) to provide a basic technical foundation for CFD, and (3) to convey how CFD is incorporated into engineering product and process design.

Challenges of biological sample preparation for SIMS imaging of elements and molecules at subcellular resolution

International Nuclear Information System (INIS)

Chandra, Subhash

2008-01-01

Secondary ion mass spectrometry (SIMS) based imaging techniques capable of subcellular resolution characterization of elements and molecules are becoming valuable tools in many areas of biology and medicine. Due to high vacuum requirements of SIMS, the live cells cannot be analyzed directly in the instrument. The sample preparation, therefore, plays a critical role in preserving the native chemical composition for SIMS analysis. This work focuses on the evaluation of frozen-hydrated and frozen freeze-dried sample preparations for SIMS studies of cultured cells with a CAMECA IMS-3f dynamic SIMS ion microscope instrument capable of producing SIMS images with a spatial resolution of 500 nm. The sandwich freeze-fracture method was used for fracturing the cells. The complimentary fracture planes in the plasma membrane were characterized by field-emission secondary electron microscopy (FESEM) in the frozen-hydrated state. The cells fractured at the dorsal surface were used for SIMS analysis. The frozen-hydrated SIMS analysis of individual cells under dynamic primary ion beam (O 2 + ) revealed local secondary ion signal enhancements correlated with the water image signals of 19 (H 3 O) + . A preferential removal of water from the frozen cell matrix in the Z-axis was also observed. These complications render the frozen-hydrated sample type less desirable for subcellular dynamic SIMS studies. The freeze-drying of frozen-hydrated cells, either inside the instrument or externally in a freeze-drier, allowed SIMS imaging of subcellular chemical composition. Morphological evaluations of fractured freeze-dried cells with SEM and confocal laser scanning microscopy (CLSM) revealed well-preserved mitochondria, Golgi apparatus, and stress fibers. SIMS analysis of fractured freeze-dried cells revealed well-preserved chemical composition of even the most highly diffusible ions like K + and Na + in physiologically relevant concentrations. The high K-low Na signature in individual cells

Challenges of biological sample preparation for SIMS imaging of elements and molecules at subcellular resolution

Science.gov (United States)

Chandra, Subhash

2008-12-01

Secondary ion mass spectrometry (SIMS) based imaging techniques capable of subcellular resolution characterization of elements and molecules are becoming valuable tools in many areas of biology and medicine. Due to high vacuum requirements of SIMS, the live cells cannot be analyzed directly in the instrument. The sample preparation, therefore, plays a critical role in preserving the native chemical composition for SIMS analysis. This work focuses on the evaluation of frozen-hydrated and frozen freeze-dried sample preparations for SIMS studies of cultured cells with a CAMECA IMS-3f dynamic SIMS ion microscope instrument capable of producing SIMS images with a spatial resolution of 500 nm. The sandwich freeze-fracture method was used for fracturing the cells. The complimentary fracture planes in the plasma membrane were characterized by field-emission secondary electron microscopy (FESEM) in the frozen-hydrated state. The cells fractured at the dorsal surface were used for SIMS analysis. The frozen-hydrated SIMS analysis of individual cells under dynamic primary ion beam (O 2+) revealed local secondary ion signal enhancements correlated with the water image signals of 19(H 3O) +. A preferential removal of water from the frozen cell matrix in the Z-axis was also observed. These complications render the frozen-hydrated sample type less desirable for subcellular dynamic SIMS studies. The freeze-drying of frozen-hydrated cells, either inside the instrument or externally in a freeze-drier, allowed SIMS imaging of subcellular chemical composition. Morphological evaluations of fractured freeze-dried cells with SEM and confocal laser scanning microscopy (CLSM) revealed well-preserved mitochondria, Golgi apparatus, and stress fibers. SIMS analysis of fractured freeze-dried cells revealed well-preserved chemical composition of even the most highly diffusible ions like K + and Na + in physiologically relevant concentrations. The high K-low Na signature in individual cells

An introduction to Computational Fluid Dynamics

DEFF Research Database (Denmark)

Sørensen, Lars Schiøtt

1999-01-01

CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building.......CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building....

Sub-cellular localisation of a 15N-labelled peptide vector using NanoSIMS imaging

Science.gov (United States)

Römer, Winfried; Wu, Ting-Di; Duchambon, Patricia; Amessou, Mohamed; Carrez, Danièle; Johannes, Ludger; Guerquin-Kern, Jean-Luc

2006-07-01

Dynamic SIMS imaging is proposed to map sub-cellular distributions of isotopically labelled, exogenous compounds. NanoSIMS imaging allows the characterisation of the intracellular transport pathways of exogenous molecules, including peptide vectors employed in innovative therapies, using stable isotopes as molecular markers to detect the compound of interest. Shiga toxin B-subunit (STxB) was chosen as a representative peptide vector. The recombinant protein ( 15N-STxB) was synthesised in Escherichia coli using 15NH 4Cl as sole nitrogen source resulting in 15N enrichment in the molecule. Using the NanoSIMS 50 ion microprobe (Cameca), different ion species ( 12C 14N -, 12C 15N -, 31P -) originating from the same sputtered micro volume were simultaneously detected. High mass resolving power enabled the discrimination of 12C 15N - from its polyatomic isobars of mass 27. We imaged the membrane binding and internalisation of 15N-STxB in HeLa cells at spatial resolutions of less than 100 nm. Thus, the use of rare stable isotopes like 15N with dynamic SIMS imaging permits sub-cellular detection of isotopically labelled, exogenous molecules and imaging of their transport pathways at high mass and spatial resolution. Application of stable isotopes as markers can replace the large and chemically complex tags used for fluorescence microscopy, without altering the chemical and physical properties of the molecule.

Predicting the subcellular localization of viral proteins within a mammalian host cell

Directory of Open Access Journals (Sweden)

Thomas DY

2006-04-01

Full Text Available Abstract Background The bioinformatic prediction of protein subcellular localization has been extensively studied for prokaryotic and eukaryotic organisms. However, this is not the case for viruses whose proteins are often involved in extensive interactions at various subcellular localizations with host proteins. Results Here, we investigate the extent of utilization of human cellular localization mechanisms by viral proteins and we demonstrate that appropriate eukaryotic subcellular localization predictors can be used to predict viral protein localization within the host cell. Conclusion Such predictions provide a method to rapidly annotate viral proteomes with subcellular localization information. They are likely to have widespread applications both in the study of the functions of viral proteins in the host cell and in the design of antiviral drugs.

Prediction of essential proteins based on subcellular localization and gene expression correlation.

Science.gov (United States)

Fan, Yetian; Tang, Xiwei; Hu, Xiaohua; Wu, Wei; Ping, Qing

2017-12-01

Essential proteins are indispensable to the survival and development process of living organisms. To understand the functional mechanisms of essential proteins, which can be applied to the analysis of disease and design of drugs, it is important to identify essential proteins from a set of proteins first. As traditional experimental methods designed to test out essential proteins are usually expensive and laborious, computational methods, which utilize biological and topological features of proteins, have attracted more attention in recent years. Protein-protein interaction networks, together with other biological data, have been explored to improve the performance of essential protein prediction. The proposed method SCP is evaluated on Saccharomyces cerevisiae datasets and compared with five other methods. The results show that our method SCP outperforms the other five methods in terms of accuracy of essential protein prediction. In this paper, we propose a novel algorithm named SCP, which combines the ranking by a modified PageRank algorithm based on subcellular compartments information, with the ranking by Pearson correlation coefficient (PCC) calculated from gene expression data. Experiments show that subcellular localization information is promising in boosting essential protein prediction.

Computational Fluid Dynamics and Room Air Movement

DEFF Research Database (Denmark)

Nielsen, Peter Vilhelm

2004-01-01

on the mass fraction transport equation. The importance of ?false? or numerical diffusion is also addressed in connection with the simple description of a supply opening. The different aspects of boundary conditions in the indoor environment as e.g. the simulation of Air Terminal Devices and the simulation......Nielsen, P.V. Computational Fluid Dynamics and Room Air Movement. Indoor Air, International Journal of Indoor Environment and Health, Vol. 14, Supplement 7, pp. 134-143, 2004. ABSTRACT Computational Fluid Dynamics (CFD) and new developments of CFD in the indoor environment as well as quality...... considerations are important elements in the study of energy consumption, thermal comfort and indoor air quality in buildings. The paper discusses the quality level of Computational Fluid Dynamics and the involved schemes (first, second and third order schemes) by the use of the Smith and Hutton problem...

Computer processing of dynamic scintigraphic studies

International Nuclear Information System (INIS)

Ullmann, V.

1985-01-01

The methods are discussed of the computer processing of dynamic scintigraphic studies which were developed, studied or implemented by the authors within research task no. 30-02-03 in nuclear medicine within the five year plan 1981 to 85. This was mainly the method of computer processing radionuclide angiography, phase radioventriculography, regional lung ventilation, dynamic sequential scintigraphy of kidneys and radionuclide uroflowmetry. The problems are discussed of the automatic definition of fields of interest, the methodology of absolute volumes of the heart chamber in radionuclide cardiology, the design and uses are described of the multipurpose dynamic phantom of heart activity for radionuclide angiocardiography and ventriculography developed within the said research task. All methods are documented with many figures showing typical clinical (normal and pathological) and phantom measurements. (V.U.)

Sub-cellular force microscopy in single normal and cancer cells

Energy Technology Data Exchange (ETDEWEB)

Babahosseini, H. [VT MEMS Laboratory, The Bradley Department of Electrical and Computer Engineering, Blacksburg, VA 24061 (United States); Carmichael, B. [Nonlinear Intelligent Structures Laboratory, Department of Mechanical Engineering, University of Alabama, Tuscaloosa, AL 35487-0276 (United States); Strobl, J.S. [VT MEMS Laboratory, The Bradley Department of Electrical and Computer Engineering, Blacksburg, VA 24061 (United States); Mahmoodi, S.N., E-mail: nmahmoodi@eng.ua.edu [Nonlinear Intelligent Structures Laboratory, Department of Mechanical Engineering, University of Alabama, Tuscaloosa, AL 35487-0276 (United States); Agah, M., E-mail: agah@vt.edu [VT MEMS Laboratory, The Bradley Department of Electrical and Computer Engineering, Blacksburg, VA 24061 (United States)

2015-08-07

This work investigates the biomechanical properties of sub-cellular structures of breast cells using atomic force microscopy (AFM). The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity, and the relaxation time of sub-cellular structures. The triple-layered modeling results allow for determination and comparison of the biomechanical properties of the three major sub-cellular structures between normal and cancerous cells: the up plasma membrane/actin cortex, the mid cytoplasm/nucleus, and the low nuclear/integrin sub-domains. The results reveal that the sub-domains become stiffer and significantly more viscous with depth, regardless of cell type. In addition, there is a decreasing trend in the average elastic modulus and apparent viscosity of the all corresponding sub-cellular structures from normal to cancerous cells, which becomes most remarkable in the deeper sub-domain. The presented modeling in this work constitutes a unique AFM-based experimental framework to study the biomechanics of sub-cellular structures. - Highlights: • The cells are modeled as a triple-layered structure using Generalized Maxwell model. • The sub-domains include membrane/cortex, cytoplasm/nucleus, and nuclear/integrin. • Biomechanics of corresponding sub-domains are compared among normal and cancer cells. • Viscoelasticity of sub-domains show a decreasing trend from normal to cancer cells. • The decreasing trend becomes most significant in the deeper sub-domain.

Sub-cellular force microscopy in single normal and cancer cells

International Nuclear Information System (INIS)

Babahosseini, H.; Carmichael, B.; Strobl, J.S.; Mahmoodi, S.N.; Agah, M.

2015-01-01

This work investigates the biomechanical properties of sub-cellular structures of breast cells using atomic force microscopy (AFM). The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity, and the relaxation time of sub-cellular structures. The triple-layered modeling results allow for determination and comparison of the biomechanical properties of the three major sub-cellular structures between normal and cancerous cells: the up plasma membrane/actin cortex, the mid cytoplasm/nucleus, and the low nuclear/integrin sub-domains. The results reveal that the sub-domains become stiffer and significantly more viscous with depth, regardless of cell type. In addition, there is a decreasing trend in the average elastic modulus and apparent viscosity of the all corresponding sub-cellular structures from normal to cancerous cells, which becomes most remarkable in the deeper sub-domain. The presented modeling in this work constitutes a unique AFM-based experimental framework to study the biomechanics of sub-cellular structures. - Highlights: • The cells are modeled as a triple-layered structure using Generalized Maxwell model. • The sub-domains include membrane/cortex, cytoplasm/nucleus, and nuclear/integrin. • Biomechanics of corresponding sub-domains are compared among normal and cancer cells. • Viscoelasticity of sub-domains show a decreasing trend from normal to cancer cells. • The decreasing trend becomes most significant in the deeper sub-domain

Computer Modelling of Dynamic Processes

Directory of Open Access Journals (Sweden)

B. Rybakin

2000-10-01

Full Text Available Results of numerical modeling of dynamic problems are summed in the article up. These problems are characteristic for various areas of human activity, in particular for problem solving in ecology. The following problems are considered in the present work: computer modeling of dynamic effects on elastic-plastic bodies, calculation and determination of performances of gas streams in gas cleaning equipment, modeling of biogas formation processes.

Computational plasticity algorithm for particle dynamics simulations

Science.gov (United States)

Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.

2018-01-01

The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.

Subcellular analysis by laser ablation electrospray ionization mass spectrometry

Science.gov (United States)

Vertes, Akos; Stolee, Jessica A; Shrestha, Bindesh

2014-12-02

In various embodiments, a method of laser ablation electrospray ionization mass spectrometry (LAESI-MS) may generally comprise micro-dissecting a cell comprising at least one of a cell wall and a cell membrane to expose at least one subcellular component therein, ablating the at least one subcellular component by an infrared laser pulse to form an ablation plume, intercepting the ablation plume by an electrospray plume to form ions, and detecting the ions by mass spectrometry.

Programming Unconventional Computers: Dynamics, Development, Self-Reference

Directory of Open Access Journals (Sweden)

Susan Stepney

2012-10-01

Full Text Available Classical computing has well-established formalisms for specifying, refining, composing, proving, and otherwise reasoning about computations. These formalisms have matured over the past 70 years or so. Unconventional Computing includes the use of novel kinds of substrates–from black holes and quantum effects, through to chemicals, biomolecules, even slime moulds–to perform computations that do not conform to the classical model. Although many of these unconventional substrates can be coerced into performing classical computation, this is not how they “naturally” compute. Our ability to exploit unconventional computing is partly hampered by a lack of corresponding programming formalisms: we need models for building, composing, and reasoning about programs that execute in these substrates. What might, say, a slime mould programming language look like? Here I outline some of the issues and properties of these unconventional substrates that need to be addressed to find “natural” approaches to programming them. Important concepts include embodied real values, processes and dynamical systems, generative systems and their meta-dynamics, and embodied self-reference.

Dynamic Subcellular Localization of Iron during Embryo Development in Brassicaceae Seeds

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Miguel A. Ibeas

2017-12-01

Full Text Available Iron is an essential micronutrient for plants. Little is know about how iron is loaded in embryo during seed development. In this article we used Perls/DAB staining in order to reveal iron localization at the cellular and subcellular levels in different Brassicaceae seed species. In dry seeds of Brassica napus, Nasturtium officinale, Lepidium sativum, Camelina sativa, and Brassica oleracea iron localizes in vacuoles of cells surrounding provasculature in cotyledons and hypocotyl. Using B. napus and N. officinale as model plants we determined where iron localizes during seed development. Our results indicate that iron is not detectable by Perls/DAB staining in heart stage embryo cells. Interestingly, at torpedo development stage iron localizes in nuclei of different cells type, including integument, free cell endosperm and almost all embryo cells. Later, iron is detected in cytoplasmic structures in different embryo cell types. Our results indicate that iron accumulates in nuclei in specific stages of embryo maturation before to be localized in vacuoles of cells surrounding provasculature in mature seeds.

Subcellular distribution of glutathione and cysteine in cyanobacteria.

Science.gov (United States)

Zechmann, Bernd; Tomasić, Ana; Horvat, Lucija; Fulgosi, Hrvoje

2010-10-01

Glutathione plays numerous important functions in eukaryotic and prokaryotic cells. Whereas it can be found in virtually all eukaryotic cells, its production in prokaryotes is restricted to cyanobacteria and proteobacteria and a few strains of gram-positive bacteria. In bacteria, it is involved in the protection against reactive oxygen species (ROS), osmotic shock, acidic conditions, toxic chemicals, and heavy metals. Glutathione synthesis in bacteria takes place in two steps out of cysteine, glutamate, and glycine. Cysteine is the limiting factor for glutathione biosynthesis which can be especially crucial for cyanobacteria, which rely on both the sufficient sulfur supply from the growth media and on the protection of glutathione against ROS that are produced during photosynthesis. In this study, we report a method that allows detection and visualization of the subcellular distribution of glutathione in Synechocystis sp. This method is based on immunogold cytochemistry with glutathione and cysteine antisera and computer-supported transmission electron microscopy. Labeling of glutathione and cysteine was restricted to the cytosol and interthylakoidal spaces. Glutathione and cysteine could not be detected in carboxysomes, cyanophycin granules, cell walls, intrathylakoidal spaces, periplasm, and vacuoles. The accuracy of the glutathione and cysteine labeling is supported by two observations. First, preadsorption of the antiglutathione and anticysteine antisera with glutathione and cysteine, respectively, reduced the density of the gold particles to background levels. Second, labeling of glutathione and cysteine was strongly decreased by 98.5% and 100%, respectively, in Synechocystis sp. cells grown on media without sulfur. This study indicates a strong similarity of the subcellular distribution of glutathione and cysteine in cyanobacteria and plastids of plants and provides a deeper insight into glutathione metabolism in bacteria.

The Dynamic Geometrisation of Computer Programming

Science.gov (United States)

Sinclair, Nathalie; Patterson, Margaret

2018-01-01

The goal of this paper is to explore dynamic geometry environments (DGE) as a type of computer programming language. Using projects created by secondary students in one particular DGE, we analyse the extent to which the various aspects of computational thinking--including both ways of doing things and particular concepts--were evident in their…

Subcellular site and nature of intracellular cadmium in plants

International Nuclear Information System (INIS)

Wagner, G.J.

1979-01-01

The mechanisms underlying heavy metal accumulation, toxicity and tolerance in higher plants are poorly understood. Since subcellular processes are undoubtedly involved in all these phenomena, it is of interest to study the extent of, subcellular site of and nature of intracellularly accumulated cadmium in higher plants. Whole plants supplied 109 CdCl 2 or 112 CdSO 4 accumulated Cd into roots and aerial tissues. Preparation of protoplasts from aerial tissue followed by subcellular fractionation of the protoplasts to obtain intact vacuoles, chloroplasts and cytosol revealed the presence of Cd in the cytosol but not in vacuoles or chloroplasts. Particulate materials containing other cell components were also labeled. Of the 109 Cd supplied to plants, 2 to 10% was recovered in both cytosol preparations and in particulate materials. Cytosol contained proteinaceous--Cd complexes, free metal and low molecular weight Cd complexes. Labeling of protoplasts gave similar results. No evidence was obtained for the production of volatile Cd complexes in tobacco

Fluid dynamics applications of the Illiac IV computer

Science.gov (United States)

Maccormack, R. W.; Stevens, K. G., Jr.

1976-01-01

The Illiac IV is a parallel-structure computer with computing power an order of magnitude greater than that of conventional computers. It can be used for experimental tasks in fluid dynamics which can be simulated more economically, for simulating flows that cannot be studied by experiment, and for combining computer and experimental simulations. The architecture of Illiac IV is described, and the use of its parallel operation is demonstrated on the example of its solution of the one-dimensional wave equation. For fluid dynamics problems, a special FORTRAN-like vector programming language was devised, called CFD language. Two applications are described in detail: (1) the determination of the flowfield around the space shuttle, and (2) the computation of transonic turbulent separated flow past a thick biconvex airfoil.

Protein Subcellular Localization with Gaussian Kernel Discriminant Analysis and Its Kernel Parameter Selection.

Science.gov (United States)

Wang, Shunfang; Nie, Bing; Yue, Kun; Fei, Yu; Li, Wenjia; Xu, Dongshu

2017-12-15

Kernel discriminant analysis (KDA) is a dimension reduction and classification algorithm based on nonlinear kernel trick, which can be novelly used to treat high-dimensional and complex biological data before undergoing classification processes such as protein subcellular localization. Kernel parameters make a great impact on the performance of the KDA model. Specifically, for KDA with the popular Gaussian kernel, to select the scale parameter is still a challenging problem. Thus, this paper introduces the KDA method and proposes a new method for Gaussian kernel parameter selection depending on the fact that the differences between reconstruction errors of edge normal samples and those of interior normal samples should be maximized for certain suitable kernel parameters. Experiments with various standard data sets of protein subcellular localization show that the overall accuracy of protein classification prediction with KDA is much higher than that without KDA. Meanwhile, the kernel parameter of KDA has a great impact on the efficiency, and the proposed method can produce an optimum parameter, which makes the new algorithm not only perform as effectively as the traditional ones, but also reduce the computational time and thus improve efficiency.

Computer-graphic visualization of dynamics

International Nuclear Information System (INIS)

Stewart, H.B.

1986-01-01

As engineered systems become increasingly sophisticated and complex, questions of efficiency, reliability, and safety demand the application of more powerful methods of analysis. One indication of this is the accelerating trend away from purely static or quasi-steady system modeling toward models that include essentially dynamic behavior. It is here that the qualitative ideas of nonlinear dynamics, dealing as they do with the most typical behavior in real dynamical systems, can be expected to play an increasingly prominent role. As part of a continuing investigation of the most important low-order differential equations, an interactive computer graphics environment has been created for the study of systems in three-dimensional phase space. This environment makes available the basic control of both numerical simulation and graphic visualization by a specially designed menu system. A key ingredient in this environment is the possibility of graphic communication not only from machine to man, but also from man to machine. Thus to specify the starting point for a numerical integration, for example, the user points to a location in phase space on the screen of the graphics terminal (using crosshairs or a mouse and cursor), bypassing the necessity to give numerical values of the phase-space coordinates. By devising a flexible computer interface which implements conceptual approaches to phase-space analysis of dynamical systems, significant advances in understanding of prototypical differential equations have been achieved

Neptunium 237 behaviour in subcellular fractions of rat kidneys

International Nuclear Information System (INIS)

Kreslov, V.V.; Maksutova, A.Ya.; Mushkacheva, G.S.

1978-01-01

Subcellular distribution of intravenously injected (1 and 0.5 μCi/rat) neptunium nitrate (5- and 6-valent) in kidneys of rat males and females has been investigated. It has been shown that the radionuclide was unevenly distributed within the cell. As early as 24 hours after administration, about 50 per cent of neptunium were concentrated in the mitochondrial fraction. The data are presented on variations in neptunium behaviour within subcellular fractions of rat kidneys depending on the sex of animals, valency and dose of the isotope

Multi-Label Learning via Random Label Selection for Protein Subcellular Multi-Locations Prediction.

Science.gov (United States)

Wang, Xiao; Li, Guo-Zheng

2013-03-12

Prediction of protein subcellular localization is an important but challenging problem, particularly when proteins may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular localization methods are only used to deal with the single-location proteins. In the past few years, only a few methods have been proposed to tackle proteins with multiple locations. However, they only adopt a simple strategy, that is, transforming the multi-location proteins to multiple proteins with single location, which doesn't take correlations among different subcellular locations into account. In this paper, a novel method named RALS (multi-label learning via RAndom Label Selection), is proposed to learn from multi-location proteins in an effective and efficient way. Through five-fold cross validation test on a benchmark dataset, we demonstrate our proposed method with consideration of label correlations obviously outperforms the baseline BR method without consideration of label correlations, indicating correlations among different subcellular locations really exist and contribute to improvement of prediction performance. Experimental results on two benchmark datasets also show that our proposed methods achieve significantly higher performance than some other state-of-the-art methods in predicting subcellular multi-locations of proteins. The prediction web server is available at http://levis.tongji.edu.cn:8080/bioinfo/MLPred-Euk/ for the public usage.

Development of real-time visualization system for Computational Fluid Dynamics on parallel computers

International Nuclear Information System (INIS)

Muramatsu, Kazuhiro; Otani, Takayuki; Matsumoto, Hideki; Takei, Toshifumi; Doi, Shun

1998-03-01

A real-time visualization system for computational fluid dynamics in a network connecting between a parallel computing server and the client terminal was developed. Using the system, a user can visualize the results of a CFD (Computational Fluid Dynamics) simulation on the parallel computer as a client terminal during the actual computation on a server. Using GUI (Graphical User Interface) on the client terminal, to user is also able to change parameters of the analysis and visualization during the real-time of the calculation. The system carries out both of CFD simulation and generation of a pixel image data on the parallel computer, and compresses the data. Therefore, the amount of data from the parallel computer to the client is so small in comparison with no compression that the user can enjoy the swift image appearance comfortably. Parallelization of image data generation is based on Owner Computation Rule. GUI on the client is built on Java applet. A real-time visualization is thus possible on the client PC only if Web browser is implemented on it. (author)

Computer Programme for the Dynamic Analysis of Tall Regular ...

African Journals Online (AJOL)

The traditional method of dynamic analysis of tall rigid frames assumes the shear frame model. Models that allow joint rotations with/without the inclusion of the column axial loads give improved results but pose much more computational difficulty. In this work a computer program Natfrequency that determines the dynamic ...

Subcellular sites for bacterial protein export

NARCIS (Netherlands)

Campo, Nathalie; Tjalsma, Harold; Buist, Girbe; Stepniak, Dariusz; Meijer, Michel; Veenhuis, Marten; Westermann, Martin; Müller, Jörg P.; Bron, Sierd; Kok, Jan; Kuipers, Oscar P.; Jongbloed, Jan D.H.

2004-01-01

Most bacterial proteins destined to leave the cytoplasm are exported to extracellular compartments or imported into the cytoplasmic membrane via the highly conserved SecA-YEG pathway. In the present studies, the subcellular distributions of core components of this pathway, SecA and SecY, and of the

Subcellular sites for bacterial protein export.

NARCIS (Netherlands)

Campo, N.; Tjalsma, H.; Buist, G.; Stepniak, D.; Meijer, M.; Veenhuis, M.; Westermann, M.; Muller, J.P.; Bron, S.; Kok, J.; Kuipers, O.P.; Jongbloed, J.D.

2004-01-01

Most bacterial proteins destined to leave the cytoplasm are exported to extracellular compartments or imported into the cytoplasmic membrane via the highly conserved SecA-YEG pathway. In the present studies, the subcellular distributions of core components of this pathway, SecA and SecY, and of the

Interface between computational fluid dynamics (CFD) and plant analysis computer codes

International Nuclear Information System (INIS)

Coffield, R.D.; Dunckhorst, F.F.; Tomlinson, E.T.; Welch, J.W.

1993-01-01

Computational fluid dynamics (CFD) can provide valuable input to the development of advanced plant analysis computer codes. The types of interfacing discussed in this paper will directly contribute to modeling and accuracy improvements throughout the plant system and should result in significant reduction of design conservatisms that have been applied to such analyses in the past

Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.

Science.gov (United States)

Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

2013-12-01

Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au). © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Computational fluid dynamics a practical approach

CERN Document Server

Tu, Jiyuan; Liu, Chaoqun

2018-01-01

Computational Fluid Dynamics: A Practical Approach, Third Edition, is an introduction to CFD fundamentals and commercial CFD software to solve engineering problems. The book is designed for a wide variety of engineering students new to CFD, and for practicing engineers learning CFD for the first time. Combining an appropriate level of mathematical background, worked examples, computer screen shots, and step-by-step processes, this book walks the reader through modeling and computing, as well as interpreting CFD results. This new edition has been updated throughout, with new content and improved figures, examples and problems.

Monoterpene biosynthesis potential of plant subcellular compartments

NARCIS (Netherlands)

Dong, L.; Jongedijk, E.J.; Bouwmeester, H.J.; Krol, van der A.R.

2016-01-01

Subcellular monoterpene biosynthesis capacity based on local geranyl diphosphate (GDP) availability or locally boosted GDP production was determined for plastids, cytosol and mitochondria. A geraniol synthase (GES) was targeted to plastids, cytosol, or mitochondria. Transient expression in Nicotiana

Biomechanics of subcellular structures by non-invasive Brillouin microscopy

Science.gov (United States)

Antonacci, Giuseppe; Braakman, Sietse

2016-11-01

Cellular biomechanics play a pivotal role in the pathophysiology of several diseases. Unfortunately, current methods to measure biomechanical properties are invasive and mostly limited to the surface of a cell. As a result, the mechanical behaviour of subcellular structures and organelles remains poorly characterised. Here, we show three-dimensional biomechanical images of single cells obtained with non-invasive, non-destructive Brillouin microscopy with an unprecedented spatial resolution. Our results quantify the longitudinal elastic modulus of subcellular structures. In particular, we found the nucleoli to be stiffer than both the nuclear envelope (p biomechanics and its role in pathophysiology.

Neural Computations in a Dynamical System with Multiple Time Scales.

Science.gov (United States)

Mi, Yuanyuan; Lin, Xiaohan; Wu, Si

2016-01-01

Neural systems display rich short-term dynamics at various levels, e.g., spike-frequency adaptation (SFA) at the single-neuron level, and short-term facilitation (STF) and depression (STD) at the synapse level. These dynamical features typically cover a broad range of time scales and exhibit large diversity in different brain regions. It remains unclear what is the computational benefit for the brain to have such variability in short-term dynamics. In this study, we propose that the brain can exploit such dynamical features to implement multiple seemingly contradictory computations in a single neural circuit. To demonstrate this idea, we use continuous attractor neural network (CANN) as a working model and include STF, SFA and STD with increasing time constants in its dynamics. Three computational tasks are considered, which are persistent activity, adaptation, and anticipative tracking. These tasks require conflicting neural mechanisms, and hence cannot be implemented by a single dynamical feature or any combination with similar time constants. However, with properly coordinated STF, SFA and STD, we show that the network is able to implement the three computational tasks concurrently. We hope this study will shed light on the understanding of how the brain orchestrates its rich dynamics at various levels to realize diverse cognitive functions.

Modeling Computer Virus and Its Dynamics

Directory of Open Access Journals (Sweden)

Mei Peng

2013-01-01

Full Text Available Based on that the computer will be infected by infected computer and exposed computer, and some of the computers which are in suscepitible status and exposed status can get immunity by antivirus ability, a novel coumputer virus model is established. The dynamic behaviors of this model are investigated. First, the basic reproduction number R0, which is a threshold of the computer virus spreading in internet, is determined. Second, this model has a virus-free equilibrium P0, which means that the infected part of the computer disappears, and the virus dies out, and P0 is a globally asymptotically stable equilibrium if R01 then this model has only one viral equilibrium P*, which means that the computer persists at a constant endemic level, and P* is also globally asymptotically stable. Finally, some numerical examples are given to demonstrate the analytical results.

STUDY OF SUBCELLULAR DISTRIBUTION OF CRYSTALLINE MESO-TETRA(3-PYRIDYLBACTERIOCHLORIN NANOPARTICLES

Directory of Open Access Journals (Sweden)

Yu. S. Maklygina

2016-01-01

Full Text Available The results of the study of subcellular distribution of molecular meso-tetra(3-pyridylbacteriochlorin nanocrystals proposed as therapeutic agents for photodynamic therapy are represented in the article. Investigations and measurement of spectroscopic properties of molecular crystals of near-infrared photosensitizer were conducted using special device complex based on fiber-optic spectrometer. Investigation and analysis of the pattern of subcellular accumulation of meso-tetra(3-pyridylbacteriochlorin in molecular (dimethyl sulfoxide (DMSO as solvent and nanocrystalline forms on different cell lines: human monocytes (THP-1, human cervical cancer cells (HeLa and mouse malignant brain tumor cells (glioma C6. The dynamics of subcellylar accumulation of the agent at concentration of 5 and 10 mg/l was assessed with laser microscope-spectrum analyzer and by confocal microscopy. The study showed that in the course of interaction with cell lines molecular nanocrystals of the agent developed ability to fluorescence. Hence, in the cellular environment meso-tetra(3-pyridyl bacteriochlorin nanoparticles became phototoxic giving opportunities for their use for fluorescence diagnosis and photodynamic therapy. Specific role of meso-tetra(3-pyridylbacteriochlorin in the range of photosensitizers is determined by its spectral characteristics, i.e. absorption and fluorescence in near-infrared band, which allows measuring and affecting on deeper layers of biotissue. Thus, the use of meso-tetra(3-pyridylbacteriochlorin nanoparticles as nanophotosensitizers may improve the efficacy of diagnosis and treatment of deep-seated tumors.

ClubSub-P: Cluster-based subcellular localization prediction for Gram-negative bacteria and Archaea.

Directory of Open Access Journals (Sweden)

Nagarajan eParamasivam

2011-11-01

Full Text Available The subcellular localization of proteins provides important clues to their function in a cell. In our efforts to predict useful vaccine targets against Gram-negative bacteria, we noticed that misannotated start codons frequently lead to wrongly assigned subcellular localizations. This and other problems in subcellular localization prediction, such as the relatively high false positive and false negative rates of some tools, can be avoided by applying multiple prediction tools to groups of homologous proteins. Here we present ClubSub-P, an online database that combines existing subcellular localization prediction tools into a consensus pipeline from more than 600 proteomes of fully sequenced microorganisms. On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false positive and false negative predictions. ClubSub-P can assign the subcellular localization of proteins from Gram-negative bacteria and Archaea with high precision. The database is searchable, and can easily be expanded using either new bacterial genomes or new prediction tools as they become available. This will further improve the performance of the subcellular localization prediction, as well as the detection of misannotated start codons and other annotation errors. ClubSub-P is available online at http://toolkit.tuebingen.mpg.de/clubsubp/

Dynamical Models for Computer Viruses Propagation

Directory of Open Access Journals (Sweden)

José R. C. Piqueira

2008-01-01

Full Text Available Nowadays, digital computer systems and networks are the main engineering tools, being used in planning, design, operation, and control of all sizes of building, transportation, machinery, business, and life maintaining devices. Consequently, computer viruses became one of the most important sources of uncertainty, contributing to decrease the reliability of vital activities. A lot of antivirus programs have been developed, but they are limited to detecting and removing infections, based on previous knowledge of the virus code. In spite of having good adaptation capability, these programs work just as vaccines against diseases and are not able to prevent new infections based on the network state. Here, a trial on modeling computer viruses propagation dynamics relates it to other notable events occurring in the network permitting to establish preventive policies in the network management. Data from three different viruses are collected in the Internet and two different identification techniques, autoregressive and Fourier analyses, are applied showing that it is possible to forecast the dynamics of a new virus propagation by using the data collected from other viruses that formerly infected the network.

Statistical properties of dynamical systems – Simulation and abstract computation

International Nuclear Information System (INIS)

Galatolo, Stefano; Hoyrup, Mathieu; Rojas, Cristóbal

2012-01-01

Highlights: ► A survey on results about computation and computability on the statistical properties of dynamical systems. ► Computability and non-computability results for invariant measures. ► A short proof for the computability of the convergence speed of ergodic averages. ► A kind of “constructive” version of the pointwise ergodic theorem. - Abstract: We survey an area of recent development, relating dynamics to theoretical computer science. We discuss some aspects of the theoretical simulation and computation of the long term behavior of dynamical systems. We will focus on the statistical limiting behavior and invariant measures. We present a general method allowing the algorithmic approximation at any given accuracy of invariant measures. The method can be applied in many interesting cases, as we shall explain. On the other hand, we exhibit some examples where the algorithmic approximation of invariant measures is not possible. We also explain how it is possible to compute the speed of convergence of ergodic averages (when the system is known exactly) and how this entails the computation of arbitrarily good approximations of points of the space having typical statistical behaviour (a sort of constructive version of the pointwise ergodic theorem).

SD-CAS: Spin Dynamics by Computer Algebra System.

Science.gov (United States)

Filip, Xenia; Filip, Claudiu

2010-11-01

A computer algebra tool for describing the Liouville-space quantum evolution of nuclear 1/2-spins is introduced and implemented within a computational framework named Spin Dynamics by Computer Algebra System (SD-CAS). A distinctive feature compared with numerical and previous computer algebra approaches to solving spin dynamics problems results from the fact that no matrix representation for spin operators is used in SD-CAS, which determines a full symbolic character to the performed computations. Spin correlations are stored in SD-CAS as four-entry nested lists of which size increases linearly with the number of spins into the system and are easily mapped into analytical expressions in terms of spin operator products. For the so defined SD-CAS spin correlations a set of specialized functions and procedures is introduced that are essential for implementing basic spin algebra operations, such as the spin operator products, commutators, and scalar products. They provide results in an abstract algebraic form: specific procedures to quantitatively evaluate such symbolic expressions with respect to the involved spin interaction parameters and experimental conditions are also discussed. Although the main focus in the present work is on laying the foundation for spin dynamics symbolic computation in NMR based on a non-matrix formalism, practical aspects are also considered throughout the theoretical development process. In particular, specific SD-CAS routines have been implemented using the YACAS computer algebra package (http://yacas.sourceforge.net), and their functionality was demonstrated on a few illustrative examples. Copyright © 2010 Elsevier Inc. All rights reserved.

Movies of cellular and sub-cellular motion by digital holographic microscopy

Directory of Open Access Journals (Sweden)

Yu Lingfeng

2006-03-01

Full Text Available Abstract Background Many biological specimens, such as living cells and their intracellular components, often exhibit very little amplitude contrast, making it difficult for conventional bright field microscopes to distinguish them from their surroundings. To overcome this problem phase contrast techniques such as Zernike, Normarsky and dark-field microscopies have been developed to improve specimen visibility without chemically or physically altering them by the process of staining. These techniques have proven to be invaluable tools for studying living cells and furthering scientific understanding of fundamental cellular processes such as mitosis. However a drawback of these techniques is that direct quantitative phase imaging is not possible. Quantitative phase imaging is important because it enables determination of either the refractive index or optical thickness variations from the measured optical path length with sub-wavelength accuracy. Digital holography is an emergent phase contrast technique that offers an excellent approach in obtaining both qualitative and quantitative phase information from the hologram. A CCD camera is used to record a hologram onto a computer and numerical methods are subsequently applied to reconstruct the hologram to enable direct access to both phase and amplitude information. Another attractive feature of digital holography is the ability to focus on multiple focal planes from a single hologram, emulating the focusing control of a conventional microscope. Methods A modified Mach-Zender off-axis setup in transmission is used to record and reconstruct a number of holographic amplitude and phase images of cellular and sub-cellular features. Results Both cellular and sub-cellular features are imaged with sub-micron, diffraction-limited resolution. Movies of holographic amplitude and phase images of living microbes and cells are created from a series of holograms and reconstructed with numerically adjustable

Subcellular Nanoparticle Distribution from Light Transmission Spectroscopy

Science.gov (United States)

Deatsch, Alison; Sun, Nan; Johnson, Jeffrey; Stack, Sharon; Tanner, Carol; Ruggiero, Steven

We have measured the particle-size distribution (PSD) of subcellular structures in plant and animal cells. We have employed a new technique developed by our group, Light Transmission Spectroscopy-combined with cell fractionation-to accurately measure PSDs over a wide size range: from 10 nm to 3000nm, which includes objects from the size of individual proteins to organelles. To date our experiments have included cultured human oral cells and spinach cells. These results show a power-law dependence of particle density with particle diameter, implying a universality of the packing distribution. We discuss modeling the cell as a self-similar (fractal) body comprised of spheres on all size scales. This goal of this work is to obtain a better understanding of the fundamental nature of particle packing within cells in order to enrich our knowledge of the structure, function, and interactions of sub-cellular nanostructures across cell types.

Dynamic X-ray computed tomography

International Nuclear Information System (INIS)

Grangeat, P.

2003-01-01

Paper Dynamic computed tomography (CT) imaging aims at reconstructing image sequences where the dynamic nature of the living human body is of primary interest. Main concerned applications are image-guided interventional procedures, functional studies and cardiac imaging. The introduction of ultra-fast rotating gantries along with multi-row detectors and in near future area detectors allows a huge progress toward the imaging of moving organs with low-contrast resolution. This paper gives an overview of the different concepts used in dynamic CT. A new reconstruction algorithm based on a voxel-specific dynamic evolution compensation is also presented. It provides four-dimensional image sequences with accurate spatio-temporal information, where each frame is reconstructed using a long-scan acquisition mode on several half-turns. In the same time, this technique permits to reduce the dose delivered per rotation while keeping the same signal to noise ratio for every frame using an adaptive motion-compensated temporal averaging. Results are illustrated on simulated data. (authors)

Computational Fluid Dynamics in Ventilation

DEFF Research Database (Denmark)

Nielsen, Peter V.; Allard, Francis; Awbi, Hazim B.

2008-01-01

Computational Fluid Dynamics in Ventilation Design is a new title in the is a new title in the REHVA guidebook series. The guidebook is written for people who need to use and discuss results based on CFD predictions, and it gives insight into the subject for those who are not used to work with CFD...

Studies on proinsulin and proglucagon biosynthesis and conversion at the subcellular level: I. Fractionation procedure and characterization of the subcellular fractions

Science.gov (United States)

Noe, BD; Baste, CA; Bauer, GE

1977-01-01

Anglerfish islets were homogenized in 0.25 M sucrose and separated into seven separate subcellular fractions by differential and discontinuous density gradient centrifugation. The objective was to isolate microsomes and secretory granules in a highly purified state. The fractions were characterized by electron microscopy and chemical analyses. Each fraction was assayed for its content of protein, RNA, DNA, immunoreactive insulin (IRI), and immunoreactive glucagon (IRG). Ultrastructural examination showed that two of the seven subcellular fractions contain primarily mitochondria, and that two others consist almost exclusively of secretory granules. A fifth fraction contains rough and smooth microsomal vesicles. The remaining two fractions are the cell supernate and the nuclei and cell debris. The content of DNA and RNA in all fractions is consistent with the observed ultrastructure. More than 82 percent of the total cellular IRI and 89(percent) of the total cellular IRG are found in the fractions of secretory granules. The combined fractions of secretory granules and microsomes consistently yield >93 percent of the total IRG. These results indicate that the fractionation procedure employed yields fractions of microsomes and secretory granules that contain nearly all the immunoassayable insulin and glucagons found in whole islet tissue. These fractions are thus considered suitable for study of proinsulin and proglucagon biosynthesis and their metabolic conversion at the subcellular level. PMID:328517

Subcellular localization of cadmium in hyperaccumulator Populus ...

African Journals Online (AJOL)

In this study, subcellular localization of cadmium in hyperaccumulator grey poplar (Populus × canescens) was investigated by the transmission electron microscopy (TEM) method. Young Populus × canescens were grown and hydroponic experiments were conducted under four Cd2+ concentrations (10, 30, 50, and 70 μM) ...

The Efficient Use of Vector Computers with Emphasis on Computational Fluid Dynamics : a GAMM-Workshop

CERN Document Server

Gentzsch, Wolfgang

1986-01-01

The GAMM Committee for Numerical Methods in Fluid Mechanics organizes workshops which should bring together experts of a narrow field of computational fluid dynamics (CFD) to exchange ideas and experiences in order to speed-up the development in this field. In this sense it was suggested that a workshop should treat the solution of CFD problems on vector computers. Thus we organized a workshop with the title "The efficient use of vector computers with emphasis on computational fluid dynamics". The workshop took place at the Computing Centre of the University of Karlsruhe, March 13-15,1985. The participation had been restricted to 22 people of 7 countries. 18 papers have been presented. In the announcement of the workshop we wrote: "Fluid mechanics has actively stimulated the development of superfast vector computers like the CRAY's or CYBER 205. Now these computers on their turn stimulate the development of new algorithms which result in a high degree of vectorization (sca1ar/vectorized execution-time). But w...

Computational fluid dynamic applications

Energy Technology Data Exchange (ETDEWEB)

Chang, S.-L.; Lottes, S. A.; Zhou, C. Q.

2000-04-03

The rapid advancement of computational capability including speed and memory size has prompted the wide use of computational fluid dynamics (CFD) codes to simulate complex flow systems. CFD simulations are used to study the operating problems encountered in system, to evaluate the impacts of operation/design parameters on the performance of a system, and to investigate novel design concepts. CFD codes are generally developed based on the conservation laws of mass, momentum, and energy that govern the characteristics of a flow. The governing equations are simplified and discretized for a selected computational grid system. Numerical methods are selected to simplify and calculate approximate flow properties. For turbulent, reacting, and multiphase flow systems the complex processes relating to these aspects of the flow, i.e., turbulent diffusion, combustion kinetics, interfacial drag and heat and mass transfer, etc., are described in mathematical models, based on a combination of fundamental physics and empirical data, that are incorporated into the code. CFD simulation has been applied to a large variety of practical and industrial scale flow systems.

Physiological aspects of the subcellular localization of glycogen in skeletal muscle

DEFF Research Database (Denmark)

Nielsen, Joachim; Ørtenblad, Niels

2013-01-01

Glucose is stored in skeletal muscle fibers as glycogen, a branched-chain polymer observed in electron microscopy images as roughly spherical particles (known as β-particles of 10-45 nm in diameter), which are distributed in distinct localizations within the myofibers and are physically associated...... investigated the role and regulation of these distinct deposits of glycogen. In this report, we review the available literature regarding the subcellular localization of glycogen in skeletal muscle as investigated by electron microscopy studies and put this into perspective in terms of the architectural......, topological, and dynamic organization of skeletal muscle fibers. In summary, the distribution of glycogen within skeletal muscle fibers has been shown to depend on the fiber phenotype, individual training status, short-term immobilization, and exercise and to influence both muscle contractility...

Computational Methods in Stochastic Dynamics Volume 2

CERN Document Server

Stefanou, George; Papadopoulos, Vissarion

2013-01-01

The considerable influence of inherent uncertainties on structural behavior has led the engineering community to recognize the importance of a stochastic approach to structural problems. Issues related to uncertainty quantification and its influence on the reliability of the computational models are continuously gaining in significance. In particular, the problems of dynamic response analysis and reliability assessment of structures with uncertain system and excitation parameters have been the subject of continuous research over the last two decades as a result of the increasing availability of powerful computing resources and technology.   This book is a follow up of a previous book with the same subject (ISBN 978-90-481-9986-0) and focuses on advanced computational methods and software tools which can highly assist in tackling complex problems in stochastic dynamic/seismic analysis and design of structures. The selected chapters are authored by some of the most active scholars in their respective areas and...

Symbolic mathematical computing: orbital dynamics and application to accelerators

International Nuclear Information System (INIS)

Fateman, R.

1986-01-01

Computer-assisted symbolic mathematical computation has become increasingly useful in applied mathematics. A brief introduction to such capabilitites and some examples related to orbital dynamics and accelerator physics are presented. (author)

Visualization of unsteady computational fluid dynamics

Science.gov (United States)

Haimes, Robert

1994-11-01

A brief summary of the computer environment used for calculating three dimensional unsteady Computational Fluid Dynamic (CFD) results is presented. This environment requires a super computer as well as massively parallel processors (MPP's) and clusters of workstations acting as a single MPP (by concurrently working on the same task) provide the required computational bandwidth for CFD calculations of transient problems. The cluster of reduced instruction set computers (RISC) is a recent advent based on the low cost and high performance that workstation vendors provide. The cluster, with the proper software can act as a multiple instruction/multiple data (MIMD) machine. A new set of software tools is being designed specifically to address visualizing 3D unsteady CFD results in these environments. Three user's manuals for the parallel version of Visual3, pV3, revision 1.00 make up the bulk of this report.

Subcellular partitioning of metals in Aporrectodea caliginosa along a gradient of metal exposure in 31 field-contaminated soils

Energy Technology Data Exchange (ETDEWEB)

Beaumelle, Léa [INRA, UR 251 PESSAC, 78026 Versailles Cedex (France); Gimbert, Frédéric [Laboratoire Chrono-Environnement, UMR 6249 University of Franche-Comté/CNRS Usc INRA, 16 route de Gray, 25030 Besançon Cedex (France); Hedde, Mickaël [INRA, UR 251 PESSAC, 78026 Versailles Cedex (France); Guérin, Annie [INRA, US 0010 LAS Laboratoire d' analyses des sols, 273 rue de Cambrai, 62000 Arras (France); Lamy, Isabelle, E-mail: lamy@versailles.inra.fr [INRA, UR 251 PESSAC, 78026 Versailles Cedex (France)

2015-07-01

Subcellular fractionation of metals in organisms was proposed as a better way to characterize metal bioaccumulation. Here we report the impact of a laboratory exposure to a wide range of field-metal contaminated soils on the subcellular partitioning of metals in the earthworm Aporrectodea caliginosa. Soils moderately contaminated were chosen to create a gradient of soil metal availability; covering ranges of both soil metal contents and of several soil parameters. Following exposure, Cd, Pb and Zn concentrations were determined both in total earthworm body and in three subcellular compartments: cytosolic, granular and debris fractions. Three distinct proxies of soil metal availability were investigated: CaCl{sub 2}-extractable content dissolved content predicted by a semi-mechanistic model and free ion concentration predicted by a geochemical speciation model. Subcellular partitionings of Cd and Pb were modified along the gradient of metal exposure, while stable Zn partitioning reflected regulation processes. Cd subcellular distribution responded more strongly to increasing soil Cd concentration than the total internal content, when Pb subcellular distribution and total internal content were similarly affected. Free ion concentrations were better descriptors of Cd and Pb subcellular distribution than CaCl{sub 2} extractable and dissolved metal concentrations. However, free ion concentrations and soil total metal contents were equivalent descriptors of the subcellular partitioning of Cd and Pb because they were highly correlated. Considering lowly contaminated soils, our results raise the question of the added value of three proxies of metal availability compared to soil total metal content in the assessment of metal bioavailability to earthworm. - Highlights: • Earthworms were exposed to a wide panel of historically contaminated soils • Subcellular partitioning of Cd, Pb and Zn was investigated in earthworms • Three proxies of soil metal availability were

Dynamic computing random access memory

International Nuclear Information System (INIS)

Traversa, F L; Bonani, F; Pershin, Y V; Di Ventra, M

2014-01-01

The present von Neumann computing paradigm involves a significant amount of information transfer between a central processing unit and memory, with concomitant limitations in the actual execution speed. However, it has been recently argued that a different form of computation, dubbed memcomputing (Di Ventra and Pershin 2013 Nat. Phys. 9 200–2) and inspired by the operation of our brain, can resolve the intrinsic limitations of present day architectures by allowing for computing and storing of information on the same physical platform. Here we show a simple and practical realization of memcomputing that utilizes easy-to-build memcapacitive systems. We name this architecture dynamic computing random access memory (DCRAM). We show that DCRAM provides massively-parallel and polymorphic digital logic, namely it allows for different logic operations with the same architecture, by varying only the control signals. In addition, by taking into account realistic parameters, its energy expenditures can be as low as a few fJ per operation. DCRAM is fully compatible with CMOS technology, can be realized with current fabrication facilities, and therefore can really serve as an alternative to the present computing technology. (paper)

Detrended cross-correlation coefficient: Application to predict apoptosis protein subcellular localization.

Science.gov (United States)

Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

2016-12-01

Apoptosis, or programed cell death, plays a central role in the development and homeostasis of an organism. Obtaining information on subcellular location of apoptosis proteins is very helpful for understanding the apoptosis mechanism. The prediction of subcellular localization of an apoptosis protein is still a challenging task, and existing methods mainly based on protein primary sequences. In this paper, we introduce a new position-specific scoring matrix (PSSM)-based method by using detrended cross-correlation (DCCA) coefficient of non-overlapping windows. Then a 190-dimensional (190D) feature vector is constructed on two widely used datasets: CL317 and ZD98, and support vector machine is adopted as classifier. To evaluate the proposed method, objective and rigorous jackknife cross-validation tests are performed on the two datasets. The results show that our approach offers a novel and reliable PSSM-based tool for prediction of apoptosis protein subcellular localization. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantitative Analysis of Subcellular Distribution of the SUMO Conjugation System by Confocal Microscopy Imaging.

Science.gov (United States)

Mas, Abraham; Amenós, Montse; Lois, L Maria

2016-01-01

Different studies point to an enrichment in SUMO conjugation in the cell nucleus, although non-nuclear SUMO targets also exist. In general, the study of subcellular localization of proteins is essential for understanding their function within a cell. Fluorescence microscopy is a powerful tool for studying subcellular protein partitioning in living cells, since fluorescent proteins can be fused to proteins of interest to determine their localization. Subcellular distribution of proteins can be influenced by binding to other biomolecules and by posttranslational modifications. Sometimes these changes affect only a portion of the protein pool or have a partial effect, and a quantitative evaluation of fluorescence images is required to identify protein redistribution among subcellular compartments. In order to obtain accurate data about the relative subcellular distribution of SUMO conjugation machinery members, and to identify the molecular determinants involved in their localization, we have applied quantitative confocal microscopy imaging. In this chapter, we will describe the fluorescent protein fusions used in these experiments, and how to measure, evaluate, and compare average fluorescence intensities in cellular compartments by image-based analysis. We show the distribution of some components of the Arabidopsis SUMOylation machinery in epidermal onion cells and how they change their distribution in the presence of interacting partners or even when its activity is affected.

In Situ Spatiotemporal Mapping of Flow Fields around Seeded Stem Cells at the Subcellular Length Scale

Science.gov (United States)

Song, Min Jae; Dean, David; Knothe Tate, Melissa L.

2010-01-01

A major hurdle to understanding and exploiting interactions between the stem cell and its environment is the lack of a tool for precise delivery of mechanical cues concomitant to observing sub-cellular adaptation of structure. These studies demonstrate the use of microscale particle image velocimetry (μ-PIV) for in situ spatiotemporal mapping of flow fields around mesenchymal stem cells, i.e. murine embryonic multipotent cell line C3H10T1/2, at the subcellular length scale, providing a tool for real time observation and analysis of stem cell adaptation to the prevailing mechanical milieu. In the absence of cells, computational fluid dynamics (CFD) predicts flow regimes within 12% of μ-PIV measures, achieving the technical specifications of the chamber and the flow rates necessary to deliver target shear stresses at a particular height from the base of the flow chamber. However, our μ-PIV studies show that the presence of cells per se as well as the density at which cells are seeded significantly influences local flow fields. Furthermore, for any given cell or cell seeding density, flow regimes vary significantly along the vertical profile of the cell. Hence, the mechanical milieu of the stem cell exposed to shape changing shear stresses, induced by fluid drag, varies with respect to proximity of surrounding cells as well as with respect to apical height. The current study addresses a previously unmet need to predict and observe both flow regimes as well as mechanoadaptation of cells in flow chambers designed to deliver precisely controlled mechanical signals to live cells. An understanding of interactions and adaptation in response to forces at the interface between the surface of the cell and its immediate local environment may be key for de novo engineering of functional tissues from stem cell templates as well as for unraveling the mechanisms underlying multiscale development, growth and adaptation of organisms. PMID:20862249

In situ spatiotemporal mapping of flow fields around seeded stem cells at the subcellular length scale.

Directory of Open Access Journals (Sweden)

Min Jae Song

2010-09-01

Full Text Available A major hurdle to understanding and exploiting interactions between the stem cell and its environment is the lack of a tool for precise delivery of mechanical cues concomitant to observing sub-cellular adaptation of structure. These studies demonstrate the use of microscale particle image velocimetry (μ-PIV for in situ spatiotemporal mapping of flow fields around mesenchymal stem cells, i.e. murine embryonic multipotent cell line C3H10T1/2, at the subcellular length scale, providing a tool for real time observation and analysis of stem cell adaptation to the prevailing mechanical milieu. In the absence of cells, computational fluid dynamics (CFD predicts flow regimes within 12% of μ-PIV measures, achieving the technical specifications of the chamber and the flow rates necessary to deliver target shear stresses at a particular height from the base of the flow chamber. However, our μ-PIV studies show that the presence of cells per se as well as the density at which cells are seeded significantly influences local flow fields. Furthermore, for any given cell or cell seeding density, flow regimes vary significantly along the vertical profile of the cell. Hence, the mechanical milieu of the stem cell exposed to shape changing shear stresses, induced by fluid drag, varies with respect to proximity of surrounding cells as well as with respect to apical height. The current study addresses a previously unmet need to predict and observe both flow regimes as well as mechanoadaptation of cells in flow chambers designed to deliver precisely controlled mechanical signals to live cells. An understanding of interactions and adaptation in response to forces at the interface between the surface of the cell and its immediate local environment may be key for de novo engineering of functional tissues from stem cell templates as well as for unraveling the mechanisms underlying multiscale development, growth and adaptation of organisms.

Computational modeling of turn-taking dynamics in spoken conversations

OpenAIRE

Chowdhury, Shammur Absar

2017-01-01

The study of human interaction dynamics has been at the center for multiple research disciplines in- cluding computer and social sciences, conversational analysis and psychology, for over decades. Recent interest has been shown with the aim of designing computational models to improve human-machine interaction system as well as support humans in their decision-making process. Turn-taking is one of the key aspects of conversational dynamics in dyadic conversations and is an integral part of hu...

Subcellular compartmentation, interdependency and dynamics of the cyclic AMP-dependent PKA subunits during pathogenic differentiation in rice blast.

Science.gov (United States)

Selvaraj, Poonguzhali; Tham, Hong Fai; Ramanujam, Ravikrishna; Naqvi, Naweed I

2017-08-01

The cAMP-dependent PKA signalling plays a central role in growth, asexual development and pathogenesis in fungal pathogens. Here, we functionally characterised RPKA, the regulatory subunit of cAMP/PKA and studied the dynamics and organisation of the PKA subunits in the rice blast pathogen Magnaporthe oryzae. The RPKA subunit was essential for proper vegetative growth, asexual sporulation and surface hydrophobicity in M. oryzae. A spontaneous suppressor mutation, SMR19, that restored growth and conidiation in the RPKA deletion mutant was isolated and characterised. SMR19 enhanced conidiation and appressorium formation but failed to suppress the pathogenesis defects in rpkAΔ. The PKA activity was undetectable in the mycelial extracts of SMR19, which showed a single mutation (val242leu) in the highly conserved active site of the catalytic subunit (CPKA) of cAMP/PKA. The two subunits of cAMP/PKA showed different subcellular localisation patterns with RpkA being predominantly nucleocytoplasmic in conidia, while CpkA was largely cytosolic and/or vesicular. The CpkA anchored RpkA in cytoplasmic vesicles, and localisation of PKA in the cytoplasm was governed by CpkA in a cAMP-dependant or independent manner. We show that there exists a tight regulation of PKA subunits at the level of transcription, and the cAMP signalling is differentially compartmentalised in a stage-specific manner in rice blast. © 2017 John Wiley & Sons Ltd.

Engineering applications of computational fluid dynamics

CERN Document Server

Awang, Mokhtar

2015-01-01

This volume presents the results of Computational Fluid Dynamics (CFD) analysis that can be used for conceptual studies of product design, detail product development, process troubleshooting. It demonstrates the benefit of CFD modeling as a cost saving, timely, safe and easy to scale-up methodology.

Computational Fluid Dynamics Methods and Their Applications in Medical Science

Directory of Open Access Journals (Sweden)

Kowalewski Wojciech

2016-12-01

Full Text Available As defined by the National Institutes of Health: “Biomedical engineering integrates physical, chemical, mathematical, and computational sciences and engineering principles to study biology, medicine, behavior, and health”. Many issues in this area are closely related to fluid dynamics. This paper provides an overview of the basic concepts concerning Computational Fluid Dynamics and its applications in medicine.

Principles of computational fluid dynamics

CERN Document Server

Wesseling, Pieter

2001-01-01

The book is aimed at graduate students, researchers, engineers and physicists involved in flow computations. An up-to-date account is given of the present state-of-the-art of numerical methods employed in computational fluid dynamics. The underlying numerical principles are treated with a fair amount of detail, using elementary mathematical analysis. Attention is given to difficulties arising from geometric complexity of the flow domain and of nonuniform structured boundary-fitted grids. Uniform accuracy and efficiency for singular perturbation problems is studied, pointing the way to accurate computation of flows at high Reynolds number. Much attention is given to stability analysis, and useful stability conditions are provided, some of them new, for many numerical schemes used in practice. Unified methods for compressible and incompressible flows are discussed. Numerical analysis of the shallow-water equations is included. The theory of hyperbolic conservation laws is treated. Godunov's order barrier and ho...

Capillary electrophoretic analysis reveals subcellular binding between individual mitochondria and cytoskeleton

Science.gov (United States)

Kostal, Vratislav; Arriaga, Edgar A.

2011-01-01

Interactions between the cytoskeleton and mitochondria are essential for normal cellular function. An assessment of such interactions is commonly based on bulk analysis of mitochondrial and cytoskeletal markers present in a given sample, which assumes complete binding between these two organelle types. Such measurements are biased because they rarely account for non-bound ‘free’ subcellular species. Here we report on the use of capillary electrophoresis with dual laser induced fluorescence detection (CE-LIF) to identify, classify, count and quantify properties of individual binding events of mitochondria and cytoskeleton. Mitochondria were fluorescently labeled with DsRed2 while F-actin, a major cytoskeletal component, was fluorescently labeled with Alexa488-phalloidin. In a typical subcellular fraction of L6 myoblasts, 79% of mitochondrial events did not have detectable levels of F-actin, while the rest had on average ~2 zeptomole F-actin, which theoretically represents a ~ 2.5-μm long network of actin filaments per event. Trypsin treatment of L6 subcellular fractions prior to analysis decreased the fraction of mitochondrial events with detectable levels of F-actin, which is expected from digestion of cytoskeletal proteins on the surface of mitochondria. The electrophoretic mobility distributions of the individual events were also used to further distinguish between cytoskeleton-bound from cytoskeleton-free mitochondrial events. The CE-LIF approach described here could be further developed to explore cytoskeleton interactions with other subcellular structures, the effects of cytoskeleton destabilizing drugs, and the progression of viral infections. PMID:21309532

Towards Dynamic Remote Data Auditing in Computational Clouds

Science.gov (United States)

Khurram Khan, Muhammad; Anuar, Nor Badrul

2014-01-01

Cloud computing is a significant shift of computational paradigm where computing as a utility and storing data remotely have a great potential. Enterprise and businesses are now more interested in outsourcing their data to the cloud to lessen the burden of local data storage and maintenance. However, the outsourced data and the computation outcomes are not continuously trustworthy due to the lack of control and physical possession of the data owners. To better streamline this issue, researchers have now focused on designing remote data auditing (RDA) techniques. The majority of these techniques, however, are only applicable for static archive data and are not subject to audit the dynamically updated outsourced data. We propose an effectual RDA technique based on algebraic signature properties for cloud storage system and also present a new data structure capable of efficiently supporting dynamic data operations like append, insert, modify, and delete. Moreover, this data structure empowers our method to be applicable for large-scale data with minimum computation cost. The comparative analysis with the state-of-the-art RDA schemes shows that the proposed scheme is secure and highly efficient in terms of the computation and communication overhead on the auditor and server. PMID:25121114

Towards Dynamic Remote Data Auditing in Computational Clouds

Directory of Open Access Journals (Sweden)

Mehdi Sookhak

2014-01-01

Full Text Available Cloud computing is a significant shift of computational paradigm where computing as a utility and storing data remotely have a great potential. Enterprise and businesses are now more interested in outsourcing their data to the cloud to lessen the burden of local data storage and maintenance. However, the outsourced data and the computation outcomes are not continuously trustworthy due to the lack of control and physical possession of the data owners. To better streamline this issue, researchers have now focused on designing remote data auditing (RDA techniques. The majority of these techniques, however, are only applicable for static archive data and are not subject to audit the dynamically updated outsourced data. We propose an effectual RDA technique based on algebraic signature properties for cloud storage system and also present a new data structure capable of efficiently supporting dynamic data operations like append, insert, modify, and delete. Moreover, this data structure empowers our method to be applicable for large-scale data with minimum computation cost. The comparative analysis with the state-of-the-art RDA schemes shows that the proposed scheme is secure and highly efficient in terms of the computation and communication overhead on the auditor and server.

Expression and subcellular localization of antiporter regulating ...

African Journals Online (AJOL)

We examined the expression and subcellular localization of antiporter regulating protein OsARP in a submergence tolerant rice (Oryza sativa L.) cultivar FR13A. In the public databases, this protein was designated as putative Os02g0465900 protein. The cDNA containing the full-length sequence of OsARP gene was ...

Wingless signalling alters the levels, subcellular distribution and dynamics of Armadillo and E-cadherin in third instar larval wing imaginal discs.

Directory of Open Access Journals (Sweden)

Ildiko M L Somorjai

2008-08-01

Full Text Available Armadillo, the Drosophila orthologue of vertebrate ss-catenin, plays a dual role as the key effector of Wingless/Wnt1 signalling, and as a bridge between E-Cadherin and the actin cytoskeleton. In the absence of ligand, Armadillo is phosphorylated and targeted to the proteasome. Upon binding of Wg to its receptors, the "degradation complex" is inhibited; Armadillo is stabilised and enters the nucleus to transcribe targets.Although the relationship between signalling and adhesion has been extensively studied, few in vivo data exist concerning how the "transcriptional" and "adhesive" pools of Armadillo are regulated to orchestrate development. We have therefore addressed how the subcellular distribution of Armadillo and its association with E-Cadherin change in larval wing imaginal discs, under wild type conditions and upon signalling. Using confocal microscopy, we show that Armadillo and E-Cadherin are spatio-temporally regulated during development, and that a punctate species becomes concentrated in a subapical compartment in response to Wingless. In order to further dissect this phenomenon, we overexpressed Armadillo mutants exhibiting different levels of activity and stability, but retaining E-Cadherin binding. Arm(S10 displaces endogenous Armadillo from the AJ and the basolateral membrane, while leaving E-Cadherin relatively undisturbed. Surprisingly, DeltaNArm(1-155 caused displacement of both Armadillo and E-Cadherin, results supported by our novel method of quantification. However, only membrane-targeted Myr-DeltaNArm(1-155 produced comparable nuclear accumulation of Armadillo and signalling to Arm(S10. These experiments also highlighted a row of cells at the A/P boundary depleted of E-Cadherin at the AJ, but containing actin.Taken together, our results provide in vivo evidence for a complex non-linear relationship between Armadillo levels, subcellular distribution and Wingless signalling. Moreover, this study highlights the importance of

Subcellular distribution of styrene oxide in rat liver

International Nuclear Information System (INIS)

Pacifici, G.M.; Cuoci, L.; Rane, A.

1984-01-01

The subcellular distribution of ( 3 H)-styrene-7,8-oxide was studied in the rat liver. The compound was added to liver homogenate to give a final concentration of 2 X 10(-5); 2 X 10(-4) and 2 X 10(-3) M. Subcellular fractions were obtained by differential centrifugation. Most of styrene oxide (59-88%) was associated with the cytosolic fraction. Less than 15 percent of the compound was retrieved in each of the nuclear, mitochondrial and microsomal fractions. A considerable percentage of radioactivity was found unextractable with the organic solvents, suggesting that styrene oxide reacted with the endogenous compounds. The intracellular distribution of this epoxide was also studied in the perfused rat liver. Comparable results with those previously described were obtained. The binding of styrene oxide to the cytosolic protein was investigated by equilibrium dialysis and ultrafiltration. Only a small percentage of the compound was bound to protein

Computational methods for fluid dynamics

CERN Document Server

Ferziger, Joel H

2002-01-01

In its 3rd revised and extended edition the book offers an overview of the techniques used to solve problems in fluid mechanics on computers and describes in detail those most often used in practice. Included are advanced methods in computational fluid dynamics, like direct and large-eddy simulation of turbulence, multigrid methods, parallel computing, moving grids, structured, block-structured and unstructured boundary-fitted grids, free surface flows. The 3rd edition contains a new section dealing with grid quality and an extended description of discretization methods. The book shows common roots and basic principles for many different methods. The book also contains a great deal of practical advice for code developers and users, it is designed to be equally useful to beginners and experts. The issues of numerical accuracy, estimation and reduction of numerical errors are dealt with in detail, with many examples. A full-feature user-friendly demo-version of a commercial CFD software has been added, which ca...

Modelling the WWER-type reactor dynamics using a hybrid computer. Part 1

International Nuclear Information System (INIS)

Karpeta, C.

Results of simulation studies into reactor and steam generator dynamics of a WWER type power plant are presented. Spatial kinetics of the reactor core is described by a nodal approximation to diffusion equations, xenon poisoning equations and heat transfer equations. The simulation of the reactor model dynamics was performed on a hybrid computer. Models of both a horizontal and a vertical steam generator were developed. The dynamics was investigated over a large range of power by computing the transients on a digital computer. (author)

Predicting Subcellular Localization of Proteins by Bioinformatic Algorithms

DEFF Research Database (Denmark)

Nielsen, Henrik

2015-01-01

was used. Various statistical and machine learning algorithms are used with all three approaches, and various measures and standards are employed when reporting the performances of the developed methods. This chapter presents a number of available methods for prediction of sorting signals and subcellular...

Tip chip : Subcellular sampling from single cancer cells

NARCIS (Netherlands)

Quist, Jos; Sarajlic, Edin; Lai, Stanley C.S.; Lemay, Serge G.

2016-01-01

To analyze the molecular content of single cells, cell lysis is typically required, yielding a snapshot of cell behavior only. To follow complex molecular profiles over time, subcellular sampling methods potentially can be used, but to date these methods involve laborious offline analysis. Here we

Subcellular interactions of dietary cadmium, copper and zinc in rainbow trout (Oncorhynchus mykiss)

International Nuclear Information System (INIS)

Kamunde, Collins; MacPhail, Ruth

2011-01-01

Highlights: Interactions of Cu, Cd and Zn were studied at the subcellular level in rainbow trout. Metals accumulated in the liver were predominantly metabolically active. Cd, Cu and Zn exhibited both competitive and cooperative interactions. The metal–metal interactions altered subcellular metals partitioning. - Abstract: Interactions of Cu, Cd and Zn were studied at the subcellular level in juvenile rainbow trout (Oncorhynchus mykiss) fed diets containing (μg/g) 500 Cu, 1000 Zn and 500 Cd singly and as a ternary mixture for 28 days. Livers were harvested and submitted to differential centrifugation to isolate components of metabolically active metal pool (MAP: heat-denaturable proteins (HDP), organelles, nuclei) and metabolically detoxified metal pool (MDP: heat stable proteins (HSP), NaOH-resistant granules). Results indicated that Cd accumulation was enhanced in all the subcellular compartments, albeit at different time points, in fish exposed to the metals mixture relative to those exposed to Cd alone, whereas Cu alone exposure increased Cd partitioning. Exposure to the metals mixture reduced (HDP) and enhanced (HSP, nuclei and granules) Cu accumulation while exposure to Zn alone enhanced Cu concentration in all the fractions analyzed without altering proportional distribution in MAP and MDP. Although subcellular Zn accumulation was less pronounced than that of either Cu or Cd, concentrations of Zn were enhanced in HDP, nuclei and granules from fish exposed to the metals mixture relative to those exposed to Zn alone. Cadmium alone exposure mobilized Zn and Cu from the nuclei and increased Zn accumulation in organelles and Cu in granules, while Cu alone exposure stimulated Zn accumulation in HSP, HDP and organelles. Interestingly, Cd alone exposure increased the partitioning of the three metals in MDP indicative of enhanced detoxification. Generally the accumulated metals were predominantly metabolically active: Cd, 67–83%; Cu, 68–79% and Zn, 60–76

Subcellular interactions of dietary cadmium, copper and zinc in rainbow trout (Oncorhynchus mykiss)

Energy Technology Data Exchange (ETDEWEB)

Kamunde, Collins, E-mail: ckamunde@upei.ca [Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE, C1A 4P3 (Canada); MacPhail, Ruth [Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE, C1A 4P3 (Canada)

2011-10-15

Highlights: Interactions of Cu, Cd and Zn were studied at the subcellular level in rainbow trout. Metals accumulated in the liver were predominantly metabolically active. Cd, Cu and Zn exhibited both competitive and cooperative interactions. The metal-metal interactions altered subcellular metals partitioning. - Abstract: Interactions of Cu, Cd and Zn were studied at the subcellular level in juvenile rainbow trout (Oncorhynchus mykiss) fed diets containing ({mu}g/g) 500 Cu, 1000 Zn and 500 Cd singly and as a ternary mixture for 28 days. Livers were harvested and submitted to differential centrifugation to isolate components of metabolically active metal pool (MAP: heat-denaturable proteins (HDP), organelles, nuclei) and metabolically detoxified metal pool (MDP: heat stable proteins (HSP), NaOH-resistant granules). Results indicated that Cd accumulation was enhanced in all the subcellular compartments, albeit at different time points, in fish exposed to the metals mixture relative to those exposed to Cd alone, whereas Cu alone exposure increased Cd partitioning. Exposure to the metals mixture reduced (HDP) and enhanced (HSP, nuclei and granules) Cu accumulation while exposure to Zn alone enhanced Cu concentration in all the fractions analyzed without altering proportional distribution in MAP and MDP. Although subcellular Zn accumulation was less pronounced than that of either Cu or Cd, concentrations of Zn were enhanced in HDP, nuclei and granules from fish exposed to the metals mixture relative to those exposed to Zn alone. Cadmium alone exposure mobilized Zn and Cu from the nuclei and increased Zn accumulation in organelles and Cu in granules, while Cu alone exposure stimulated Zn accumulation in HSP, HDP and organelles. Interestingly, Cd alone exposure increased the partitioning of the three metals in MDP indicative of enhanced detoxification. Generally the accumulated metals were predominantly metabolically active: Cd, 67-83%; Cu, 68-79% and Zn, 60-76%. Taken

Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications

Directory of Open Access Journals (Sweden)

Huang Yong

2009-11-01

Full Text Available Abstract Background Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families. Results The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64% consisted of both mitochondrial and cytosolic (non-mitochondrial proteins (mt-cy families while the remaining 33 (36% were composed of mitochondrial proteins (mt-mt families. Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1 relocalization from mitochondria to cytosol, 2 from cytosol to mitochondria and 3 multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on

Mapping the Subcellular Proteome of Shewanella oneidensis MR-1 using Sarkosyl-based fractionation and LC-MS/MS protein identification

Energy Technology Data Exchange (ETDEWEB)

Brown, Roslyn N.; Romine, Margaret F.; Schepmoes, Athena A.; Smith, Richard D.; Lipton, Mary S.

2010-07-19

A simple and effective subcellular proteomic method for fractionation and analysis of gram-negative bacterial cytoplasm, periplasm, inner, and outer membranes was applied to Shewanella oneidensis to gain insight into its subcellular architecture. A combination of differential centrifugation, Sarkosyl solubilization, and osmotic lysis was used to prepare subcellular fractions. Global differences in protein fractions were observed by SDS PAGE and heme staining, and tryptic peptides were analyzed using high-resolution LC-MS/MS. Compared to crude cell lysates, the fractionation method achieved a significant enrichment (average ~2-fold) in proteins predicted to be localized to each subcellular fraction. Compared to other detergent, organic solvent, and density-based methods previously reported, Sarkosyl most effectively facilitated separation of the inner and outer membranes and was amenable to mass spectrometry, making this procedure ideal for probing the subcellular proteome of gram-negative bacteria via LC-MS/MS. With 40% of the observable proteome represented, this study has provided extensive information on both subcellular architecture and relative abundance of proteins in S. oneidensis and provides a foundation for future work on subcellular organization and protein-membrane interactions in other gram-negative bacteria.

A full computation-relevant topological dynamics classification of elementary cellular automata.

Science.gov (United States)

Schüle, Martin; Stoop, Ruedi

2012-12-01

Cellular automata are both computational and dynamical systems. We give a complete classification of the dynamic behaviour of elementary cellular automata (ECA) in terms of fundamental dynamic system notions such as sensitivity and chaoticity. The "complex" ECA emerge to be sensitive, but not chaotic and not eventually weakly periodic. Based on this classification, we conjecture that elementary cellular automata capable of carrying out complex computations, such as needed for Turing-universality, are at the "edge of chaos."

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

Science.gov (United States)

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Fluid dynamics computer programs for NERVA turbopump

Science.gov (United States)

Brunner, J. J.

1972-01-01

During the design of the NERVA turbopump, numerous computer programs were developed for the analyses of fluid dynamic problems within the machine. Program descriptions, example cases, users instructions, and listings for the majority of these programs are presented.

Computer Vision Based Measurement of Wildfire Smoke Dynamics

Directory of Open Access Journals (Sweden)

BUGARIC, M.

2015-02-01

Full Text Available This article presents a novel method for measurement of wildfire smoke dynamics based on computer vision and augmented reality techniques. The aspect of smoke dynamics is an important feature in video smoke detection that could distinguish smoke from visually similar phenomena. However, most of the existing smoke detection systems are not capable of measuring the real-world size of the detected smoke regions. Using computer vision and GIS-based augmented reality, we measure the real dimensions of smoke plumes, and observe the change in size over time. The measurements are performed on offline video data with known camera parameters and location. The observed data is analyzed in order to create a classifier that could be used to eliminate certain categories of false alarms induced by phenomena with different dynamics than smoke. We carried out an offline evaluation where we measured the improvement in the detection process achieved using the proposed smoke dynamics characteristics. The results show a significant increase in algorithm performance, especially in terms of reducing false alarms rate. From this it follows that the proposed method for measurement of smoke dynamics could be used to improve existing smoke detection algorithms, or taken into account when designing new ones.

Exponential rise of dynamical complexity in quantum computing through projections.

Science.gov (United States)

Burgarth, Daniel Klaus; Facchi, Paolo; Giovannetti, Vittorio; Nakazato, Hiromichi; Pascazio, Saverio; Yuasa, Kazuya

2014-10-10

The ability of quantum systems to host exponentially complex dynamics has the potential to revolutionize science and technology. Therefore, much effort has been devoted to developing of protocols for computation, communication and metrology, which exploit this scaling, despite formidable technical difficulties. Here we show that the mere frequent observation of a small part of a quantum system can turn its dynamics from a very simple one into an exponentially complex one, capable of universal quantum computation. After discussing examples, we go on to show that this effect is generally to be expected: almost any quantum dynamics becomes universal once 'observed' as outlined above. Conversely, we show that any complex quantum dynamics can be 'purified' into a simpler one in larger dimensions. We conclude by demonstrating that even local noise can lead to an exponentially complex dynamics.

Guidelines for Computing Longitudinal Dynamic Stability Characteristics of a Subsonic Transport

Science.gov (United States)

Thompson, Joseph R.; Frank, Neal T.; Murphy, Patrick C.

2010-01-01

A systematic study is presented to guide the selection of a numerical solution strategy for URANS computation of a subsonic transport configuration undergoing simulated forced oscillation about its pitch axis. Forced oscillation is central to the prevalent wind tunnel methodology for quantifying aircraft dynamic stability derivatives from force and moment coefficients, which is the ultimate goal for the computational simulations. Extensive computations are performed that lead in key insights of the critical numerical parameters affecting solution convergence. A preliminary linear harmonic analysis is included to demonstrate the potential of extracting dynamic stability derivatives from computational solutions.

A parametric study of a solar calcinator using computational fluid dynamics

International Nuclear Information System (INIS)

Fidaros, D.K.; Baxevanou, C.A.; Vlachos, N.S.

2007-01-01

In this work a horizontal rotating solar calcinator is studied numerically using computational fluid dynamics. The specific solar reactor is a 10 kW model designed and used for efficiency studies. The numerical model is based on the solution of the Navier-Stokes equations for the gas flow, and on Lagrangean dynamics for the discrete particles. All necessary mathematical models were developed and incorporated into a computational fluid dynamics model with the influence of turbulence simulated by a two-equation (RNG k-ε) model. The efficiency of the reactor was calculated for different thermal inputs, feed rates, rotational speeds and particle diameters. The numerically computed degrees of calcination compared well with equivalent experimental results

Subcellular Redox Targeting: Bridging in Vitro and in Vivo Chemical Biology.

Science.gov (United States)

Long, Marcus J C; Poganik, Jesse R; Ghosh, Souradyuti; Aye, Yimon

2017-03-17

Networks of redox sensor proteins within discrete microdomains regulate the flow of redox signaling. Yet, the inherent reactivity of redox signals complicates the study of specific redox events and pathways by traditional methods. Herein, we review designer chemistries capable of measuring flux and/or mimicking subcellular redox signaling at the cellular and organismal level. Such efforts have begun to decipher the logic underlying organelle-, site-, and target-specific redox signaling in vitro and in vivo. These data highlight chemical biology as a perfect gateway to interrogate how nature choreographs subcellular redox chemistry to drive precision redox biology.

Subcellular localization for Gram positive and Gram negative bacterial proteins using linear interpolation smoothing model.

Science.gov (United States)

Saini, Harsh; Raicar, Gaurav; Dehzangi, Abdollah; Lal, Sunil; Sharma, Alok

2015-12-07

Protein subcellular localization is an important topic in proteomics since it is related to a protein׳s overall function, helps in the understanding of metabolic pathways, and in drug design and discovery. In this paper, a basic approximation technique from natural language processing called the linear interpolation smoothing model is applied for predicting protein subcellular localizations. The proposed approach extracts features from syntactical information in protein sequences to build probabilistic profiles using dependency models, which are used in linear interpolation to determine how likely is a sequence to belong to a particular subcellular location. This technique builds a statistical model based on maximum likelihood. It is able to deal effectively with high dimensionality that hinders other traditional classifiers such as Support Vector Machines or k-Nearest Neighbours without sacrificing performance. This approach has been evaluated by predicting subcellular localizations of Gram positive and Gram negative bacterial proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computational Fluid Dynamics (CFD) Computations With Zonal Navier-Stokes Flow Solver (ZNSFLOW) Common High Performance Computing Scalable Software Initiative (CHSSI) Software

National Research Council Canada - National Science Library

Edge, Harris

1999-01-01

...), computational fluid dynamics (CFD) 6 project. Under the project, a proven zonal Navier-Stokes solver was rewritten for scalable parallel performance on both shared memory and distributed memory high performance computers...

Essential Computational Fluid Dynamics

CERN Document Server

Zikanov, Oleg

2011-01-01

This book serves as a complete and self-contained introduction to the principles of Computational Fluid Dynamic (CFD) analysis. It is deliberately short (at approximately 300 pages) and can be used as a text for the first part of the course of applied CFD followed by a software tutorial. The main objectives of this non-traditional format are: 1) To introduce and explain, using simple examples where possible, the principles and methods of CFD analysis and to demystify the `black box’ of a CFD software tool, and 2) To provide a basic understanding of how CFD problems are set and

Arterioportal shunts on dynamic computed tomography

International Nuclear Information System (INIS)

Nakayama, T.; Hiyama, Y.; Ohnishi, K.; Tsuchiya, S.; Kohno, K.; Nakajima, Y.; Okuda, K.

1983-01-01

Thirty-two patients, 20 with hepatocelluar carcinoma and 12 with liver cirrhosis, were examined by dynamic computed tomography (CT) using intravenous bolus injection of contrast medium and by celiac angiography. Dynamic CT disclosed arterioportal shunting in four cases of hepatocellular carcinoma and in one of cirrhosis. In three of the former, the arterioportal shunt was adjacent to a mass lesion on CT, suggesting tumor invasion into the portal branch. In one with hepatocellular carcinoma, the shunt was remote from the mass. In the case with cirrhosis, there was no mass. In these last two cases, the shunt might have been caused by prior percutaneous needle puncture. In another case of hepatocellular carcinoma, celiac angiography but not CT demonstrated an arterioportal shunt. Thus, dynamic CT was diagnostic in five of six cases of arteriographically demonstrated arterioportal shunts

Subcellular partitioning of cadmium in the freshwater bivalve, Pyganodon grandis, after separate short-term exposures to waterborne or diet-borne metal

Energy Technology Data Exchange (ETDEWEB)

Cooper, Sophie; Hare, Landis [INRS-Eau, Terre et Environnement, Universite du Quebec, 490 rue de la Couronne, Quebec, QC, G1K 9A9 (Canada); Campbell, Peter G.C., E-mail: peter.campbell@ete.inrs.ca [INRS-Eau, Terre et Environnement, Universite du Quebec, 490 rue de la Couronne, Quebec, QC, G1K 9A9 (Canada)

2010-11-15

The dynamics of cadmium uptake and subcellular partitioning were studied in laboratory experiments conducted on Pyganodon grandis, a freshwater unionid bivalve that shows promise as a biomonitor for metal pollution. Bivalves were collected from an uncontaminated lake, allowed to acclimate to laboratory conditions ({>=}25 days), and then either exposed to a low, environmentally relevant, concentration of dissolved Cd (5 nM; 6, 12 and 24 h), or fed Cd-contaminated algae ({approx}70 nmol Cd g{sup -1} dry weight; 4 x 4 h). In this latter case, the bivalves were allowed to depurate for up to 8 days after the end of the feeding phase. As anticipated, the gills were the main target organ during the aqueous Cd exposure whereas the intestine was the initial site of Cd accumulation during the dietary exposure; during the subsequent depuration period, the dietary Cd accumulated in both the digestive gland and in the gills. For the gills, the distribution of Cd among the subcellular fractions (i.e., granules > heat-denatured proteins (HDP) {approx} heat-stable proteins (HSP) > mitochondria {approx} lysosomes + microsomes) was insensitive to the exposure route; both waterborne and diet-borne Cd ended up largely bound to the granule fraction. The subcellular distribution of Cd in the digestive gland differed markedly from that in the gills (HDP > HSP {approx} granules {approx} mitochondria > lysosomes + microsomes), but as in the case of the gills, this distribution was relatively insensitive to the exposure route. For both the gills and the digestive gland, the subcellular distributions of Cd differed from those observed in native bivalves that are chronically exposed to Cd in the field - in the short-term experimental exposures of P. grandis, metal detoxification was less effective than in chronically exposed native bivalves.

Development of tight-binding, chemical-reaction-dynamics simulator for combinatorial computational chemistry

International Nuclear Information System (INIS)

Kubo, Momoji; Ando, Minako; Sakahara, Satoshi; Jung, Changho; Seki, Kotaro; Kusagaya, Tomonori; Endou, Akira; Takami, Seiichi; Imamura, Akira; Miyamoto, Akira

2004-01-01

Recently, we have proposed a new concept called 'combinatorial computational chemistry' to realize a theoretical, high-throughput screening of catalysts and materials. We have already applied our combinatorial, computational-chemistry approach, mainly based on static first-principles calculations, to various catalysts and materials systems and its applicability to the catalysts and materials design was strongly confirmed. In order to realize more effective and efficient combinatorial, computational-chemistry screening, a high-speed, chemical-reaction-dynamics simulator based on quantum-chemical, molecular-dynamics method is essential. However, to the best of our knowledge, there is no chemical-reaction-dynamics simulator, which has an enough high-speed ability to perform a high-throughput screening. In the present study, we have succeeded in the development of a chemical-reaction-dynamics simulator based on our original, tight-binding, quantum-chemical, molecular-dynamics method, which is more than 5000 times faster than the regular first-principles, molecular-dynamics method. Moreover, its applicability and effectiveness to the atomistic clarification of the methanol-synthesis dynamics at reaction temperature were demonstrated

HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins.

Science.gov (United States)

Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

2014-01-01

Protein subcellular localization prediction, as an essential step to elucidate the functions in vivo of proteins and identify drugs targets, has been extensively studied in previous decades. Instead of only determining subcellular localization of single-label proteins, recent studies have focused on predicting both single- and multi-location proteins. Computational methods based on Gene Ontology (GO) have been demonstrated to be superior to methods based on other features. However, existing GO-based methods focus on the occurrences of GO terms and disregard their relationships. This paper proposes a multi-label subcellular-localization predictor, namely HybridGO-Loc, that leverages not only the GO term occurrences but also the inter-term relationships. This is achieved by hybridizing the GO frequencies of occurrences and the semantic similarity between GO terms. Given a protein, a set of GO terms are retrieved by searching against the gene ontology database, using the accession numbers of homologous proteins obtained via BLAST search as the keys. The frequency of GO occurrences and semantic similarity (SS) between GO terms are used to formulate frequency vectors and semantic similarity vectors, respectively, which are subsequently hybridized to construct fusion vectors. An adaptive-decision based multi-label support vector machine (SVM) classifier is proposed to classify the fusion vectors. Experimental results based on recent benchmark datasets and a new dataset containing novel proteins show that the proposed hybrid-feature predictor significantly outperforms predictors based on individual GO features as well as other state-of-the-art predictors. For readers' convenience, the HybridGO-Loc server, which is for predicting virus or plant proteins, is available online at http://bioinfo.eie.polyu.edu.hk/HybridGoServer/.

Computation of magnetic suspension of maglev systems using dynamic circuit theory

Science.gov (United States)

He, J. L.; Rote, D. M.; Coffey, H. T.

1992-01-01

Dynamic circuit theory is applied to several magnetic suspensions associated with maglev systems. These suspension systems are the loop-shaped coil guideway, the figure-eight-shaped null-flux coil guideway, and the continuous sheet guideway. Mathematical models, which can be used for the development of computer codes, are provided for each of these suspension systems. The differences and similarities of the models in using dynamic circuit theory are discussed in the paper. The paper emphasizes the transient and dynamic analysis and computer simulation of maglev systems. In general, the method discussed here can be applied to many electrodynamic suspension system design concepts. It is also suited for the computation of the performance of maglev propulsion systems. Numerical examples are presented in the paper.

Domain of attraction computation for tumor dynamics

NARCIS (Netherlands)

Doban, A.I.; Lazar, M.

2014-01-01

In this paper we propose the use of rational Lyapunov functions to estimate the domain of attraction of the tumor dormancy equilibrium of immune cells-malignant cells interaction dynamics. A procedure for computing rational Lyapunov functions is worked out, with focus on obtaining a meaningful

Plasma effects on subcellular structures

International Nuclear Information System (INIS)

Gweon, Bomi; Kim, Dan Bee; Jung, Heesoo; Choe, Wonho; Kim, Daeyeon; Shin, Jennifer H.

2010-01-01

Atmospheric pressure helium plasma treated human hepatocytes exhibit distinctive zones of necrotic and live cells separated by a void. We propose that plasma induced necrosis is attributed to plasma species such as oxygen radicals, charged particles, metastables and/or severe disruption of charged cytoskeletal proteins. Interestingly, uncharged cytoskeletal intermediate filaments are only minimally disturbed by plasma, elucidating the possibility of plasma induced electrostatic effects selectively destroying charged proteins. These bona fide plasma effects, which inflict alterations in specific subcellular structures leading to necrosis and cellular detachment, were not observed by application of helium flow or electric field alone.

Subcellular distribution of curium in beagle liver

International Nuclear Information System (INIS)

Bruenger, F.W.; Grube, B.J.; Atherton, D.R.; Taylor, G.N.; Stevens, W.

1976-01-01

The subcellular distribution of curium ( 243 244 Cm) was studied in canine liver from 2 hr to 47 days after injection of 3 μCi 243 244 Cm/kg of body weight. The pattern of distribution for Cm was similar to other trivalent actinide elements studied previously (Am, Cf). Initially (2 hr), most of the nuclide was found in the cytosol and at least 90 percent was protein bound. About 70 percent of the Cm was bound to ferritin, approximately 5 percent was associated with a protein of MW approximately 200,000, and approximately 25 percent was found in the low-molecular-weight region (approximately 5000). The decrease in the Cm content of cytosol, nuclei, and microsomes coincided with an increase in the amount associated with mitochondria and lysosomes. The concentration of the Cm in the mitochondrial fraction was higher than it was in the lysosomal fraction at each time studied. In the mitochondrial fraction approximately 30 percent of the Cm was bound to membranous or granular material, and 70 percent was found in the soluble fraction. The Cm concentration initially associated with cell nuclei was high but had diminished to 20 percent of the 2 hr concentration by 20 days post injection (PI). The subcellular distribution of Cm in the liver of a dog which had received the same dose and was terminated because of severe liver damage was studied at 384 days PI. The liver weighed 130 g and contained approximately 30 percent of the injected Cm. In contrast, a normal liver weighs 280 g and at 2 hr PI contains approximately 40 percent of the injected dose. The subcellular distribution of Cm in this severely damaged liver differed from the pattern observed at earlier times after injection. The relative concentration of Cm in the cytosol was doubled; it was higher in the nuclei-debris fraction; and it was lower in the mitochondrial and lysosomal fractions when compared to earlier times

Distribution of polycyclic aromatic hydrocarbons in subcellular root tissues of ryegrass (Lolium multiflorum Lam.)

Science.gov (United States)

2010-01-01

Background Because of the increasing quantity and high toxicity to humans of polycyclic aromatic hydrocarbons (PAHs) in the environment, several bioremediation mechanisms and protocols have been investigated to restore PAH-contaminated sites. The transport of organic contaminants among plant cells via tissues and their partition in roots, stalks, and leaves resulting from transpiration and lipid content have been extensively investigated. However, information about PAH distributions in intracellular tissues is lacking, thus limiting the further development of a mechanism-based phytoremediation strategy to improve treatment efficiency. Results Pyrene exhibited higher uptake and was more recalcitrant to metabolism in ryegrass roots than was phenanthrene. The kinetic processes of uptake from ryegrass culture medium revealed that these two PAHs were first adsorbed onto root cell walls, and they then penetrated cell membranes and were distributed in intracellular organelle fractions. At the beginning of uptake (< 50 h), adsorption to cell walls dominated the subcellular partitioning of the PAHs. After 96 h of uptake, the subcellular partition of PAHs approached a stable state in the plant water system, with the proportion of PAH distributed in subcellular fractions being controlled by the lipid contents of each component. Phenanthrene and pyrene primarily accumulated in plant root cell walls and organelles, with about 45% of PAHs in each of these two fractions, and the remainder was retained in the dissolved fraction of the cells. Because of its higher lipophilicity, pyrene displayed greater accumulation factors in subcellular walls and organelle fractions than did phenanthrene. Conclusions Transpiration and the lipid content of root cell fractions are the main drivers of the subcellular partition of PAHs in roots. Initially, PAHs adsorb to plant cell walls, and they then gradually diffuse into subcellular fractions of tissues. The lipid content of intracellular

A dynamical-systems approach for computing ice-affected streamflow

Science.gov (United States)

Holtschlag, David J.

1996-01-01

A dynamical-systems approach was developed and evaluated for computing ice-affected streamflow. The approach provides for dynamic simulation and parameter estimation of site-specific equations relating ice effects to routinely measured environmental variables. Comparison indicates that results from the dynamical-systems approach ranked higher than results from 11 analytical methods previously investigated on the basis of accuracy and feasibility criteria. Additional research will likely lead to further improvements in the approach.

The incorporation of labelled amino acids into the subcellular fractions of the rabbit brain

International Nuclear Information System (INIS)

Ogrodnik, W.

1980-01-01

Radioactive amino acids were injected into the fourth ventriculum of adult rabbits. After 3, 6 and 13 hours the animals were killed and tissue subcellular fractions were prepared from their brains. Nucleic acids were extracted and quantitatively determined from nucleic, myelin, mitochondrial, microsomal and cytoplasmic fractions. The radioactivity was determined in the protein and nucleic acid fractions. It was found out that the incorporation of radioactive amino acids increased in relation to time. In the analyzed subcellular fractions a very rapid incorporation of glutamic acid and leucine into cytoplasmic proteins was observed. The chromatographic analysis of the nucleic acids showed that radioactivity in the nucleic acid fractions depended on a radioactive protein contamination. Radioactive aminoacyl-tRNA was not found in the nucleic acid fractions, extracted from different subcellular fractions. (author)

Neural Computations in a Dynamical System with Multiple Time Scales

Directory of Open Access Journals (Sweden)

Yuanyuan Mi

2016-09-01

Full Text Available Neural systems display rich short-term dynamics at various levels, e.g., spike-frequencyadaptation (SFA at single neurons, and short-term facilitation (STF and depression (STDat neuronal synapses. These dynamical features typically covers a broad range of time scalesand exhibit large diversity in different brain regions. It remains unclear what the computationalbenefit for the brain to have such variability in short-term dynamics is. In this study, we proposethat the brain can exploit such dynamical features to implement multiple seemingly contradictorycomputations in a single neural circuit. To demonstrate this idea, we use continuous attractorneural network (CANN as a working model and include STF, SFA and STD with increasing timeconstants in their dynamics. Three computational tasks are considered, which are persistent activity,adaptation, and anticipative tracking. These tasks require conflicting neural mechanisms, andhence cannot be implemented by a single dynamical feature or any combination with similar timeconstants. However, with properly coordinated STF, SFA and STD, we show that the network isable to implement the three computational tasks concurrently. We hope this study will shed lighton the understanding of how the brain orchestrates its rich dynamics at various levels to realizediverse cognitive functions.

Computational fluid dynamics modelling of displacement natural ventilation.

OpenAIRE

Ji, Yingchun

2005-01-01

Natural ventilation is widely recognised as contributing towards low-energy building design. The requirement to reduce energy usage in new buildings has rejuvenated interest in natural ventilation. This thesis deals with computer modelling of natural displacement ventilation driven either by buoyancy or buoyancy combined with wind forces. Two benchmarks have been developed using computational fluid dynamics (CFD) in order to evaluate the accuracy with which CFD is able to mo...

Organelle-targeting surface-enhanced Raman scattering (SERS) nanosensors for subcellular pH sensing.

Science.gov (United States)

Shen, Yanting; Liang, Lijia; Zhang, Shuqin; Huang, Dianshuai; Zhang, Jing; Xu, Shuping; Liang, Chongyang; Xu, Weiqing

2018-01-25

The pH value of subcellular organelles in living cells is a significant parameter in the physiological activities of cells. Its abnormal fluctuations are commonly believed to be associated with cancers and other diseases. Herein, a series of surface-enhanced Raman scattering (SERS) nanosensors with high sensitivity and targeting function was prepared for the quantification and monitoring of pH values in mitochondria, nucleus, and lysosome. The nanosensors were composed of gold nanorods (AuNRs) functionalized with a pH-responsive molecule (4-mercaptopyridine, MPy) and peptides that could specifically deliver the AuNRs to the targeting subcellular organelles. The localization of our prepared nanoprobes in specific organelles was confirmed by super-high resolution fluorescence imaging and bio-transmission electron microscopy (TEM) methods. By the targeting ability, the pH values of the specific organelles can be determined by monitoring the vibrational spectral changes of MPy with different pH values. Compared to the cases of reported lysosome and cytoplasm SERS pH sensors, more accurate pH values of mitochondria and nucleus, which could be two additional intracellular tracers for subcellular microenvironments, were disclosed by this SERS approach, further improving the accuracy of discrimination of related diseases. Our sensitive SERS strategy can also be employed to explore crucial physiological and biological processes that are related to subcellular pH fluctuations.

Graphics supercomputer for computational fluid dynamics research

Science.gov (United States)

Liaw, Goang S.

1994-11-01

The objective of this project is to purchase a state-of-the-art graphics supercomputer to improve the Computational Fluid Dynamics (CFD) research capability at Alabama A & M University (AAMU) and to support the Air Force research projects. A cutting-edge graphics supercomputer system, Onyx VTX, from Silicon Graphics Computer Systems (SGI), was purchased and installed. Other equipment including a desktop personal computer, PC-486 DX2 with a built-in 10-BaseT Ethernet card, a 10-BaseT hub, an Apple Laser Printer Select 360, and a notebook computer from Zenith were also purchased. A reading room has been converted to a research computer lab by adding some furniture and an air conditioning unit in order to provide an appropriate working environments for researchers and the purchase equipment. All the purchased equipment were successfully installed and are fully functional. Several research projects, including two existing Air Force projects, are being performed using these facilities.

Computational Fluid Dynamics in Ventilation Design

DEFF Research Database (Denmark)

Nielsen, Peter V.

2008-01-01

This paper is based on the new REHVA Guidebook Computational Fluid  Dynamics in Ventilation Design (Nielsen et al. 2007) written by Peter V. Nielsen, Francis(Nielsen 2007) written by Peter V. Nielsen, Francis Allard, Hazim B. Awbi, Lars Davidson and Alois Schälin. The guidebook is made for people....... The guidebook introduces rules for good quality prediction work, and it is the purpose of the guidebook to improve the technical level of CFD work in ventilation.......This paper is based on the new REHVA Guidebook Computational Fluid  Dynamics in Ventilation Design (Nielsen et al. 2007) written by Peter V. Nielsen, Francis(Nielsen 2007) written by Peter V. Nielsen, Francis Allard, Hazim B. Awbi, Lars Davidson and Alois Schälin. The guidebook is made for people...... who need to use and discuss results based on CFD predictions, and it gives insight into the subject for those who are not used to work with CFD. The guidebook is also written for people working with CFD who have to be more aware of how this numerical method is applied in the area of ventilation...

Self-study manual for introduction to computational fluid dynamics

OpenAIRE

Nabatov, Andrey

2017-01-01

Computational Fluid Dynamics (CFD) is the branch of Fluid Mechanics and Computational Physics that plays a decent role in modern Mechanical Engineering Design process due to such advantages as relatively low cost of simulation comparing with conduction of real experiment, an opportunity to easily correct the design of a prototype prior to manufacturing of the final product and a wide range of application: mixing, acoustics, cooling and aerodynamics. This makes CFD particularly and Computation...

Dynamic modelling of an adsorption storage tank using a hybrid approach combining computational fluid dynamics and process simulation

Science.gov (United States)

Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.

2004-01-01

A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.

Computational Fluid Dynamics (CFD) Technology Programme 1995- 1999

Energy Technology Data Exchange (ETDEWEB)

Haekkinen, R.J.; Hirsch, C.; Krause, E.; Kytoemaa, H.K. [eds.

1997-12-31

The report is a mid-term evaluation of the Computational Fluid Dynamics (CFD) Technology Programme started by Technology Development Centre Finland (TEKES) in 1995 as a five-year initiative to be concluded in 1999. The main goal of the programme is to increase the know-how and application of CFD in Finnish industry, to coordinate and thus provide a better basis for co-operation between national CFD activities and encouraging research laboratories and industry to establish co-operation with the international CFD community. The projects of the programme focus on the following areas: (1) studies of modeling the physics and dynamics of the behaviour of fluid material, (2) expressing the physical models in a numerical mode and developing a computer codes, (3) evaluating and testing current physical models and developing new ones, (4) developing new numerical algorithms, solvers, and pre- and post-processing software, and (5) applying the new computational tools to problems relevant to their ultimate industrial use. The report consists of two sections. The first considers issues concerning the whole programme and the second reviews each project

Computational fluid dynamics in ventilation design

CERN Document Server

Allard, Francis; Awbi, Hazim B; Davidson, Lars; Schälin, Alois

2007-01-01

CFD-calculations have been rapidly developed to a powerful tool for the analysis of air pollution distribution in various spaces. However, the user of CFD-calculation should be aware of the basic principles of calculations and specifically the boundary conditions. Computational Fluid Dynamics (CFD) – in Ventilation Design models is written by a working group of highly qualified international experts representing research, consulting and design.

Subcellular SIMS imaging of isotopically labeled amino acids in cryogenically prepared cells

International Nuclear Information System (INIS)

Chandra, Subhash

2004-01-01

Ion microscopy is a potentially powerful technique for localization of isotopically labeled molecules. In this study, L-arginine and phenylalanine amino acids labeled with stable isotopes 13 C and 15 N were localized in cultured cells with the ion microscope at 500 nm spatial resolution. Cells were exposed to the labeled amino acids and cryogenically prepared. SIMS analyses were made in fractured freeze-dried cells. A dynamic distribution was observed from labeled arginine-treated LLC-PK 1 kidney cells at mass 28 ( 13 C 15 N) in negative secondaries, revealing cell-to-cell heterogeneity and preferential accumulation of the amino acid (or its metabolite) in the nucleus and nucleolus of some cells. The smaller nucleolus inside the nucleus was clearly resolved in SIMS images and confirmed by correlative light microscopy. The distribution of labeled phenylalanine contrasted with arginine as it was rather homogeneously distributed in T98G human glioblastoma cells. Images of 39 K, 23 Na and 40 Ca were also recorded to confirm the reliability of sample preparation and authenticity of the observed amino acid distributions. These observations indicate that SIMS techniques can provide a valuable technology for subcellular localization of nitrogen-containing molecules in proteomics since nitrogen does not have a radionuclide tracer isotope. Amino acids labeled with stable isotopes can be used as tracers for studying their transport and metabolism in distinct subcellular compartments with SIMS. Further studies of phenylalanine uptake in human glioblastoma cells may have special significance in boron neutron capture therapy (BNCT) as a boron analogue of phenylalanine, boronophenylalanine is a clinically approved compound for the treatment of brain tumors

Subcellular SIMS imaging of isotopically labeled amino acids in cryogenically prepared cells

Energy Technology Data Exchange (ETDEWEB)

Chandra, Subhash

2004-06-15

Ion microscopy is a potentially powerful technique for localization of isotopically labeled molecules. In this study, L-arginine and phenylalanine amino acids labeled with stable isotopes {sup 13}C and {sup 15}N were localized in cultured cells with the ion microscope at 500 nm spatial resolution. Cells were exposed to the labeled amino acids and cryogenically prepared. SIMS analyses were made in fractured freeze-dried cells. A dynamic distribution was observed from labeled arginine-treated LLC-PK{sub 1} kidney cells at mass 28 ({sup 13}C{sup 15}N) in negative secondaries, revealing cell-to-cell heterogeneity and preferential accumulation of the amino acid (or its metabolite) in the nucleus and nucleolus of some cells. The smaller nucleolus inside the nucleus was clearly resolved in SIMS images and confirmed by correlative light microscopy. The distribution of labeled phenylalanine contrasted with arginine as it was rather homogeneously distributed in T98G human glioblastoma cells. Images of {sup 39}K, {sup 23}Na and {sup 40}Ca were also recorded to confirm the reliability of sample preparation and authenticity of the observed amino acid distributions. These observations indicate that SIMS techniques can provide a valuable technology for subcellular localization of nitrogen-containing molecules in proteomics since nitrogen does not have a radionuclide tracer isotope. Amino acids labeled with stable isotopes can be used as tracers for studying their transport and metabolism in distinct subcellular compartments with SIMS. Further studies of phenylalanine uptake in human glioblastoma cells may have special significance in boron neutron capture therapy (BNCT) as a boron analogue of phenylalanine, boronophenylalanine is a clinically approved compound for the treatment of brain tumors.

A novel representation for apoptosis protein subcellular localization prediction using support vector machine.

Science.gov (United States)

Zhang, Li; Liao, Bo; Li, Dachao; Zhu, Wen

2009-07-21

Apoptosis, or programmed cell death, plays an important role in development of an organism. Obtaining information on subcellular location of apoptosis proteins is very helpful to understand the apoptosis mechanism. In this paper, based on the concept that the position distribution information of amino acids is closely related with the structure and function of proteins, we introduce the concept of distance frequency [Matsuda, S., Vert, J.P., Ueda, N., Toh, H., Akutsu, T., 2005. A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci. 14, 2804-2813] and propose a novel way to calculate distance frequencies. In order to calculate the local features, each protein sequence is separated into p parts with the same length in our paper. Then we use the novel representation of protein sequences and adopt support vector machine to predict subcellular location. The overall prediction accuracy is significantly improved by jackknife test.

Dissertation Defense Computational Fluid Dynamics Uncertainty Analysis for Payload Fairing Spacecraft Environmental Control Systems

Science.gov (United States)

Groves, Curtis Edward

2014-01-01

Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This paper describes an approach to quantify the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft without the use of test data. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional "validation by test only" mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions. Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computational Fluid Dynamics can be used to verify these requirements; however, the model must be validated by test data. This research includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available and open source solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT, STARCCM+, and OPENFOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid Dynamics model using the methodology found in "Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations". This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics

Dissertation Defense: Computational Fluid Dynamics Uncertainty Analysis for Payload Fairing Spacecraft Environmental Control Systems

Science.gov (United States)

Groves, Curtis Edward

2014-01-01

Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This paper describes an approach to quantify the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft without the use of test data. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional validation by test only mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions.Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computational Fluid Dynamics can be used to verify these requirements; however, the model must be validated by test data. This research includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available and open source solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT, STARCCM+, and OPENFOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid Dynamics model using the methodology found in Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations. This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics predictions

DeepLoc: prediction of protein subcellular localization using deep learning

DEFF Research Database (Denmark)

Almagro Armenteros, Jose Juan; Sønderby, Casper Kaae; Sønderby, Søren Kaae

2017-01-01

The prediction of eukaryotic protein subcellular localization is a well-studied topic in bioinformatics due to its relevance in proteomics research. Many machine learning methods have been successfully applied in this task, but in most of them, predictions rely on annotation of homologues from...... knowledge databases. For novel proteins where no annotated homologues exist, and for predicting the effects of sequence variants, it is desirable to have methods for predicting protein properties from sequence information only. Here, we present a prediction algorithm using deep neural networks to predict...... current state-of-the-art algorithms, including those relying on homology information. The method is available as a web server at http://www.cbs.dtu.dk/services/DeepLoc . Example code is available at https://github.com/JJAlmagro/subcellular_localization . The dataset is available at http...

Reference Computational Meshing Strategy for Computational Fluid Dynamics Simulation of Departure from Nucleate BoilingReference Computational Meshing Strategy for Computational Fluid Dynamics Simulation of Departure from Nucleate Boiling

Energy Technology Data Exchange (ETDEWEB)

Pointer, William David [ORNL

2017-08-01

The objective of this effort is to establish a strategy and process for generation of suitable computational mesh for computational fluid dynamics simulations of departure from nucleate boiling in a 5 by 5 fuel rod assembly held in place by PWR mixing vane spacer grids. This mesh generation process will support ongoing efforts to develop, demonstrate and validate advanced multi-phase computational fluid dynamics methods that enable more robust identification of dryout conditions and DNB occurrence.Building upon prior efforts and experience, multiple computational meshes were developed using the native mesh generation capabilities of the commercial CFD code STAR-CCM+. These meshes were used to simulate two test cases from the Westinghouse 5 by 5 rod bundle facility. The sensitivity of predicted quantities of interest to the mesh resolution was then established using two evaluation methods, the Grid Convergence Index method and the Least Squares method. This evaluation suggests that the Least Squares method can reliably establish the uncertainty associated with local parameters such as vector velocity components at a point in the domain or surface averaged quantities such as outlet velocity magnitude. However, neither method is suitable for characterization of uncertainty in global extrema such as peak fuel surface temperature, primarily because such parameters are not necessarily associated with a fixed point in space. This shortcoming is significant because the current generation algorithm for identification of DNB event conditions relies on identification of such global extrema. Ongoing efforts to identify DNB based on local surface conditions will address this challenge

Morphing-Based Shape Optimization in Computational Fluid Dynamics

Science.gov (United States)

Rousseau, Yannick; Men'Shov, Igor; Nakamura, Yoshiaki

In this paper, a Morphing-based Shape Optimization (MbSO) technique is presented for solving Optimum-Shape Design (OSD) problems in Computational Fluid Dynamics (CFD). The proposed method couples Free-Form Deformation (FFD) and Evolutionary Computation, and, as its name suggests, relies on the morphing of shape and computational domain, rather than direct shape parameterization. Advantages of the FFD approach compared to traditional parameterization are first discussed. Then, examples of shape and grid deformations by FFD are presented. Finally, the MbSO approach is illustrated and applied through an example: the design of an airfoil for a future Mars exploration airplane.

Studies on the turnover and subcellular localization of membrane gangliosides in cultured neuroblastoma cells

International Nuclear Information System (INIS)

Clarke, J.T.; Cook, H.W.; Spence, M.W.

1985-01-01

To compare the subcellular distribution of endogenously synthesized and exogenous gangliosides, cultured murine neuroblastoma cells (N1E-115) were incubated in suspension for 22 h in the presence of D-[1- 3 H]galactose or [ 3 H]GM1 ganglioside, transferred to culture medium containing no radioisotope for periods of up to 72 hr, and then subjected to subcellular fractionation and analysis of lipid-sialic acid and radiolabeled ganglioside levels. The results indicated that GM2 and GM3 were the principal gangliosides in the cells with only traces of GM1 and small amounts of disialogangliosides present. About 50% of the endogenously synthesized radiolabelled ganglioside in the four major subcellular membrane fractions studied was recovered from plasma membrane and only 10-15% from the crude mitochondrial membrane fraction. In contrast, 45% of the exogenous [ 3 H]GM1 taken up into the same subcellular membrane fractions was recovered from the crude mitochondrial fraction; less than 15% was localized in the plasma membrane fraction. The results are similar to those obtained from previously reported studies on membrane phospholipid turnover. They suggest that exogenous GM1 ganglioside, like exogenous phosphatidylcholine, does not intermix freely with any quantitatively major pool of endogenous membrane lipid

Principles of computational fluid dynamics

International Nuclear Information System (INIS)

Wesseling, P.

2001-01-01

The book is aimed at graduate students, researchers, engineers and physicists involved in flow computations. An up-to-date account is given of the present state- of-the-art of numerical methods employed in computational fluid dynamics. The underlying numerical principles are treated with a fair amount of detail, using elementary mathematical analysis. Attention is given to difficulties arising from geometric complexity of the flow domain and of nonuniform structured boundary-fitted grids. Uniform accuracy and efficiency for singular perturbation problems is studied, pointing the way to accurate computation of flows at high Reynolds number. Much attention is given to stability analysis, and useful stability conditions are provided, some of them new, for many numerical schemes used in practice. Unified methods for compressible and incompressible flows are discussed. Numerical analysis of the shallow-water equations is included. The theory of hyperbolic conservation laws is treated. Godunov's order barrier and how to overcome it by means of slope-limited schemes is discussed. An introduction is given to efficient iterative solution methods, using Krylov subspace and multigrid acceleration. Many pointers are given to recent literature, to help the reader to quickly reach the current research frontier. (orig.)

A computationally efficient OMP-based compressed sensing reconstruction for dynamic MRI

International Nuclear Information System (INIS)

Usman, M; Prieto, C; Schaeffter, T; Batchelor, P G; Odille, F; Atkinson, D

2011-01-01

Compressed sensing (CS) methods in MRI are computationally intensive. Thus, designing novel CS algorithms that can perform faster reconstructions is crucial for everyday applications. We propose a computationally efficient orthogonal matching pursuit (OMP)-based reconstruction, specifically suited to cardiac MR data. According to the energy distribution of a y-f space obtained from a sliding window reconstruction, we label the y-f space as static or dynamic. For static y-f space images, a computationally efficient masked OMP reconstruction is performed, whereas for dynamic y-f space images, standard OMP reconstruction is used. The proposed method was tested on a dynamic numerical phantom and two cardiac MR datasets. Depending on the field of view composition of the imaging data, compared to the standard OMP method, reconstruction speedup factors ranging from 1.5 to 2.5 are achieved. (note)

Computational Fluid and Particle Dynamics in the Human Respiratory System

CERN Document Server

Tu, Jiyuan; Ahmadi, Goodarz

2013-01-01

Traditional research methodologies in the human respiratory system have always been challenging due to their invasive nature. Recent advances in medical imaging and computational fluid dynamics (CFD) have accelerated this research. This book compiles and details recent advances in the modelling of the respiratory system for researchers, engineers, scientists, and health practitioners. It breaks down the complexities of this field and provides both students and scientists with an introduction and starting point to the physiology of the respiratory system, fluid dynamics and advanced CFD modeling tools. In addition to a brief introduction to the physics of the respiratory system and an overview of computational methods, the book contains best-practice guidelines for establishing high-quality computational models and simulations. Inspiration for new simulations can be gained through innovative case studies as well as hands-on practice using pre-made computational code. Last but not least, students and researcher...

A future for computational fluid dynamics at CERN

CERN Document Server

Battistin, M

2005-01-01

Computational Fluid Dynamics (CFD) is an analysis of fluid flow, heat transfer and associated phenomena in physical systems using computers. CFD has been used at CERN since 1993 by the TS-CV group, to solve thermo-fluid related problems, particularly during the development, design and construction phases of the LHC experiments. Computer models based on CFD techniques can be employed to reduce the effort required for prototype testing, saving not only time and money but offering possibilities of additional investigations and design optimisation. The development of a more efficient support team at CERN depends on to two important factors: available computing power and experienced engineers. Available computer power IS the limiting resource of CFD. Only the recent increase of computer power had allowed important high tech and industrial applications. Computer Grid is already now (OpenLab at CERN) and will be more so in the future natural environment for CFD science. At CERN, CFD activities have been developed by...

Exploiting short-term memory in soft body dynamics as a computational resource.

Science.gov (United States)

Nakajima, K; Li, T; Hauser, H; Pfeifer, R

2014-11-06

Soft materials are not only highly deformable, but they also possess rich and diverse body dynamics. Soft body dynamics exhibit a variety of properties, including nonlinearity, elasticity and potentially infinitely many degrees of freedom. Here, we demonstrate that such soft body dynamics can be employed to conduct certain types of computation. Using body dynamics generated from a soft silicone arm, we show that they can be exploited to emulate functions that require memory and to embed robust closed-loop control into the arm. Our results suggest that soft body dynamics have a short-term memory and can serve as a computational resource. This finding paves the way towards exploiting passive body dynamics for control of a large class of underactuated systems. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Nanodiamond Landmarks for Subcellular Multimodal Optical and Electron Imaging

Science.gov (United States)

Zurbuchen, Mark A.; Lake, Michael P.; Kohan, Sirus A.; Leung, Belinda; Bouchard, Louis-S.

2013-01-01

There is a growing need for biolabels that can be used in both optical and electron microscopies, are non-cytotoxic, and do not photobleach. Such biolabels could enable targeted nanoscale imaging of sub-cellular structures, and help to establish correlations between conjugation-delivered biomolecules and function. Here we demonstrate a sub-cellular multi-modal imaging methodology that enables localization of inert particulate probes, consisting of nanodiamonds having fluorescent nitrogen-vacancy centers. These are functionalized to target specific structures, and are observable by both optical and electron microscopies. Nanodiamonds targeted to the nuclear pore complex are rapidly localized in electron-microscopy diffraction mode to enable “zooming-in” to regions of interest for detailed structural investigations. Optical microscopies reveal nanodiamonds for in-vitro tracking or uptake-confirmation. The approach is general, works down to the single nanodiamond level, and can leverage the unique capabilities of nanodiamonds, such as biocompatibility, sensitive magnetometry, and gene and drug delivery. PMID:24036840

A semiautomated computer-interactive dynamic impact testing system

International Nuclear Information System (INIS)

Alexander, D.J.; Nanstad, R.K.; Corwin, W.R.; Hutton, J.T.

1989-01-01

A computer-assisted semiautomated system has been developed for testing a variety of specimen types under dynamic impact conditions. The primary use of this system is for the testing of Charpy specimens. Full-, half-, and third-size specimens have been tested, both in the lab and remotely in a hot cell for irradiated specimens. Specimens are loaded into a transfer device which moves the specimen into a chamber, where a hot air gun is used to heat the specimen, or cold nitrogen gas is used for cooling, as required. The specimen is then quickly transferred from the furnace to the anvils and then broken. This system incorporates an instrumented tup to determine the change in voltage during the fracture process. These data are analyzed by the computer system after the test is complete. The voltage-time trace is recorded with a digital oscilloscope, transferred to the computer, and analyzed. The analysis program incorporates several unique features. It interacts with the operator and identifies the maximum voltage during the test, the amount of rapid fracture during the test (if any), and the end of the fracture process. The program then calculates the area to maximum voltage and the total area under the voltage-time curve. The data acquisition and analysis part of the system can also be used to conduct other dynamic testing. Dynamic tear and precracked specimens can be tested with an instrumented tup and analyzed in a similar manner. 3 refs., 7 figs

Combining dynamical decoupling with fault-tolerant quantum computation

International Nuclear Information System (INIS)

Ng, Hui Khoon; Preskill, John; Lidar, Daniel A.

2011-01-01

We study how dynamical decoupling (DD) pulse sequences can improve the reliability of quantum computers. We prove upper bounds on the accuracy of DD-protected quantum gates and derive sufficient conditions for DD-protected gates to outperform unprotected gates. Under suitable conditions, fault-tolerant quantum circuits constructed from DD-protected gates can tolerate stronger noise and have a lower overhead cost than fault-tolerant circuits constructed from unprotected gates. Our accuracy estimates depend on the dynamics of the bath that couples to the quantum computer and can be expressed either in terms of the operator norm of the bath's Hamiltonian or in terms of the power spectrum of bath correlations; we explain in particular how the performance of recursively generated concatenated pulse sequences can be analyzed from either viewpoint. Our results apply to Hamiltonian noise models with limited spatial correlations.

Determining the sub-cellular localization of proteins within Caenorhabditis elegans body wall muscle.

Science.gov (United States)

Meissner, Barbara; Rogalski, Teresa; Viveiros, Ryan; Warner, Adam; Plastino, Lorena; Lorch, Adam; Granger, Laure; Segalat, Laurent; Moerman, Donald G

2011-01-01

Determining the sub-cellular localization of a protein within a cell is often an essential step towards understanding its function. In Caenorhabditis elegans, the relatively large size of the body wall muscle cells and the exquisite organization of their sarcomeres offer an opportunity to identify the precise position of proteins within cell substructures. Our goal in this study is to generate a comprehensive "localizome" for C. elegans body wall muscle by GFP-tagging proteins expressed in muscle and determining their location within the cell. For this project, we focused on proteins that we know are expressed in muscle and are orthologs or at least homologs of human proteins. To date we have analyzed the expression of about 227 GFP-tagged proteins that show localized expression in the body wall muscle of this nematode (e.g. dense bodies, M-lines, myofilaments, mitochondria, cell membrane, nucleus or nucleolus). For most proteins analyzed in this study no prior data on sub-cellular localization was available. In addition to discrete sub-cellular localization we observe overlapping patterns of localization including the presence of a protein in the dense body and the nucleus, or the dense body and the M-lines. In total we discern more than 14 sub-cellular localization patterns within nematode body wall muscle. The localization of this large set of proteins within a muscle cell will serve as an invaluable resource in our investigation of muscle sarcomere assembly and function.

Accumulation, subcellular distribution and toxicity of inorganic mercury and methylmercury in marine phytoplankton

Energy Technology Data Exchange (ETDEWEB)

Wu Yun [Division of Life Science, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong); Wang Wenxiong, E-mail: wwang@ust.hk [Division of Life Science, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon (Hong Kong)

2011-10-15

We examined the accumulation, subcellular distribution, and toxicity of Hg(II) and MeHg in three marine phytoplankton (the diatom Thalassiosira pseudonana, the green alga Chlorella autotrophica, and the flagellate Isochrysis galbana). For MeHg, the inter-species toxic difference could be best interpreted by the total cellular or intracellular accumulation. For Hg(II), both I. galbana and T. pseudonana exhibited similar sensitivity, but they each accumulated a different level of Hg(II). A higher percentage of Hg(II) was bound to the cellular debris fraction in T. pseudonana than in I. galbana, implying that the cellular debris may play an important role in Hg(II) detoxification. Furthermore, heat-stable proteins were a major binding pool for MeHg, while the cellular debris was an important binding pool for Hg(II). Elucidating the different subcellular fates of Hg(II) and MeHg may help us understand their toxicity in marine phytoplankton at the bottom of aquatic food chains. - Highlights: > The inter-species toxic difference of methylmercury in marine phytoplankton can be explained by its total cellular or intracellular accumulation. > The inter-species toxic difference of inorganic mercury in marine phytoplankton can be explained by its subcellular distribution. > Heat-stable protein was a major binding pool for MeHg, while the cellular debris was an important binding pool for Hg(II). - The inter-species difference in methylmercury and inorganic mercury toxicity in phytoplankton can be explained by cellular accumulation and subcellular distribution.

Accumulation, subcellular distribution and toxicity of inorganic mercury and methylmercury in marine phytoplankton

International Nuclear Information System (INIS)

Wu Yun; Wang Wenxiong

2011-01-01

We examined the accumulation, subcellular distribution, and toxicity of Hg(II) and MeHg in three marine phytoplankton (the diatom Thalassiosira pseudonana, the green alga Chlorella autotrophica, and the flagellate Isochrysis galbana). For MeHg, the inter-species toxic difference could be best interpreted by the total cellular or intracellular accumulation. For Hg(II), both I. galbana and T. pseudonana exhibited similar sensitivity, but they each accumulated a different level of Hg(II). A higher percentage of Hg(II) was bound to the cellular debris fraction in T. pseudonana than in I. galbana, implying that the cellular debris may play an important role in Hg(II) detoxification. Furthermore, heat-stable proteins were a major binding pool for MeHg, while the cellular debris was an important binding pool for Hg(II). Elucidating the different subcellular fates of Hg(II) and MeHg may help us understand their toxicity in marine phytoplankton at the bottom of aquatic food chains. - Highlights: → The inter-species toxic difference of methylmercury in marine phytoplankton can be explained by its total cellular or intracellular accumulation. → The inter-species toxic difference of inorganic mercury in marine phytoplankton can be explained by its subcellular distribution. → Heat-stable protein was a major binding pool for MeHg, while the cellular debris was an important binding pool for Hg(II). - The inter-species difference in methylmercury and inorganic mercury toxicity in phytoplankton can be explained by cellular accumulation and subcellular distribution.

Dynamic integration of remote cloud resources into local computing clusters

Energy Technology Data Exchange (ETDEWEB)

Fleig, Georg; Erli, Guenther; Giffels, Manuel; Hauth, Thomas; Quast, Guenter; Schnepf, Matthias [Institut fuer Experimentelle Kernphysik, Karlsruher Institut fuer Technologie (Germany)

2016-07-01

In modern high-energy physics (HEP) experiments enormous amounts of data are analyzed and simulated. Traditionally dedicated HEP computing centers are built or extended to meet this steadily increasing demand for computing resources. Nowadays it is more reasonable and more flexible to utilize computing power at remote data centers providing regular cloud services to users as they can be operated in a more efficient manner. This approach uses virtualization and allows the HEP community to run virtual machines containing a dedicated operating system and transparent access to the required software stack on almost any cloud site. The dynamic management of virtual machines depending on the demand for computing power is essential for cost efficient operation and sharing of resources with other communities. For this purpose the EKP developed the on-demand cloud manager ROCED for dynamic instantiation and integration of virtualized worker nodes into the institute's computing cluster. This contribution will report on the concept of our cloud manager and the implementation utilizing a remote OpenStack cloud site and a shared HPC center (bwForCluster located in Freiburg).

Image communication scheme based on dynamic visual cryptography and computer generated holography

Science.gov (United States)

Palevicius, Paulius; Ragulskis, Minvydas

2015-01-01

Computer generated holograms are often exploited to implement optical encryption schemes. This paper proposes the integration of dynamic visual cryptography (an optical technique based on the interplay of visual cryptography and time-averaging geometric moiré) with Gerchberg-Saxton algorithm. A stochastic moiré grating is used to embed the secret into a single cover image. The secret can be visually decoded by a naked eye if only the amplitude of harmonic oscillations corresponds to an accurately preselected value. The proposed visual image encryption scheme is based on computer generated holography, optical time-averaging moiré and principles of dynamic visual cryptography. Dynamic visual cryptography is used both for the initial encryption of the secret image and for the final decryption. Phase data of the encrypted image are computed by using Gerchberg-Saxton algorithm. The optical image is decrypted using the computationally reconstructed field of amplitudes.

Subcellular location of the enzymes of purine breakdown in the yeast Candida famata grown on uric acid

NARCIS (Netherlands)

Large, Peter J.; Waterham, Hans R.; Veenhuis, Marten

1990-01-01

The subcellular location of the enzymes of purine breakdown in the yeast Candida famata, which grows on uric acid as sole carbon and nitrogen source, has been examined by subcellular fractionation methods. Uricase was confirmed as being peroxisomal, but the other three enzymes, allantoinase,

Decomposition and Cross-Product-Based Method for Computing the Dynamic Equation of Robots

Directory of Open Access Journals (Sweden)

Ching-Long Shih

2012-08-01

Full Text Available This paper aims to demonstrate a clear relationship between Lagrange equations and Newton-Euler equations regarding computational methods for robot dynamics, from which we derive a systematic method for using either symbolic or on-line numerical computations. Based on the decomposition approach and cross-product operation, a computing method for robot dynamics can be easily developed. The advantages of this computing framework are that: it can be used for both symbolic and on-line numeric computation purposes, and it can also be applied to biped systems, as well as some simple closed-chain robot systems.

Pathways and Subcellular Compartmentation of NAD Biosynthesis in Human Cells

Science.gov (United States)

Nikiforov, Andrey; Dölle, Christian; Niere, Marc; Ziegler, Mathias

2011-01-01

NAD is a vital redox carrier, and its degradation is a key element of important regulatory pathways. NAD-mediated functions are compartmentalized and have to be fueled by specific biosynthetic routes. However, little is known about the different pathways, their subcellular distribution, and regulation in human cells. In particular, the route(s) to generate mitochondrial NAD, the largest subcellular pool, is still unknown. To visualize organellar NAD changes in cells, we targeted poly(ADP-ribose) polymerase activity into the mitochondrial matrix. This activity synthesized immunodetectable poly(ADP-ribose) depending on mitochondrial NAD availability. Based on this novel detector system, detailed subcellular enzyme localizations, and pharmacological inhibitors, we identified extracellular NAD precursors, their cytosolic conversions, and the pathway of mitochondrial NAD generation. Our results demonstrate that, besides nicotinamide and nicotinic acid, only the corresponding nucleosides readily enter the cells. Nucleotides (e.g. NAD and NMN) undergo extracellular degradation resulting in the formation of permeable precursors. These precursors can all be converted to cytosolic and mitochondrial NAD. For mitochondrial NAD synthesis, precursors are converted to NMN in the cytosol. When taken up into the organelles, NMN (together with ATP) serves as substrate of NMNAT3 to form NAD. NMNAT3 was conclusively localized to the mitochondrial matrix and is the only known enzyme of NAD synthesis residing within these organelles. We thus present a comprehensive dissection of mammalian NAD biosynthesis, the groundwork to understand regulation of NAD-mediated processes, and the organismal homeostasis of this fundamental molecule. PMID:21504897

Spatiotemporal Dynamics and Reliable Computations in Recurrent Spiking Neural Networks

Science.gov (United States)

Pyle, Ryan; Rosenbaum, Robert

2017-01-01

Randomly connected networks of excitatory and inhibitory spiking neurons provide a parsimonious model of neural variability, but are notoriously unreliable for performing computations. We show that this difficulty is overcome by incorporating the well-documented dependence of connection probability on distance. Spatially extended spiking networks exhibit symmetry-breaking bifurcations and generate spatiotemporal patterns that can be trained to perform dynamical computations under a reservoir computing framework.

Spatiotemporal Dynamics and Reliable Computations in Recurrent Spiking Neural Networks.

Science.gov (United States)

Pyle, Ryan; Rosenbaum, Robert

2017-01-06

Randomly connected networks of excitatory and inhibitory spiking neurons provide a parsimonious model of neural variability, but are notoriously unreliable for performing computations. We show that this difficulty is overcome by incorporating the well-documented dependence of connection probability on distance. Spatially extended spiking networks exhibit symmetry-breaking bifurcations and generate spatiotemporal patterns that can be trained to perform dynamical computations under a reservoir computing framework.

Computational Fluid Dynamics and Building Energy Performance Simulation

DEFF Research Database (Denmark)

Nielsen, Peter V.; Tryggvason, Tryggvi

An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution will be introduced for improvement of the predictions of both the energy consumption and the indoor environment. The building energy performance...

Dynamic Docking: A Paradigm Shift in Computational Drug Discovery

Directory of Open Access Journals (Sweden)

Dario Gioia

2017-11-01

Full Text Available Molecular docking is the methodology of choice for studying in silico protein-ligand binding and for prioritizing compounds to discover new lead candidates. Traditional docking simulations suffer from major limitations, mostly related to the static or semi-flexible treatment of ligands and targets. They also neglect solvation and entropic effects, which strongly limits their predictive power. During the last decade, methods based on full atomistic molecular dynamics (MD have emerged as a valid alternative for simulating macromolecular complexes. In principle, compared to traditional docking, MD allows the full exploration of drug-target recognition and binding from both the mechanistic and energetic points of view (dynamic docking. Binding and unbinding kinetic constants can also be determined. While dynamic docking is still too computationally expensive to be routinely used in fast-paced drug discovery programs, the advent of faster computing architectures and advanced simulation methodologies are changing this scenario. It is feasible that dynamic docking will replace static docking approaches in the near future, leading to a major paradigm shift in in silico drug discovery. Against this background, we review the key achievements that have paved the way for this progress.

Accurate prediction of subcellular location of apoptosis proteins combining Chou’s PseAAC and PsePSSM based on wavelet denoising

Science.gov (United States)

Chen, Cheng; Chen, Rui-Xin; Wang, Lei; Wang, Ming-Hui; Zhang, Yan

2017-01-01

Apoptosis proteins subcellular localization information are very important for understanding the mechanism of programmed cell death and the development of drugs. The prediction of subcellular localization of an apoptosis protein is still a challenging task because the prediction of apoptosis proteins subcellular localization can help to understand their function and the role of metabolic processes. In this paper, we propose a novel method for protein subcellular localization prediction. Firstly, the features of the protein sequence are extracted by combining Chou's pseudo amino acid composition (PseAAC) and pseudo-position specific scoring matrix (PsePSSM), then the feature information of the extracted is denoised by two-dimensional (2-D) wavelet denoising. Finally, the optimal feature vectors are input to the SVM classifier to predict subcellular location of apoptosis proteins. Quite promising predictions are obtained using the jackknife test on three widely used datasets and compared with other state-of-the-art methods. The results indicate that the method proposed in this paper can remarkably improve the prediction accuracy of apoptosis protein subcellular localization, which will be a supplementary tool for future proteomics research. PMID:29296195

Dynamical duality of type- and token-computation as an abstract brain

Energy Technology Data Exchange (ETDEWEB)

Gunji, Yukio-Pegio [Department of Earth and Planetary Sciences, Faculty of Science, Kobe University (Japan); Graduate School of Science and Technology, Kobe University (Japan)] e-mail: yukio@kobe-u.ac.jp; Miyoshi, Hiroyuki [Department of Computer Sciences, Faculty of Science, Kyoto Sangyo University (Japan); Takahashi, Tatsuji [Graduate School of Science and Technology, Kobe University (Japan); Kamiura, Moto [Graduate School of Science and Technology, Kobe University (Japan)

2006-03-01

In brain science, there are few researches focusing on the theoretical relation between cognition (top-down processing) and perception (bottom-up processing). Philosophically they were regarded as the alternative leading to the dualism of mind and body, while it is an adequate problem for the endo-physics. Qualia are conjectured as the hard problem under those situations. To overcome such an impasse, we propose an abstract brain model featuring the dynamical duality of two parts of computations in a brain, in a term of endo-physics and internal measurement. Two parts of computations are expressed as binary relations, and the relationship between them is expressed as a pair of maps, called an infomorphism [Barwise J, Seligman J. Information flow, the logic of distributed systems. Cambridge University Press 1997]. Dynamical duality is implemented by the interaction between a binary relation and an infomorphism, and that leads to a dynamical change of a pair of binary relations. When a binary relation is expressed as a partial ordered set, one can check whether a part of computation is closed with respect to logical operations (i.e., a lattice) or not. By estimating a binary relation in terms of properties of lattice, we show that dynamical infomorphism robustly develops to a pair of logical computations corresponding to type cognition and non-logical one corresponding to qualia perception. It implies origin of differentiation and robust co-existence of type-cognition and qualia-perception. It is easy to see that dynamical infomorphism can also develop to a pair of singleton sets corresponding to savants' special cognitive style.

Dynamical duality of type- and token-computation as an abstract brain

International Nuclear Information System (INIS)

Gunji, Yukio-Pegio; Miyoshi, Hiroyuki; Takahashi, Tatsuji; Kamiura, Moto

2006-01-01

In brain science, there are few researches focusing on the theoretical relation between cognition (top-down processing) and perception (bottom-up processing). Philosophically they were regarded as the alternative leading to the dualism of mind and body, while it is an adequate problem for the endo-physics. Qualia are conjectured as the hard problem under those situations. To overcome such an impasse, we propose an abstract brain model featuring the dynamical duality of two parts of computations in a brain, in a term of endo-physics and internal measurement. Two parts of computations are expressed as binary relations, and the relationship between them is expressed as a pair of maps, called an infomorphism [Barwise J, Seligman J. Information flow, the logic of distributed systems. Cambridge University Press 1997]. Dynamical duality is implemented by the interaction between a binary relation and an infomorphism, and that leads to a dynamical change of a pair of binary relations. When a binary relation is expressed as a partial ordered set, one can check whether a part of computation is closed with respect to logical operations (i.e., a lattice) or not. By estimating a binary relation in terms of properties of lattice, we show that dynamical infomorphism robustly develops to a pair of logical computations corresponding to type cognition and non-logical one corresponding to qualia perception. It implies origin of differentiation and robust co-existence of type-cognition and qualia-perception. It is easy to see that dynamical infomorphism can also develop to a pair of singleton sets corresponding to savants' special cognitive style

Metabolic dynamics in skeletal muscle during acute reduction in blood flow and oxygen supply to mitochondria: in-silico studies using a multi-scale, top-down integrated model.

Science.gov (United States)

Dash, Ranjan K; Li, Yanjun; Kim, Jaeyeon; Beard, Daniel A; Saidel, Gerald M; Cabrera, Marco E

2008-09-09

Control mechanisms of cellular metabolism and energetics in skeletal muscle that may become evident in response to physiological stresses such as reduction in blood flow and oxygen supply to mitochondria can be quantitatively understood using a multi-scale computational model. The analysis of dynamic responses from such a model can provide insights into mechanisms of metabolic regulation that may not be evident from experimental studies. For the purpose, a physiologically-based, multi-scale computational model of skeletal muscle cellular metabolism and energetics was developed to describe dynamic responses of key chemical species and reaction fluxes to muscle ischemia. The model, which incorporates key transport and metabolic processes and subcellular compartmentalization, is based on dynamic mass balances of 30 chemical species in both capillary blood and tissue cells (cytosol and mitochondria) domains. The reaction fluxes in cytosol and mitochondria are expressed in terms of a general phenomenological Michaelis-Menten equation involving the compartmentalized energy controller ratios ATP/ADP and NADH/NAD(+). The unknown transport and reaction parameters in the model are estimated simultaneously by minimizing the differences between available in vivo experimental data on muscle ischemia and corresponding model outputs in coupled with the resting linear flux balance constraints using a robust, nonlinear, constrained-based, reduced gradient optimization algorithm. With the optimal parameter values, the model is able to simulate dynamic responses to reduced blood flow and oxygen supply to mitochondria associated with muscle ischemia of several key metabolite concentrations and metabolic fluxes in the subcellular cytosolic and mitochondrial compartments, some that can be measured and others that can not be measured with the current experimental techniques. The model can be applied to test complex hypotheses involving dynamic regulation of cellular metabolism and

pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC.

Science.gov (United States)

Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen

2017-09-10

Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions. This kind of multiplex proteins is particularly important for both basic research and drug design. Using the multi-label theory, we present a new predictor called "pLoc-mVirus" by extracting the optimal GO (Gene Ontology) information into the general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validation on a same stringent benchmark dataset indicated that the proposed pLoc-mVirus predictor is remarkably superior to iLoc-Virus, the state-of-the-art method in predicting virus protein subcellular localization. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mVirus/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. Copyright © 2017 Elsevier B.V. All rights reserved.

Trainable hardware for dynamical computing using error backpropagation through physical media.

Science.gov (United States)

Hermans, Michiel; Burm, Michaël; Van Vaerenbergh, Thomas; Dambre, Joni; Bienstman, Peter

2015-03-24

Neural networks are currently implemented on digital Von Neumann machines, which do not fully leverage their intrinsic parallelism. We demonstrate how to use a novel class of reconfigurable dynamical systems for analogue information processing, mitigating this problem. Our generic hardware platform for dynamic, analogue computing consists of a reciprocal linear dynamical system with nonlinear feedback. Thanks to reciprocity, a ubiquitous property of many physical phenomena like the propagation of light and sound, the error backpropagation-a crucial step for tuning such systems towards a specific task-can happen in hardware. This can potentially speed up the optimization process significantly, offering important benefits for the scalability of neuro-inspired hardware. In this paper, we show, using one experimentally validated and one conceptual example, that such systems may provide a straightforward mechanism for constructing highly scalable, fully dynamical analogue computers.

Computational fluid dynamics simulations of light water reactor flows

International Nuclear Information System (INIS)

Tzanos, C.P.; Weber, D.P.

1999-01-01

Advances in computational fluid dynamics (CFD), turbulence simulation, and parallel computing have made feasible the development of three-dimensional (3-D) single-phase and two-phase flow CFD codes that can simulate fluid flow and heat transfer in realistic reactor geometries with significantly reduced reliance, especially in single phase, on empirical correlations. The objective of this work was to assess the predictive power and computational efficiency of a CFD code in the analysis of a challenging single-phase light water reactor problem, as well as to identify areas where further improvements are needed

Computational electrochemo-fluid dynamics modeling in a uranium electrowinning cell

International Nuclear Information System (INIS)

Kim, K.R.; Choi, S.Y.; Kim, S.H.; Shim, J.B.; Paek, S.; Kim, I.T.

2014-01-01

A computational electrochemo-fluid dynamics model has been developed to describe the electrowinning behavior in an electrolyte stream through a planar electrode cell system. Electrode reaction of the uranium electrowinning process from a molten-salt electrolyte stream was modeled to illustrate the details of the flow-assisted mass transport of ions to the cathode. This modeling approach makes it possible to represent variations of the convective diffusion limited current density by taking into account the concentration profile at the electrode surface as a function of the flow characteristics and applied current density in a commercially available computational fluid dynamics platform. It was possible to predict the conventional current-voltage relation in addition to details of electrolyte fluid dynamics and electrochemical variables, such as the flow field, species concentrations, potential, and current distributions throughout the galvanostatic electrolysis cell. (author)

Imaging cells and sub-cellular structures with ultrahigh resolution full-field X-ray microscopy.

Science.gov (United States)

Chien, C C; Tseng, P Y; Chen, H H; Hua, T E; Chen, S T; Chen, Y Y; Leng, W H; Wang, C H; Hwu, Y; Yin, G C; Liang, K S; Chen, F R; Chu, Y S; Yeh, H I; Yang, Y C; Yang, C S; Zhang, G L; Je, J H; Margaritondo, G

2013-01-01

Our experimental results demonstrate that full-field hard-X-ray microscopy is finally able to investigate the internal structure of cells in tissues. This result was made possible by three main factors: the use of a coherent (synchrotron) source of X-rays, the exploitation of contrast mechanisms based on the real part of the refractive index and the magnification provided by high-resolution Fresnel zone-plate objectives. We specifically obtained high-quality microradiographs of human and mouse cells with 29 nm Rayleigh spatial resolution and verified that tomographic reconstruction could be implemented with a final resolution level suitable for subcellular features. We also demonstrated that a phase retrieval method based on a wave propagation algorithm could yield good subcellular images starting from a series of defocused microradiographs. The concluding discussion compares cellular and subcellular hard-X-ray microradiology with other techniques and evaluates its potential impact on biomedical research. Copyright © 2012 Elsevier Inc. All rights reserved.

Subcellular localization of ammonium transporters in Dictyostelium discoideum

Directory of Open Access Journals (Sweden)

Davis Carter T

2008-12-01

Full Text Available Abstract Background With the exception of vertebrates, most organisms have plasma membrane associated ammonium transporters which primarily serve to import a source of nitrogen for nutritional purposes. Dictyostelium discoideum has three ammonium transporters, Amts A, B and C. Our present work used fluorescent fusion proteins to determine the cellular localization of the Amts and tested the hypothesis that the transporters mediate removal of ammonia generated endogenously from the elevated protein catabolism common to many protists. Results Using RFP and YFP fusion constructs driven by the actin 15 promoter, we found that the three ammonium transporters were localized on the plasma membrane and on the membranes of subcellular organelles. AmtA and AmtB were localized on the membranes of endolysosomes and phagosomes, with AmtB further localized on the membranes of contractile vacuoles. AmtC also was localized on subcellular organelles when it was stabilized by coexpression with either the AmtA or AmtB fusion transporter. The three ammonium transporters exported ammonia linearly with regard to time during the first 18 hours of the developmental program as revealed by reduced export in the null strains. The fluorescently tagged transporters rescued export when expressed in the null strains, and thus they were functional transporters. Conclusion Unlike ammonium transporters in most organisms, which import NH3/NH4+ as a nitrogen source, those of Dictyostelium export ammonia/ammonium as a waste product from extensive catabolism of exogenously derived and endogenous proteins. Localization on proteolytic organelles and on the neutral contractile vacuole suggests that Dictyostelium ammonium transporters may have unique subcellular functions and play a role in the maintenance of intracellular ammonium distribution. A lack of correlation between the null strain phenotypes and ammonia excretion properties of the ammonium transporters suggests that it is not

Subcellular SIMS imaging of gadolinium isotopes in human glioblastoma cells treated with a gadolinium containing MRI agent

Science.gov (United States)

Smith, Duane R.; Lorey, Daniel R.; Chandra, Subhash

2004-06-01

Neutron capture therapy is an experimental binary radiotherapeutic modality for the treatment of brain tumors such as glioblastoma multiforme. Recently, neutron capture therapy with gadolinium-157 has gained attention, and techniques for studying the subcellular distribution of gadolinium-157 are needed. In this preliminary study, we have been able to image the subcellular distribution of gadolinium-157, as well as the other six naturally abundant isotopes of gadolinium, with SIMS ion microscopy. T98G human glioblastoma cells were treated for 24 h with 25 mg/ml of the metal ion complex diethylenetriaminepentaacetic acid Gd(III) dihydrogen salt hydrate (Gd-DTPA). Gd-DTPA is a contrast enhancing agent used for MRI of brain tumors, blood-brain barrier impairment, diseases of the central nervous system, etc. A highly heterogeneous subcellular distribution was observed for gadolinium-157. The nuclei in each cell were distinctly lower in gadolinium-157 than in the cytoplasm. Even within the cytoplasm the gadolinium-157 was heterogeneously distributed. The other six naturally abundant isotopes of gadolinium were imaged from the same cells and exhibited a subcellular distribution consistent with that observed for gadolinium-157. These observations indicate that SIMS ion microscopy may be a viable approach for subcellular studies of gadolinium containing neutron capture therapy drugs and may even play a major role in the development and validation of new gadolinium contrast enhancing agents for diagnostic MRI applications.

Prospects for Computational Fluid Dynamics in Room Air Contaminant Control

DEFF Research Database (Denmark)

Nielsen, Peter V.

The fluid dynamics research is strongly influenced by the increasing computer power which has been available for the last decades. This development is obvious from the curve in figure 1 which shows the computation cost as a function of years. It is obvious that the cost for a given job will decre...

A Simple Method for Dynamic Scheduling in a Heterogeneous Computing System

OpenAIRE

Žumer, Viljem; Brest, Janez

2002-01-01

A simple method for the dynamic scheduling on a heterogeneous computing system is proposed in this paper. It was implemented to minimize the parallel program execution time. The proposed method decomposes the program workload into computationally homogeneous subtasks, which may be of the different size, depending on the current load of each machine in a heterogeneous computing system.

Dynamical Trust and Reputation Computation Model for B2C E-Commerce

Directory of Open Access Journals (Sweden)

Bo Tian

2015-10-01

Full Text Available Trust is one of the most important factors that influence the successful application of network service environments, such as e-commerce, wireless sensor networks, and online social networks. Computation models associated with trust and reputation have been paid special attention in both computer societies and service science in recent years. In this paper, a dynamical computation model of reputation for B2C e-commerce is proposed. Firstly, conceptions associated with trust and reputation are introduced, and the mathematical formula of trust for B2C e-commerce is given. Then a dynamical computation model of reputation is further proposed based on the conception of trust and the relationship between trust and reputation. In the proposed model, classical varying processes of reputation of B2C e-commerce are discussed. Furthermore, the iterative trust and reputation computation models are formulated via a set of difference equations based on the closed-loop feedback mechanism. Finally, a group of numerical simulation experiments are performed to illustrate the proposed model of trust and reputation. Experimental results show that the proposed model is effective in simulating the dynamical processes of trust and reputation for B2C e-commerce.

Formal Analysis of Dynamics Within Philosophy of Mind by Computer Simulation

NARCIS (Netherlands)

Bosse, T.; Schut, M.C.; Treur, J.

2009-01-01

Computer simulations can be useful tools to support philosophers in validating their theories, especially when these theories concern phenomena showing nontrivial dynamics. Such theories are usually informal, whilst for computer simulation a formally described model is needed. In this paper, a

On Computational Fluid Dynamics Tools in Architectural Design

DEFF Research Database (Denmark)

Kirkegaard, Poul Henning; Hougaard, Mads; Stærdahl, Jesper Winther

engineering computational fluid dynamics (CFD) simulation program ANSYS CFX and a CFD based representative program RealFlow are investigated. These two programs represent two types of CFD based tools available for use during phases of an architectural design process. However, as outlined in two case studies...

Direct modeling for computational fluid dynamics

Science.gov (United States)

Xu, Kun

2015-06-01

All fluid dynamic equations are valid under their modeling scales, such as the particle mean free path and mean collision time scale of the Boltzmann equation and the hydrodynamic scale of the Navier-Stokes (NS) equations. The current computational fluid dynamics (CFD) focuses on the numerical solution of partial differential equations (PDEs), and its aim is to get the accurate solution of these governing equations. Under such a CFD practice, it is hard to develop a unified scheme that covers flow physics from kinetic to hydrodynamic scales continuously because there is no such governing equation which could make a smooth transition from the Boltzmann to the NS modeling. The study of fluid dynamics needs to go beyond the traditional numerical partial differential equations. The emerging engineering applications, such as air-vehicle design for near-space flight and flow and heat transfer in micro-devices, do require further expansion of the concept of gas dynamics to a larger domain of physical reality, rather than the traditional distinguishable governing equations. At the current stage, the non-equilibrium flow physics has not yet been well explored or clearly understood due to the lack of appropriate tools. Unfortunately, under the current numerical PDE approach, it is hard to develop such a meaningful tool due to the absence of valid PDEs. In order to construct multiscale and multiphysics simulation methods similar to the modeling process of constructing the Boltzmann or the NS governing equations, the development of a numerical algorithm should be based on the first principle of physical modeling. In this paper, instead of following the traditional numerical PDE path, we introduce direct modeling as a principle for CFD algorithm development. Since all computations are conducted in a discretized space with limited cell resolution, the flow physics to be modeled has to be done in the mesh size and time step scales. Here, the CFD is more or less a direct

Parallel Computational Fluid Dynamics 2007 : Implementations and Experiences on Large Scale and Grid Computing

CERN Document Server

2009-01-01

At the 19th Annual Conference on Parallel Computational Fluid Dynamics held in Antalya, Turkey, in May 2007, the most recent developments and implementations of large-scale and grid computing were presented. This book, comprised of the invited and selected papers of this conference, details those advances, which are of particular interest to CFD and CFD-related communities. It also offers the results related to applications of various scientific and engineering problems involving flows and flow-related topics. Intended for CFD researchers and graduate students, this book is a state-of-the-art presentation of the relevant methodology and implementation techniques of large-scale computing.

ALG-2 oscillates in subcellular localization, unitemporally with calcium oscillations

DEFF Research Database (Denmark)

la Cour, Jonas Marstrand; Mollerup, Jens; Berchtold, Martin Werner

2007-01-01

discovered that the subcellular distribution of a tagged version of ALG-2 could be directed by physiological external stimuli (including ATP, EGF, prostaglandin, histamine), which provoke intracellular Ca2+ oscillations. Cellular stimulation led to a redistribution of ALG-2 from the cytosol to a punctate...

Analysis of the subcellular localization of the human histone methyltransferase SETDB1

Energy Technology Data Exchange (ETDEWEB)

Tachibana, Keisuke, E-mail: nya@phs.osaka-u.ac.jp [Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 (Japan); Gotoh, Eiko; Kawamata, Natsuko [Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 (Japan); Ishimoto, Kenji [Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 (Japan); Laboratory for System Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Uchihara, Yoshie [Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 (Japan); Iwanari, Hiroko [Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Sugiyama, Akira; Kawamura, Takeshi [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032 (Japan); Mochizuki, Yasuhiro [Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Tanaka, Toshiya [Laboratory for System Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Sakai, Juro [Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Hamakubo, Takao [Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Kodama, Tatsuhiko [Laboratory for System Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); and others

2015-10-02

SET domain, bifurcated 1 (SETDB1) is a histone methyltransferase that methylates lysine 9 on histone H3. Although it is important to know the localization of proteins to elucidate their physiological function, little is known of the subcellular localization of human SETDB1. In the present study, to investigate the subcellular localization of hSETDB1, we established a human cell line constitutively expressing enhanced green fluorescent protein fused to hSETDB1. We then generated a monoclonal antibody against the hSETDB1 protein. Expression of both exogenous and endogenous hSETDB1 was observed mainly in the cytoplasm of various human cell lines. Combined treatment with the nuclear export inhibitor leptomycin B and the proteasome inhibitor MG132 led to the accumulation of hSETDB1 in the nucleus. These findings suggest that hSETDB1, localized in the nucleus, might undergo degradation by the proteasome and be exported to the cytosol, resulting in its detection mainly in the cytosol. - Highlights: • Endogenous human SETDB1 was localized mainly in the cytoplasm. • Combined treatment with LMB and MG132 led to accumulation of human SETDB1 in the nucleus. • HeLa cells expressing EFGP-hSETDB1 are useful for subcellular localization analyses.

Distribution of physostigmine and metabolites in brain subcellular fractions of the rat

International Nuclear Information System (INIS)

King, B.F.; Somani, S.M.

1987-01-01

The distribution of 3 H-physostigmine (Phy) has been studied in the rat brain subcellular fractions at various time intervals following i.v. injection. 3 H-Phy or its metabolites rapidly accumulate into the cytoplasm of cells and penetrates the intracellular compartments. Kinetic studies of the subcellular distribution of radioactivity (RA) per gm of rat brain following i.v. injection of 3 H-Phy show peak concentrations at 30 min in all subcellular fractions with the exception of mitochondria. In the mitochondrial fraction the RA levels continue to rise from 4682 +/- 875 DPM/gm at 5 min to 27,474 +/- 2825 DPM/gm at 60 min (P < .05). The cytosol contains the highest RA: 223,341 +/- 21,044 DPM/gm at 30 min which declined to 53,475 +/- 3756 DPM/gm at 60 min. RA in synaptosome, microsomes and myelin increases from 5 to 30 min, and declines at 60 min. In vitro studies did not show a greater uptake of RA by the mitochondrial or synaptosomal fractions. The finding of relatively high concentrations of RA in the mitochondrial fraction at 60 min increases the likelihood that Phy or its metabolites could interfere with the physiological function of the organelle. 21 references, 1 figure, 2 tables

Analysis of the subcellular localization of the human histone methyltransferase SETDB1

International Nuclear Information System (INIS)

Tachibana, Keisuke; Gotoh, Eiko; Kawamata, Natsuko; Ishimoto, Kenji; Uchihara, Yoshie; Iwanari, Hiroko; Sugiyama, Akira; Kawamura, Takeshi; Mochizuki, Yasuhiro; Tanaka, Toshiya; Sakai, Juro; Hamakubo, Takao; Kodama, Tatsuhiko

2015-01-01

SET domain, bifurcated 1 (SETDB1) is a histone methyltransferase that methylates lysine 9 on histone H3. Although it is important to know the localization of proteins to elucidate their physiological function, little is known of the subcellular localization of human SETDB1. In the present study, to investigate the subcellular localization of hSETDB1, we established a human cell line constitutively expressing enhanced green fluorescent protein fused to hSETDB1. We then generated a monoclonal antibody against the hSETDB1 protein. Expression of both exogenous and endogenous hSETDB1 was observed mainly in the cytoplasm of various human cell lines. Combined treatment with the nuclear export inhibitor leptomycin B and the proteasome inhibitor MG132 led to the accumulation of hSETDB1 in the nucleus. These findings suggest that hSETDB1, localized in the nucleus, might undergo degradation by the proteasome and be exported to the cytosol, resulting in its detection mainly in the cytosol. - Highlights: • Endogenous human SETDB1 was localized mainly in the cytoplasm. • Combined treatment with LMB and MG132 led to accumulation of human SETDB1 in the nucleus. • HeLa cells expressing EFGP-hSETDB1 are useful for subcellular localization analyses.

Real-time quantification of subcellular H2O2 and glutathione redox potential in living cardiovascular tissues.

Science.gov (United States)

Panieri, Emiliano; Millia, Carlo; Santoro, Massimo M

2017-08-01

Detecting and measuring the dynamic redox events that occur in vivo is a prerequisite for understanding the impact of oxidants and redox events in normal and pathological conditions. These aspects are particularly relevant in cardiovascular tissues wherein alterations of the redox balance are associated with stroke, aging, and pharmacological intervention. An ambiguous aspect of redox biology is how redox events occur in subcellular organelles including mitochondria, and nuclei. Genetically-encoded Rogfp2 fluorescent probes have become powerful tools for real-time detection of redox events. These probes detect hydrogen peroxide (H 2 O 2 ) levels and glutathione redox potential (E GSH ), both with high spatiotemporal resolution. By generating novel transgenic (Tg) zebrafish lines that express compartment-specific Rogfp2-Orp1 and Grx1-Rogfp2 sensors we analyzed cytosolic, mitochondrial, and the nuclear redox state of endothelial cells and cardiomyocytes of living zebrafish embryos. We provide evidence for the usefulness of these Tg lines for pharmacological compounds screening by addressing the blocking of pentose phosphate pathways (PPP) and glutathione synthesis, thus altering subcellular redox state in vivo. Rogfp2-based transgenic zebrafish lines represent valuable tools to characterize the impact of redox changes in living tissues and offer new opportunities for studying metabolic driven antioxidant response in biomedical research. Copyright © 2017 Elsevier Inc. All rights reserved.

New Frontiers in Analyzing Dynamic Group Interactions: Bridging Social and Computer Science.

Science.gov (United States)

Lehmann-Willenbrock, Nale; Hung, Hayley; Keyton, Joann

2017-10-01

This special issue on advancing interdisciplinary collaboration between computer scientists and social scientists documents the joint results of the international Lorentz workshop, "Interdisciplinary Insights into Group and Team Dynamics," which took place in Leiden, The Netherlands, July 2016. An equal number of scholars from social and computer science participated in the workshop and contributed to the papers included in this special issue. In this introduction, we first identify interaction dynamics as the core of group and team models and review how scholars in social and computer science have typically approached behavioral interactions in groups and teams. Next, we identify key challenges for interdisciplinary collaboration between social and computer scientists, and we provide an overview of the different articles in this special issue aimed at addressing these challenges.

Computational and experimental investigation of dynamic shock reflection phenomena

CSIR Research Space (South Africa)

Naidoo, K

2007-07-01

Full Text Available wedge are used to analyse dynamic flow field phenomena and response of the triple point below and within the dual solution domain. Computed, unsteady pressure traces on the reflection plane are also analysed...

Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report Phase I

Energy Technology Data Exchange (ETDEWEB)

Schmalz, Mark S

2011-07-24

Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G} for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient

Forward and adjoint sensitivity computation of chaotic dynamical systems

Energy Technology Data Exchange (ETDEWEB)

Wang, Qiqi, E-mail: qiqi@mit.edu [Department of Aeronautics and Astronautics, MIT, 77 Mass Ave., Cambridge, MA 02139 (United States)

2013-02-15

This paper describes a forward algorithm and an adjoint algorithm for computing sensitivity derivatives in chaotic dynamical systems, such as the Lorenz attractor. The algorithms compute the derivative of long time averaged “statistical” quantities to infinitesimal perturbations of the system parameters. The algorithms are demonstrated on the Lorenz attractor. We show that sensitivity derivatives of statistical quantities can be accurately estimated using a single, short trajectory (over a time interval of 20) on the Lorenz attractor.

Zonal methods and computational fluid dynamics

International Nuclear Information System (INIS)

Atta, E.H.

1985-01-01

Recent advances in developing numerical algorithms for solving fluid flow problems, and the continuing improvement in the speed and storage of large scale computers have made it feasible to compute the flow field about complex and realistic configurations. Current solution methods involve the use of a hierarchy of mathematical models ranging from the linearized potential equation to the Navier Stokes equations. Because of the increasing complexity of both the geometries and flowfields encountered in practical fluid flow simulation, there is a growing emphasis in computational fluid dynamics on the use of zonal methods. A zonal method is one that subdivides the total flow region into interconnected smaller regions or zones. The flow solutions in these zones are then patched together to establish the global flow field solution. Zonal methods are primarily used either to limit the complexity of the governing flow equations to a localized region or to alleviate the grid generation problems about geometrically complex and multicomponent configurations. This paper surveys the application of zonal methods for solving the flow field about two and three-dimensional configurations. Various factors affecting their accuracy and ease of implementation are also discussed. From the presented review it is concluded that zonal methods promise to be very effective for computing complex flowfields and configurations. Currently there are increasing efforts to improve their efficiency, versatility, and accuracy

[L-arginine metabolism enzyme activities in rat liver subcellular fractions under condition of protein deprivation].

Science.gov (United States)

Kopyl'chuk, G P; Buchkovskaia, I M

2014-01-01

The features of arginase and NO-synthase pathways of arginine's metabolism have been studied in rat liver subcellular fractions under condition of protein deprivation. During the experimental period (28 days) albino male rats were kept on semi synthetic casein diet AIN-93. The protein deprivation conditions were designed as total absence of protein in the diet and consumption of the diet partially deprived with 1/2 of the casein amount compared to in the regular diet. Daily diet consumption was regulated according to the pair feeding approach. It has been shown that the changes of enzyme activities, involved in L-arginine metabolism, were characterized by 1.4-1.7 fold decrease in arginase activity, accompanied with unchanged NO-synthase activity in cytosol. In mitochondrial fraction the unchanged arginase activity was accompanied by 3-5 fold increase of NO-synthase activity. At the terminal stages of the experiment the monodirectional dynamics in the studied activities have been observed in the mitochondrial and cytosolfractions in both experimental groups. In the studied subcellular fractions arginase activity decreased (2.4-2.7 fold with no protein in the diet and 1.5 fold with partly supplied protein) and was accompanied by NO-synthase activity increase by 3.8 fold in cytosole fraction, by 7.2 fold in mitochondrial fraction in the group with no protein in the diet and by 2.2 and 3.5 fold in the group partialy supplied with protein respectively. The observed tendency is presumably caused by the switch of L-arginine metabolism from arginase into oxidizing NO-synthase parthway.

High-Precision Computation: Mathematical Physics and Dynamics

International Nuclear Information System (INIS)

Bailey, D.H.; Barrio, R.; Borwein, J.M.

2010-01-01

At the present time, IEEE 64-bit oating-point arithmetic is suficiently accurate for most scientic applications. However, for a rapidly growing body of important scientic computing applications, a higher level of numeric precision is required. Such calculations are facilitated by high-precision software packages that include high-level language translation modules to minimize the conversion e ort. This pa- per presents a survey of recent applications of these techniques and provides someanalysis of their numerical requirements. These applications include supernova simulations, climate modeling, planetary orbit calculations, Coulomb n-body atomic systems, studies of the one structure constant, scattering amplitudes of quarks, glu- ons and bosons, nonlinear oscillator theory, experimental mathematics, evaluation of orthogonal polynomials, numerical integration of ODEs, computation of periodic orbits, studies of the splitting of separatrices, detection of strange nonchaotic at- tractors, Ising theory, quantum held theory, and discrete dynamical systems. We conclude that high-precision arithmetic facilities are now an indispensable compo- nent of a modern large-scale scientic computing environment.

High-Precision Computation: Mathematical Physics and Dynamics

Energy Technology Data Exchange (ETDEWEB)

Bailey, D. H.; Barrio, R.; Borwein, J. M.

2010-04-01

At the present time, IEEE 64-bit oating-point arithmetic is suficiently accurate for most scientic applications. However, for a rapidly growing body of important scientic computing applications, a higher level of numeric precision is required. Such calculations are facilitated by high-precision software packages that include high-level language translation modules to minimize the conversion e ort. This pa- per presents a survey of recent applications of these techniques and provides someanalysis of their numerical requirements. These applications include supernova simulations, climate modeling, planetary orbit calculations, Coulomb n-body atomic systems, studies of the one structure constant, scattering amplitudes of quarks, glu- ons and bosons, nonlinear oscillator theory, experimental mathematics, evaluation of orthogonal polynomials, numerical integration of ODEs, computation of periodic orbits, studies of the splitting of separatrices, detection of strange nonchaotic at- tractors, Ising theory, quantum held theory, and discrete dynamical systems. We conclude that high-precision arithmetic facilities are now an indispensable compo- nent of a modern large-scale scientic computing environment.

Structure and dynamics of amorphous polymers: computer simulations compared to experiment and theory

International Nuclear Information System (INIS)

Paul, Wolfgang; Smith, Grant D

2004-01-01

This contribution considers recent developments in the computer modelling of amorphous polymeric materials. Progress in our capabilities to build models for the computer simulation of polymers from the detailed atomistic scale up to coarse-grained mesoscopic models, together with the ever-improving performance of computers, have led to important insights from computer simulations into the structural and dynamic properties of amorphous polymers. Structurally, chain connectivity introduces a range of length scales from that of the chemical bond to the radius of gyration of the polymer chain covering 2-4 orders of magnitude. Dynamically, this range of length scales translates into an even larger range of time scales observable in relaxation processes in amorphous polymers ranging from about 10 -13 to 10 -3 s or even to 10 3 s when glass dynamics is concerned. There is currently no single simulation technique that is able to describe all these length and time scales efficiently. On large length and time scales basic topology and entropy become the governing properties and this fact can be exploited using computer simulations of coarse-grained polymer models to study universal aspects of the structure and dynamics of amorphous polymers. On the largest length and time scales chain connectivity is the dominating factor leading to the strong increase in longest relaxation times described within the reptation theory of polymer melt dynamics. Recently, many of the universal aspects of this behaviour have been further elucidated by computer simulations of coarse-grained polymer models. On short length scales the detailed chemistry and energetics of the polymer are important, and one has to be able to capture them correctly using chemically realistic modelling of specific polymers, even when the aim is to extract generic physical behaviour exhibited by the specific chemistry. Detailed studies of chemically realistic models highlight the central importance of torsional dynamics

Spatio-temporal manipulation of small GTPase activity at subcellular level and on timescale of seconds in living cells.

Science.gov (United States)

DeRose, Robert; Pohlmeyer, Christopher; Umeda, Nobuhiro; Ueno, Tasuku; Nagano, Tetsuo; Kuo, Scot; Inoue, Takanari

2012-03-09

Dynamic regulation of the Rho family of small guanosine triphosphatases (GTPases) with great spatiotemporal precision is essential for various cellular functions and events(1, 2). Their spatiotemporally dynamic nature has been revealed by visualization of their activity and localization in real time(3). In order to gain deeper understanding of their roles in diverse cellular functions at the molecular level, the next step should be perturbation of protein activities at a precise subcellular location and timing. To achieve this goal, we have developed a method for light-induced, spatio-temporally controlled activation of small GTPases by combining two techniques: (1) rapamycin-induced FKBP-FRB heterodimerization and (2) a photo-caging method of rapamycin. With the use of rapamycin-mediated FKBP-FRB heterodimerization, we have developed a method for rapidly inducible activation or inactivation of small GTPases including Rac(4), Cdc42(4), RhoA(4) and Ras(5), in which rapamycin induces translocation of FKBP-fused GTPases, or their activators, to the plasma membrane where FRB is anchored. For coupling with this heterodimerization system, we have also developed a photo-caging system of rapamycin analogs. A photo-caged compound is a small molecule whose activity is suppressed with a photocleavable protecting group known as a caging group. To suppress heterodimerization activity completely, we designed a caged rapamycin that is tethered to a macromolecule such that the resulting large complex cannot cross the plasma membrane, leading to virtually no background activity as a chemical dimerizer inside cells(6). Figure 1 illustrates a scheme of our system. With the combination of these two systems, we locally recruited a Rac activator to the plasma membrane on a timescale of seconds and achieved light-induced Rac activation at the subcellular level(6).

Computational Psychometrics for Modeling System Dynamics during Stressful Disasters

Directory of Open Access Journals (Sweden)

Pietro Cipresso

2017-08-01

Full Text Available Disasters can be very stressful events. However, computational models of stress require data that might be very difficult to collect during disasters. Moreover, personal experiences are not repeatable, so it is not possible to collect bottom-up information when building a coherent model. To overcome these problems, we propose the use of computational models and virtual reality integration to recreate disaster situations, while examining possible dynamics in order to understand human behavior and relative consequences. By providing realistic parameters associated with disaster situations, computational scientists can work more closely with emergency responders to improve the quality of interventions in the future.

Subcellular and supracellular mechanical stress prescribes cytoskeleton behavior in Arabidopsis cotyledon pavement cells

Science.gov (United States)

Sampathkumar, Arun; Krupinski, Pawel; Wightman, Raymond; Milani, Pascale; Berquand, Alexandre; Boudaoud, Arezki; Hamant, Olivier; Jönsson, Henrik; Meyerowitz, Elliot M

2014-01-01

Although it is a central question in biology, how cell shape controls intracellular dynamics largely remains an open question. Here, we show that the shape of Arabidopsis pavement cells creates a stress pattern that controls microtubule orientation, which then guides cell wall reinforcement. Live-imaging, combined with modeling of cell mechanics, shows that microtubules align along the maximal tensile stress direction within the cells, and atomic force microscopy demonstrates that this leads to reinforcement of the cell wall parallel to the microtubules. This feedback loop is regulated: cell-shape derived stresses could be overridden by imposed tissue level stresses, showing how competition between subcellular and supracellular cues control microtubule behavior. Furthermore, at the microtubule level, we identified an amplification mechanism in which mechanical stress promotes the microtubule response to stress by increasing severing activity. These multiscale feedbacks likely contribute to the robustness of microtubule behavior in plant epidermis. DOI: http://dx.doi.org/10.7554/eLife.01967.001 PMID:24740969

Bioaccumulation and subcellular partitioning of zinc in rainbow trout (Oncorhynchus mykiss): Cross-talk between waterborne and dietary uptake

International Nuclear Information System (INIS)

Sappal, Ravinder; Burka, John; Dawson, Susan; Kamunde, Collins

2009-01-01

Zinc homeostasis was studied at the tissue and gill subcellular levels in rainbow trout (Oncorhynchus mykiss) following waterborne and dietary exposures, singly and in combination. Juvenile rainbow trout were exposed to 150 or 600 μg l -1 waterborne Zn, 1500 or 4500 μg g -1 dietary Zn, and a combination of 150 μg l -1 waterborne and 1500 μg g -1 dietary Zn for 40 days. Accumulation of Zn in tissues and gill subcellular fractions was measured. At the tissue level, the carcass acted as the main Zn depot containing 84-90% of whole body Zn burden whereas the gill held 4-6%. At the subcellular level, the majority of gill Zn was bioavailable with the estimated metabolically active pool being 81-90%. Interestingly, the nuclei-cellular debris fraction bound the highest amount (40%) of the gill Zn burden. There was low partitioning of Zn into the detoxified pool (10-19%) suggesting that sequestration and chelation are not major mechanisms of cellular Zn homeostasis in rainbow trout. Further, the subcellular partitioning of Zn did not conform to the spill-over model of metal toxicity because Zn binding was indiscriminate irrespective of exposure concentration and duration. The contribution of the branchial and gastrointestinal uptake pathways to Zn accumulation depended on the tissue. Specifically, in plasma, blood cells, and gill, uptake from water was dominant whereas both pathways appeared to contribute equally to Zn accumulation in the carcass. Subcellularly, additive uptake from the two pathways was observed in the heat-stable proteins (HSP) fraction. Toxicologically, Zn exposure caused minimal adverse effects manifested by a transitory inhibition of protein synthesis in gills in the waterborne exposure. Overall, subcellular fractionation appears to have value in the quest for a better understanding of Zn homeostasis and interactions between branchial and gastrointestinal uptake pathways

Bioaccumulation and subcellular partitioning of zinc in rainbow trout (Oncorhynchus mykiss): Cross-talk between waterborne and dietary uptake

Energy Technology Data Exchange (ETDEWEB)

Sappal, Ravinder; Burka, John; Dawson, Susan [Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3 (Canada); Kamunde, Collins [Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3 (Canada)], E-mail: ckamunde@upei.ca

2009-03-09

Zinc homeostasis was studied at the tissue and gill subcellular levels in rainbow trout (Oncorhynchus mykiss) following waterborne and dietary exposures, singly and in combination. Juvenile rainbow trout were exposed to 150 or 600 {mu}g l{sup -1} waterborne Zn, 1500 or 4500 {mu}g g{sup -1} dietary Zn, and a combination of 150 {mu}g l{sup -1} waterborne and 1500 {mu}g g{sup -1} dietary Zn for 40 days. Accumulation of Zn in tissues and gill subcellular fractions was measured. At the tissue level, the carcass acted as the main Zn depot containing 84-90% of whole body Zn burden whereas the gill held 4-6%. At the subcellular level, the majority of gill Zn was bioavailable with the estimated metabolically active pool being 81-90%. Interestingly, the nuclei-cellular debris fraction bound the highest amount (40%) of the gill Zn burden. There was low partitioning of Zn into the detoxified pool (10-19%) suggesting that sequestration and chelation are not major mechanisms of cellular Zn homeostasis in rainbow trout. Further, the subcellular partitioning of Zn did not conform to the spill-over model of metal toxicity because Zn binding was indiscriminate irrespective of exposure concentration and duration. The contribution of the branchial and gastrointestinal uptake pathways to Zn accumulation depended on the tissue. Specifically, in plasma, blood cells, and gill, uptake from water was dominant whereas both pathways appeared to contribute equally to Zn accumulation in the carcass. Subcellularly, additive uptake from the two pathways was observed in the heat-stable proteins (HSP) fraction. Toxicologically, Zn exposure caused minimal adverse effects manifested by a transitory inhibition of protein synthesis in gills in the waterborne exposure. Overall, subcellular fractionation appears to have value in the quest for a better understanding of Zn homeostasis and interactions between branchial and gastrointestinal uptake pathways.

Hepatic blood perfusion estimated by dynamic contrast-enhanced computed tomography in pigs

DEFF Research Database (Denmark)

Winterdahl, Michael; Sørensen, Michael; Keiding, Inger Susanne

2012-01-01

The aim of this study was to determine whether dynamic contrast-enhanced computed tomography (DCE-CT) and the slope method can provide absolute measures of hepatic blood perfusion from the hepatic artery (HA) and portal vein (PV) at experimentally varied blood flow rates.......The aim of this study was to determine whether dynamic contrast-enhanced computed tomography (DCE-CT) and the slope method can provide absolute measures of hepatic blood perfusion from the hepatic artery (HA) and portal vein (PV) at experimentally varied blood flow rates....

Fluid dynamics parallel computer development at NASA Langley Research Center

Science.gov (United States)

Townsend, James C.; Zang, Thomas A.; Dwoyer, Douglas L.

1987-01-01

To accomplish more detailed simulations of highly complex flows, such as the transition to turbulence, fluid dynamics research requires computers much more powerful than any available today. Only parallel processing on multiple-processor computers offers hope for achieving the required effective speeds. Looking ahead to the use of these machines, the fluid dynamicist faces three issues: algorithm development for near-term parallel computers, architecture development for future computer power increases, and assessment of possible advantages of special purpose designs. Two projects at NASA Langley address these issues. Software development and algorithm exploration is being done on the FLEX/32 Parallel Processing Research Computer. New architecture features are being explored in the special purpose hardware design of the Navier-Stokes Computer. These projects are complementary and are producing promising results.

Computational fluid-dynamic model of laser-induced breakdown in air

International Nuclear Information System (INIS)

Dors, Ivan G.; Parigger, Christian G.

2003-01-01

Temperature and pressure profiles are computed by the use of a two-dimensional, axially symmetric, time-accurate computational fluid-dynamic model for nominal 10-ns optical breakdown laser pulses. The computational model includes a kinetics mechanism that implements plasma equilibrium kinetics in ionized regions and nonequilibrium, multistep, finite-rate reactions in nonionized regions. Fluid-physics phenomena following laser-induced breakdown are recorded with high-speed shadowgraph techniques. The predicted fluid phenomena are shown by direct comparison with experimental records to agree with the flow patterns that are characteristic of laser spark decay

Prion subcellular fractionation reveals infectivity spectrum, with a high titre-low PrPres level disparity

Directory of Open Access Journals (Sweden)

Lewis Victoria

2012-04-01

Full Text Available Abstract Background Prion disease transmission and pathogenesis are linked to misfolded, typically protease resistant (PrPres conformers of the normal cellular prion protein (PrPC, with the former posited to be the principal constituent of the infectious 'prion'. Unexplained discrepancies observed between detectable PrPres and infectivity levels exemplify the complexity in deciphering the exact biophysical nature of prions and those host cell factors, if any, which contribute to transmission efficiency. In order to improve our understanding of these important issues, this study utilized a bioassay validated cell culture model of prion infection to investigate discordance between PrPres levels and infectivity titres at a subcellular resolution. Findings Subcellular fractions enriched in lipid rafts or endoplasmic reticulum/mitochondrial marker proteins were equally highly efficient at prion transmission, despite lipid raft fractions containing up to eight times the levels of detectable PrPres. Brain homogenate infectivity was not differentially enhanced by subcellular fraction-specific co-factors, and proteinase K pre-treatment of selected fractions modestly, but equally reduced infectivity. Only lipid raft associated infectivity was enhanced by sonication. Conclusions This study authenticates a subcellular disparity in PrPres and infectivity levels, and eliminates simultaneous divergence of prion strains as the explanation for this phenomenon. On balance, the results align best with the concept that transmission efficiency is influenced more by intrinsic characteristics of the infectious prion, rather than cellular microenvironment conditions or absolute PrPres levels.

Applied Computational Fluid Dynamics at NASA Ames Research Center

Science.gov (United States)

Holst, Terry L.; Kwak, Dochan (Technical Monitor)

1994-01-01

The field of Computational Fluid Dynamics (CFD) has advanced to the point where it can now be used for many applications in fluid mechanics research and aerospace vehicle design. A few applications being explored at NASA Ames Research Center will be presented and discussed. The examples presented will range in speed from hypersonic to low speed incompressible flow applications. Most of the results will be from numerical solutions of the Navier-Stokes or Euler equations in three space dimensions for general geometry applications. Computational results will be used to highlight the presentation as appropriate. Advances in computational facilities including those associated with NASA's CAS (Computational Aerosciences) Project of the Federal HPCC (High Performance Computing and Communications) Program will be discussed. Finally, opportunities for future research will be presented and discussed. All material will be taken from non-sensitive, previously-published and widely-disseminated work.

Parallel algorithms and architecture for computation of manipulator forward dynamics

Science.gov (United States)

Fijany, Amir; Bejczy, Antal K.

1989-01-01

Parallel computation of manipulator forward dynamics is investigated. Considering three classes of algorithms for the solution of the problem, that is, the O(n), the O(n exp 2), and the O(n exp 3) algorithms, parallelism in the problem is analyzed. It is shown that the problem belongs to the class of NC and that the time and processors bounds are of O(log2/2n) and O(n exp 4), respectively. However, the fastest stable parallel algorithms achieve the computation time of O(n) and can be derived by parallelization of the O(n exp 3) serial algorithms. Parallel computation of the O(n exp 3) algorithms requires the development of parallel algorithms for a set of fundamentally different problems, that is, the Newton-Euler formulation, the computation of the inertia matrix, decomposition of the symmetric, positive definite matrix, and the solution of triangular systems. Parallel algorithms for this set of problems are developed which can be efficiently implemented on a unique architecture, a triangular array of n(n+2)/2 processors with a simple nearest-neighbor interconnection. This architecture is particularly suitable for VLSI and WSI implementations. The developed parallel algorithm, compared to the best serial O(n) algorithm, achieves an asymptotic speedup of more than two orders-of-magnitude in the computation the forward dynamics.

Quinoa - Adaptive Computational Fluid Dynamics, 0.2

Energy Technology Data Exchange (ETDEWEB)

2017-09-22

Quinoa is a set of computational tools that enables research and numerical analysis in fluid dynamics. At this time it remains a test-bed to experiment with various algorithms using fully asynchronous runtime systems. Currently, Quinoa consists of the following tools: (1) Walker, a numerical integrator for systems of stochastic differential equations in time. It is a mathematical tool to analyze and design the behavior of stochastic differential equations. It allows the estimation of arbitrary coupled statistics and probability density functions and is currently used for the design of statistical moment approximations for multiple mixing materials in variable-density turbulence. (2) Inciter, an overdecomposition-aware finite element field solver for partial differential equations using 3D unstructured grids. Inciter is used to research asynchronous mesh-based algorithms and to experiment with coupling asynchronous to bulk-synchronous parallel code. Two planned new features of Inciter, compared to the previous release (LA-CC-16-015), to be implemented in 2017, are (a) a simple Navier-Stokes solver for ideal single-material compressible gases, and (b) solution-adaptive mesh refinement (AMR), which enables dynamically concentrating compute resources to regions with interesting physics. Using the NS-AMR problem we plan to explore how to scale such high-load-imbalance simulations, representative of large production multiphysics codes, to very large problems on very large computers using an asynchronous runtime system. (3) RNGTest, a test harness to subject random number generators to stringent statistical tests enabling quantitative ranking with respect to their quality and computational cost. (4) UnitTest, a unit test harness, running hundreds of tests per second, capable of testing serial, synchronous, and asynchronous functions. (5) MeshConv, a mesh file converter that can be used to convert 3D tetrahedron meshes from and to either of the following formats: Gmsh

Operational computer graphics in the flight dynamics environment

Science.gov (United States)

Jeletic, James F.

1989-01-01

Over the past five years, the Flight Dynamics Division of the National Aeronautics and Space Administration's (NASA's) Goddard Space Flight Center has incorporated computer graphics technology into its operational environment. In an attempt to increase the effectiveness and productivity of the Division, computer graphics software systems have been developed that display spacecraft tracking and telemetry data in 2-d and 3-d graphic formats that are more comprehensible than the alphanumeric tables of the past. These systems vary in functionality from real-time mission monitoring system, to mission planning utilities, to system development tools. Here, the capabilities and architecture of these systems are discussed.

Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation.

Science.gov (United States)

Neve, Jonathan; Burger, Kaspar; Li, Wencheng; Hoque, Mainul; Patel, Radhika; Tian, Bin; Gullerova, Monika; Furger, Andre

2016-01-01

Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we used a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape APA profiles in different subcellular locations. Here, we show that APA isoforms with shorter 3' UTRs tend to be overrepresented in the cytoplasm and appear to be cell-type-specific events. Nuclear retention of longer APA isoforms occurs and is partly a result of incomplete splicing contributing to the observed cytoplasmic bias of transcripts with shorter 3' UTRs. We demonstrate that the endoribonuclease III, DICER1, contributes to the establishment of subcellular APA profiles not only by expected cytoplasmic miRNA-mediated destabilization of APA mRNA isoforms, but also by affecting polyadenylation site choice. © 2016 Neve et al.; Published by Cold Spring Harbor Laboratory Press.

Computational modeling of intraocular gas dynamics

International Nuclear Information System (INIS)

Noohi, P; Abdekhodaie, M J; Cheng, Y L

2015-01-01

The purpose of this study was to develop a computational model to simulate the dynamics of intraocular gas behavior in pneumatic retinopexy (PR) procedure. The presented model predicted intraocular gas volume at any time and determined the tolerance angle within which a patient can maneuver and still gas completely covers the tear(s). Computational fluid dynamics calculations were conducted to describe PR procedure. The geometrical model was constructed based on the rabbit and human eye dimensions. SF_6 in the form of pure and diluted with air was considered as the injected gas. The presented results indicated that the composition of the injected gas affected the gas absorption rate and gas volume. After injection of pure SF_6, the bubble expanded to 2.3 times of its initial volume during the first 23 h, but when diluted SF_6 was used, no significant expansion was observed. Also, head positioning for the treatment of retinal tear influenced the rate of gas absorption. Moreover, the determined tolerance angle depended on the bubble and tear size. More bubble expansion and smaller retinal tear caused greater tolerance angle. For example, after 23 h, for the tear size of 2 mm the tolerance angle of using pure SF_6 is 1.4 times more than that of using diluted SF_6 with 80% air. Composition of the injected gas and conditions of the tear in PR may dramatically affect the gas absorption rate and gas volume. Quantifying these effects helps to predict the tolerance angle and improve treatment efficiency. (paper)

Modelling Emission from Building Materials with Computational Fluid Dynamics

DEFF Research Database (Denmark)

Topp, Claus; Nielsen, Peter V.; Heiselberg, Per

This paper presents a numerical model that by means of computational fluid dynamics (CFD) is capable of dealing with both pollutant transport across the boundary layer and internal diffusion in the source without prior knowledge of which is the limiting process. The model provides the concentration...

A Parameter Estimation Method for Dynamic Computational Cognitive Models

NARCIS (Netherlands)

Thilakarathne, D.J.

2015-01-01

A dynamic computational cognitive model can be used to explore a selected complex cognitive phenomenon by providing some features or patterns over time. More specifically, it can be used to simulate, analyse and explain the behaviour of such a cognitive phenomenon. It generates output data in the

Developments of multibody system dynamics: computer simulations and experiments

International Nuclear Information System (INIS)

Yoo, Wan-Suk; Kim, Kee-Nam; Kim, Hyun-Woo; Sohn, Jeong-Hyun

2007-01-01

It is an exceptional success when multibody dynamics researchers Multibody System Dynamics journal one of the most highly ranked journals in the last 10 years. In the inaugural issue, Professor Schiehlen wrote an interesting article explaining the roots and perspectives of multibody system dynamics. Professor Shabana also wrote an interesting article to review developments in flexible multibody dynamics. The application possibilities of multibody system dynamics have grown wider and deeper, with many application examples being introduced with multibody techniques in the past 10 years. In this paper, the development of multibody dynamics is briefly reviewed and several applications of multibody dynamics are described according to the author's research results. Simulation examples are compared to physical experiments, which show reasonableness and accuracy of the multibody formulation applied to real problems. Computer simulations using the absolute nodal coordinate formulation (ANCF) were also compared to physical experiments; therefore, the validity of ANCF for large-displacement and large-deformation problems was shown. Physical experiments for large deformation problems include beam, plate, chain, and strip. Other research topics currently being carried out in the author's laboratory are also briefly explained

Nano-Modeling and Computation in Bio and Brain Dynamics

Directory of Open Access Journals (Sweden)

Paolo Di Sia

2016-04-01

Full Text Available The study of brain dynamics currently utilizes the new features of nanobiotechnology and bioengineering. New geometric and analytical approaches appear very promising in all scientific areas, particularly in the study of brain processes. Efforts to engage in deep comprehension lead to a change in the inner brain parameters, in order to mimic the external transformation by the proper use of sensors and effectors. This paper highlights some crossing research areas of natural computing, nanotechnology, and brain modeling and considers two interesting theoretical approaches related to brain dynamics: (a the memory in neural network, not as a passive element for storing information, but integrated in the neural parameters as synaptic conductances; and (b a new transport model based on analytical expressions of the most important transport parameters, which works from sub-pico-level to macro-level, able both to understand existing data and to give new predictions. Complex biological systems are highly dependent on the context, which suggests a “more nature-oriented” computational philosophy.

Dynamics of number systems computation with arbitrary precision

CERN Document Server

Kurka, Petr

2016-01-01

This book is a source of valuable and useful information on the topics of dynamics of number systems and scientific computation with arbitrary precision. It is addressed to scholars, scientists and engineers, and graduate students. The treatment is elementary and self-contained with relevance both for theory and applications. The basic prerequisite of the book is linear algebra and matrix calculus. .

Novel Reporter for Faithful Monitoring of ERK2 Dynamics in Living Cells and Model Organisms

Science.gov (United States)

Sipieter, François; Cappe, Benjamin; Gonzalez Pisfil, Mariano; Spriet, Corentin; Bodart, Jean-François; Cailliau-Maggio, Katia; Vandenabeele, Peter; Héliot, Laurent; Riquet, Franck B.

2015-01-01

Uncoupling of ERK1/2 phosphorylation from subcellular localization is essential towards the understanding of molecular mechanisms that control ERK1/2-mediated cell-fate decision. ERK1/2 non-catalytic functions and discoveries of new specific anchors responsible of the subcellular compartmentalization of ERK1/2 signaling pathway have been proposed as regulation mechanisms for which dynamic monitoring of ERK1/2 localization is necessary. However, studying the spatiotemporal features of ERK2, for instance, in different cellular processes in living cells and tissues requires a tool that can faithfully report on its subcellular distribution. We developed a novel molecular tool, ERK2-LOC, based on the T2A-mediated coexpression of strictly equimolar levels of eGFP-ERK2 and MEK1, to faithfully visualize ERK2 localization patterns. MEK1 and eGFP-ERK2 were expressed reliably and functionally both in vitro and in single living cells. We then assessed the subcellular distribution and mobility of ERK2-LOC using fluorescence microscopy in non-stimulated conditions and after activation/inhibition of the MAPK/ERK1/2 signaling pathway. Finally, we used our coexpression system in Xenopus laevis embryos during the early stages of development. This is the first report on MEK1/ERK2 T2A-mediated coexpression in living embryos, and we show that there is a strong correlation between the spatiotemporal subcellular distribution of ERK2-LOC and the phosphorylation patterns of ERK1/2. Our approach can be used to study the spatiotemporal localization of ERK2 and its dynamics in a variety of processes in living cells and embryonic tissues. PMID:26517832

Subcellular localization of pituitary enzymes

Science.gov (United States)

Smith, R. E.

1970-01-01

A cytochemical procedure is reported for identifying subcellular sites of enzymes hydrolyzing beta-naphthylamine substrates, and to study the sites of reaction product localization in cells of various tissues. Investigations using the substrate Leu 4-methoxy-8-naphthylamine, a capture with hexonium pararosaniline, and the final chelation of osmium have identified the hydrolyzing enzyme of rat liver cells; this enzyme localized on cell membranes with intense deposition in the areas of the parcanaliculi. The study of cells in the anterior pituitary of the rat showed the deposition of reaction product on cell membrane; and on the membranes of secretion granules contained within the cell. The deposition of reaction product on the cell membrane however showed no increase or decrease with changes in the physiological state of the gland and release of secretion granules from specific cells.

FRET biosensors reveal AKAP-mediated shaping of subcellular PKA activity and a novel mode of Ca(2+)/PKA crosstalk.

Science.gov (United States)

Schott, Micah B; Gonowolo, Faith; Maliske, Benjamin; Grove, Bryon

2016-04-01

Scaffold proteins play a critical role in cellular homeostasis by anchoring signaling enzymes in close proximity to downstream effectors. In addition to anchoring static enzyme complexes, some scaffold proteins also form dynamic signalosomes that can traffic to different subcellular compartments upon stimulation. Gravin (AKAP12), a multivalent scaffold, anchors PKA and other enzymes to the plasma membrane under basal conditions, but upon [Ca(2+)]i elevation, is rapidly redistributed to the cytosol. Because gravin redistribution also impacts PKA localization, we postulate that gravin acts as a calcium "switch" that modulates PKA-substrate interactions at the plasma membrane, thus facilitating a novel crosstalk mechanism between Ca(2+) and PKA-dependent pathways. To assess this, we measured the impact of gravin-V5/His expression on compartmentalized PKA activity using the FRET biosensor AKAR3 in cultured cells. Upon treatment with forskolin or isoproterenol, cells expressing gravin-V5/His showed elevated levels of plasma membrane PKA activity, but cytosolic PKA activity levels were reduced compared with control cells lacking gravin. This effect required both gravin interaction with PKA and localization at the plasma membrane. Pretreatment with calcium-elevating agents thapsigargin or ATP caused gravin redistribution away from the plasma membrane and prevented gravin from elevating PKA activity levels at the membrane. Importantly, this mode of Ca(2+)/PKA crosstalk was not observed in cells expressing a gravin mutant that resisted calcium-mediated redistribution from the cell periphery. These results reveal that gravin impacts subcellular PKA activity levels through the spatial targeting of PKA, and that calcium elevation modulates downstream β-adrenergic/PKA signaling through gravin redistribution, thus supporting the hypothesis that gravin mediates crosstalk between Ca(2+) and PKA-dependent signaling pathways. Based on these results, AKAP localization dynamics may

FRET biosensors reveal AKAP-mediated shaping of subcellular PKA activity and a novel mode of Ca2+/PKA crosstalk

Science.gov (United States)

Schott, Micah; Gonowolo, Faith; Maliske, Ben; Grove, Bryon

2016-01-01

Scaffold proteins play a critical role in cellular homeostasis by anchoring signaling enzymes in close proximity to downstream effectors. In addition to anchoring static enzyme complexes, some scaffold proteins also form dynamic signalosomes that can traffic to different subcellular compartments upon stimulation. Gravin (AKAP12), a multivalent scaffold, anchors PKA and other enzymes to the plasma membrane under basal conditions, but upon [Ca2+]i elevation, is rapidly redistributed to the cytosol. Because gravin redistribution also impacts PKA localization, we postulate that gravin acts as a calcium “switch” that modulates PKA-substrate interactions at the plasma membrane, thus facilitating a novel crosstalk mechanism between Ca2+ and PKA-dependent pathways. To assess this, we measured the impact of gravin-V5/His expression on compartmentalized PKA activity using the FRET biosensor AKAR3 in cultured cells. Upon treatment with forskolin or isoproterenol, cells expressing gravin-V5/His showed elevated levels of plasma membrane PKA activity, but cytosolic PKA activity levels were reduced compared with control cells lacking gravin. This effect required both gravin interaction with PKA and localization at the plasma membrane. Pretreatment with calcium-elevating agents thapsigargin or ATP caused gravin redistribution away from the plasma membrane and prevented gravin from elevating PKA activity levels at the membrane. Importantly, this mode of Ca2+/PKA crosstalk was not observed in cells expressing a gravin mutant that resists calcium-mediated redistribution from the cell periphery. These results reveal that gravin impacts subcellular PKA activity levels through the spatial targeting of PKA, and that calcium elevation modulates downstream β-adrenergic/PKA signaling through gravin redistribution, thus supporting the hypothesis that gravin mediates crosstalk between Ca2+ and PKA-dependent signaling pathways. Based on these results, AKAP localization dynamics may

Parasites modify sub-cellular partitioning of metals in the gut of fish

Energy Technology Data Exchange (ETDEWEB)

Oyoo-Okoth, Elijah, E-mail: elijaoyoo2009@gmail.com [Division of Environmental Health, School of Environmental Studies, Moi University, P.O. Box 3900, Eldoret (Kenya); Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 9424/1090 GE (Netherlands); Admiraal, Wim [Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 9424/1090 GE (Netherlands); Osano, Odipo [Division of Environmental Health, School of Environmental Studies, Moi University, P.O. Box 3900, Eldoret (Kenya); Kraak, Michiel H.S. [Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 9424/1090 GE (Netherlands); Gichuki, John; Ogwai, Caleb [Kenya Marine and Fisheries Research Institute, P.O. Box 1881, Kisumu (Kenya)

2012-01-15

Infestation of fish by parasites may influence metal accumulation patterns in the host. However, the subcellular mechanisms of these processes have rarely been studied. Therefore, this study determined how a cyprinid fish (Rastrineobola argentea) partitioned four metals (Cd, Cr, Zn and Cu) in the subcellular fractions of the gut in presence of an endoparasite (Ligula intestinalis). The fish were sampled along four sites in Lake Victoria, Kenya differing in metal contamination. Accumulation of Cd, Cr and Zn was higher in the whole body and in the gut of parasitized fish compared to non-parasitized fish, while Cu was depleted in parasitized fish. Generally, for both non-parasitized and parasitized fish, Cd, Cr and Zn partitioned in the cytosolic fractions and Cu in the particulate fraction. Metal concentrations in organelles within the particulate fractions of the non-parasitized fish were statistically similar except for Cd in the lysosome, while in the parasitized fish, Cd, Cr and Zn were accumulated more by the lysosome and microsomes. In the cytosolic fractions, the non-parasitized fish accumulated Cd, Cr and Zn in the heat stable proteins (HSP), while in the parasitized fish the metals were accumulated in the heat denatured proteins (HDP). On the contrary, Cu accumulated in the HSP in parasitized fish. The present study revealed specific binding of metals to potentially sensitive sub-cellular fractions in fish in the presence of parasites, suggesting interference with metal detoxification, and potentially affecting the health status of fish hosts in Lake Victoria.

The coupling of fluids, dynamics, and controls on advanced architecture computers

Science.gov (United States)

Atwood, Christopher

1995-01-01

This grant provided for the demonstration of coupled controls, body dynamics, and fluids computations in a workstation cluster environment; and an investigation of the impact of peer-peer communication on flow solver performance and robustness. The findings of these investigations were documented in the conference articles.The attached publication, 'Towards Distributed Fluids/Controls Simulations', documents the solution and scaling of the coupled Navier-Stokes, Euler rigid-body dynamics, and state feedback control equations for a two-dimensional canard-wing. The poor scaling shown was due to serialized grid connectivity computation and Ethernet bandwidth limits. The scaling of a peer-to-peer communication flow code on an IBM SP-2 was also shown. The scaling of the code on the switched fabric-linked nodes was good, with a 2.4 percent loss due to communication of intergrid boundary point information. The code performance on 30 worker nodes was 1.7 (mu)s/point/iteration, or a factor of three over a Cray C-90 head. The attached paper, 'Nonlinear Fluid Computations in a Distributed Environment', documents the effect of several computational rate enhancing methods on convergence. For the cases shown, the highest throughput was achieved using boundary updates at each step, with the manager process performing communication tasks only. Constrained domain decomposition of the implicit fluid equations did not degrade the convergence rate or final solution. The scaling of a coupled body/fluid dynamics problem on an Ethernet-linked cluster was also shown.

Dynamic computer simulation of the Fort St. Vrain steam turbines

International Nuclear Information System (INIS)

Conklin, J.C.

1983-01-01

A computer simulation is described for the dynamic response of the Fort St. Vrain nuclear reactor regenerative intermediate- and low-pressure steam turbines. The fundamental computer-modeling assumptions for the turbines and feedwater heaters are developed. A turbine heat balance specifying steam and feedwater conditions at a given generator load and the volumes of the feedwater heaters are all that are necessary as descriptive input parameters. Actual plant data for a generator load reduction from 100 to 50% power (which occurred as part of a plant transient on November 9, 1981) are compared with computer-generated predictions, with reasonably good agreement

Thirteenth Workshop for Computational Fluid Dynamic Applications in Rocket Propulsion and Launch Vehicle Technology. Volume 2

Science.gov (United States)

Williams, R. W. (Compiler)

1996-01-01

This conference publication includes various abstracts and presentations given at the 13th Workshop for Computational Fluid Dynamic Applications in Rocket Propulsion and Launch Vehicle Technology held at the George C. Marshall Space Flight Center April 25-27 1995. The purpose of the workshop was to discuss experimental and computational fluid dynamic activities in rocket propulsion and launch vehicles. The workshop was an open meeting for government, industry, and academia. A broad number of topics were discussed including computational fluid dynamic methodology, liquid and solid rocket propulsion, turbomachinery, combustion, heat transfer, and grid generation.

Integrating aerodynamic surface modeling for computational fluid dynamics with computer aided structural analysis, design, and manufacturing

Science.gov (United States)

Thorp, Scott A.

1992-01-01

This presentation will discuss the development of a NASA Geometry Exchange Specification for transferring aerodynamic surface geometry between LeRC systems and grid generation software used for computational fluid dynamics research. The proposed specification is based on a subset of the Initial Graphics Exchange Specification (IGES). The presentation will include discussion of how the NASA-IGES standard will accommodate improved computer aided design inspection methods and reverse engineering techniques currently being developed. The presentation is in viewgraph format.

Direct speciation analysis of arsenic in sub-cellular compartments using micro-X-ray absorption spectroscopy

International Nuclear Information System (INIS)

Bacquart, Thomas; Deves, Guillaume; Ortega, Richard

2010-01-01

Identification of arsenic chemical species at a sub-cellular level is a key to understanding the mechanisms involved in arsenic toxicology and antitumor pharmacology. When performed with a microbeam, X-ray absorption near-edge structure (μ-XANES) enables the direct speciation analysis of arsenic in sub-cellular compartments avoiding cell fractionation and other preparation steps that might modify the chemical species. This methodology couples tracking of cellular organelles in a single cell by confocal or epifluorescence microscopy with local analysis of chemical species by μ-XANES. Here we report the results obtained with a μ-XANES experimental setup based on Kirkpatrick-Baez X-ray focusing optics that maintains high flux of incoming radiation (>10 11 ph/s) at micrometric spatial resolution (1.5x4.0 μm 2 ). This original experimental setup enabled the direct speciation analysis of arsenic in sub-cellular organelles with a 10 -15 g detection limit. μ-XANES shows that inorganic arsenite, As(OH) 3 , is the main form of arsenic in the cytosol, nucleus, and mitochondrial network of cultured cancer cells exposed to As 2 O 3 . On the other hand, a predominance of As(III) species is observed in HepG2 cells exposed to As(OH) 3 with, in some cases, oxidation to a pentavalent form in nuclear structures of HepG2 cells. The observation of intra-nuclear mixed redox states suggests an inter-individual variability in a cell population that can only be evidenced with direct sub-cellular speciation analysis.

A hybrid computer simulation of reactor spatial dynamics

International Nuclear Information System (INIS)

Hinds, H.W.

1977-08-01

The partial differential equations describing the one-speed spatial dynamics of thermal neutron reactors were converted to a set of ordinary differential equations, using finite-difference approximations for the spatial derivatives. The variables were then normalized to a steady-state reference condition in a novel manner, to yield an equation set particularly suitable for implementation on a hybrid computer. One Applied Dynamics AD/FIVE analog-computer console is capable of solving, all in parallel, up to 30 simultaneous differential equations. This corresponds roughly to eight reactor nodes, each with two active delayed-neutron groups. To improve accuracy, an increase in the number of nodes is usually required. Using the Hsu-Howe multiplexing technique, an 8-node, one-dimensional module was switched back and forth between the left and right halves of the reactor, to simulate a 16-node model, also in one dimension. These two versions (8 or 16 nodes) of the model were tested on benchmark problems of the loss-of-coolant type, which were also solved using the digital code FORSIM, with two energy groups and 26 nodes. Good agreement was obtained between the two solution techniques. (author)

Evaluation on subcellular partitioning and biodynamics of pulse copper toxicity in tilapia reveals impacts of a major environmental disturbance.

Science.gov (United States)

Ju, Yun-Ru; Yang, Ying-Fei; Tsai, Jeng-Wei; Cheng, Yi-Hsien; Chen, Wei-Yu; Liao, Chung-Min

2017-07-01

Fluctuation exposure of trace metal copper (Cu) is ubiquitous in aquatic environments. The purpose of this study was to investigate the impacts of chronically pulsed exposure on biodynamics and subcellular partitioning of Cu in freshwater tilapia (Oreochromis mossambicus). Long-term 28-day pulsed Cu exposure experiments were performed to explore subcellular partitioning and toxicokinetics/toxicodynamics of Cu in tilapia. Subcellular partitioning linking with a metal influx scheme was used to estimate detoxification and elimination rates. A biotic ligand model-based damage assessment model was used to take into account environmental effects and biological mechanisms of Cu toxicity. We demonstrated that the probability causing 50% of susceptibility risk in response to pulse Cu exposure in generic Taiwan aquaculture ponds was ~33% of Cu in adverse physiologically associated, metabolically active pool, implicating no significant susceptibility risk for tilapia. We suggest that our integrated ecotoxicological models linking chronic exposure measurements with subcellular partitioning can facilitate a risk assessment framework that provides a predictive tool for preventive susceptibility reduction strategies for freshwater fish exposed to pulse metal stressors.

Dynamic Scaffolding of Socially Regulated Learning in a Computer-Based Learning Environment

NARCIS (Netherlands)

Molenaar, I.; Roda, Claudia; van Boxtel, Carla A.M.; Sleegers, P.J.C.

2012-01-01

The aim of this study is to test the effects of dynamically scaffolding social regulation of middle school students working in a computer-based learning environment. Dyads in the scaffolding condition (N = 56) are supported with computer-generated scaffolds and students in the control condition (N =

Further development of the Dynamic Control Assemblies Worth Measurement Method for Advanced Reactivity Computers

International Nuclear Information System (INIS)

Petenyi, V.; Strmensky, C.; Jagrik, J.; Minarcin, M.; Sarvaic, I.

2005-01-01

The dynamic control assemblies worth measurement technique is a quick method for validation of predicted control assemblies worth. The dynamic control assemblies worth measurement utilize space-time corrections for the measured out of core ionization chamber readings calculated by DYN 3D computer code. The space-time correction arising from the prompt neutron density redistribution in the measured ionization chamber reading can be directly applied in the advanced reactivity computer. The second correction concerning the difference of spatial distribution of delayed neutrons can be calculated by simulation the measurement procedure by dynamic version of the DYN 3D code. In the paper some results of dynamic control assemblies worth measurement applied for NPP Mochovce are presented (Authors)

Computer studies of multiple-quantum spin dynamics

Energy Technology Data Exchange (ETDEWEB)

Murdoch, J.B.

1982-11-01

The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment.

Computer studies of multiple-quantum spin dynamics

International Nuclear Information System (INIS)

Murdoch, J.B.

1982-11-01

The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment

Colour in visualisation for computational fluid dynamics

OpenAIRE

Kinnear, D; Atherton, MA; Collins, MW; Dokhan, J; Karayiannis, TG

2006-01-01

Colour is used in computational fluid dynamic (CFD) simulations in two key ways. First it is used to visualise the geometry and allow the engineers to be confident that the model constructed is a good representation of the engineering situation. Once an analysis has been completed, colour is used in post-processing the data from the simulations to illustrate the complex fluid mechanic phenomena under investigation. This paper describes these two uses of colour and provides some examples to il...

Biodynamics of copper oxide nanoparticles and copper ions in an oligochaete - Part II: Subcellular distribution following sediment exposure

Energy Technology Data Exchange (ETDEWEB)

Thit, Amalie, E-mail: athitj@ruc.dk [U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA 94025 (United States); Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000 (Denmark); Ramskov, Tina, E-mail: tramskov@hotmail.com [U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA 94025 (United States); Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000 (Denmark); Croteau, Marie-Noële, E-mail: mcroteau@usgs.gov [Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000 (Denmark); Selck, Henriette [U.S. Geological Survey, 345 Middlefield Road, Menlo Park, CA 94025 (United States); Department of Science and Environment, Roskilde University, Universitetsvej 1, Roskilde DK-4000 (Denmark)

2016-11-15

Highlights: • L. variegatus was exposed to sediment spiked with either aqueous Cu or nanoparticulate CuO. • Both aqueous and nanoparticulate Cu were marginally accumulated by L. variegatus. • Elimination of Cu accumulated from both forms was limited. • The subcellular distribution of accumulated Cu varied between Cu forms. • The use of a tracer, greater exposure concentration and duration are recommended. - Abstract: The use and likely incidental release of metal nanoparticles (NPs) is steadily increasing. Despite the increasing amount of published literature on metal NP toxicity in the aquatic environment, very little is known about the biological fate of NPs after sediment exposures. Here, we compare the bioavailability and subcellular distribution of copper oxide (CuO) NPs and aqueous Cu (Cu-Aq) in the sediment-dwelling worm Lumbriculus variegatus. Ten days (d) sediment exposure resulted in marginal Cu bioaccumulation in L. variegatus for both forms of Cu. Bioaccumulation was detected because isotopically enriched {sup 65}Cu was used as a tracer. Neither burrowing behavior or survival was affected by the exposure. Once incorporated into tissue, Cu loss was negligible over 10 d of elimination in clean sediment (Cu elimination rate constants were not different from zero). With the exception of day 10, differences in bioaccumulation and subcellular distribution between Cu forms were either not detectable or marginal. After 10 d of exposure to Cu-Aq, the accumulated Cu was primarily partitioned in the subcellular fraction containing metallothionein-like proteins (MTLP, ≈40%) and cellular debris (CD, ≈30%). Cu concentrations in these fractions were significantly higher than in controls. For worms exposed to CuO NPs for 10 d, most of the accumulated Cu was partitioned in the CD fraction (≈40%), which was the only subcellular fraction where the Cu concentration was significantly higher than for the control group. Our results indicate that L. variegatus

Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E

2017-01-01

Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach...... to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration....... The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure...

GASFLOW-MPI. A scalable computational fluid dynamics code for gases, aerosols and combustion. Vol. 1. Theory and computational model (Revision 1.0)

Energy Technology Data Exchange (ETDEWEB)

Xiao, Jianjun; Travis, Jack; Royl, Peter; Necker, Gottfried; Svishchev, Anatoly; Jordan, Thomas

2016-07-01

Karlsruhe Institute of Technology (KIT) is developing the parallel computational fluid dynamics code GASFLOW-MPI as a best-estimate tool for predicting transport, mixing, and combustion of hydrogen and other gases in nuclear reactor containments and other facility buildings. GASFLOW-MPI is a finite-volume code based on proven computational fluid dynamics methodology that solves the compressible Navier-Stokes equations for three-dimensional volumes in Cartesian or cylindrical coordinates.

Rapid and dynamic subcellular reorganization following mechanical stimulation of Arabidopsis epidermal cells mimics responses to fungal and oomycete attack

Directory of Open Access Journals (Sweden)

Takemoto Daigo

2008-06-01

Full Text Available Abstract Background Plant cells respond to the presence of potential fungal or oomycete pathogens by mounting a basal defence response that involves aggregation of cytoplasm, reorganization of cytoskeletal, endomembrane and other cell components and development of cell wall appositions beneath the infection site. This response is induced by non-adapted, avirulent and virulent pathogens alike, and in the majority of cases achieves penetration resistance against the microorganism on the plant surface. To explore the nature of signals that trigger this subcellular response and to determine the timing of its induction, we have monitored the reorganization of GFP-tagged actin, microtubules, endoplasmic reticulum (ER and peroxisomes in Arabidopsis plants – after touching the epidermal surface with a microneedle. Results Within 3 to 5 minutes of touching the surface of Arabidopsis cotyledon epidermal cells with fine glass or tungsten needles, actin microfilaments, ER and peroxisomes began to accumulate beneath the point of contact with the needle. Formation of a dense patch of actin was followed by focusing of actin cables on the site of contact. Touching the cell surface induced localized depolymerization of microtubules to form a microtubule-depleted zone surrounding a dense patch of GFP-tubulin beneath the needle tip. The concentration of actin, GFP-tubulin, ER and peroxisomes remained focused on the contact site as the needle moved across the cell surface and quickly dispersed when the needle was removed. Conclusion Our results show that plant cells can detect the gentle pressure of a microneedle on the epidermal cell surface and respond by reorganizing subcellular components in a manner similar to that induced during attack by potential fungal or oomycete pathogens. The results of our study indicate that during plant-pathogen interactions, the basal defence response may be induced by the plant's perception of the physical force exerted by the

Correlation of N-myc downstream-regulated gene 1 subcellular localization and lymph node metastases of colorectal neoplasms

Energy Technology Data Exchange (ETDEWEB)

Song, Yan [Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014 (China); Lv, Liyang [Department of Health, Jinan Military Area Command, Jinan 250022 (China); Du, Juan; Yue, Longtao [Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014 (China); Cao, Lili, E-mail: cllly22@163.com [Medical Research Center, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan 250014 (China)

2013-09-20

Highlights: •We clarified NDRG1 subcellular location in colorectal cancer. •We found the changes of NDRG1 distribution during colorectal cancer progression. •We clarified the correlation between NDRG1 distribution and lymph node metastasis. •It is possible that NDRG1 subcellular localization may determine its function. •Maybe NDRG1 is valuable early diagnostic markers for metastasis. -- Abstract: In colorectal neoplasms, N-myc downstream-regulated gene 1 (NDRG1) is a primarily cytoplasmic protein, but it is also expressed on the cell membrane and in the nucleus. NDRG1 is involved in various stages of tumor development in colorectal cancer, and it is possible that the different subcellular localizations may determine the function of NDRG1 protein. Here, we attempt to clarify the characteristics of NDRG1 protein subcellular localization during the progression of colorectal cancer. We examined NDRG1 expression in 49 colorectal cancer patients in cancerous, non-cancerous, and corresponding lymph node tissues. Cytoplasmic and membrane NDRG1 expression was higher in the lymph nodes with metastases than in those without metastases (P < 0.01). Nuclear NDRG1 expression in colorectal neoplasms was significantly higher than in the normal colorectal mucosa, and yet the normal colorectal mucosa showed no nuclear expression. Furthermore, our results showed higher cytoplasmic NDRG1 expression was better for differentiation, and higher membrane NDRG1 expression resulted in a greater possibility of lymph node metastasis. These data indicate that a certain relationship between the cytoplasmic and membrane expression of NDRG1 in lymph nodes exists with lymph node metastasis. NDRG1 expression may translocate from the membrane of the colorectal cancer cells to the nucleus, where it is involved in lymph node metastasis. Combination analysis of NDRG1 subcellular expression and clinical variables will help predict the incidence of lymph node metastasis.

Correlation of N-myc downstream-regulated gene 1 subcellular localization and lymph node metastases of colorectal neoplasms

International Nuclear Information System (INIS)

Song, Yan; Lv, Liyang; Du, Juan; Yue, Longtao; Cao, Lili

2013-01-01

Highlights: •We clarified NDRG1 subcellular location in colorectal cancer. •We found the changes of NDRG1 distribution during colorectal cancer progression. •We clarified the correlation between NDRG1 distribution and lymph node metastasis. •It is possible that NDRG1 subcellular localization may determine its function. •Maybe NDRG1 is valuable early diagnostic markers for metastasis. -- Abstract: In colorectal neoplasms, N-myc downstream-regulated gene 1 (NDRG1) is a primarily cytoplasmic protein, but it is also expressed on the cell membrane and in the nucleus. NDRG1 is involved in various stages of tumor development in colorectal cancer, and it is possible that the different subcellular localizations may determine the function of NDRG1 protein. Here, we attempt to clarify the characteristics of NDRG1 protein subcellular localization during the progression of colorectal cancer. We examined NDRG1 expression in 49 colorectal cancer patients in cancerous, non-cancerous, and corresponding lymph node tissues. Cytoplasmic and membrane NDRG1 expression was higher in the lymph nodes with metastases than in those without metastases (P < 0.01). Nuclear NDRG1 expression in colorectal neoplasms was significantly higher than in the normal colorectal mucosa, and yet the normal colorectal mucosa showed no nuclear expression. Furthermore, our results showed higher cytoplasmic NDRG1 expression was better for differentiation, and higher membrane NDRG1 expression resulted in a greater possibility of lymph node metastasis. These data indicate that a certain relationship between the cytoplasmic and membrane expression of NDRG1 in lymph nodes exists with lymph node metastasis. NDRG1 expression may translocate from the membrane of the colorectal cancer cells to the nucleus, where it is involved in lymph node metastasis. Combination analysis of NDRG1 subcellular expression and clinical variables will help predict the incidence of lymph node metastasis

Cell segmentation in time-lapse fluorescence microscopy with temporally varying sub-cellular fusion protein patterns.

Science.gov (United States)

Bunyak, Filiz; Palaniappan, Kannappan; Chagin, Vadim; Cardoso, M

2009-01-01

Fluorescently tagged proteins such as GFP-PCNA produce rich dynamically varying textural patterns of foci distributed in the nucleus. This enables the behavioral study of sub-cellular structures during different phases of the cell cycle. The varying punctuate patterns of fluorescence, drastic changes in SNR, shape and position during mitosis and abundance of touching cells, however, require more sophisticated algorithms for reliable automatic cell segmentation and lineage analysis. Since the cell nuclei are non-uniform in appearance, a distribution-based modeling of foreground classes is essential. The recently proposed graph partitioning active contours (GPAC) algorithm supports region descriptors and flexible distance metrics. We extend GPAC for fluorescence-based cell segmentation using regional density functions and dramatically improve its efficiency for segmentation from O(N(4)) to O(N(2)), for an image with N(2) pixels, making it practical and scalable for high throughput microscopy imaging studies.

Techniques for animation of CFD results. [computational fluid dynamics

Science.gov (United States)

Horowitz, Jay; Hanson, Jeffery C.

1992-01-01

Video animation is becoming increasingly vital to the computational fluid dynamics researcher, not just for presentation, but for recording and comparing dynamic visualizations that are beyond the current capabilities of even the most powerful graphic workstation. To meet these needs, Lewis Research Center has recently established a facility to provide users with easy access to advanced video animation capabilities. However, producing animation that is both visually effective and scientifically accurate involves various technological and aesthetic considerations that must be understood both by the researcher and those supporting the visualization process. These considerations include: scan conversion, color conversion, and spatial ambiguities.

Computational fluid dynamics (CFD) simulation of hot air flow ...

African Journals Online (AJOL)

Computational Fluid Dynamics simulation of air flow distribution, air velocity and pressure field pattern as it will affect moisture transient in a cabinet tray dryer is performed using SolidWorks Flow Simulation (SWFS) 2014 SP 4.0 program. The model used for the drying process in this experiment was designed with Solid ...

A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements.

Directory of Open Access Journals (Sweden)

Daniel Durstewitz

2017-06-01

Full Text Available The computational and cognitive properties of neural systems are often thought to be implemented in terms of their (stochastic network dynamics. Hence, recovering the system dynamics from experimentally observed neuronal time series, like multiple single-unit recordings or neuroimaging data, is an important step toward understanding its computations. Ideally, one would not only seek a (lower-dimensional state space representation of the dynamics, but would wish to have access to its statistical properties and their generative equations for in-depth analysis. Recurrent neural networks (RNNs are a computationally powerful and dynamically universal formal framework which has been extensively studied from both the computational and the dynamical systems perspective. Here we develop a semi-analytical maximum-likelihood estimation scheme for piecewise-linear RNNs (PLRNNs within the statistical framework of state space models, which accounts for noise in both the underlying latent dynamics and the observation process. The Expectation-Maximization algorithm is used to infer the latent state distribution, through a global Laplace approximation, and the PLRNN parameters iteratively. After validating the procedure on toy examples, and using inference through particle filters for comparison, the approach is applied to multiple single-unit recordings from the rodent anterior cingulate cortex (ACC obtained during performance of a classical working memory task, delayed alternation. Models estimated from kernel-smoothed spike time data were able to capture the essential computational dynamics underlying task performance, including stimulus-selective delay activity. The estimated models were rarely multi-stable, however, but rather were tuned to exhibit slow dynamics in the vicinity of a bifurcation point. In summary, the present work advances a semi-analytical (thus reasonably fast maximum-likelihood estimation framework for PLRNNs that may enable to recover

Single-polymer dynamics under constraints: scaling theory and computer experiment

International Nuclear Information System (INIS)

Milchev, Andrey

2011-01-01

The relaxation, diffusion and translocation dynamics of single linear polymer chains in confinement is briefly reviewed with emphasis on the comparison between theoretical scaling predictions and observations from experiment or, most frequently, from computer simulations. Besides cylindrical, spherical and slit-like constraints, related problems such as the chain dynamics in a random medium and the translocation dynamics through a nanopore are also considered. Another particular kind of confinement is imposed by polymer adsorption on attractive surfaces or selective interfaces-a short overview of single-chain dynamics is also contained in this survey. While both theory and numerical experiments consider predominantly coarse-grained models of self-avoiding linear chain molecules with typically Rouse dynamics, we also note some recent studies which examine the impact of hydrodynamic interactions on polymer dynamics in confinement. In all of the aforementioned cases we focus mainly on the consequences of imposed geometric restrictions on single-chain dynamics and try to check our degree of understanding by assessing the agreement between theoretical predictions and observations. (topical review)

Apparatus and method for measuring single cell and sub-cellular photosynthetic efficiency

Science.gov (United States)

Davis, Ryan Wesley; Singh, Seema; Wu, Huawen

2013-07-09

Devices for measuring single cell changes in photosynthetic efficiency in algal aquaculture are disclosed that include a combination of modulated LED trans-illumination of different intensities with synchronized through objective laser illumination and confocal detection. Synchronization and intensity modulation of a dual illumination scheme were provided using a custom microcontroller for a laser beam block and constant current LED driver. Therefore, single whole cell photosynthetic efficiency, and subcellular (diffraction limited) photosynthetic efficiency measurement modes are permitted. Wide field rapid light scanning actinic illumination is provided for both by an intensity modulated 470 nm LED. For the whole cell photosynthetic efficiency measurement, the same LED provides saturating pulses for generating photosynthetic induction curves. For the subcellular photosynthetic efficiency measurement, a switched through objective 488 nm laser provides saturating pulses for generating photosynthetic induction curves. A second near IR LED is employed to generate dark adapted states in the system under study.

A Scheduling Algorithm for Cloud Computing System Based on the Driver of Dynamic Essential Path.

Science.gov (United States)

Xie, Zhiqiang; Shao, Xia; Xin, Yu

2016-01-01

To solve the problem of task scheduling in the cloud computing system, this paper proposes a scheduling algorithm for cloud computing based on the driver of dynamic essential path (DDEP). This algorithm applies a predecessor-task layer priority strategy to solve the problem of constraint relations among task nodes. The strategy assigns different priority values to every task node based on the scheduling order of task node as affected by the constraint relations among task nodes, and the task node list is generated by the different priority value. To address the scheduling order problem in which task nodes have the same priority value, the dynamic essential long path strategy is proposed. This strategy computes the dynamic essential path of the pre-scheduling task nodes based on the actual computation cost and communication cost of task node in the scheduling process. The task node that has the longest dynamic essential path is scheduled first as the completion time of task graph is indirectly influenced by the finishing time of task nodes in the longest dynamic essential path. Finally, we demonstrate the proposed algorithm via simulation experiments using Matlab tools. The experimental results indicate that the proposed algorithm can effectively reduce the task Makespan in most cases and meet a high quality performance objective.

The performance model of dynamic virtual organization (VO) formations within grid computing context

International Nuclear Information System (INIS)

Han Liangxiu

2009-01-01

Grid computing aims to enable 'resource sharing and coordinated problem solving in dynamic, multi-institutional virtual organizations (VOs)'. Within the grid computing context, successful dynamic VO formations mean a number of individuals and institutions associated with certain resources join together and form new VOs in order to effectively execute tasks within given time steps. To date, while the concept of VOs has been accepted, few research has been done on the impact of effective dynamic virtual organization formations. In this paper, we develop a performance model of dynamic VOs formation and analyze the effect of different complex organizational structures and their various statistic parameter properties on dynamic VO formations from three aspects: (1) the probability of a successful VO formation under different organizational structures and statistic parameters change, e.g. average degree; (2) the effect of task complexity on dynamic VO formations; (3) the impact of network scales on dynamic VO formations. The experimental results show that the proposed model can be used to understand the dynamic VO formation performance of the simulated organizations. The work provides a good path to understand how to effectively schedule and utilize resources based on the complex grid network and therefore improve the overall performance within grid environment.

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity.

Science.gov (United States)

Liang, Jie; Qian, Hong

2010-01-01

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand "complex behavior" and complexity theory, and from which important biological insight can be gained.

Distinct cellular and subcellular distributions of G protein-coupled receptor kinase and arrestin isoforms in the striatum.

Directory of Open Access Journals (Sweden)

Evgeny Bychkov

Full Text Available G protein-coupled receptor kinases (GRKs and arrestins mediate desensitization of G protein-coupled receptors (GPCR. Arrestins also mediate G protein-independent signaling via GPCRs. Since GRK and arrestins demonstrate no strict receptor specificity, their functions in the brain may depend on their cellular complement, expression level, and subcellular targeting. However, cellular expression and subcellular distribution of GRKs and arrestins in the brain is largely unknown. We show that GRK isoforms GRK2 and GRK5 are similarly expressed in direct and indirect pathway neurons in the rat striatum. Arrestin-2 and arrestin-3 are also expressed in neurons of both pathways. Cholinergic interneurons are enriched in GRK2, arrestin-3, and GRK5. Parvalbumin-positive interneurons express more of GRK2 and less of arrestin-2 than medium spiny neurons. The GRK5 subcellular distribution in the human striatal neurons is altered by its phosphorylation: unphosphorylated enzyme preferentially localizes to synaptic membranes, whereas phosphorylated GRK5 is found in plasma membrane and cytosolic fractions. Both GRK isoforms are abundant in the nucleus of human striatal neurons, whereas the proportion of both arrestins in the nucleus was equally low. However, overall higher expression of arrestin-2 yields high enough concentration in the nucleus to mediate nuclear functions. These data suggest cell type- and subcellular compartment-dependent differences in GRK/arrestin-mediated desensitization and signaling.

Hybrid computer simulation of the dynamics of the Hoger Onderwijs Reactor

International Nuclear Information System (INIS)

Moers, J.C.; Vries, J.W. de.

1976-01-01

A distributed parameter model for the dynamics of the Hoger Onderwijs Reactor (HOR) at Delft is presented. The neutronic and the thermodynamic part of this model have been separately implemented on the AD4-IBM1800 Hybrid Computer of the Delft University of Technology Computation Centre. A continuous Space/Discrete Time solution method has been employed. Some test results of the simulation are included

Global dynamics of a novel multi-group model for computer worms

International Nuclear Information System (INIS)

Gong Yong-Wang; Song Yu-Rong; Jiang Guo-Ping

2013-01-01

In this paper, we study worm dynamics in computer networks composed of many autonomous systems. A novel multi-group SIQR (susceptible-infected-quarantined-removed) model is proposed for computer worms by explicitly considering anti-virus measures and the network infrastructure. Then, the basic reproduction number of worm R 0 is derived and the global dynamics of the model are established. It is shown that if R 0 is less than or equal to 1, the disease-free equilibrium is globally asymptotically stable and the worm dies out eventually, whereas, if R 0 is greater than 1, one unique endemic equilibrium exists and it is globally asymptotically stable, thus the worm persists in the network. Finally, numerical simulations are given to illustrate the theoretical results. (general)

A Model for the Acceptance of Cloud Computing Technology Using DEMATEL Technique and System Dynamics Approach

Directory of Open Access Journals (Sweden)

seyyed mohammad zargar

2018-03-01

Full Text Available Cloud computing is a new method to provide computing resources and increase computing power in organizations. Despite the many benefits this method shares, it has not been universally used because of some obstacles including security issues and has become a concern for IT managers in organization. In this paper, the general definition of cloud computing is presented. In addition, having reviewed previous studies, the researchers identified effective variables on technology acceptance and, especially, cloud computing technology. Then, using DEMATEL technique, the effectiveness and permeability of the variable were determined. The researchers also designed a model to show the existing dynamics in cloud computing technology using system dynamics approach. The validity of the model was confirmed through evaluation methods in dynamics model by using VENSIM software. Finally, based on different conditions of the proposed model, a variety of scenarios were designed. Then, the implementation of these scenarios was simulated within the proposed model. The results showed that any increase in data security, government support and user training can lead to the increase in the adoption and use of cloud computing technology.

Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning

Directory of Open Access Journals (Sweden)

Tanel Pärnamaa

2017-05-01

Full Text Available High-throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently-tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held-out images. We confirm that low-level network features correspond to basic image characteristics, while deeper layers separate localization classes. Using this network as a feature calculator, we train standard classifiers that assign proteins to previously unseen compartments after observing only a small number of training examples. Our results are the most accurate subcellular localization classifications to date, and demonstrate the usefulness of deep learning for high-throughput microscopy.

Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning.

Science.gov (United States)

Pärnamaa, Tanel; Parts, Leopold

2017-05-05

High-throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently-tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held-out images. We confirm that low-level network features correspond to basic image characteristics, while deeper layers separate localization classes. Using this network as a feature calculator, we train standard classifiers that assign proteins to previously unseen compartments after observing only a small number of training examples. Our results are the most accurate subcellular localization classifications to date, and demonstrate the usefulness of deep learning for high-throughput microscopy. Copyright © 2017 Parnamaa and Parts.

Extensive use of computational fluid dynamics in the upgrading of hydraulic turbines

Energy Technology Data Exchange (ETDEWEB)

Sabourin, M.; Eremeef, R.; De Henau, V.

1995-12-31

Computational fluid dynamics codes, based on turbulent Navier-Stokes equations, allow evaluation of the hydraulic losses of each turbine component with precision. Using those codes with the new generation of computers enables a wide variety of component geometries to be modelled and compared to the original designs under flow conditions obtained from testing, at a reasonable cost and in a relatively short time. This paper reviews the actual method used in the design of a solution to a turbine rehabilitation project involving runner replacement, redesign of upstream components (stay vanes and wicket gates), and downstream components (draft tubes and runner outlets). The paper shows how computational fluid dynamics can help hydraulic engineers to obtain valuable information not only on performance enhancement but also on the phenomena that produce the enhancement, and to reduce the variety of modifications to be tested.

Fast Virtual Fractional Flow Reserve Based Upon Steady-State Computational Fluid Dynamics Analysis

Directory of Open Access Journals (Sweden)

Paul D. Morris, PhD

2017-08-01

Full Text Available Fractional flow reserve (FFR-guided percutaneous intervention is superior to standard assessment but remains underused. The authors have developed a novel “pseudotransient” analysis protocol for computing virtual fractional flow reserve (vFFR based upon angiographic images and steady-state computational fluid dynamics. This protocol generates vFFR results in 189 s (cf >24 h for transient analysis using a desktop PC, with <1% error relative to that of full-transient computational fluid dynamics analysis. Sensitivity analysis demonstrated that physiological lesion significance was influenced less by coronary or lesion anatomy (33% and more by microvascular physiology (59%. If coronary microvascular resistance can be estimated, vFFR can be accurately computed in less time than it takes to make invasive measurements.

Privacy context model for dynamic privacy adaptation in ubiquitous computing

NARCIS (Netherlands)

Schaub, Florian; Koenings, Bastian; Dietzel, Stefan; Weber, M.; Kargl, Frank

Ubiquitous computing is characterized by the merger of physical and virtual worlds as physical artifacts gain digital sensing, processing, and communication capabilities. Maintaining an appropriate level of privacy in the face of such complex and often highly dynamic systems is challenging. We argue

Computational Fluid Dynamics model of stratified atmospheric boundary-layer flow

DEFF Research Database (Denmark)

Koblitz, Tilman; Bechmann, Andreas; Sogachev, Andrey

2015-01-01

For wind resource assessment, the wind industry is increasingly relying on computational fluid dynamics models of the neutrally stratified surface-layer. So far, physical processes that are important to the whole atmospheric boundary-layer, such as the Coriolis effect, buoyancy forces and heat...

Dynamical Trust and Reputation Computation Model for B2C E-Commerce

OpenAIRE

Bo Tian; Kecheng Liu; Yuanzhong Chen

2015-01-01

Trust is one of the most important factors that influence the successful application of network service environments, such as e-commerce, wireless sensor networks, and online social networks. Computation models associated with trust and reputation have been paid special attention in both computer societies and service science in recent years. In this paper, a dynamical computation model of reputation for B2C e-commerce is proposed. Firstly, conceptions associated with trust and reputation are...

Subcellular partitioning kinetics, metallothionein response and oxidative damage in the marine mussel Mytilus galloprovincialis exposed to cadmium-based quantum dots

Energy Technology Data Exchange (ETDEWEB)

Rocha, Thiago Lopes [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Gomes, Tânia [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo (Norway); Durigon, Emerson Giuliani [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Bebianno, Maria João, E-mail: mbebian@ualg.pt [CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139 Faro (Portugal)

2016-06-01

The environmental health impact of metal-based nanomaterials is of emerging concern, but their metabolism and detoxification pathways in marine bioindicator species remain unclear. This study investigated the role of subcellular partitioning kinetics, metallothioneins (MTs) response and oxidative damage (lipid peroxidation – LPO) in the marine mussel Mytilus galloprovincialis exposed to CdTe quantum dots (QDs) in comparison with its dissolved counterpart. Mussels were exposed to QDs and dissolved Cd for 21 days at 10 μg Cd L{sup −1} followed by a 50 days depuration. Higher Cd concentrations were detected in fractions containing mitochondria, nucleus and lysosomes, suggesting potential subcellular targets of QDs toxicity in mussel tissues. Tissue specific metabolism patterns were observed in mussels exposed to both Cd forms. Although MT levels were directly associated with Cd in both forms, QDs subcellular partitioning is linked to biologically active metal (BAM), but no increase in LPO occurred, while in the case of dissolved Cd levels are in the biologically detoxified metal (BDM) form, indicating nano-specific effects. Mussel gills showed lower detoxification capability of QDs, while the digestive gland is the major tissue for storage and detoxification of both Cd forms. Both mussel tissues were unable to completely eliminate the Cd accumulated in the QDs form (estimated half-life time > 50 days), highlighting the potential source of Cd and QDs toxicity for human and environmental health. Results indicate tissue specific metabolism patterns and nano-specific effects in marine mussel exposed to QDs. - Highlights: • Subcellular partitioning and MT response are Cd form, tissue and time dependent. • Tissue specific metabolism of Cd-based quantum dots (QDs) in marine mussels. • QDs are slower biologically detoxified when compared to dissolved Cd. • Subcellular partitioning and biomarker responses indicate nano-specific effects. • Subcellular

Dynamic Scaffolding of Socially Regulated Learning in a Computer-Based Learning Environment

Science.gov (United States)

Molenaar, Inge; Roda, Claudia; van Boxtel, Carla; Sleegers, Peter

2012-01-01

The aim of this study is to test the effects of dynamically scaffolding social regulation of middle school students working in a computer-based learning environment. Dyads in the scaffolding condition (N=56) are supported with computer-generated scaffolds and students in the control condition (N=54) do not receive scaffolds. The scaffolds are…

Subcellular distribution and chemical forms of cadmium in Phytolacca americana L

Energy Technology Data Exchange (ETDEWEB)

Fu Xiaoping; Dou Changming [Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029 (China); Chen Yingxu, E-mail: yingxu_chen@hotmail.com [Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029 (China); Chen Xincai; Shi Jiyan; Yu Mingge; Xu Jie [Ministry of Agriculture Key Laboratory of Non-point Source Pollution Control, Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310029 (China)

2011-02-15

Phytolacca americana L. (pokeweed) is a promising species for Cd phytoextraction with large biomass and fast growth rate. To further understand the mechanisms involved in Cd tolerance and detoxification, the present study investigated subcellular distribution and chemical forms of Cd in pokeweed. Subcellular fractionation of Cd-containing tissues indicated that both in root and leaves, the majority of the element was located in soluble fraction and cell walls. Meanwhile, Cd taken up by pokeweed existed in different chemical forms. Results showed that the greatest amount of Cd was found in the extraction of 80% ethanol in roots, followed by 1 M NaCl, d-H{sub 2}O and 2% HAc, while in leaves and stems, most of the Cd was extracted by 1 M NaCl, and the subdominant amount of Cd was extracted by 80% ethanol. It could be suggested that Cd compartmentation with organo-ligands in vacuole or integrated with pectates and proteins in cell wall might be responsible for the adaptation of pokeweed to Cd stress.

Radioimmunoassay of steroids in homogenates and subcellular fractions of testicular tissue

International Nuclear Information System (INIS)

Campo, S.; Nicolau, G.; Pellizari, E.; Rivarola, M.A.

1977-01-01

Radioimmunoassays for testosterone (T), dihydrotestosterone (DHT) and 5alpha-androstan-3alpha, 17beta-diol (DIOL) in homogenates of whole testis, interstitial tissue and seminiferous tubules as well as subcellular fractions of the latter were developed. Steroids were extracted with acetone, submitted to several solvent partitions and isolated by a celite: propylene glycol: ethylene glycol column chromatography. Anit-T serum was used for the assay of T and DTH, and a specific anti-Diol serum for DIOL. Subcellular fractions were separated by differential centrifugation. The nuclear fraction was purified by centrifugation in a dense sucrose buffer followed by several washings. Losses were corrected according to recovery of DNA. Optimal conditions for purification of acetone extracts at minimal losses were established. Validation of the method was studied testing linear regression of logit-log transformations of standard curves and parallelism with unknowns. T was the steroid present in higher concentrations in all samples studied. It is concluded that the present method for determination of endogenous androgen concentrations in testicular tissue is valid and might be useful in studing testicular function. (orig.) [de

Computational approach to large quantum dynamical problems

International Nuclear Information System (INIS)

Friesner, R.A.; Brunet, J.P.; Wyatt, R.E.; Leforestier, C.; Binkley, S.

1987-01-01

The organizational structure is described for a new program that permits computations on a variety of quantum mechanical problems in chemical dynamics and spectroscopy. Particular attention is devoted to developing and using algorithms that exploit the capabilities of current vector supercomputers. A key component in this procedure is the recursive transformation of the large sparse Hamiltonian matrix into a much smaller tridiagonal matrix. An application to time-dependent laser molecule energy transfer is presented. Rate of energy deposition in the multimode molecule for systematic variations in the molecular intermode coupling parameters is emphasized

High performance computations using dynamical nucleation theory

International Nuclear Information System (INIS)

Windus, T L; Crosby, L D; Kathmann, S M

2008-01-01

Chemists continue to explore the use of very large computations to perform simulations that describe the molecular level physics of critical challenges in science. In this paper, we describe the Dynamical Nucleation Theory Monte Carlo (DNTMC) model - a model for determining molecular scale nucleation rate constants - and its parallel capabilities. The potential for bottlenecks and the challenges to running on future petascale or larger resources are delineated. A 'master-slave' solution is proposed to scale to the petascale and will be developed in the NWChem software. In addition, mathematical and data analysis challenges are described

Dynamic partitioning as a way to exploit new computing paradigms: the cloud use case

International Nuclear Information System (INIS)

Ciaschini, Vincenzo; Dal Pra, Stefano; Dell'Agnello, Luca

2015-01-01

The WLCG community and many groups in the HEP community have based their computing strategy on the Grid paradigm, which proved successful and still ensures its goals. However, Grid technology has not spread much over other communities; in the commercial world, the cloud paradigm is the emerging way to provide computing services. WLCG experiments aim to achieve integration of their existing current computing model with cloud deployments and take advantage of the so-called opportunistic resources (including HPC facilities) which are usually not Grid compliant. One missing feature in the most common cloud frameworks, is the concept of job scheduler, which plays a key role in a traditional computing centre, by enabling a fairshare based access at the resources to the experiments in a scenario where demand greatly outstrips availability. At CNAF we are investigating the possibility to access the Tier-1 computing resources as an OpenStack based cloud service. The system, exploiting the dynamic partitioning mechanism already being used to enable Multicore computing, allowed us to avoid a static splitting of the computing resources in the Tier-1 farm, while permitting a share friendly approach. The hosts in a dynamically partitioned farm may be moved to or from the partition, according to suitable policies for request and release of computing resources. Nodes being requested in the partition switch their role and become available to play a different one. In the cloud use case hosts may switch from acting as Worker Node in the Batch system farm to cloud compute node member, made available to tenants. In this paper we describe the dynamic partitioning concept, its implementation and integration with our current batch system, LSF. (paper)

Dynamic partitioning as a way to exploit new computing paradigms: the cloud use case.

Science.gov (United States)

Ciaschini, Vincenzo; Dal Pra, Stefano; dell'Agnello, Luca

2015-12-01

The WLCG community and many groups in the HEP community have based their computing strategy on the Grid paradigm, which proved successful and still ensures its goals. However, Grid technology has not spread much over other communities; in the commercial world, the cloud paradigm is the emerging way to provide computing services. WLCG experiments aim to achieve integration of their existing current computing model with cloud deployments and take advantage of the so-called opportunistic resources (including HPC facilities) which are usually not Grid compliant. One missing feature in the most common cloud frameworks, is the concept of job scheduler, which plays a key role in a traditional computing centre, by enabling a fairshare based access at the resources to the experiments in a scenario where demand greatly outstrips availability. At CNAF we are investigating the possibility to access the Tier-1 computing resources as an OpenStack based cloud service. The system, exploiting the dynamic partitioning mechanism already being used to enable Multicore computing, allowed us to avoid a static splitting of the computing resources in the Tier-1 farm, while permitting a share friendly approach. The hosts in a dynamically partitioned farm may be moved to or from the partition, according to suitable policies for request and release of computing resources. Nodes being requested in the partition switch their role and become available to play a different one. In the cloud use case hosts may switch from acting as Worker Node in the Batch system farm to cloud compute node member, made available to tenants. In this paper we describe the dynamic partitioning concept, its implementation and integration with our current batch system, LSF.

Transient hepatic attenuation difference of lobar or segmental distribution detected by dynamic computed tomography

International Nuclear Information System (INIS)

Itai, Y.; Moss, A.A.; Goldberg, H.I.

1982-01-01

Dynamic computed tomography of hepatic tumors revealed a transient attenuation difference of the liver in a lobar or segmental distribution in three cases. The difference was most prominent during the hepatogram phase. It was attributed to siphonage of arterial blood by hepatic tumors in two cases, while an increase of arterial flow induced by portal vein occlusion was inferred in the other case. Results indicate dynamic computed tomography will be usful in analysis of geometrical hemodynamics

Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease*

Science.gov (United States)

da Palma, Joel Ramos; Burri, Dominique Julien; Oppliger, Joël; Salamina, Marco; Cendron, Laura; de Laureto, Patrizia Polverino; Seidah, Nabil Georges; Kunz, Stefan; Pasquato, Antonella

2014-01-01

The proprotein convertase subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P) plays crucial roles in cellular homeostatic functions and is hijacked by pathogenic viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P involves sequential autocatalytic processing of its N-terminal prodomain at sites B′/B followed by the herein newly identified C′/C sites. We found that SKI-1/S1P autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. In contrast to other zymogen proprotein convertases, all incompletely matured intermediates of SKI-1/S1P showed full catalytic activity toward cellular substrates, whereas optimal cleavage of viral glycoproteins depended on B′/B processing. Incompletely matured forms of SKI-1/S1P further process cellular and viral substrates in distinct subcellular compartments. Using a cell-based sensor for SKI-1/S1P activity, we found that 9 amino acid residues at the cleavage site (P1–P8) and P1′ are necessary and sufficient to define the subcellular location of processing and to determine to what extent processing of a substrate depends on SKI-1/S1P maturation. In sum, our study reveals novel and unexpected features of SKI-1/S1P zymogen activation and subcellular specificity of activity toward cellular and pathogen-derived substrates. PMID:25378398

OpenDx programs for visualization of computational fluid dynamics (CFD) simulations

International Nuclear Information System (INIS)

Silva, Marcelo Mariano da

2008-01-01

The search for high performance and low cost hardware and software solutions always guides the developments performed at the IEN parallel computing laboratory. In this context, this dissertation about the building of programs for visualization of computational fluid dynamics (CFD) simulations using the open source software OpenDx was written. The programs developed are useful to produce videos and images in two or three dimensions. They are interactive, easily to use and were designed to serve fluid dynamics researchers. A detailed description about how this programs were developed and the complete instructions of how to use them was done. The use of OpenDx as development tool is also introduced. There are examples that help the reader to understand how programs can be useful for many applications. (author)

Computed tomography of hepatocellular carcinoma: Usefulness of dynamic CT

Energy Technology Data Exchange (ETDEWEB)

Takemoto, Kazumasa; Inoue, Yuichi; Matsuoka, Toshiyuki; Nakatsuka, Haruki; Oda, Junro [Osaka City Univ. (Japan). Faculty of Medicine

1983-04-01

Dynamic computed tomography (CT) scans in 65 hepatocellular carcinomas were analyzed and compared to plain and drip infusion contrast CT scans of those. Scans were obtained before, 10, 30, and 50 seconds after an intravenous bolus injection of 50ml 65% Angiografin. By this method, 49 hepatomas had moderate to marked enhancement at the arterial phase while the enhancement of normal liver parenchyma was only slight at the arterial phase and peaked at the portal phase. Compared to a drip infusion contrast CT, a dynamic CT had advantages to detect an isodense hepatoma in 4 and daughter tumors in 16 both of which were not appreciated by a plain and a drip infusion contrast CT. The tumor extension was also better delineated by a dynamic CT because a part of hepatoma had an isodense area. An arterio-portal shunt was visualized in one. Tumor thrombus in the portal vein was clearly demonstrated in 6 at the portal phase of a dynamic CT. Since a dynamic CT is convenient to perform without any special program or soft wear and gives us very useful information, we believe that it should be routinely employed as a part of a liver CT examination.

Concentration of 17 Elements in Subcellular Fractions of Beef Heart Tissue Determined by Neutron Activation Analysis

Energy Technology Data Exchange (ETDEWEB)

Wester, P O

1964-12-15

Subcellular fractions of beef heart tissue are investigated, by means of neutron activation analysis, with respect to their concentration of 17 different elements. A recently developed ion-exchange technique combined with gamma spectrometry is used. The homogeneity of the subcellular fractions is examined electron microscopically. The following elements are determined: As, Ba, Br, Cas Co, Cs, Cu, Fe, Hg, La, Mo, P, Rb, Se, Sm, W and Zn. The determination of Ag, Au, Cd, Ce, Cr, Sb and Sc is omitted, in view of contamination. Reproducible and characteristic patterns of distribution are obtained for all elements studied.

Concentration of 17 Elements in Subcellular Fractions of Beef Heart Tissue Determined by Neutron Activation Analysis

International Nuclear Information System (INIS)

Wester, P.O.

1964-12-01

Subcellular fractions of beef heart tissue are investigated, by means of neutron activation analysis, with respect to their concentration of 17 different elements. A recently developed ion-exchange technique combined with gamma spectrometry is used. The homogeneity of the subcellular fractions is examined electron microscopically. The following elements are determined: As, Ba, Br, Cas Co, Cs, Cu, Fe, Hg, La, Mo, P, Rb, Se, Sm, W and Zn. The determination of Ag, Au, Cd, Ce, Cr, Sb and Sc is omitted, in view of contamination. Reproducible and characteristic patterns of distribution are obtained for all elements studied

The dynamic micro computed tomography at SSRF

Science.gov (United States)

Chen, R.; Xu, L.; Du, G.; Deng, B.; Xie, H.; Xiao, T.

2018-05-01

Synchrotron radiation micro-computed tomography (SR-μCT) is a critical technique for quantitative characterizing the 3D internal structure of samples, recently the dynamic SR-μCT has been attracting vast attention since it can evaluate the three-dimensional structure evolution of a sample. A dynamic μCT method, which is based on monochromatic beam, was developed at the X-ray Imaging and Biomedical Application Beamline at Shanghai Synchrotron Radiation Facility, by combining the compressed sensing based CT reconstruction algorithm and hardware upgrade. The monochromatic beam based method can achieve quantitative information, and lower dose than the white beam base method in which the lower energy beam is absorbed by the sample rather than contribute to the final imaging signal. The developed method is successfully used to investigate the compression of the air sac during respiration in a bell cricket, providing new knowledge for further research on the insect respiratory system.

Computer codes for beam dynamics analysis of cyclotronlike accelerators

Science.gov (United States)

Smirnov, V.

2017-12-01

Computer codes suitable for the study of beam dynamics in cyclotronlike (classical and isochronous cyclotrons, synchrocyclotrons, and fixed field alternating gradient) accelerators are reviewed. Computer modeling of cyclotron segments, such as the central zone, acceleration region, and extraction system is considered. The author does not claim to give a full and detailed description of the methods and algorithms used in the codes. Special attention is paid to the codes already proven and confirmed at the existing accelerating facilities. The description of the programs prepared in the worldwide known accelerator centers is provided. The basic features of the programs available to users and limitations of their applicability are described.

Artificial Intelligence In Computational Fluid Dynamics

Science.gov (United States)

Vogel, Alison Andrews

1991-01-01

Paper compares four first-generation artificial-intelligence (Al) software systems for computational fluid dynamics. Includes: Expert Cooling Fan Design System (EXFAN), PAN AIR Knowledge System (PAKS), grid-adaptation program MITOSIS, and Expert Zonal Grid Generation (EZGrid). Focuses on knowledge-based ("expert") software systems. Analyzes intended tasks, kinds of knowledge possessed, magnitude of effort required to codify knowledge, how quickly constructed, performances, and return on investment. On basis of comparison, concludes Al most successful when applied to well-formulated problems solved by classifying or selecting preenumerated solutions. In contrast, application of Al to poorly understood or poorly formulated problems generally results in long development time and large investment of effort, with no guarantee of success.

Diversity and subcellular distribution of archaeal secreted proteins

Directory of Open Access Journals (Sweden)

Mechthild ePohlschroder

2012-07-01

Full Text Available Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell-wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as archaeal kingdom-specific pathways. A more comprehensive understanding of the transport pathways and post-translational modifications of secreted archaeal proteins will also generate invaluable insights that will facilitate the identification of commercially valuable archaeal enzymes and the development of heterologous systems in which to efficiently express them.

Diversity and subcellular distribution of archaeal secreted proteins.

Science.gov (United States)

Szabo, Zalan; Pohlschroder, Mechthild

2012-01-01

Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis, and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat) pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as phyla-specific pathways among the archaea. A more comprehensive understanding of the transport pathways used and post-translational modifications of secreted archaeal proteins will also facilitate the identification and heterologous expression of commercially valuable archaeal enzymes.

Thirteenth Workshop for Computational Fluid Dynamic Applications in Rocket Propulsion and Launch Vehicle Technology. Volume 1

Science.gov (United States)

Williams, R. W. (Compiler)

1996-01-01

The purpose of the workshop was to discuss experimental and computational fluid dynamic activities in rocket propulsion and launch vehicles. The workshop was an open meeting for government, industry, and academia. A broad number of topics were discussed including computational fluid dynamic methodology, liquid and solid rocket propulsion, turbomachinery, combustion, heat transfer, and grid generation.

Metabolism of polybrominated diphenyl ethers and tetrabromobisphenol A by fish liver subcellular fractions in vitro.

Science.gov (United States)

Shen, Mengnan; Cheng, Jie; Wu, Ruohan; Zhang, Shenghu; Mao, Liang; Gao, Shixiang

2012-06-15

Polybrominated diphenyl ethers (PBDEs) and tetrabromobisphenol A (TBBPA) are two major flame retardants that accumulate in fish tissues and are potentially toxic. Their debrominated and oxidated derivatives were also reported in fish tissues although the sources of theses derivatives were unidentified. Our study was to determine whether PBDEs and TBBPA could be metabolized by fish liver subcellular fractions in vitro and to identify what types of metabolites were formed. Liver microsomes and S9 fractions of crucian carp (Carassius auratus) were exposed to 4,4'-dibromodiphenyl ether (BDE 15), 2,2',4,4'-tetrabromodiphenyl ether (BDE 47) or TBBPA solutions for 4h. Exposure of liver subcellular fractions to BDE 15 resulted in the formation of bromophenol and two monohydroxylated dibromodiphenyl ether metabolites. Neither in microsomes nor in S9 studies has revealed the presence of hydroxylated metabolites with BDE 47 exposure which indicated that the oxidation reactions in vitro were hindered by the increased number of bromine substituents on the PBDEs. TBBPA underwent an oxidative cleavage near the central carbon of the molecule, which led to the production of 2,6-dibromo-4-isopropyl-phenol and three unidentified metabolites. Another metabolite of TBBPA characterized as a hexa-brominated compound with three aromatic rings was also found in the liver subcellular fractions. These results suggest that the biotransformation of BDE 15 and TBBPA in fish liver is mediated by cytochrome P450 (CYP450) enzymes, as revealed by the formation of hydroxylated metabolites and oxidative bond cleavage products. Moreover, further studies on the identification of specific CYP450 isozymes involved in the biotransformation revealed that CYP1A was the major enzyme responsible for the biotransformation of BDE 15 and TBBPA in fish liver subcellular fractions and CYP3A4 also played a major role in metabolism of TBBPA. Copyright © 2012 Elsevier B.V. All rights reserved.

Efficient conjugate gradient algorithms for computation of the manipulator forward dynamics

Science.gov (United States)

Fijany, Amir; Scheid, Robert E.

1989-01-01

The applicability of conjugate gradient algorithms for computation of the manipulator forward dynamics is investigated. The redundancies in the previously proposed conjugate gradient algorithm are analyzed. A new version is developed which, by avoiding these redundancies, achieves a significantly greater efficiency. A preconditioned conjugate gradient algorithm is also presented. A diagonal matrix whose elements are the diagonal elements of the inertia matrix is proposed as the preconditioner. In order to increase the computational efficiency, an algorithm is developed which exploits the synergism between the computation of the diagonal elements of the inertia matrix and that required by the conjugate gradient algorithm.

Adaptive Dynamic Process Scheduling on Distributed Memory Parallel Computers

Directory of Open Access Journals (Sweden)

Wei Shu

1994-01-01

Full Text Available One of the challenges in programming distributed memory parallel machines is deciding how to allocate work to processors. This problem is particularly important for computations with unpredictable dynamic behaviors or irregular structures. We present a scheme for dynamic scheduling of medium-grained processes that is useful in this context. The adaptive contracting within neighborhood (ACWN is a dynamic, distributed, load-dependent, and scalable scheme. It deals with dynamic and unpredictable creation of processes and adapts to different systems. The scheme is described and contrasted with two other schemes that have been proposed in this context, namely the randomized allocation and the gradient model. The performance of the three schemes on an Intel iPSC/2 hypercube is presented and analyzed. The experimental results show that even though the ACWN algorithm incurs somewhat larger overhead than the randomized allocation, it achieves better performance in most cases due to its adaptiveness. Its feature of quickly spreading the work helps it outperform the gradient model in performance and scalability.

A Symbolic and Graphical Computer Representation of Dynamical Systems

Science.gov (United States)

Gould, Laurence I.

2005-04-01

AUTONO is a Macsyma/Maxima program, designed at the University of Hartford, for solving autonomous systems of differential equations as well as for relating Lagrangians and Hamiltonians to their associated dynamical equations. AUTONO can be used in a number of fields to decipher a variety of complex dynamical systems with ease, producing their Lagrangian and Hamiltonian equations in seconds. These equations can then be incorporated into VisSim, a modeling and simulation program, which yields graphical representations of motion in a given system through easily chosen input parameters. The program, along with the VisSim differential-equations graphical package, allows for resolution and easy understanding of complex problems in a relatively short time; thus enabling quicker and more advanced computing of dynamical systems on any number of platforms---from a network of sensors on a space probe, to the behavior of neural networks, to the effects of an electromagnetic field on components in a dynamical system. A flowchart of AUTONO, along with some simple applications and VisSim output, will be shown.

Parallel computing and molecular dynamics of biological membranes

International Nuclear Information System (INIS)

La Penna, G.; Letardi, S.; Minicozzi, V.; Morante, S.; Rossi, G.C.; Salina, G.

1998-01-01

In this talk I discuss the general question of the portability of molecular dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision of the today available platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on possible programming strategies. Liquids can be satisfactorily simulated using the ''systolic'' method. For more complex systems, like the biological ones at which we are ultimately interested in, the ''domain decomposition'' approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of atoms of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed. (orig.)

An Automated High Aspect Ratio Mesher for Computational Fluid Dynamics, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — Computational fluid dynamics (CFD) simulations are routinely used while designing, analyzing, and optimizing air- and spacecraft. An important component of CFD...

Dynamic enhanced computed tomographic findings of a perirenal capillary hemangioma

Energy Technology Data Exchange (ETDEWEB)

Lee, Jung Min; Kim, Sang Won; Kim, Hyun Cheol; Yang, Dal Mo; Ryu, Jung Kyu; Lim, Sung Jig [Kyung Hee University Hospital at Gangdong, Seoul (Korea, Republic of)

2016-05-15

Hemangiomas are benign mesenchymal neoplasms that rarely occur in the kidney and perirenal space. Perirenal hemangiomas can mimic the appearance of exophytic renal cell carcinoma or various retroperitoneal tumors. We report a case of perirenal hemangioma detected by dynamic enhanced computed tomography in a 43-year-old female.

Mesh and Time-Step Independent Computational Fluid Dynamics (CFD) Solutions

Science.gov (United States)

Nijdam, Justin J.

2013-01-01

A homework assignment is outlined in which students learn Computational Fluid Dynamics (CFD) concepts of discretization, numerical stability and accuracy, and verification in a hands-on manner by solving physically realistic problems of practical interest to engineers. The students solve a transient-diffusion problem numerically using the common…

On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems

Science.gov (United States)

Junge, Oliver; Kevrekidis, Ioannis G.

2017-06-01

We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.

Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization.

Directory of Open Access Journals (Sweden)

Kuo-Chen Chou

Full Text Available One of the fundamental goals in proteomics and cell biology is to identify the functions of proteins in various cellular organelles and pathways. Information of subcellular locations of proteins can provide useful insights for revealing their functions and understanding how they interact with each other in cellular network systems. Most of the existing methods in predicting plant protein subcellular localization can only cover three or four location sites, and none of them can be used to deal with multiplex plant proteins that can simultaneously exist at two, or move between, two or more different location sits. Actually, such multiplex proteins might have special biological functions worthy of particular notice. The present study was devoted to improve the existing plant protein subcellular location predictors from the aforementioned two aspects. A new predictor called "Plant-mPLoc" is developed by integrating the gene ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo amino acid composition. It can be used to identify plant proteins among the following 12 location sites: (1 cell membrane, (2 cell wall, (3 chloroplast, (4 cytoplasm, (5 endoplasmic reticulum, (6 extracellular, (7 Golgi apparatus, (8 mitochondrion, (9 nucleus, (10 peroxisome, (11 plastid, and (12 vacuole. Compared with the existing methods for predicting plant protein subcellular localization, the new predictor is much more powerful and flexible. Particularly, it also has the capacity to deal with multiple-location proteins, which is beyond the reach of any existing predictors specialized for identifying plant protein subcellular localization. As a user-friendly web-server, Plant-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to

Dynamic Computation of Change Operations in Version Management of Business Process Models

Science.gov (United States)

Küster, Jochen Malte; Gerth, Christian; Engels, Gregor

Version management of business process models requires that changes can be resolved by applying change operations. In order to give a user maximal freedom concerning the application order of change operations, position parameters of change operations must be computed dynamically during change resolution. In such an approach, change operations with computed position parameters must be applicable on the model and dependencies and conflicts of change operations must be taken into account because otherwise invalid models can be constructed. In this paper, we study the concept of partially specified change operations where parameters are computed dynamically. We provide a formalization for partially specified change operations using graph transformation and provide a concept for their applicability. Based on this, we study potential dependencies and conflicts of change operations and show how these can be taken into account within change resolution. Using our approach, a user can resolve changes of business process models without being unnecessarily restricted to a certain order.

Retention and subcellular distribution of 67Ga in normal organs

International Nuclear Information System (INIS)

Ando, A.; Ando, I.; Hiraki, T.

1986-01-01

Using normal rats, retention values and subcellular distribution of 67 Ga in each organ were investigated. At 10 min after administration of 67 Ga-citrate the retention value of 67 Ga in blood was 6.77% dose/g, and this value decreased with time. The values for skeletal muscle, lung, pancreas, adrenal, heart muscle, brain, small intestine, large intestine and spinal cord were the highest at 10 min after administration, and they decreased with time. Conversely this value in bone increased until 10 days after injection. But in the liver, kidney, and stomach, these values increased with time after administration and were highest 24 h or 48 h after injection. After that, they decreased with time. The value in spleen reached a plateau 48 h after administration, and hardly varied for 10 days. From the results of subcellular fractionation, it was deduced that lysosome plays quite an important role in the concentration of 67 Ga in small intestine, stomach, lung, kidney and pancreas; a lesser role in its concentration in heart muscle, and hardly any role in the 67 Ga accumulation in skeletal muscle. In spleen, the contents in nuclear, mitochrondrial, microsomal, and supernatant fractions all contributed to the accumulation of 67 Ga. (orig.) [de

mPLR-Loc: an adaptive decision multi-label classifier based on penalized logistic regression for protein subcellular localization prediction.

Science.gov (United States)

Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

2015-03-15

Proteins located in appropriate cellular compartments are of paramount importance to exert their biological functions. Prediction of protein subcellular localization by computational methods is required in the post-genomic era. Recent studies have been focusing on predicting not only single-location proteins but also multi-location proteins. However, most of the existing predictors are far from effective for tackling the challenges of multi-label proteins. This article proposes an efficient multi-label predictor, namely mPLR-Loc, based on penalized logistic regression and adaptive decisions for predicting both single- and multi-location proteins. Specifically, for each query protein, mPLR-Loc exploits the information from the Gene Ontology (GO) database by using its accession number (AC) or the ACs of its homologs obtained via BLAST. The frequencies of GO occurrences are used to construct feature vectors, which are then classified by an adaptive decision-based multi-label penalized logistic regression classifier. Experimental results based on two recent stringent benchmark datasets (virus and plant) show that mPLR-Loc remarkably outperforms existing state-of-the-art multi-label predictors. In addition to being able to rapidly and accurately predict subcellular localization of single- and multi-label proteins, mPLR-Loc can also provide probabilistic confidence scores for the prediction decisions. For readers' convenience, the mPLR-Loc server is available online (http://bioinfo.eie.polyu.edu.hk/mPLRLocServer). Copyright © 2014 Elsevier Inc. All rights reserved.

Subcellular Localization of Cadmium in Chlorella vulgaris Beijerinck Strain Bt-09

Directory of Open Access Journals (Sweden)

P.B. Lintongan

2004-06-01

Full Text Available Growth response curves of Chlorella vulgaris Beijerinck strain Bt-09 to sublethal concentrations of cadmium were evaluated. The growth responses of this microalgal isolate was determined through analysis of chlorophyll a levels. Cadmium was effectively taken up by the cells as determined by Flame Atomic Absorption Spectrophotometry (F-AAS. Subcellular fractionation was undertaken to locate sites that accumulate cadmium.

Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

Science.gov (United States)

Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

2018-02-01

Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.

Body dynamics and hydrodynamics of swimming larvae: a computational study

NARCIS (Netherlands)

Li, G.; Müller, U.K.; Leeuwen, van J.L.; Liu, H.

2012-01-01

To understand the mechanics of fish swimming, we need to know the forces exerted by the fluid and how these forces affect the motion of the fish. To this end, we developed a 3-D computational approach that integrates hydrodynamics and body dynamics. This study quantifies the flow around a swimming

Trusted Bytecode Virtual Machine Module: A Novel Method for Dynamic Remote Attestation in Cloud Computing

Directory of Open Access Journals (Sweden)

Songzhu Mei

2012-09-01

Full Text Available Cloud computing bring a tremendous complexity to information security. Remote attestation can be used to establish trust relationship in cloud. TBVMM is designed to extend the existing chain of trust into the software layers to support dynamic remote attestation for cloud computing. TBVMM uses Bayesian network and Kalman filter to solve the dynamicity of the trusted relationship. It is proposed to fill the trust gap between the infrastructure and upper software stacks.

Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

International Nuclear Information System (INIS)

Ko, Soon Heum; Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel; Jha, Shantenu

2014-01-01

Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

Predict subcellular locations of singleplex and multiplex proteins by semi-supervised learning and dimension-reducing general mode of Chou's PseAAC.

Science.gov (United States)

Pacharawongsakda, Eakasit; Theeramunkong, Thanaruk

2013-12-01

Predicting protein subcellular location is one of major challenges in Bioinformatics area since such knowledge helps us understand protein functions and enables us to select the targeted proteins during drug discovery process. While many computational techniques have been proposed to improve predictive performance for protein subcellular location, they have several shortcomings. In this work, we propose a method to solve three main issues in such techniques; i) manipulation of multiplex proteins which may exist or move between multiple cellular compartments, ii) handling of high dimensionality in input and output spaces and iii) requirement of sufficient labeled data for model training. Towards these issues, this work presents a new computational method for predicting proteins which have either single or multiple locations. The proposed technique, namely iFLAST-CORE, incorporates the dimensionality reduction in the feature and label spaces with co-training paradigm for semi-supervised multi-label classification. For this purpose, the Singular Value Decomposition (SVD) is applied to transform the high-dimensional feature space and label space into the lower-dimensional spaces. After that, due to limitation of labeled data, the co-training regression makes use of unlabeled data by predicting the target values in the lower-dimensional spaces of unlabeled data. In the last step, the component of SVD is used to project labels in the lower-dimensional space back to those in the original space and an adaptive threshold is used to map a numeric value to a binary value for label determination. A set of experiments on viral proteins and gram-negative bacterial proteins evidence that our proposed method improve the classification performance in terms of various evaluation metrics such as Aiming (or Precision), Coverage (or Recall) and macro F-measure, compared to the traditional method that uses only labeled data.

Investigation of Swirling Flow in Rod Bundle Subchannels Using Computational Fluid Dynamics

International Nuclear Information System (INIS)

Holloway, Mary V.; Beasley, Donald E.; Conner, Michael E.

2006-01-01

The fluid dynamics for turbulent flow through rod bundles representative of those used in pressurized water reactors is examined using computational fluid dynamics (CFD). The rod bundles of the pressurized water reactor examined in this study consist of a square array of parallel rods that are held on a constant pitch by support grids spaced axially along the rod bundle. Split-vane pair support grids are often used to create swirling flow in the rod bundle in an effort to improve the heat transfer characteristics for the rod bundle during both normal operating conditions and in accident condition scenarios. Computational fluid dynamics simulations for a two subchannel portion of the rod bundle were used to model the flow downstream of a split-vane pair support grid. A high quality computational mesh was used to investigate the choice of turbulence model appropriate for the complex swirling flow in the rod bundle subchannels. Results document a central swirling flow structure in each of the subchannels downstream of the split-vane pairs. Strong lateral flows along the surface of the rods, as well as impingement regions of lateral flow on the rods are documented. In addition, regions of lateral flow separation and low axial velocity are documented next to the rods. Results of the CFD are compared to experimental particle image velocimetry (PIV) measurements documenting the lateral flow structures downstream of the split-vane pairs. Good agreement is found between the computational simulation and experimental measurements for locations close to the support grid. (authors)

Computer Processing and Display of Positron Scintigrams and Dynamic Function Curves

Energy Technology Data Exchange (ETDEWEB)

Wilensky, S.; Ashare, A. B.; Pizer, S. M.; Hoop, B. Jr.; Brownell, G. L. [Massachusetts General Hospital, Boston, MA (United States)

1969-01-15

A computer processing and display system for handling radioisotope data is described. The system has been used to upgrade and display brain scans and to process dynamic function curves. The hardware and software are described, and results are presented. (author)

Estimation of numerical uncertainty in computational fluid dynamics simulations of a passively controlled wave energy converter

DEFF Research Database (Denmark)

Wang, Weizhi; Wu, Minghao; Palm, Johannes

2018-01-01

for almost linear incident waves. First, we show that the computational fluid dynamics simulations have acceptable agreement to experimental data. We then present a verification and validation study focusing on the solution verification covering spatial and temporal discretization, iterative and domain......The wave loads and the resulting motions of floating wave energy converters are traditionally computed using linear radiation–diffraction methods. Yet for certain cases such as survival conditions, phase control and wave energy converters operating in the resonance region, more complete...... dynamics simulations have largely been overlooked in the wave energy sector. In this article, we apply formal verification and validation techniques to computational fluid dynamics simulations of a passively controlled point absorber. The phase control causes the motion response to be highly nonlinear even...

Dynamic computer model for the metallogenesis and tectonics of the Circum-North Pacific

Science.gov (United States)

Scotese, Christopher R.; Nokleberg, Warren J.; Monger, James W.H.; Norton, Ian O.; Parfenov, Leonid M.; Khanchuk, Alexander I.; Bundtzen, Thomas K.; Dawson, Kenneth M.; Eremin, Roman A.; Frolov, Yuri F.; Fujita, Kazuya; Goryachev, Nikolai A.; Pozdeev, Anany I.; Ratkin, Vladimir V.; Rodinov, Sergey M.; Rozenblum, Ilya S.; Scholl, David W.; Shpikerman, Vladimir I.; Sidorov, Anatoly A.; Stone, David B.

2001-01-01

The digital files on this report consist of a dynamic computer model of the metallogenesis and tectonics of the Circum-North Pacific, and background articles, figures, and maps. The tectonic part of the dynamic computer model is derived from a major analysis of the tectonic evolution of the Circum-North Pacific which is also contained in directory tectevol. The dynamic computer model and associated materials on this CD-ROM are part of a project on the major mineral deposits, metallogenesis, and tectonics of the Russian Far East, Alaska, and the Canadian Cordillera. The project provides critical information on bedrock geology and geophysics, tectonics, major metalliferous mineral resources, metallogenic patterns, and crustal origin and evolution of mineralizing systems for this region. The major scientific goals and benefits of the project are to: (1) provide a comprehensive international data base on the mineral resources of the region that is the first, extensive knowledge available in English; (2) provide major new interpretations of the origin and crustal evolution of mineralizing systems and their host rocks, thereby enabling enhanced, broad-scale tectonic reconstructions and interpretations; and (3) promote trade and scientific and technical exchanges between North America and Eastern Asia.

Determination of platinum in human subcellular microsamples by inductively coupled plasma mass spectrometry

DEFF Research Database (Denmark)

Björn, Erik; Nygren, Yvonne; Nguyen, Tam T. T. N.

2007-01-01

A fast and robust method for the determination of platinum in human subcellular microsamples by inductively coupled plasma mass spectrometry was developed, characterized, and validated. Samples of isolated DNA and exosome fractions from human ovarian (2008) and melanoma (T289) cancer cell lines w...

Analysis of potato virus X replicase and TGBp3 subcellular locations

International Nuclear Information System (INIS)

Bamunusinghe, Devinka; Hemenway, Cynthia L.; Nelson, Richard S.; Sanderfoot, Anton A.; Ye, Chang M.; Silva, Muniwarage A.T.; Payton, M.; Verchot-Lubicz, Jeanmarie

2009-01-01

Potato virus X (PVX) infection leads to certain cytopathological modifications of the host endomembrane system. The subcellular location of the PVX replicase was previously unknown while the PVX TGBp3 protein was previously reported to reside in the ER. Using PVX infectious clones expressing the green fluorescent protein reporter, and antisera detecting the PVX replicase and host membrane markers, we examined the subcellular distribution of the PVX replicase in relation to the TGBp3. Confocal and electron microscopic observations revealed that the replicase localizes in membrane bound structures that derive from the ER. A subset of TGBp3 resides in the ER at the same location as the replicase. Sucrose gradient fractionation showed that the PVX replicase and TGBp3 proteins co-fractionate with ER marker proteins. This localization represents a region where both proteins may be synthesized and/or function. There is no evidence to indicate that either PVX protein moves into the Golgi apparatus. Cerulenin, a drug that inhibits de novo membrane synthesis, also inhibited PVX replication. These combined data indicate that PVX replication relies on ER-derived membrane recruitment and membrane proliferation.

Dynamic X-ray computed tomography; Tomographie dynamique a rayons X

Energy Technology Data Exchange (ETDEWEB)

Grangeat, P

2003-07-01

Paper Dynamic computed tomography (CT) imaging aims at reconstructing image sequences where the dynamic nature of the living human body is of primary interest. Main concerned applications are image-guided interventional procedures, functional studies and cardiac imaging. The introduction of ultra-fast rotating gantries along with multi-row detectors and in near future area detectors allows a huge progress toward the imaging of moving organs with low-contrast resolution. This paper gives an overview of the different concepts used in dynamic CT. A new reconstruction algorithm based on a voxel-specific dynamic evolution compensation is also presented. It provides four-dimensional image sequences with accurate spatio-temporal information, where each frame is reconstructed using a long-scan acquisition mode on several half-turns. In the same time, this technique permits to reduce the dose delivered per rotation while keeping the same signal to noise ratio for every frame using an adaptive motion-compensated temporal averaging. Results are illustrated on simulated data. (authors)

Modeling behavior dynamics using computational psychometrics within virtual worlds.

Science.gov (United States)

Cipresso, Pietro

2015-01-01

In case of fire in a building, how will people behave in the crowd? The behavior of each individual affects the behavior of others and, conversely, each one behaves considering the crowd as a whole and the individual others. In this article, I propose a three-step method to explore a brand new way to study behavior dynamics. The first step relies on the creation of specific situations with standard techniques (such as mental imagery, text, video, and audio) and an advanced technique [Virtual Reality (VR)] to manipulate experimental settings. The second step concerns the measurement of behavior in one, two, or many individuals focusing on parameters extractions to provide information about the behavior dynamics. Finally, the third step, which uses the parameters collected and measured in the previous two steps in order to simulate possible scenarios to forecast through computational models, understand, and explain behavior dynamics at the social level. An experimental study was also included to demonstrate the three-step method and a possible scenario.

Computer Assisted Comprehension of Distant Worlds: Understanding Hunger Dynamics in Africa.

Science.gov (United States)

Moseley, William G.

2001-01-01

Describes a computer program called RiskMap. Explains that after completing an assignment on rural economics and hunger dynamics in Africa, students showed an increased level of understanding and felt that using RiskMap was helpful in learning the material. Includes references. (DAJ)

Computational Fluid Dynamic (CFD) Analysis of a Generic Missile With Grid Fins

National Research Council Canada - National Science Library

DeSpirito, James

2000-01-01

This report presents the results of a study demonstrating an approach for using viscous computational fluid dynamic simulations to calculate the flow field and aerodynamic coefficients for a missile with grid fin...

Analysis of molten salt thermal-hydraulics using computational fluid dynamics

International Nuclear Information System (INIS)

Yamaji, B.; Csom, G.; Aszodi, A.

2003-01-01

To give a good solution for the problem of high level radioactive waste partitioning and transmutation is expected to be a pro missing option. Application of this technology also could extend the possibilities of nuclear energy. Large number of liquid-fuelled reactor concepts or accelerator driven subcritical systems was proposed as transmutors. Several of these consider fluoride based molten salts as the liquid fuel and coolant medium. The thermal-hydraulic behaviour of these systems is expected to be fundamentally different than the behaviour of widely used water-cooled reactors with solid fuel. Considering large flow domains three-dimensional thermal-hydraulic analysis is the method seeming to be applicable. Since the fuel is the coolant medium as well, one can expect a strong coupling between neutronics and thermal-hydraulics too. In the present paper the application of Computational Fluid Dynamics for three-dimensional thermal-hydraulics simulations of molten salt reactor concepts is introduced. In our past and recent works several calculations were carried out to investigate the capabilities of Computational Fluid Dynamics through the analysis of different molten salt reactor concepts. Homogenous single region molten salt reactor concept is studied and optimised. Another single region reactor concept is introduced also. This concept has internal heat exchanges in the flow domain and the molten salt is circulated by natural convection. The analysis of the MSRE experiment is also a part of our work since it may form a good background from the validation point of view. In the paper the results of the Computational Fluid Dynamics calculations with these concepts are presented. In the further work our objective is to investigate the thermal-hydraulics of the multi-region molten salt reactor (Authors)

Cadmium Disrupts Subcellular Organelles, Including Chloroplasts, Resulting in Melatonin Induction in Plants

Directory of Open Access Journals (Sweden)

Hyoung-Yool Lee

2017-10-01

Full Text Available Cadmium is a well-known elicitor of melatonin synthesis in plants, including rice. However, the mechanisms by which cadmium induces melatonin induction remain elusive. To investigate whether cadmium influences physical integrities in subcellular organelles, we treated tobacco leaves with either CdCl2 or AlCl3 and monitored the structures of subcellular organelles—such as chloroplasts, mitochondria, and the endoplasmic reticulum (ER—using confocal microscopic analysis. Unlike AlCl3 treatment, CdCl2 (0.5 mM treatment significantly disrupted chloroplasts, mitochondria, and ER. In theory, the disruption of chloroplasts enabled chloroplast-expressed serotonin N-acetyltransferase (SNAT to encounter serotonin in the cytoplasm, leading to the synthesis of N-acetylserotonin followed by melatonin synthesis. In fact, the disruption of chloroplasts by cadmium, not by aluminum, gave rise to a huge induction of melatonin in rice leaves, which suggests that cadmium-treated chloroplast disruption plays an important role in inducing melatonin in plants by removing physical barriers, such as chloroplast double membranes, allowing SNAT to gain access to the serotonin substrate enriched in the cytoplasm.

DNA-programmed dynamic assembly of quantum dots for molecular computation.

Science.gov (United States)

He, Xuewen; Li, Zhi; Chen, Muzi; Ma, Nan

2014-12-22

Despite the widespread use of quantum dots (QDs) for biosensing and bioimaging, QD-based bio-interfaceable and reconfigurable molecular computing systems have not yet been realized. DNA-programmed dynamic assembly of multi-color QDs is presented for the construction of a new class of fluorescence resonance energy transfer (FRET)-based QD computing systems. A complete set of seven elementary logic gates (OR, AND, NOR, NAND, INH, XOR, XNOR) are realized using a series of binary and ternary QD complexes operated by strand displacement reactions. The integration of different logic gates into a half-adder circuit for molecular computation is also demonstrated. This strategy is quite versatile and straightforward for logical operations and would pave the way for QD-biocomputing-based intelligent molecular diagnostics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational Fluid Dynamics Analysis of High Injection Pressure Blended Biodiesel

Science.gov (United States)

Khalid, Amir; Jaat, Norrizam; Faisal Hushim, Mohd; Manshoor, Bukhari; Zaman, Izzuddin; Sapit, Azwan; Razali, Azahari

2017-08-01

Biodiesel have great potential for substitution with petrol fuel for the purpose of achieving clean energy production and emission reduction. Among the methods that can control the combustion properties, controlling of the fuel injection conditions is one of the successful methods. The purpose of this study is to investigate the effect of high injection pressure of biodiesel blends on spray characteristics using Computational Fluid Dynamics (CFD). Injection pressure was observed at 220 MPa, 250 MPa and 280 MPa. The ambient temperature was kept held at 1050 K and ambient pressure 8 MPa in order to simulate the effect of boost pressure or turbo charger during combustion process. Computational Fluid Dynamics were used to investigate the spray characteristics of biodiesel blends such as spray penetration length, spray angle and mixture formation of fuel-air mixing. The results shows that increases of injection pressure, wider spray angle is produced by biodiesel blends and diesel fuel. The injection pressure strongly affects the mixture formation, characteristics of fuel spray, longer spray penetration length thus promotes the fuel and air mixing.

Computational strong-field quantum dynamics. Intense light-matter interactions

International Nuclear Information System (INIS)

Bauer, Dieter

2017-01-01

This graduate textbook introduces the computational techniques to study ultra-fast quantum dynamics of matter exposed to strong laser fields. Coverage includes methods to propagate wavefunctions according to the time dependent Schroedinger, Klein-Gordon or Dirac equation, the calculation of typical observables, time-dependent density functional theory, multi configurational time-dependent Hartree-Fock, time-dependent configuration interaction singles, the strong-field approximation, and the microscopic particle-in-cell approach.

Computational strong-field quantum dynamics. Intense light-matter interactions

Energy Technology Data Exchange (ETDEWEB)

Bauer, Dieter (ed.) [Rostock Univ. (Germany). Inst. fuer Physik

2017-09-01

This graduate textbook introduces the computational techniques to study ultra-fast quantum dynamics of matter exposed to strong laser fields. Coverage includes methods to propagate wavefunctions according to the time dependent Schroedinger, Klein-Gordon or Dirac equation, the calculation of typical observables, time-dependent density functional theory, multi configurational time-dependent Hartree-Fock, time-dependent configuration interaction singles, the strong-field approximation, and the microscopic particle-in-cell approach.

Recent Development in Rigorous Computational Methods in Dynamical Systems

OpenAIRE

Arai, Zin; Kokubu, Hiroshi; Pilarczyk, Paweł

2009-01-01

We highlight selected results of recent development in the area of rigorous computations which use interval arithmetic to analyse dynamical systems. We describe general ideas and selected details of different ways of approach and we provide specific sample applications to illustrate the effectiveness of these methods. The emphasis is put on a topological approach, which combined with rigorous calculations provides a broad range of new methods that yield mathematically rel...

Computational strong-field quantum dynamics intense light-matter interactions

CERN Document Server

2017-01-01

This graduate textbook introduces the computational techniques to study ultra-fast quantum dynamics of matter exposed to strong laser fields. Coverage includes methods to propagate wavefunctions according to the time-dependent Schrödinger, Klein-Gordon or Dirac equation, the calculation of typical observables, time-dependent density functional theory, multi-configurational time-dependent Hartree-Fock, time-dependent configuration interaction singles, the strong-field approximation, and the microscopic particle-in-cell approach.

Symposium on computational fluid dynamics: technology and applications

International Nuclear Information System (INIS)

1988-01-01

A symposium on the technology and applications of computational fluid dynamics (CFD) was held in Pretoria from 21-23 Nov 1988. The following aspects were covered: multilevel adaptive methods and multigrid solvers in CFD, a symbolic processing approach to CFD, interplay between CFD and analytical approximations, CFD on a transfer array, the application of CFD in high speed aerodynamics, numerical simulation of laminar blood flow, two-phase flow modelling in nuclear accident analysis, and the finite difference scheme for the numerical solution of fluid flow

Error suppression and error correction in adiabatic quantum computation: non-equilibrium dynamics

International Nuclear Information System (INIS)

Sarovar, Mohan; Young, Kevin C

2013-01-01

While adiabatic quantum computing (AQC) has some robustness to noise and decoherence, it is widely believed that encoding, error suppression and error correction will be required to scale AQC to large problem sizes. Previous works have established at least two different techniques for error suppression in AQC. In this paper we derive a model for describing the dynamics of encoded AQC and show that previous constructions for error suppression can be unified with this dynamical model. In addition, the model clarifies the mechanisms of error suppression and allows the identification of its weaknesses. In the second half of the paper, we utilize our description of non-equilibrium dynamics in encoded AQC to construct methods for error correction in AQC by cooling local degrees of freedom (qubits). While this is shown to be possible in principle, we also identify the key challenge to this approach: the requirement of high-weight Hamiltonians. Finally, we use our dynamical model to perform a simplified thermal stability analysis of concatenated-stabilizer-code encoded many-body systems for AQC or quantum memories. This work is a companion paper to ‘Error suppression and error correction in adiabatic quantum computation: techniques and challenges (2013 Phys. Rev. X 3 041013)’, which provides a quantum information perspective on the techniques and limitations of error suppression and correction in AQC. In this paper we couch the same results within a dynamical framework, which allows for a detailed analysis of the non-equilibrium dynamics of error suppression and correction in encoded AQC. (paper)

Transmitted wavefront testing with large dynamic range based on computer-aided deflectometry

Science.gov (United States)

Wang, Daodang; Xu, Ping; Gong, Zhidong; Xie, Zhongmin; Liang, Rongguang; Xu, Xinke; Kong, Ming; Zhao, Jun

2018-06-01

The transmitted wavefront testing technique is demanded for the performance evaluation of transmission optics and transparent glass, in which the achievable dynamic range is a key issue. A computer-aided deflectometric testing method with fringe projection is proposed for the accurate testing of transmitted wavefronts with a large dynamic range. Ray tracing of the modeled testing system is carried out to achieve the virtual ‘null’ testing of transmitted wavefront aberrations. The ray aberration is obtained from the ray tracing result and measured slope, with which the test wavefront aberration can be reconstructed. To eliminate testing system modeling errors, a system geometry calibration based on computer-aided reverse optimization is applied to realize accurate testing. Both numerical simulation and experiments have been carried out to demonstrate the feasibility and high accuracy of the proposed testing method. The proposed testing method can achieve a large dynamic range compared with the interferometric method, providing a simple, low-cost and accurate way for the testing of transmitted wavefronts from various kinds of optics and a large amount of industrial transmission elements.

pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites.

Science.gov (United States)

Cheng, Xiang; Zhao, Shu-Guang; Lin, Wei-Zhong; Xiao, Xuan; Chou, Kuo-Chen

2017-11-15

Cells are deemed the basic unit of life. However, many important functions of cells as well as their growth and reproduction are performed via the protein molecules located at their different organelles or locations. Facing explosive growth of protein sequences, we are challenged to develop fast and effective method to annotate their subcellular localization. However, this is by no means an easy task. Particularly, mounting evidences have indicated proteins have multi-label feature meaning that they may simultaneously exist at, or move between, two or more different subcellular location sites. Unfortunately, most of the existing computational methods can only be used to deal with the single-label proteins. Although the 'iLoc-Animal' predictor developed recently is quite powerful that can be used to deal with the animal proteins with multiple locations as well, its prediction quality needs to be improved, particularly in enhancing the absolute true rate and reducing the absolute false rate. Here we propose a new predictor called 'pLoc-mAnimal', which is superior to iLoc-Animal as shown by the compelling facts. When tested by the most rigorous cross-validation on the same high-quality benchmark dataset, the absolute true success rate achieved by the new predictor is 37% higher and the absolute false rate is four times lower in comparison with the state-of-the-art predictor. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mAnimal/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. xxiao@gordonlifescience.org or kcchou@gordonlifescience.org. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features.

Science.gov (United States)

Zhou, Hang; Yang, Yang; Shen, Hong-Bin

2017-03-15

Protein subcellular localization prediction has been an important research topic in computational biology over the last decade. Various automatic methods have been proposed to predict locations for large scale protein datasets, where statistical machine learning algorithms are widely used for model construction. A key step in these predictors is encoding the amino acid sequences into feature vectors. Many studies have shown that features extracted from biological domains, such as gene ontology and functional domains, can be very useful for improving the prediction accuracy. However, domain knowledge usually results in redundant features and high-dimensional feature spaces, which may degenerate the performance of machine learning models. In this paper, we propose a new amino acid sequence-based human protein subcellular location prediction approach Hum-mPLoc 3.0, which covers 12 human subcellular localizations. The sequences are represented by multi-view complementary features, i.e. context vocabulary annotation-based gene ontology (GO) terms, peptide-based functional domains, and residue-based statistical features. To systematically reflect the structural hierarchy of the domain knowledge bases, we propose a novel feature representation protocol denoted as HCM (Hidden Correlation Modeling), which will create more compact and discriminative feature vectors by modeling the hidden correlations between annotation terms. Experimental results on four benchmark datasets show that HCM improves prediction accuracy by 5-11% and F 1 by 8-19% compared with conventional GO-based methods. A large-scale application of Hum-mPLoc 3.0 on the whole human proteome reveals proteins co-localization preferences in the cell. www.csbio.sjtu.edu.cn/bioinf/Hum-mPLoc3/. hbshen@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

The self-adaptation to dynamic failures for efficient virtual organization formations in grid computing context

International Nuclear Information System (INIS)

Han Liangxiu

2009-01-01

Grid computing aims to enable 'resource sharing and coordinated problem solving in dynamic, multi-institutional virtual organizations (VOs)'. However, due to the nature of heterogeneous and dynamic resources, dynamic failures in the distributed grid environment usually occur more than in traditional computation platforms, which cause failed VO formations. In this paper, we develop a novel self-adaptive mechanism to dynamic failures during VO formations. Such a self-adaptive scheme allows an individual and member of VOs to automatically find other available or replaceable one once a failure happens and therefore makes systems automatically recover from dynamic failures. We define dynamic failure situations of a system by using two standard indicators: mean time between failures (MTBF) and mean time to recover (MTTR). We model both MTBF and MTTR as Poisson distributions. We investigate and analyze the efficiency of the proposed self-adaptation mechanism to dynamic failures by comparing the success probability of VO formations before and after adopting it in three different cases: (1) different failure situations; (2) different organizational structures and scales; (3) different task complexities. The experimental results show that the proposed scheme can automatically adapt to dynamic failures and effectively improve the dynamic VO formation performance in the event of node failures, which provide a valuable addition to the field.

A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana

Directory of Open Access Journals (Sweden)

Thomas eNägele

2013-12-01

Full Text Available During the last decade genome sequencing has experienced a rapid technological development resulting in numerous sequencing projects and applications in life science. In plant molecular biology, the availability of sequence data on whole genomes has enabled the reconstruction of metabolic networks. Enzymatic reactions are predicted by the sequence information. Pathways arise due to the participation of chemical compounds as substrates and products in these reactions. Although several of these comprehensive networks have been reconstructed for the genetic model plant Arabidopsis thaliana, the integration of experimental data is still challenging. Particularly the analysis of subcellular organization of plant cells limits the understanding of regulatory instances in these metabolic networks in vivo. In this study, we develop an approach for the functional integration of experimental high-throughput data into such large-scale networks. We present a subcellular metabolic network model comprising 524 metabolic intermediates and 548 metabolic interactions derived from a total of 2769 reactions. We demonstrate how to link the metabolite covariance matrix of different Arabidopsis thaliana accessions with the subcellular metabolic network model for the inverse calculation of the biochemical Jacobian, finally resulting in the calculation of a matrix which satisfies a Lyaponov equation involving a covariance matrix. In this way, differential strategies of metabolite compartmentation and involved reactions were identified in the accessions when exposed to low temperature.

Regorafenib effects on human colon carcinoma xenografts monitored by dynamic contrast-enhanced computed tomography with immunohistochemical validation.

Directory of Open Access Journals (Sweden)

Clemens C Cyran

Full Text Available To investigate dynamic contrast-enhanced computed tomography for monitoring the effects of regorafenib on experimental colon carcinomas in rats by quantitative assessments of tumor microcirculation parameters with immunohistochemical validation.Colon carcinoma xenografts (HT-29 implanted subcutaneously in female athymic rats (n = 15 were imaged at baseline and after a one-week treatment with regorafenib by dynamic contrast-enhanced computed tomography (128-slice dual-source computed tomography. The therapy group (n = 7 received regorafenib daily (10 mg/kg bodyweight. Quantitative parameters of tumor microcirculation (plasma flow, mL/100 mL/min, endothelial permeability (PS, mL/100 mL/min, and tumor vascularity (plasma volume, % were calculated using a 2-compartment uptake model. Dynamic contrast-enhanced computed tomography parameters were validated with immunohistochemical assessments of tumor microvascular density (CD-31, tumor cell apoptosis (TUNEL, and proliferation (Ki-67.Regorafenib suppressed tumor vascularity (15.7±5.3 to 5.5±3.5%; p<0.05 and tumor perfusion (12.8±2.3 to 8.8±2.9 mL/100 mL/min; p = 0.063. Significantly lower microvascular density was observed in the therapy group (CD-31; 48±10 vs. 113±25, p<0.05. In regorafenib-treated tumors, significantly more apoptotic cells (TUNEL; 11844±2927 vs. 5097±3463, p<0.05 were observed. Dynamic contrast-enhanced computed tomography tumor perfusion and tumor vascularity correlated significantly (p<0.05 with microvascular density (CD-31; r = 0.84 and 0.66 and inversely with apoptosis (TUNEL; r = -0.66 and -0.71.Regorafenib significantly suppressed tumor vascularity (plasma volume quantified by dynamic contrast-enhanced computed tomography in experimental colon carcinomas in rats with good-to-moderate correlations to an immunohistochemical gold standard. Tumor response biomarkers assessed by dynamic contrast-enhanced computed tomography may be a promising future

Issues in computational fluid dynamics code verification and validation

Energy Technology Data Exchange (ETDEWEB)

Oberkampf, W.L.; Blottner, F.G.

1997-09-01

A broad range of mathematical modeling errors of fluid flow physics and numerical approximation errors are addressed in computational fluid dynamics (CFD). It is strongly believed that if CFD is to have a major impact on the design of engineering hardware and flight systems, the level of confidence in complex simulations must substantially improve. To better understand the present limitations of CFD simulations, a wide variety of physical modeling, discretization, and solution errors are identified and discussed. Here, discretization and solution errors refer to all errors caused by conversion of the original partial differential, or integral, conservation equations representing the physical process, to algebraic equations and their solution on a computer. The impact of boundary conditions on the solution of the partial differential equations and their discrete representation will also be discussed. Throughout the article, clear distinctions are made between the analytical mathematical models of fluid dynamics and the numerical models. Lax`s Equivalence Theorem and its frailties in practical CFD solutions are pointed out. Distinctions are also made between the existence and uniqueness of solutions to the partial differential equations as opposed to the discrete equations. Two techniques are briefly discussed for the detection and quantification of certain types of discretization and grid resolution errors.

Data Point Averaging for Computational Fluid Dynamics Data

Science.gov (United States)

Norman, Jr., David (Inventor)

2016-01-01

A system and method for generating fluid flow parameter data for use in aerodynamic heating analysis. Computational fluid dynamics data is generated for a number of points in an area on a surface to be analyzed. Sub-areas corresponding to areas of the surface for which an aerodynamic heating analysis is to be performed are identified. A computer system automatically determines a sub-set of the number of points corresponding to each of the number of sub-areas and determines a value for each of the number of sub-areas using the data for the sub-set of points corresponding to each of the number of sub-areas. The value is determined as an average of the data for the sub-set of points corresponding to each of the number of sub-areas. The resulting parameter values then may be used to perform an aerodynamic heating analysis.

Aerodynamic research of a racing car based on wind tunnel test and computational fluid dynamics

Directory of Open Access Journals (Sweden)

Wang Jianfeng

2018-01-01

Full Text Available Wind tunnel test and computational fluid dynamics (CFD simulation are two main methods for the study of automotive aerodynamics. CFD simulation software solves the results in calculation by using the basic theory of aerodynamic. Calculation will inevitably lead to bias, and the wind tunnel test can effectively simulate the real driving condition, which is the most effective aerodynamics research method. This paper researches the aerodynamic characteristics of the wing of a racing car. Aerodynamic model of a racing car is established. Wind tunnel test is carried out and compared with the simulation results of computational fluid dynamics. The deviation of the two methods is small, and the accuracy of computational fluid dynamics simulation is verified. By means of CFD software simulation, the coefficients of six aerodynamic forces are fitted and the aerodynamic equations are obtained. Finally, the aerodynamic forces and torques of the racing car travel in bend are calculated.

High Accumulation and Subcellular Distribution of Thallium in Green Cabbage (Brassica Oleracea L. Var. Capitata L.).

Science.gov (United States)

Ning, Zengping; He, Libin; Xiao, Tangfu; Márton, László

2015-01-01

The accumulation of thallium (Tl) in brassicaceous crops is widely known, but both the uptake extents of Tl by the individual cultivars of green cabbage and the distribution of Tl in the tissues of green cabbage are not well understood. Five commonly available cultivars of green cabbage grown in the Tl-spiked pot-culture trials were studied for the uptake extent and subcellular distribution of Tl. The results showed that all the trial cultivars mainly concentrated Tl in the leaves (101∼192 mg/kg, DW) rather than in the roots or stems, with no significant differences among cultivars (p = 0.455). Tl accumulation in the leaves revealed obvious subcellular fractionation: cell cytosol and vacuole > cell wall > cell organelles. The majority (∼ 88%) of leaf-Tl was found to be in the fraction of cytosol and vacuole, which also served as the major storage site for other major elements such as Ca and Mg. This specific subcellular fractionation of Tl appeared to enable green cabbage to avoid Tl damage to its vital organelles and to help green cabbage tolerate and detoxify Tl. This study demonstrated that all the five green cabbage cultivars show a good application potential in the phytoremediation of Tl-contaminated soils.

A Dynamic Connectome Supports the Emergence of Stable Computational Function of Neural Circuits through Reward-Based Learning.

Science.gov (United States)

Kappel, David; Legenstein, Robert; Habenschuss, Stefan; Hsieh, Michael; Maass, Wolfgang

2018-01-01

Synaptic connections between neurons in the brain are dynamic because of continuously ongoing spine dynamics, axonal sprouting, and other processes. In fact, it was recently shown that the spontaneous synapse-autonomous component of spine dynamics is at least as large as the component that depends on the history of pre- and postsynaptic neural activity. These data are inconsistent with common models for network plasticity and raise the following questions: how can neural circuits maintain a stable computational function in spite of these continuously ongoing processes, and what could be functional uses of these ongoing processes? Here, we present a rigorous theoretical framework for these seemingly stochastic spine dynamics and rewiring processes in the context of reward-based learning tasks. We show that spontaneous synapse-autonomous processes, in combination with reward signals such as dopamine, can explain the capability of networks of neurons in the brain to configure themselves for specific computational tasks, and to compensate automatically for later changes in the network or task. Furthermore, we show theoretically and through computer simulations that stable computational performance is compatible with continuously ongoing synapse-autonomous changes. After reaching good computational performance it causes primarily a slow drift of network architecture and dynamics in task-irrelevant dimensions, as observed for neural activity in motor cortex and other areas. On the more abstract level of reinforcement learning the resulting model gives rise to an understanding of reward-driven network plasticity as continuous sampling of network configurations.

Hypertensive disease and renal hypertensions: renal structural and functional studies by using dynamic computed tomography

International Nuclear Information System (INIS)

Arabidze, G.G.; Pogrebnaya, G.N.; Todua, F.I.; Sokolova, R.I.; Kozdoba, O.A.

1989-01-01

Dynamic computed tomography was conducted by the original methods; the findings were analyzed by taking into account time-density curves which made it possible to gain an insight into the status of blood flow and filtration in each individual kidney. Computed tomography and dynamic computed tomography revealed that hypertensive disease was characterized by normal volume and thickness of the renal cortical layer and symmetric time-density curves, whereas a hypertensive type of chronic glomerulonephritis featured lower renal cartical layer thickness, reduced renal volume, symmetrically decrease amplitudes of the first and second peaks of the time-density curve, chronic pyelonephritis showed asymmetric time-density diagrams due to the lower density areas in the afflicted kidney

A Dynamic Object Behavior Model and Implementation Based on Computational Reflection

Institute of Scientific and Technical Information of China (English)

HE Cheng-wan; HE Fei; HE Ke-qing

2005-01-01

A dynamic object behavior model based on computational reflection is proposed. This model consists of function level and meta level, the meta objects in meta level manage the base objects and behaviors in function level, including dynamic binding and unbinding of base object and behavior.We implement this model with RoleJava Language, which is our self linguistic extension of the Java Language. Meta Objects are generated automatically at compile-time, this makes the reflecton mechanism transparent to programmers. Finally an example applying this model to a banking system is presented.

Evolution of perturbed dynamical systems: analytical computation with time independent accuracy

Energy Technology Data Exchange (ETDEWEB)

Gurzadyan, A.V. [Russian-Armenian (Slavonic) University, Department of Mathematics and Mathematical Modelling, Yerevan (Armenia); Kocharyan, A.A. [Monash University, School of Physics and Astronomy, Clayton (Australia)

2016-12-15

An analytical method for investigation of the evolution of dynamical systems with independent on time accuracy is developed for perturbed Hamiltonian systems. The error-free estimation using of computer algebra enables the application of the method to complex multi-dimensional Hamiltonian and dissipative systems. It also opens principal opportunities for the qualitative study of chaotic trajectories. The performance of the method is demonstrated on perturbed two-oscillator systems. It can be applied to various non-linear physical and astrophysical systems, e.g. to long-term planetary dynamics. (orig.)

Computational Fluid Dynamics of Choanoflagellate Filter-Feeding

DEFF Research Database (Denmark)

Asadzadeh, Seyed Saeed; Walther, Jens Honore; Nielsen, Lasse Tor

Choanoflagellates are unicellular aquatic organisms with a single flagellum that drives a feeding current through a funnel-shaped collar filter on which bacteria-sized prey are caught. Using computational fluid dynamics (CFD) we model the beating flagellum and the complex filter flow of the choanoflagell...... to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), and addition of a wide vane in our CFD model allows us to correctly predict the observed clearance rate....

Quality control of computational fluid dynamics in indoor environments

DEFF Research Database (Denmark)

Sørensen, Dan Nørtoft; Nielsen, P. V.

2003-01-01

Computational fluid dynamics (CFD) is used routinely to predict air movement and distributions of temperature and concentrations in indoor environments. Modelling and numerical errors are inherent in such studies and must be considered when the results are presented. Here, we discuss modelling as...... the quality of CFD calculations, as well as guidelines for the minimum information that should accompany all CFD-related publications to enable a scientific judgment of the quality of the study....

Internalization and Subcellular Trafficking of Poly-l-lysine Dendrimers Are Impacted by the Site of Fluorophore Conjugation.

Science.gov (United States)

Avaritt, Brittany R; Swaan, Peter W

2015-06-01

Internalization and intracellular trafficking of dendrimer-drug conjugates play an important role in achieving successful drug delivery. In this study, we aimed to elucidate the endocytosis mechanisms and subcellular localization of poly-l-lysine (PLL) dendrimers in Caco-2 cells. We also investigated the impact of fluorophore conjugation on cytotoxicity, uptake, and transepithelial transport. Oregon green 514 (OG) was conjugated to PLL G3 at either the dendrimer periphery or the core. Chemical inhibitors of clathrin-, caveolin-, cholesterol-, and dynamin-mediated endocytosis pathways and macropinocytosis were employed to establish internalization mechanisms, while colocalization with subcellular markers was used to determine dendrimer trafficking. Cell viability, internalization, and uptake were all influenced by the site of fluorophore conjugation. Uptake was found to be highly dependent on cholesterol- and dynamin-mediated endocytosis as well as macropinocytosis. Dendrimers were trafficked to endosomes and lysosomes, and subcellular localization was impacted by the fluorophore conjugation site. The results of this study indicate that PLL dendrimers exploit multiple pathways for cellular entry, and internalization and trafficking can be impacted by conjugation. Therefore, design of dendrimer-drug conjugates requires careful consideration to achieve successful drug delivery.

Computer aided instrumented Charpy test applied dynamic fracture toughness evaluation system

International Nuclear Information System (INIS)

Kobayashi, Toshiro; Niinomi, Mitsuo

1986-01-01

Micro computer aided data treatment system and personal computer aided data analysis system were applied to the traditional instrumented Charpy impact test system. The analysis of Charpy absorbed energy (E i , E p , E t ) and load (P y , P m ), and the evaluation of dynamic toughness through whole fracture process, i.e. J Id , J R curve and T mat was examined using newly developed computer aided instrumented Charpy impact test system. E i , E p , E t , P y and P m were effectively analyzed using moving average method and printed out automatically by micro computer aided data treatment system. J Id , J R curve and T mat could be measured by stop block test method. Then, J Id , J R curve and T mat were effectively estimated using compliance changing rate method and key curve method on the load-load point displacement curve of single fatigue cracked specimen by personal computer aided data analysis system. (author)

Multitasking the code ARC3D. [for computational fluid dynamics

Science.gov (United States)

Barton, John T.; Hsiung, Christopher C.

1986-01-01

The CRAY multitasking system was developed in order to utilize all four processors and sharply reduce the wall clock run time. This paper describes the techniques used to modify the computational fluid dynamics code ARC3D for this run and analyzes the achieved speedup. The ARC3D code solves either the Euler or thin-layer N-S equations using an implicit approximate factorization scheme. Results indicate that multitask processing can be used to achieve wall clock speedup factors of over three times, depending on the nature of the program code being used. Multitasking appears to be particularly advantageous for large-memory problems running on multiple CPU computers.

Computational fluid dynamics study of viscous fingering in supercritical fluid chromatography.

Science.gov (United States)

Subraveti, Sai Gokul; Nikrityuk, Petr; Rajendran, Arvind

2018-01-26

Axi-symmetric numerical simulations are carried out to study the dynamics of a plug introduced through a mixed-stream injection in supercritical fluid chromatographic columns. The computational fluid dynamics model developed in this work takes into account both the hydrodynamics and adsorption equilibria to describe the phenomena of viscous fingering and plug effect that contribute to peak distortions in mixed-stream injections. The model was implemented into commercial computational fluid dynamics software using user-defined functions. The simulations describe the propagation of both the solute and modifier highlighting the interplay between the hydrodynamics and plug effect. The simulated peaks showed good agreement with experimental data published in the literature involving different injection volumes (5 μL, 50 μL, 1 mL and 2 mL) of flurbiprofen on Chiralpak AD-H column using a mobile phase of CO 2 and methanol. The study demonstrates that while viscous fingering is the main source of peak distortions for large-volume injections (1 mL and 2 mL) it has negligible impact on small-volume injections (5 μL and 50 μL). Band broadening in small-volume injections arise mainly due to the plug effect. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Moving finite elements: A continuously adaptive method for computational fluid dynamics

International Nuclear Information System (INIS)

Glasser, A.H.; Miller, K.; Carlson, N.

1991-01-01

Moving Finite Elements (MFE), a recently developed method for computational fluid dynamics, promises major advances in the ability of computers to model the complex behavior of liquids, gases, and plasmas. Applications of computational fluid dynamics occur in a wide range of scientifically and technologically important fields. Examples include meteorology, oceanography, global climate modeling, magnetic and inertial fusion energy research, semiconductor fabrication, biophysics, automobile and aircraft design, industrial fluid processing, chemical engineering, and combustion research. The improvements made possible by the new method could thus have substantial economic impact. Moving Finite Elements is a moving node adaptive grid method which has a tendency to pack the grid finely in regions where it is most needed at each time and to leave it coarse elsewhere. It does so in a manner which is simple and automatic, and does not require a large amount of human ingenuity to apply it to each particular problem. At the same time, it often allows the time step to be large enough to advance a moving shock by many shock thicknesses in a single time step, moving the grid smoothly with the solution and minimizing the number of time steps required for the whole problem. For 2D problems (two spatial variables) the grid is composed of irregularly shaped and irregularly connected triangles which are very flexible in their ability to adapt to the evolving solution. While other adaptive grid methods have been developed which share some of these desirable properties, this is the only method which combines them all. In many cases, the method can save orders of magnitude of computing time, equivalent to several generations of advancing computer hardware

Brain systems for probabilistic and dynamic prediction: computational specificity and integration.

Directory of Open Access Journals (Sweden)

Jill X O'Reilly

2013-09-01

Full Text Available A computational approach to functional specialization suggests that brain systems can be characterized in terms of the types of computations they perform, rather than their sensory or behavioral domains. We contrasted the neural systems associated with two computationally distinct forms of predictive model: a reinforcement-learning model of the environment obtained through experience with discrete events, and continuous dynamic forward modeling. By manipulating the precision with which each type of prediction could be used, we caused participants to shift computational strategies within a single spatial prediction task. Hence (using fMRI we showed that activity in two brain systems (typically associated with reward learning and motor control could be dissociated in terms of the forms of computations that were performed there, even when both systems were used to make parallel predictions of the same event. A region in parietal cortex, which was sensitive to the divergence between the predictions of the models and anatomically connected to both computational networks, is proposed to mediate integration of the two predictive modes to produce a single behavioral output.

Prequels to Synthetic Biology: From Candidate Gene Identification and Validation to Enzyme Subcellular Localization in Plant and Yeast Cells.

Science.gov (United States)

Foureau, E; Carqueijeiro, I; Dugé de Bernonville, T; Melin, C; Lafontaine, F; Besseau, S; Lanoue, A; Papon, N; Oudin, A; Glévarec, G; Clastre, M; St-Pierre, B; Giglioli-Guivarc'h, N; Courdavault, V

2016-01-01

Natural compounds extracted from microorganisms or plants constitute an inexhaustible source of valuable molecules whose supply can be potentially challenged by limitations in biological sourcing. The recent progress in synthetic biology combined to the increasing access to extensive transcriptomics and genomics data now provide new alternatives to produce these molecules by transferring their whole biosynthetic pathway in heterologous production platforms such as yeasts or bacteria. While the generation of high titer producing strains remains per se an arduous field of investigation, elucidation of the biosynthetic pathways as well as characterization of their complex subcellular organization are essential prequels to the efficient development of such bioengineering approaches. Using examples from plants and yeasts as a framework, we describe potent methods to rationalize the study of partially characterized pathways, including the basics of computational applications to identify candidate genes in transcriptomics data and the validation of their function by an improved procedure of virus-induced gene silencing mediated by direct DNA transfer to get around possible resistance to Agrobacterium-delivery of viral vectors. To identify potential alterations of biosynthetic fluxes resulting from enzyme mislocalizations in reconstituted pathways, we also detail protocols aiming at characterizing subcellular localizations of protein in plant cells by expression of fluorescent protein fusions through biolistic-mediated transient transformation, and localization of transferred enzymes in yeast using similar fluorescence procedures. Albeit initially developed for the Madagascar periwinkle, these methods may be applied to other plant species or organisms in order to establish synthetic biology platform. © 2016 Elsevier Inc. All rights reserved.

Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes

Directory of Open Access Journals (Sweden)

Kaznessis Yiannis N

2007-01-01

Full Text Available Abstract Background Tightly regulated gene networks, precisely controlling the expression of protein molecules, have received considerable interest by the biomedical community due to their promising applications. Among the most well studied inducible transcription systems are the tetracycline regulatory expression systems based on the tetracycline resistance operon of Escherichia coli, Tet-Off (tTA and Tet-On (rtTA. Despite their initial success and improved designs, limitations still persist, such as low inducer sensitivity. Instead of looking at these networks statically, and simply changing or mutating the promoter and operator regions with trial and error, a systematic investigation of the dynamic behavior of the network can result in rational design of regulatory gene expression systems. Sophisticated algorithms can accurately capture the dynamical behavior of gene networks. With computer aided design, we aim to improve the synthesis of regulatory networks and propose new designs that enable tighter control of expression. Results In this paper we engineer novel networks by recombining existing genes or part of genes. We synthesize four novel regulatory networks based on the Tet-Off and Tet-On systems. We model all the known individual biomolecular interactions involved in transcription, translation, regulation and induction. With multiple time-scale stochastic-discrete and stochastic-continuous models we accurately capture the transient and steady state dynamics of these networks. Important biomolecular interactions are identified and the strength of the interactions engineered to satisfy design criteria. A set of clear design rules is developed and appropriate mutants of regulatory proteins and operator sites are proposed. Conclusion The complexity of biomolecular interactions is accurately captured through computer simulations. Computer simulations allow us to look into the molecular level, portray the dynamic behavior of gene regulatory

Preliminary study of selenium and mercury distribution in some porcine tissues and their subcellular fractions by NAA and HG-AFS

International Nuclear Information System (INIS)

Jiujiang Zhao; Chunying Chen; Peiqun Zhang; Zhifang Chai

2004-01-01

Selenium and mercury distribution in porcine tissues and their subcellular fractions from a mercury-polluted area of Guizhou Province and from a not mercury-exposed area of Beijing in China have been studied with neutron activation analysis and hydride generation-atomic fluorescence spectrometry. Both the selenium and mercury levels are higher in Guizhou porcine tissues and their subcellular fractions than those in Beijing. These two elements are highly enriched in kidney and liver of Guizhou pig, while selenium is only enriched in the kidney of Beijing pig. Exposure of mercury may result in redistribution of Se and Hg in vivo. The Hg/Se molar ratio of the subcellular fractions is very low in the case of relatively low mercury level and gradually reaches to a high constant value with increasing level of mercury, which implies that selenium and mercury may form some special complexes in the organisms. (author)

Organ accumulation and subcellular location of Cicer arietinum ST1 protein.

Science.gov (United States)

Albornos, Lucía; Cabrera, Javier; Hernández-Nistal, Josefina; Martín, Ignacio; Labrador, Emilia; Dopico, Berta

2014-07-01

The ST (ShooT Specific) proteins are a new family of proteins characterized by a signal peptide, tandem repeats of 25/26 amino acids, and a domain of unknown function (DUF2775), whose presence is limited to a few families of dicotyledonous plants, mainly Fabaceae and Asteraceae. Their function remains unknown, although involvement in plant growth, fruit morphogenesis or in biotic and abiotic interactions have been suggested. This work is focused on ST1, a Cicer arietinum ST protein. We established the protein accumulation in different tissues and organs of chickpea seedlings and plants and its subcellular localization, which could indicate the possible function of ST1. The raising of specific antibodies against ST1 protein revealed that its accumulation in epicotyls and radicles was related to their elongation rate. Its pattern of tissue location in cotyledons during seed formation and early seed germination, as well as its localization in the perivascular fibres of epicotyls and radicles, indicated a possible involvement in seed germination and seedling growth. ST1 protein appears both inside the cell and in the cell wall. This double subcellular localization was found in every organ in which the ST1 protein was detected: seeds, cotyledons and seedling epicotyls and radicles. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Subcellular distribution of zinc in the benign and malignant human prostate

International Nuclear Information System (INIS)

Leake, A.; Chrisholm, G.D.; Busuttil, A.; Habib, F.K

1984-01-01

The subcellular distribution of zinc and its interaction with androgens has been examined in the benign and malignant human prostate. Endogenously, most of the zinc was associated with the nuclear fraction but signigicant concentrations were also found in the cytosol. Furthermore, the epithelium contained more zinc than that found in either the stroma or the intact gland. Zinc concentrations were lower in the subcellular fractions of the cancerous tissue when compared to hyperplastic specimens. In vitro uptake of zinc into prostatic homogenates was rapid and at equilibrium the binding was stable for both the 4degC and the 37degC incubations. At low zinc concentrations (<5mM) the uptake was higher in the nucleus, whereas at higher concentraions, the cancerous tissue exhibited a greater capacity for the metal which was predominantly retained by the cytosol. Our data suggest the presence of a saturable zinc retention mechanism in the nucleus. The zinc uptake was found to be independent of any added androgen. In contrast, the total androgen uptake by the prostate was significantly enhanced by the addition of zinc. This effect was not due to increases in the nuclear and cytosolic receptor binding since zinc inhibited the binding of the androgen to these receptors. (author)

Modeling Behavior Dynamics using Computational Psychometrics within Virtual Worlds

Directory of Open Access Journals (Sweden)

Pietro eCipresso

2015-11-01

Full Text Available In case of fire in a building, how will people behave in the crowd? The behavior of each individual affects the behavior of others and, conversely, each one behaves considering the crowd as a whole and the individual others. In this article, I propose a three-step method to explore a brand new way to study behavior dynamics. The first step relies on the creation of specific situations with standard techniques (such as mental imagery, text, video and audio and an advanced technique (Virtual Reality to manipulate experimental settings. The second step concerns the measurement of behavior in one, two or many individuals focusing on parameters extractions to provide information about the behavior dynamics. Finally, the third step, which uses the parameters collected and measured in the previous two steps in order to simulate possible scenarios to forecast through computational models, understand and explain behavior dynamics at the social level. An experimental study was also included to demonstrate the three-step method and a possible scenario.

The effect of dynamic workstations on the performance of various computer and office-based tasks

NARCIS (Netherlands)

Burford, E.M.; Botter, J.; Commissaris, D.; Könemann, R.; Hiemstra-Van Mastrigt, S.; Ellegast, R.P.

2013-01-01

The effect of different workstations, conventional and dynamic, on different types of performance measures for several different office and computer based task was investigated in this research paper. The two dynamic workstations assessed were the Lifespan Treadmill Desk and the RightAngle

Fast reactor safety and computational thermo-fluid dynamics approaches

International Nuclear Information System (INIS)

Ninokata, Hisashi; Shimizu, Takeshi

1993-01-01

This article provides a brief description of the safety principle on which liquid metal cooled fast breeder reactors (LMFBRs) is based and the roles of computations in the safety practices. A number of thermohydraulics models have been developed to date that successfully describe several of the important types of fluids and materials motion encountered in the analysis of postulated accidents in LMFBRs. Most of these models use a mixture of implicit and explicit numerical solution techniques in solving a set of conservation equations formulated in Eulerian coordinates, with special techniques included to specific situations. Typical computational thermo-fluid dynamics approaches are discussed in particular areas of analyses of the physical phenomena relevant to the fuel subassembly thermohydraulics design and that involve describing the motion of molten materials in the core over a large scale. (orig.)

COMPUTER TOOLS OF DYNAMIC MATHEMATIC SOFTWARE AND METHODICAL PROBLEMS OF THEIR USE

OpenAIRE

Olena V. Semenikhina; Maryna H. Drushliak

2014-01-01

The article presents results of analyses of standard computer tools of dynamic mathematic software which are used in solving tasks, and tools on which the teacher can support in the teaching of mathematics. Possibility of the organization of experimental investigating of mathematical objects on the basis of these tools and the wording of new tasks on the basis of the limited number of tools, fast automated check are specified. Some methodological comments on application of computer tools and ...

Subcellular binding of 239Pu in the liver of selected species of rodents

International Nuclear Information System (INIS)

Winter, R.

1980-01-01

The subcellular distribution of 239 Pu in the liver of selected rodent species was investigated as well as the relation between 239 Pu and the iron metabolism. The goal of the investigation was to find out why the liver discharge of 239 Pu from the liver varies so much between species. (orig.) [de

A paradigm for modeling and computation of gas dynamics

Science.gov (United States)

Xu, Kun; Liu, Chang

2017-02-01

In the continuum flow regime, the Navier-Stokes (NS) equations are usually used for the description of gas dynamics. On the other hand, the Boltzmann equation is applied for the rarefied flow. These two equations are based on distinguishable modeling scales for flow physics. Fortunately, due to the scale separation, i.e., the hydrodynamic and kinetic ones, both the Navier-Stokes equations and the Boltzmann equation are applicable in their respective domains. However, in real science and engineering applications, they may not have such a distinctive scale separation. For example, around a hypersonic flying vehicle, the flow physics at different regions may correspond to different regimes, where the local Knudsen number can be changed significantly in several orders of magnitude. With a variation of flow physics, theoretically a continuous governing equation from the kinetic Boltzmann modeling to the hydrodynamic Navier-Stokes dynamics should be used for its efficient description. However, due to the difficulties of a direct modeling of flow physics in the scale between the kinetic and hydrodynamic ones, there is basically no reliable theory or valid governing equations to cover the whole transition regime, except resolving flow physics always down to the mean free path scale, such as the direct Boltzmann solver and the Direct Simulation Monte Carlo (DSMC) method. In fact, it is an unresolved problem about the exact scale for the validity of the NS equations, especially in the small Reynolds number cases. The computational fluid dynamics (CFD) is usually based on the numerical solution of partial differential equations (PDEs), and it targets on the recovering of the exact solution of the PDEs as mesh size and time step converging to zero. This methodology can be hardly applied to solve the multiple scale problem efficiently because there is no such a complete PDE for flow physics through a continuous variation of scales. For the non-equilibrium flow study, the direct

Distributed interactive graphics applications in computational fluid dynamics

International Nuclear Information System (INIS)

Rogers, S.E.; Buning, P.G.; Merritt, F.J.

1987-01-01

Implementation of two distributed graphics programs used in computational fluid dynamics is discussed. Both programs are interactive in nature. They run on a CRAY-2 supercomputer and use a Silicon Graphics Iris workstation as the front-end machine. The hardware and supporting software are from the Numerical Aerodynamic Simulation project. The supercomputer does all numerically intensive work and the workstation, as the front-end machine, allows the user to perform real-time interactive transformations on the displayed data. The first program was written as a distributed program that computes particle traces for fluid flow solutions existing on the supercomputer. The second is an older post-processing and plotting program modified to run in a distributed mode. Both programs have realized a large increase in speed over that obtained using a single machine. By using these programs, one can learn quickly about complex features of a three-dimensional flow field. Some color results are presented

Optically-controlled platforms for transfection and single- and sub-cellular surgery

DEFF Research Database (Denmark)

Villangca, Mark Jayson; Casey, Duncan; Glückstad, Jesper

2015-01-01

and specificity of optical trapping in conjunction with other modalities to perform single and sub-cellular surgery. These tools form highly tuneable platforms for the delivery or removal of material from cells of interest, but can simultaneously excite fluorescent probes for imaging purposes or plasmonic...... structures for very local heating. We discuss both the history and recent applications of the field, highlighting the key findings and developments over the last 40 years of biophotonics research....

Dynamic stability calculations for power grids employing a parallel computer

Energy Technology Data Exchange (ETDEWEB)

Schmidt, K

1982-06-01

The aim of dynamic contingency calculations in power systems is to estimate the effects of assumed disturbances, such as loss of generation. Due to the large dimensions of the problem these simulations require considerable computing time and costs, to the effect that they are at present only used in a planning state but not for routine checks in power control stations. In view of the homogeneity of the problem, where a multitude of equal generator models, having different parameters, are to be integrated simultaneously, the use of a parallel computer looks very attractive. The results of this study employing a prototype parallel computer (SMS 201) are presented. It consists of up to 128 equal microcomputers bus-connected to a control computer. Each of the modules is programmed to simulate a node of the power grid. Generators with their associated control are represented by models of 13 states each. Passive nodes are complemented by 'phantom'-generators, so that the whole power grid is homogenous, thus removing the need for load-flow-iterations. Programming of microcomputers is essentially performed in FORTRAN.

New Frontiers in Analyzing Dynamic Group Interactions : Bridging Social and Computer Science

NARCIS (Netherlands)

Lehmann-Willenbrock, Nale; Hung, H.S.; Keyton, Joann

2017-01-01

This special issue on advancing interdisciplinary collaboration between computer scientists and social scientists documents the joint results of the international Lorentz workshop, “Interdisciplinary Insights into Group and Team Dynamics,” which took place in Leiden, The Netherlands, July 2016.

Sub-cellular distribution and translocation of TRP channels.

Science.gov (United States)

Toro, Carlos A; Arias, Luis A; Brauchi, Sebastian

2011-01-01

Cellular electrical activity is the result of a highly complex processes that involve the activation of ion channel proteins. Ion channels make pores on cell membranes that rapidly transit between conductive and non-conductive states, allowing different ions to flow down their electrochemical gradients across cell membranes. In the case of neuronal cells, ion channel activity orchestrates action potentials traveling through axons, enabling electrical communication between cells in distant parts of the body. Somatic sensation -our ability to feel touch, temperature and noxious stimuli- require ion channels able to sense and respond to our peripheral environment. Sensory integration involves the summing of various environmental cues and their conversion into electrical signals. Members of the Transient Receptor Potential (TRP) family of ion channels have emerged as important mediators of both cellular sensing and sensory integration. The regulation of the spatial and temporal distribution of membrane receptors is recognized as an important mechanism for controlling the magnitude of the cellular response and the time scale on which cellular signaling occurs. Several studies have shown that this mechanism is also used by TRP channels to modulate cellular response and ultimately fulfill their physiological function as sensors. However, the inner-working of this mode of control for TRP channels remains poorly understood. The question of whether TRPs intrinsically regulate their own vesicular trafficking or weather the dynamic regulation of TRP channel residence on the cell surface is caused by extrinsic changes in the rates of vesicle insertion or retrieval remain open. This review will examine the evidence that sub-cellular redistribution of TRP channels plays an important role in regulating their activity and explore the mechanisms that control the trafficking of vesicles containing TRP channels.

Prediction of protein subcellular locations by GO-FunD-PseAA predictor.

Science.gov (United States)

Chou, Kuo-Chen; Cai, Yu-Dong

2004-08-06

The localization of a protein in a cell is closely correlated with its biological function. With the explosion of protein sequences entering into DataBanks, it is highly desired to develop an automated method that can fast identify their subcellular location. This will expedite the annotation process, providing timely useful information for both basic research and industrial application. In view of this, a powerful predictor has been developed by hybridizing the gene ontology approach [Nat. Genet. 25 (2000) 25], functional domain composition approach [J. Biol. Chem. 277 (2002) 45765], and the pseudo-amino acid composition approach [Proteins Struct. Funct. Genet. 43 (2001) 246; Erratum: ibid. 44 (2001) 60]. As a showcase, the recently constructed dataset [Bioinformatics 19 (2003) 1656] was used for demonstration. The dataset contains 7589 proteins classified into 12 subcellular locations: chloroplast, cytoplasmic, cytoskeleton, endoplasmic reticulum, extracellular, Golgi apparatus, lysosomal, mitochondrial, nuclear, peroxisomal, plasma membrane, and vacuolar. The overall success rate of prediction obtained by the jackknife cross-validation was 92%. This is so far the highest success rate performed on this dataset by following an objective and rigorous cross-validation procedure.

High-performance computational fluid dynamics: a custom-code approach

International Nuclear Information System (INIS)

Fannon, James; Náraigh, Lennon Ó; Loiseau, Jean-Christophe; Valluri, Prashant; Bethune, Iain

2016-01-01

We introduce a modified and simplified version of the pre-existing fully parallelized three-dimensional Navier–Stokes flow solver known as TPLS. We demonstrate how the simplified version can be used as a pedagogical tool for the study of computational fluid dynamics (CFDs) and parallel computing. TPLS is at its heart a two-phase flow solver, and uses calls to a range of external libraries to accelerate its performance. However, in the present context we narrow the focus of the study to basic hydrodynamics and parallel computing techniques, and the code is therefore simplified and modified to simulate pressure-driven single-phase flow in a channel, using only relatively simple Fortran 90 code with MPI parallelization, but no calls to any other external libraries. The modified code is analysed in order to both validate its accuracy and investigate its scalability up to 1000 CPU cores. Simulations are performed for several benchmark cases in pressure-driven channel flow, including a turbulent simulation, wherein the turbulence is incorporated via the large-eddy simulation technique. The work may be of use to advanced undergraduate and graduate students as an introductory study in CFDs, while also providing insight for those interested in more general aspects of high-performance computing. (paper)

High-performance computational fluid dynamics: a custom-code approach

Science.gov (United States)

Fannon, James; Loiseau, Jean-Christophe; Valluri, Prashant; Bethune, Iain; Náraigh, Lennon Ó.

2016-07-01

We introduce a modified and simplified version of the pre-existing fully parallelized three-dimensional Navier-Stokes flow solver known as TPLS. We demonstrate how the simplified version can be used as a pedagogical tool for the study of computational fluid dynamics (CFDs) and parallel computing. TPLS is at its heart a two-phase flow solver, and uses calls to a range of external libraries to accelerate its performance. However, in the present context we narrow the focus of the study to basic hydrodynamics and parallel computing techniques, and the code is therefore simplified and modified to simulate pressure-driven single-phase flow in a channel, using only relatively simple Fortran 90 code with MPI parallelization, but no calls to any other external libraries. The modified code is analysed in order to both validate its accuracy and investigate its scalability up to 1000 CPU cores. Simulations are performed for several benchmark cases in pressure-driven channel flow, including a turbulent simulation, wherein the turbulence is incorporated via the large-eddy simulation technique. The work may be of use to advanced undergraduate and graduate students as an introductory study in CFDs, while also providing insight for those interested in more general aspects of high-performance computing.

Computer simulation of dynamic processes on accelerators

International Nuclear Information System (INIS)

Kol'ga, V.V.

1979-01-01

The problems of computer numerical investigation of motion of accelerated particles in accelerators and storages, an effect of different accelerator systems on the motion, determination of optimal characteristics of accelerated charged particle beams are considered. Various simulation representations are discussed which describe the accelerated particle dynamics, such as the enlarged particle method, the representation where a great number of discrete particle is substituted for a field of continuously distributed space charge, the method based on determination of averaged beam characteristics. The procedure is described of numerical studies involving the basic problems, viz. calculation of closed orbits, establishment of stability regions, investigation of resonance propagation determination of the phase stability region, evaluation of the space charge effect the problem of beam extraction. It is shown that most of such problems are reduced to solution of the Cauchy problem using a computer. The ballistic method which is applied to solution of the boundary value problem of beam extraction is considered. It is shown that introduction into the equation under study of additional members with the small positive regularization parameter is a general idea of the methods for regularization of noncorrect problems [ru

CFD: computational fluid dynamics or confounding factor dissemination? The role of hemodynamics in intracranial aneurysm rupture risk assessment.

Science.gov (United States)

Xiang, J; Tutino, V M; Snyder, K V; Meng, H

2014-10-01

Image-based computational fluid dynamics holds a prominent position in the evaluation of intracranial aneurysms, especially as a promising tool to stratify rupture risk. Current computational fluid dynamics findings correlating both high and low wall shear stress with intracranial aneurysm growth and rupture puzzle researchers and clinicians alike. These conflicting findings may stem from inconsistent parameter definitions, small datasets, and intrinsic complexities in intracranial aneurysm growth and rupture. In Part 1 of this 2-part review, we proposed a unifying hypothesis: both high and low wall shear stress drive intracranial aneurysm growth and rupture through mural cell-mediated and inflammatory cell-mediated destructive remodeling pathways, respectively. In the present report, Part 2, we delineate different wall shear stress parameter definitions and survey recent computational fluid dynamics studies, in light of this mechanistic heterogeneity. In the future, we expect that larger datasets, better analyses, and increased understanding of hemodynamic-biologic mechanisms will lead to more accurate predictive models for intracranial aneurysm risk assessment from computational fluid dynamics. © 2014 by American Journal of Neuroradiology.

High-Performance Java Codes for Computational Fluid Dynamics

Science.gov (United States)

Riley, Christopher; Chatterjee, Siddhartha; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2001-01-01

The computational science community is reluctant to write large-scale computationally -intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object-oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object-oriented design and implementation of two real-world applications from the field of Computational Fluid Dynamics (CFD): a finite-volume fluid flow solver (LAURA, from NASA Langley Research Center), and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high-performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object-oriented software design principles are not necessarily inimical to high performance.

The subcellular compartmentalization of arginine metabolizing enzymes and their role in endothelial dysfunction

Directory of Open Access Journals (Sweden)

Feng eChen

2013-07-01

Full Text Available The endothelial production of nitric oxide (NO mediates endothelium-dependent vasorelaxation and restrains vascular inflammation, smooth muscle proliferation and platelet aggregation. Impaired production of NO is a hallmark of endothelial dysfunction and promotes the development of cardiovascular disease. In endothelial cells, NO is generated by endothelial nitric oxide synthase (eNOS through the conversion of its substrate, L-arginine to L-citrulline. Reduced access to L-arginine has been proposed as a major mechanism underlying reduced eNOS activity and NO production in cardiovascular disease. The arginases (Arg1 and Arg2 metabolize L-arginine to generate L-ornithine and urea and increased expression of arginase has been proposed as a mechanism of reduced eNOS activity secondary to the depletion of L-arginine. Indeed, supplemental L-arginine and suppression of arginase activity has been shown to improve endothelium-dependent relaxation and ameliorate cardiovascular disease. However, L-arginine concentrations in endothelial cells remain sufficiently high to support NO synthesis suggesting additional mechanisms. The compartmentalization of intracellular L-arginine into poorly interchangeable pools has been proposed to allow for the local depletion of L-arginine. Indeed the subcellular location of L-arginine metabolizing enzymes plays important functional roles. In endothelial cells, eNOS is found in discrete intracellular locations and the capacity to generate NO is heavily influenced by its localtion. Arg1 and Arg2 also reside in different subcellular environments and are thought to differentially influence endothelial function. The plasma membrane solute transporter, CAT-1 and the arginine recycling enzyme, ASL, co-localize with eNOS and facilitate NO release. This review highlights the importance of the subcellular location of eNOS and arginine transporting and metabolizing enzymes to NO release and cardiovascular disease.

Applied & Computational MathematicsChallenges for the Design and Control of Dynamic Energy Systems

Energy Technology Data Exchange (ETDEWEB)

Brown, D L; Burns, J A; Collis, S; Grosh, J; Jacobson, C A; Johansen, H; Mezic, I; Narayanan, S; Wetter, M

2011-03-10

consumption. In addition the finding was that there are tools and technologies that can be assembled and deployed in the short term - the next 3-5 years - that can be used to significantly reduce the cost and time effective delivery of moderate energy savings in the U.S. building stock. Simulation tools, which are a core strength of current DOE computational research programs, provide only a part of the answer by providing a basis for simulation enabled design. New investments will be required within a broad dynamics and control research agenda which must focus on dynamics, control, optimization and simulation of multi-scale energy systems during design and operation. U.S. investments in high performance and high productivity computing (HP2C) should be leveraged and coupled with advances in dynamics and control to impact both the existing building stock through retrofits and also new construction. The essential R&D areas requiring investment are: (1) Characterizing the Dynamics of Multi-scale Energy Systems; (2) Control and Optimization Methodologies of Multi-scale Energy Systems Under Uncertainty; and (3) Multiscale Modeling and Simulation Enabled Design and Operation. The concept of using design and control specific computational tools is a new idea for the building industry. The potential payoffs in terms of accelerated design cycle times, performance optimization and optimal supervisory control to obtain and maintain energy savings are huge. Recent advances in computational power, computer science, and mathematical algorithms offer the foundations to address the control problems presented by the complex dynamics of whole building systems. The key areas for focus and associated metrics with targets for establishing competitiveness in energy efficient building design and operation are: (1) Scalability - Current methodology and tools can provide design guidance for very low energy buildings in weeks to months; what is needed is hours to days. A 50X improvement is needed. (2

Petascale molecular dynamics simulation using the fast multipole method on K computer

KAUST Repository

Ohno, Yousuke; Yokota, Rio; Koyama, Hiroshi; Morimoto, Gentaro; Hasegawa, Aki; Masumoto, Gen; Okimoto, Noriaki; Hirano, Yoshinori; Ibeid, Huda; Narumi, Tetsu; Taiji, Makoto

2014-01-01

In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.

Petascale molecular dynamics simulation using the fast multipole method on K computer

KAUST Repository

Ohno, Yousuke

2014-10-01

In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.

Application of a distributed network in computational fluid dynamic simulations

Science.gov (United States)

Deshpande, Manish; Feng, Jinzhang; Merkle, Charles L.; Deshpande, Ashish

1994-01-01

A general-purpose 3-D, incompressible Navier-Stokes algorithm is implemented on a network of concurrently operating workstations using parallel virtual machine (PVM) and compared with its performance on a CRAY Y-MP and on an Intel iPSC/860. The problem is relatively computationally intensive, and has a communication structure based primarily on nearest-neighbor communication, making it ideally suited to message passing. Such problems are frequently encountered in computational fluid dynamics (CDF), and their solution is increasingly in demand. The communication structure is explicitly coded in the implementation to fully exploit the regularity in message passing in order to produce a near-optimal solution. Results are presented for various grid sizes using up to eight processors.

Analytical, Computational Fluid Dynamics and Flight Dynamics of Coandă MAV

Science.gov (United States)

Djojodihardjo, H.; Ahmed, RI

2016-11-01

The paper establishes the basic working relationships among various relevant variables and parameters governing the aerodynamics forces and performance measures of Coandă MAV in hover and translatory motion. With such motivation, capitalizing on the basic fundamental principles, the Fluid Dynamics and Flight Mechanics of semi-spherical Coandă MAV configurations are revisited and analyzed as a baseline. To gain better understanding on the principle of Coandă MAV lift generation, a mathematical model for a spherical Coandă MAV is developed and analyzed from first physical principles. To gain further insight into the prevailing flow field around a Coandă MAV, as well as to verify the theoretical prediction presented in the work, a computational fluid dynamic CFD simulation for a Coandă MAV generic model are elaborated using commercial software FLUENT®. In addition, the equation of motion for translatory motion of Coandă MAV is elaborated. The mathematical model and derived performance measures are shown to be capable in describing the physical phenomena of the flow field of the semi-spherical Coandă MAV. The relationships between the relevant parameters of the mathematical model of the Coandă MAV to the forces acting on it are elaborated subsequently.

CSDMS2.0: Computational Infrastructure for Community Surface Dynamics Modeling

Science.gov (United States)

Syvitski, J. P.; Hutton, E.; Peckham, S. D.; Overeem, I.; Kettner, A.

2012-12-01

The Community Surface Dynamic Modeling System (CSDMS) is an NSF-supported, international and community-driven program that seeks to transform the science and practice of earth-surface dynamics modeling. CSDMS integrates a diverse community of more than 850 geoscientists representing 360 international institutions (academic, government, industry) from 60 countries and is supported by a CSDMS Interagency Committee (22 Federal agencies), and a CSDMS Industrial Consortia (18 companies). CSDMS presently distributes more 200 Open Source models and modeling tools, access to high performance computing clusters in support of developing and running models, and a suite of products for education and knowledge transfer. CSDMS software architecture employs frameworks and services that convert stand-alone models into flexible "plug-and-play" components to be assembled into larger applications. CSDMS2.0 will support model applications within a web browser, on a wider variety of computational platforms, and on other high performance computing clusters to ensure robustness and sustainability of the framework. Conversion of stand-alone models into "plug-and-play" components will employ automated wrapping tools. Methods for quantifying model uncertainty are being adapted as part of the modeling framework. Benchmarking data is being incorporated into the CSDMS modeling framework to support model inter-comparison. Finally, a robust mechanism for ingesting and utilizing semantic mediation databases is being developed within the Modeling Framework. Six new community initiatives are being pursued: 1) an earth - ecosystem modeling initiative to capture ecosystem dynamics and ensuing interactions with landscapes, 2) a geodynamics initiative to investigate the interplay among climate, geomorphology, and tectonic processes, 3) an Anthropocene modeling initiative, to incorporate mechanistic models of human influences, 4) a coastal vulnerability modeling initiative, with emphasis on deltas and

Subcellular boron and fluorine distributions with SIMS ion microscopy in BNCT and cancer research

Energy Technology Data Exchange (ETDEWEB)

Subhash Chandra

2008-05-30

The development of a secondary ion mass spectrometry (SIMS) based technique of Ion Microscopy in boron neutron capture therapy (BNCT) was the main goal of this project, so that one can study the subcellular location of boron-10 atoms and their partitioning between the normal and cancerous tissue. This information is fundamental for the screening of boronated drugs appropriate for neutron capture therapy of cancer. Our studies at Cornell concentrated mainly on studies of glioblastoma multiforme (GBM). The early years of the grant were dedicated to the development of cryogenic methods and correlative microscopic approaches so that a reliable subcellular analysis of boron-10 atoms can be made with SIMS. In later years SIMS was applied to animal models and human tissues of GBM for studying the efficacy of potential boronated agents in BNCT. Under this grant the SIMS program at Cornell attained a new level of excellence and collaborative SIMS studies were published with leading BNCT researchers in the U.S.

Accumulation of fission fragment 147Pm in subcellular level studied by electron microscopic autoradiography

International Nuclear Information System (INIS)

Zhu Shoupeng; Wang Yuanchang

1990-11-01

The subcellular localization of fission fragment 147 Pm in tissue cells by electron microscopic autoradiography was investigated. The early harm of internal contaminated accumulation of 147 Pm appeared in blood cells and endothelium cells, obviously in erythrocytes. Then 147 Pm was selectively deposited in ultrastructure of liver cells. Autoradiographic study demonstrated that dense tracks appeared in mitochondria and lysosome of podal cells within renal corpuscle. In nucleus as well as in mitochondria and microbodies of epicyte of kidney near-convoluted tubule, there are numerous radioactive 149 Pm accumulated. With the prolongation of observing time, 149 Pm was selectively and steadily deposited in subcellular level of organic component bone. The radionuclides could be accumulated in nucleus of osteoclasts and osteoblasts. In organelles, the radionuclides was mainly accumulated in rough endoplasmic reticulum and mitochondria. Autoradiographic tracks of 149 Pm was obviously found to be localized in combined point between Golgi complex and transitive vesicle of rough endoplasmic reticulum

Subcellular boron and fluorine distributions with SIMS ion microscopy in BNCT and cancer research

International Nuclear Information System (INIS)

Subhash, Chandra

2008-01-01

The development of a secondary ion mass spectrometry (SIMS) based technique of Ion Microscopy in boron neutron capture therapy (BNCT) was the main goal of this project, so that one can study the subcellular location of boron-10 atoms and their partitioning between the normal and cancerous tissue. This information is fundamental for the screening of boronated drugs appropriate for neutron capture therapy of cancer. Our studies at Cornell concentrated mainly on studies of glioblastoma multiforme (GBM). The early years of the grant were dedicated to the development of cryogenic methods and correlative microscopic approaches so that a reliable subcellular analysis of boron-10 atoms can be made with SIMS. In later years SIMS was applied to animal models and human tissues of GBM for studying the efficacy of potential boronated agents in BNCT. Under this grant the SIMS program at Cornell attained a new level of excellence and collaborative SIMS studies were published with leading BNCT researchers in the U.S.

Precision automation of cell type classification and sub-cellular fluorescence quantification from laser scanning confocal images

Directory of Open Access Journals (Sweden)

Hardy Craig Hall

2016-02-01

Full Text Available While novel whole-plant phenotyping technologies have been successfully implemented into functional genomics and breeding programs, the potential of automated phenotyping with cellular resolution is largely unexploited. Laser scanning confocal microscopy has the potential to close this gap by providing spatially highly resolved images containing anatomic as well as chemical information on a subcellular basis. However, in the absence of automated methods, the assessment of the spatial patterns and abundance of fluorescent markers with subcellular resolution is still largely qualitative and time-consuming. Recent advances in image acquisition and analysis, coupled with improvements in microprocessor performance, have brought such automated methods within reach, so that information from thousands of cells per image for hundreds of images may be derived in an experimentally convenient time-frame. Here, we present a MATLAB-based analytical pipeline to 1 segment radial plant organs into individual cells, 2 classify cells into cell type categories based upon random forest classification, 3 divide each cell into sub-regions, and 4 quantify fluorescence intensity to a subcellular degree of precision for a separate fluorescence channel. In this research advance, we demonstrate the precision of this analytical process for the relatively complex tissues of Arabidopsis hypocotyls at various stages of development. High speed and robustness make our approach suitable for phenotyping of large collections of stem-like material and other tissue types.

Mutations in the C-terminal region affect subcellular localization of crucian carp herpesvirus (CaHV) GPCR.

Science.gov (United States)

Wang, Jun; Gui, Lang; Chen, Zong-Yan; Zhang, Qi-Ya

2016-08-01

G protein-coupled receptors (GPCRs) are known as seven transmembrane domain receptors and consequently can mediate diverse biological functions via regulation of their subcellular localization. Crucian carp herpesvirus (CaHV) was recently isolated from infected fish with acute gill hemorrhage. CaHV GPCR of 349 amino acids (aa) was identified based on amino acid identity. A series of variants with truncation/deletion/substitution mutation in the C-terminal (aa 315-349) were constructed and expressed in fathead minnow (FHM) cells. The roles of three key C-terminal regions in subcellular localization of CaHV GPCR were determined. Lysine-315 (K-315) directed the aggregation of the protein preferentially at the nuclear side. Predicted N-myristoylation site (GGGWTR, aa 335-340) was responsible for punctate distribution in periplasm or throughout the cytoplasm. Predicted phosphorylation site (SSR, aa 327-329) and GGGWTR together determined the punctate distribution in cytoplasm. Detection of organelles localization by specific markers showed that the protein retaining K-315 colocalized with the Golgi apparatus. These experiments provided first evidence that different mutations of CaHV GPCR C-terminals have different affects on the subcellular localization of fish herpesvirus-encoded GPCRs. The study provided valuable information and new insights into the precise interactions between herpesvirus and fish cells, and could also provide useful targets for antiviral agents in aquaculture.

Cooperative storage of shared files in a parallel computing system with dynamic block size

Science.gov (United States)

Bent, John M.; Faibish, Sorin; Grider, Gary

2015-11-10

Improved techniques are provided for parallel writing of data to a shared object in a parallel computing system. A method is provided for storing data generated by a plurality of parallel processes to a shared object in a parallel computing system. The method is performed by at least one of the processes and comprises: dynamically determining a block size for storing the data; exchanging a determined amount of the data with at least one additional process to achieve a block of the data having the dynamically determined block size; and writing the block of the data having the dynamically determined block size to a file system. The determined block size comprises, e.g., a total amount of the data to be stored divided by the number of parallel processes. The file system comprises, for example, a log structured virtual parallel file system, such as a Parallel Log-Structured File System (PLFS).

Subcellular Characterization of Porcine Oocytes with Different Glucose-6-phosphate Dehydrogenase Activities

Directory of Open Access Journals (Sweden)

Bo Fu

2015-12-01

Full Text Available The in vitro maturation (IVM efficiency of porcine embryos is still low because of poor oocyte quality. Although brilliant cresyl blue positive (BCB+ oocytes with low glucose-6-phosphate dehydrogenase (G6PDH activity have shown superior quality than BCB negative (− oocytes with high G6PDH activity, the use of a BCB staining test before IVM is still controversial. This study aimed to shed more light on the subcellular characteristics of porcine oocytes after selection using BCB staining. We assessed germinal vesicle chromatin configuration, cortical granule (CG migration, mitochondrial distribution, the levels of acetylated lysine 9 of histone H3 (AcH3K9 and nuclear apoptosis features to investigate the correlation between G6PDH activity and these developmentally related features. A pattern of chromatin surrounding the nucleoli was seen in 53.0% of BCB+ oocytes and 77.6% of BCB+ oocytes showed peripherally distributed CGs. After IVM, 48.7% of BCB+ oocytes had a diffused mitochondrial distribution pattern. However, there were no significant differences in the levels of AcH3K9 in the nuclei of blastocysts derived from BCB+ and BCB− oocytes; at the same time, we observed a similar incidence of apoptosis in the BCB+ and control groups. Although this study indicated that G6PDH activity in porcine oocytes was correlated with several subcellular characteristics such as germinal vesicle chromatin configuration, CG migration and mitochondrial distribution, other features such as AcH3K9 level and nuclear apoptotic features were not associated with G6PDH activity and did not validate the BCB staining test. In using this test for selecting porcine oocytes, subcellular characteristics such as the AcH3K9 level and apoptotic nuclear features should also be considered. Adding histone deacetylase inhibitors or apoptosis inhibitors into the culture medium used might improve the efficiency of IVM of BCB+ oocytes.

Dynamic computed tomography scanning of benign bone lesions: Preliminary results

International Nuclear Information System (INIS)

Levine, E.; Neff, J.R.

1983-01-01

The majority of benign bone lesions can be evaluated adequately using conventional radiologic techniques. However, it is not always possible to differentiate reliably between different types of benign bone lesions on the basis of plain film appearances alone. Dynamic computed tomography (CT) scanning provides a means for further characterizing such lesions by assessing their degree of vascularity. Thus, it may help in distinguishing an osteoid osteoma, which has a hypervascular nidus, from a Brodie's abscess, which is avascular. Dynamic CT scanning may also help in the differentiation between a fluid-containing simple bone cyst, which is avascular, and other solid or semi-solid benign bone lesions which slow varying degrees of vascularity. However, because of the additional irradiation involved, dynamic CT scanning should be reserved for evaluation of selected patients with benign bone lesions in whom the plain film findings are not definitive and in whom the CT findings may have a significant influence on management. (orig.)

Introduction to focus issue: intrinsic and designed computation: information processing in dynamical systems--beyond the digital hegemony.

Science.gov (United States)

Crutchfield, James P; Ditto, William L; Sinha, Sudeshna

2010-09-01

How dynamical systems store and process information is a fundamental question that touches a remarkably wide set of contemporary issues: from the breakdown of Moore's scaling laws--that predicted the inexorable improvement in digital circuitry--to basic philosophical problems of pattern in the natural world. It is a question that also returns one to the earliest days of the foundations of dynamical systems theory, probability theory, mathematical logic, communication theory, and theoretical computer science. We introduce the broad and rather eclectic set of articles in this Focus Issue that highlights a range of current challenges in computing and dynamical systems.

Cardioplegia heat exchanger design modelling using computational fluid dynamics.

Science.gov (United States)

van Driel, M R

2000-11-01

A new cardioplegia heat exchanger has been developed by Sorin Biomedica. A three-dimensional computer-aided design (CAD) model was optimized using computational fluid dynamics (CFD) modelling. CFD optimization techniques have commonly been applied to velocity flow field analysis, but CFD analysis was also used in this study to predict the heat exchange performance of the design before prototype fabrication. The iterative results of the optimization and the actual heat exchange performance of the final configuration are presented in this paper. Based on the behaviour of this model, both the water and blood fluid flow paths of the heat exchanger were optimized. The simulation predicted superior heat exchange performance using an optimal amount of energy exchange surface area, reducing the total contact surface area, the device priming volume and the material costs. Experimental results confirm the empirical results predicted by the CFD analysis.

Subcellular compartmentalization of Cd and Zn in two bivalves. II. Significance of trophically available metal (TAM)

Science.gov (United States)

Wallace, W.G.; Luoma, S.N.

2003-01-01

This paper examines how the subcellular partitioning of Cd and Zn in the bivalves Macoma balthica and Potamocorbula amurensis may affect the trophic transfer of metal to predators. Results show that the partitioning of metals to organelles, 'enzymes' and metallothioneins (MT) comprise a subcellular compartment containing trophically available metal (TAM; i.e. metal trophically available to predators), and that because this partitioning varies with species, animal size and metal, TAM is similarly influenced. Clams from San Francisco Bay, California, were exposed for 14 d to 3.5 ??g 1-1 Cd and 20.5 ??g 1-1 Zn, including 109Cd and 65Zn as radiotracers, and were used in feeding experiments with grass shrimp Palaemon macrodatylus, or used to investigate the subcellular partitioning of metal. Grass shrimp fed Cd-contaminated P. amurensis absorbed ???60% of ingested Cd, which was in accordance with the partitioning of Cd to the bivalve's TAM compartment (i.e. Cd associated with organelles, 'enzymes' and MT); a similar relationship was found in previous studies with grass shrimp fed Cd-contaminated oligochaetes. Thus, TAM may be used as a tool to predict the trophic transfer of at least Cd. Subcellular fractionation revealed that ???34% of both the Cd and Zn accumulated by M. balthica was associated with TAM, while partitioning to TAM in P. amurensis was metal-dependent (???60% for TAM-Cd%, ???73% for TAM-Zn%). The greater TAM-Cd% of P. amurensis than M. balthica is due to preferential binding of Cd to MT and 'enzymes', while enhanced TAM-Zn% of P. amurensis results from a greater binding of Zn to organelles. TAM for most species-metal combinations was size-dependent, decreasing with increased clam size. Based on field data, it is estimated that of the 2 bivalves, P. amurensis poses the greater threat of Cd exposure to predators because of higher tissue concentrations and greater partitioning as TAM; exposure of Zn to predators would be similar between these species.

Frequency Domain Computer Programs for Prediction and Analysis of Rail Vehicle Dynamics : Volume 1. Technical Report

Science.gov (United States)

1975-12-01

Frequency domain computer programs developed or acquired by TSC for the analysis of rail vehicle dynamics are described in two volumes. Volume I defines the general analytical capabilities required for computer programs applicable to single rail vehi...

Dosimetric characterization of radionuclides for systemic tumor therapy: Influence of particle range, photon emission, and subcellular distribution

International Nuclear Information System (INIS)

Uusijaervi, Helena; Bernhardt, Peter; Ericsson, Thomas; Forssell-Aronsson, Eva

2006-01-01

Various radionuclides have been proposed for systemic tumor therapy. However, in most dosimetric analysis of proposed radionuclides the charged particles are taken into consideration while the potential photons are ignored. The photons will cause undesirable irradiation of normal tissue, and increase the probability of toxicity in, e.g., the bone marrow. The aim of this study was to investigate the dosimetric properties according to particle range, photon emission, and subcellular radionuclide distribution, of a selection of radionuclides used or proposed for radionuclide therapy, and to investigate the possibility of dividing radionuclides into groups according to their dosimetric properties. The absorbed dose rate to the tumors divided by the absorbed dose rate to the normal tissue (TND) was estimated for different tumor sizes in a mathematical model of the human body. The body was simulated as a 70-kg ellipsoid and the tumors as spheres of different sizes (1 ng-100 g). The radionuclides were either assumed to be uniformly distributed throughout the entire tumor and normal tissue, or located in the nucleus or the cytoplasm of the tumor cells and on the cell membrane of the normal cells. Fifty-nine radionuclides were studied together with monoenergetic electrons, positrons, and alpha particles. The tumor and normal tissue were assumed to be of water density. The activity concentration ratio between the tumor and normal tissue was assumed to be 25. The radionuclides emitting low-energy electrons combined with a low photon contribution, and the alpha emitters showed high TND values for most tumor sizes. Electrons with higher energy gave reduced TND values for small tumors, while a higher photon contribution reduced the TND values for large tumors. Radionuclides with high photon contributions showed low TND value for all tumor sizes studied. The radionuclides studied could be divided into four main groups according to their TND values: beta emitters, Auger electron

Cellular and Subcellular Immunohistochemical Localization and Quantification of Cadmium Ions in Wheat (Triticum aestivum.

Directory of Open Access Journals (Sweden)

Wei Gao

Full Text Available The distribution of metallic ions in plant tissues is associated with their toxicity and is important for understanding mechanisms of toxicity tolerance. A quantitative histochemical method can help advance knowledge of cellular and subcellular localization and distribution of heavy metals in plant tissues. An immunohistochemical (IHC imaging method for cadmium ions (Cd2+ was developed for the first time for the wheat Triticum aestivum grown in Cd2+-fortified soils. Also, 1-(4-Isothiocyanobenzyl-ethylenediamine-N,N,N,N-tetraacetic acid (ITCB-EDTA was used to chelate the mobile Cd2+. The ITCB-EDTA/Cd2+ complex was fixed with proteins in situ via the isothiocyano group. A new Cd2+-EDTA specific monoclonal antibody, 4F3B6D9A1, was used to locate the Cd2+-EDTA protein complex. After staining, the fluorescence intensities of sections of Cd2+-positive roots were compared with those of Cd2+-negative roots under a laser confocal scanning microscope, and the location of colloidal gold particles was determined with a transmission electron microscope. The results enable quantification of the Cd2+ content in plant tissues and illustrate Cd2+ translocation and cellular and subcellular responses of T. aestivum to Cd2+ stress. Compared to the conventional metal-S coprecipitation histochemical method, this new IHC method is quantitative, more specific and has less background interference. The subcellular location of Cd2+ was also confirmed with energy-dispersive X-ray microanalysis. The IHC method is suitable for locating and quantifying Cd2+ in plant tissues and can be extended to other heavy metallic ions.

Cellular and Subcellular Immunohistochemical Localization and Quantification of Cadmium Ions in Wheat (Triticum aestivum).

Science.gov (United States)

Gao, Wei; Nan, Tiegui; Tan, Guiyu; Zhao, Hongwei; Tan, Weiming; Meng, Fanyun; Li, Zhaohu; Li, Qing X; Wang, Baomin

2015-01-01

The distribution of metallic ions in plant tissues is associated with their toxicity and is important for understanding mechanisms of toxicity tolerance. A quantitative histochemical method can help advance knowledge of cellular and subcellular localization and distribution of heavy metals in plant tissues. An immunohistochemical (IHC) imaging method for cadmium ions (Cd2+) was developed for the first time for the wheat Triticum aestivum grown in Cd2+-fortified soils. Also, 1-(4-Isothiocyanobenzyl)-ethylenediamine-N,N,N,N-tetraacetic acid (ITCB-EDTA) was used to chelate the mobile Cd2+. The ITCB-EDTA/Cd2+ complex was fixed with proteins in situ via the isothiocyano group. A new Cd2+-EDTA specific monoclonal antibody, 4F3B6D9A1, was used to locate the Cd2+-EDTA protein complex. After staining, the fluorescence intensities of sections of Cd2+-positive roots were compared with those of Cd2+-negative roots under a laser confocal scanning microscope, and the location of colloidal gold particles was determined with a transmission electron microscope. The results enable quantification of the Cd2+ content in plant tissues and illustrate Cd2+ translocation and cellular and subcellular responses of T. aestivum to Cd2+ stress. Compared to the conventional metal-S coprecipitation histochemical method, this new IHC method is quantitative, more specific and has less background interference. The subcellular location of Cd2+ was also confirmed with energy-dispersive X-ray microanalysis. The IHC method is suitable for locating and quantifying Cd2+ in plant tissues and can be extended to other heavy metallic ions.

Subcellular distribution of glycogen and decreased tetanic Ca2+ in fatigued single intact mouse muscle fibres

DEFF Research Database (Denmark)

Nielsen, Joachim; Cheng, Arthur J; Ørtenblad, Niels

2014-01-01

In skeletal muscle fibres, glycogen has been shown to be stored at different subcellular locations: (i) between the myofibrils (intermyofibrillar); (ii) within the myofibrils (intramyofibrillar); and (iii) subsarcolemmal. Of these, intramyofibrillar glycogen has been implied as a critical regulator...... of sarcoplasmic reticulum Ca(2+) release. The aim of the present study was to test directly how the decrease in cytoplasmic free Ca(2+) ([Ca(2+)]i) during repeated tetanic contractions relates to the subcellular glycogen distribution. Single fibres of mouse flexor digitorum brevis muscles were fatigued with 70 Hz...... in tetanic [Ca(2+)]i, and hence force, is accompanied by major reductions in inter- and intramyofibrillar glycogen. The stronger correlation between decreased tetanic [Ca(2+)]i and reduced intramyofibrillar glycogen implies that sarcoplasmic reticulum Ca(2+) release critically depends on energy supply from...

Chaotic dynamics in nanoscale NbO2 Mott memristors for analogue computing

Science.gov (United States)

Kumar, Suhas; Strachan, John Paul; Williams, R. Stanley

2017-08-01

At present, machine learning systems use simplified neuron models that lack the rich nonlinear phenomena observed in biological systems, which display spatio-temporal cooperative dynamics. There is evidence that neurons operate in a regime called the edge of chaos that may be central to complexity, learning efficiency, adaptability and analogue (non-Boolean) computation in brains. Neural networks have exhibited enhanced computational complexity when operated at the edge of chaos, and networks of chaotic elements have been proposed for solving combinatorial or global optimization problems. Thus, a source of controllable chaotic behaviour that can be incorporated into a neural-inspired circuit may be an essential component of future computational systems. Such chaotic elements have been simulated using elaborate transistor circuits that simulate known equations of chaos, but an experimental realization of chaotic dynamics from a single scalable electronic device has been lacking. Here we describe niobium dioxide (NbO2) Mott memristors each less than 100 nanometres across that exhibit both a nonlinear-transport-driven current-controlled negative differential resistance and a Mott-transition-driven temperature-controlled negative differential resistance. Mott materials have a temperature-dependent metal-insulator transition that acts as an electronic switch, which introduces a history-dependent resistance into the device. We incorporate these memristors into a relaxation oscillator and observe a tunable range of periodic and chaotic self-oscillations. We show that the nonlinear current transport coupled with thermal fluctuations at the nanoscale generates chaotic oscillations. Such memristors could be useful in certain types of neural-inspired computation by introducing a pseudo-random signal that prevents global synchronization and could also assist in finding a global minimum during a constrained search. We specifically demonstrate that incorporating such

Dynamic computer simulations of electrophoresis: three decades of active research.

Science.gov (United States)

Thormann, Wolfgang; Caslavska, Jitka; Breadmore, Michael C; Mosher, Richard A

2009-06-01

Dynamic models for electrophoresis are based upon model equations derived from the transport concepts in solution together with user-inputted conditions. They are able to predict theoretically the movement of ions and are as such the most versatile tool to explore the fundamentals of electrokinetic separations. Since its inception three decades ago, the state of dynamic computer simulation software and its use has progressed significantly and Electrophoresis played a pivotal role in that endeavor as a large proportion of the fundamental and application papers were published in this periodical. Software is available that simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. This has been employed to show the detailed mechanisms of many of the fundamental phenomena that occur in electrophoretic separations. Dynamic electrophoretic simulations are relevant for separations on any scale and instrumental format, including free-fluid preparative, gel, capillary and chip electrophoresis. This review includes a historical overview, a survey of current simulators, simulation examples and a discussion of the applications and achievements of dynamic simulation.

Computational complexity of symbolic dynamics at the onset of chaos

Science.gov (United States)

Lakdawala, Porus

1996-05-01

In a variety of studies of dynamical systems, the edge of order and chaos has been singled out as a region of complexity. It was suggested by Wolfram, on the basis of qualitative behavior of cellular automata, that the computational basis for modeling this region is the universal Turing machine. In this paper, following a suggestion of Crutchfield, we try to show that the Turing machine model may often be too powerful as a computational model to describe the boundary of order and chaos. In particular we study the region of the first accumulation of period doubling in unimodal and bimodal maps of the interval, from the point of view of language theory. We show that in relation to the ``extended'' Chomsky hierarchy, the relevant computational model in the unimodal case is the nested stack automaton or the related indexed languages, while the bimodal case is modeled by the linear bounded automaton or the related context-sensitive languages.

Computational Fluid Dynamics of Choanoflagellate Filter-Feeding

Science.gov (United States)

Asadzadeh, Seyed Saeed; Walther, Jens; Nielsen, Lasse Tore; Kiorboe, Thomas; Dolger, Julia; Andersen, Anders

2017-11-01

Choanoflagellates are unicellular aquatic organisms with a single flagellum that drives a feeding current through a funnel-shaped collar filter on which bacteria-sized prey are caught. Using computational fluid dynamics (CFD) we model the beating flagellum and the complex filter flow of the choanoflagellate Diaphanoeca grandis. Our CFD simulations based on the current understanding of the morphology underestimate the experimentally observed clearance rate by more than an order of magnitude: The beating flagellum is simply unable to draw enough water through the fine filter. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), and addition of a wide vane in our CFD model allows us to correctly predict the observed clearance rate.

Advances in computational dynamics of particles, materials and structures a unified approach

CERN Document Server

Har, Jason

2012-01-01

Computational methods for the modeling and simulation of the dynamic response and behavior of particles, materials and structural systems have had a profound influence on science, engineering and technology. Complex science and engineering applications dealing with complicated structural geometries and materials that would be very difficult to treat using analytical methods have been successfully simulated using computational tools. With the incorporation of quantum, molecular and biological mechanics into new models, these methods are poised to play an even bigger role in the future. Ad

Numerical computation of soliton dynamics for NLS equations in a driving potential

Directory of Open Access Journals (Sweden)

Marco Caliari

2010-06-01

Full Text Available We provide numerical computations for the soliton dynamics of the nonlinear Schrodinger equation with an external potential. After computing the ground state solution r of a related elliptic equation we show that, in the semi-classical regime, the center of mass of the solution with initial datum built upon r is driven by the solution to $ddot x=- abla V(x$. Finally, we provide examples and analyze the numerical errors in the two dimensional case when V is a harmonic potential.

High performance computer code for molecular dynamics simulations

International Nuclear Information System (INIS)

Levay, I.; Toekesi, K.

2007-01-01

Complete text of publication follows. Molecular Dynamics (MD) simulation is a widely used technique for modeling complicated physical phenomena. Since 2005 we are developing a MD simulations code for PC computers. The computer code is written in C++ object oriented programming language. The aim of our work is twofold: a) to develop a fast computer code for the study of random walk of guest atoms in Be crystal, b) 3 dimensional (3D) visualization of the particles motion. In this case we mimic the motion of the guest atoms in the crystal (diffusion-type motion), and the motion of atoms in the crystallattice (crystal deformation). Nowadays, it is common to use Graphics Devices in intensive computational problems. There are several ways to use this extreme processing performance, but never before was so easy to programming these devices as now. The CUDA (Compute Unified Device) Architecture introduced by nVidia Corporation in 2007 is a very useful for every processor hungry application. A Unified-architecture GPU include 96-128, or more stream processors, so the raw calculation performance is 576(!) GFLOPS. It is ten times faster, than the fastest dual Core CPU [Fig.1]. Our improved MD simulation software uses this new technology, which speed up our software and the code run 10 times faster in the critical calculation code segment. Although the GPU is a very powerful tool, it has a strongly paralleled structure. It means, that we have to create an algorithm, which works on several processors without deadlock. Our code currently uses 256 threads, shared and constant on-chip memory, instead of global memory, which is 100 times slower than others. It is possible to implement the total algorithm on GPU, therefore we do not need to download and upload the data in every iteration. On behalf of maximal throughput, every thread run with the same instructions

CellMap visualizes protein-protein interactions and subcellular localization

Science.gov (United States)

Dallago, Christian; Goldberg, Tatyana; Andrade-Navarro, Miguel Angel; Alanis-Lobato, Gregorio; Rost, Burkhard

2018-01-01

Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers. PMID:29497493

Zn subcellular distribution in liver of goldfish (carassius auratus with exposure to zinc oxide nanoparticles and mechanism of hepatic detoxification.

Directory of Open Access Journals (Sweden)

Wenhong Fan

Full Text Available Zinc Oxide Nanoparticles (ZnO NPs have attracted increasing concerns because of their widespread use and toxic potential. In this study, Zn accumulations in different tissues (gills, liver, muscle, and gut of goldfish (Carassius auratus after exposure to ZnO NPs were studied in comparison with bulk ZnO and Zn(2+. And the technique of subcellular partitioning was firstly used on the liver of goldfish to study the hepatic accumulation of ZnO NPs. The results showed that at sublethal Zn concentration (2 mg/L, bioaccumulation in goldfish was tissue-specific and dependent on the exposure materials. Compared with Zn(2+, the particles of bulk ZnO and the ZnO NPs appeared to aggregate in the environmentally contacted tissues (gills and gut, rather than transport to the internal tissues (liver and muscle. The subcellular distributions of liver differed for the three exposure treatments. After ZnO NPs exposure, Zn percentage in metal-rich granule (MRG increased significantly, and after Zn(2+ exposure, it increased significantly in the organelles. Metallothionein-like proteins (MTLP were the main target for Zn(2+, while MRG played dominant role for ZnO NPs. The different results of subcellular distributions revealed that metal detoxification mechanisms of liver for ZnO NPs, bulk ZnO, and Zn(2+ were different. Overall, subcellular partitioning provided an interesting start to better understanding of the toxicity of nano- and conventional materials.

Robust dynamical decoupling for quantum computing and quantum memory.

Science.gov (United States)

Souza, Alexandre M; Alvarez, Gonzalo A; Suter, Dieter

2011-06-17

Dynamical decoupling (DD) is a popular technique for protecting qubits from the environment. However, unless special care is taken, experimental errors in the control pulses used in this technique can destroy the quantum information instead of preserving it. Here, we investigate techniques for making DD sequences robust against different types of experimental errors while retaining good decoupling efficiency in a fluctuating environment. We present experimental data from solid-state nuclear spin qubits and introduce a new DD sequence that is suitable for quantum computing and quantum memory.

Torque converter transient characteristics prediction using computational fluid dynamics

International Nuclear Information System (INIS)

Yamaguchi, T; Tanaka, K

2012-01-01

The objective of this research is to investigate the transient torque converter performance used in an automobile. A new technique in computational fluid dynamics is introduced, which includes the inertia of the turbine in a three dimensional simulation of the torque converter during a launch condition. The simulation results are compared to experimental test data with good agreement across the range of data. In addition, the simulated flow structure inside the torque converter is visualized and compared to results from a steady-state calculation.

Particle Image Velocimetry and Computational Fluid Dynamics Analysis of Fuel Cell Manifold

DEFF Research Database (Denmark)

Lebæk, Jesper; Blazniak Andreasen, Marcin; Andresen, Henrik Assenholm

2010-01-01

The inlet effect on the manifold flow in a fuel cell stack was investigated by means of numerical methods (computational fluid dynamics) and experimental methods (particle image velocimetry). At a simulated high current density situation the flow field was mapped on a 70 cell simulated cathode...

Topics in Modeling of Cochlear Dynamics: Computation, Response and Stability Analysis

Science.gov (United States)

Filo, Maurice G.

This thesis touches upon several topics in cochlear modeling. Throughout the literature, mathematical models of the cochlea vary according to the degree of biological realism to be incorporated. This thesis casts the cochlear model as a continuous space-time dynamical system using operator language. This framework encompasses a wider class of cochlear models and makes the dynamics more transparent and easier to analyze before applying any numerical method to discretize space. In fact, several numerical methods are investigated to study the computational efficiency of the finite dimensional realizations in space. Furthermore, we study the effects of the active gain perturbations on the stability of the linearized dynamics. The stability analysis is used to explain possible mechanisms underlying spontaneous otoacoustic emissions and tinnitus. Dynamic Mode Decomposition (DMD) is introduced as a useful tool to analyze the response of nonlinear cochlear models. Cochlear response features are illustrated using DMD which has the advantage of explicitly revealing the spatial modes of vibrations occurring in the Basilar Membrane (BM). Finally, we address the dynamic estimation problem of BM vibrations using Extended Kalman Filters (EKF). Due to the limitations of noninvasive sensing schemes, such algorithms are inevitable to estimate the dynamic behavior of a living cochlea.

Probabilistic Methods for the Quantification of Uncertainty and Error in Computational Fluid Dynamic Simulations

National Research Council Canada - National Science Library

Faragher, John

2004-01-01

... conservatism to allow for them. This report examines the feasibility of using a probabilistic approach for modelling the component temperatures in an engine using CFD (Computational Fluid Dynamics).

Increasing the speed of computational fluid dynamics procedure for minimization the nitrogen oxide polution from the premixed atmospheric gas burner

Directory of Open Access Journals (Sweden)

Fotev Vasko G.

2017-01-01

Full Text Available This article presents innovative method for increasing the speed of procedure which includes complex computational fluid dynamic calculations for finding the distance between flame openings of atmospheric gas burner that lead to minimal NO pollution. The method is based on standard features included in commercial computational fluid dynamic software and shortens computer working time roughly seven times in this particular case.

SciDAC advances and applications in computational beam dynamics

International Nuclear Information System (INIS)

Ryne, R; Abell, D; Adelmann, A; Amundson, J; Bohn, C; Cary, J; Colella, P; Dechow, D; Decyk, V; Dragt, A; Gerber, R; Habib, S; Higdon, D; Katsouleas, T; Ma, K-L; McCorquodale, P; Mihalcea, D; Mitchell, C; Mori, W; Mottershead, C T; Neri, F; Pogorelov, I; Qiang, J; Samulyak, R; Serafini, D; Shalf, J; Siegerist, C; Spentzouris, P; Stoltz, P; Terzic, B; Venturini, M; Walstrom, P

2005-01-01

SciDAC has had a major impact on computational beam dynamics and the design of particle accelerators. Particle accelerators-which account for half of the facilities in the DOE Office of Science Facilities for the Future of Science 20 Year Outlook-are crucial for US scientific, industrial, and economic competitiveness. Thanks to SciDAC, accelerator design calculations that were once thought impossible are now carried routinely, and new challenging and important calculations are within reach. SciDAC accelerator modeling codes are being used to get the most science out of existing facilities, to produce optimal designs for future facilities, and to explore advanced accelerator concepts that may hold the key to qualitatively new ways of accelerating charged particle beams. In this paper we present highlights from the SciDAC Accelerator Science and Technology (AST) project Beam Dynamics focus area in regard to algorithm development, software development, and applications

SciDAC Advances and Applications in Computational Beam Dynamics

International Nuclear Information System (INIS)

Ryne, R.; Abell, D.; Adelmann, A.; Amundson, J.; Bohn, C.; Cary, J.; Colella, P.; Dechow, D.; Decyk, V.; Dragt, A.; Gerber, R.; Habib, S.; Higdon, D.; Katsouleas, T.; Ma, K.-L.; McCorquodale, P.; Mihalcea, D.; Mitchell, C.; Mori, W.; Mottershead, C.T.; Neri, F.; Pogorelov, I.; Qiang, J.; Samulyak, R.; Serafini, D.; Shalf, J.; Siegerist, C.; Spentzouris, P.; Stoltz, P.; Terzic, B.; Venturini, M.; Walstrom, P.

2005-01-01

SciDAC has had a major impact on computational beam dynamics and the design of particle accelerators. Particle accelerators--which account for half of the facilities in the DOE Office of Science Facilities for the Future of Science 20 Year Outlook--are crucial for US scientific, industrial, and economic competitiveness. Thanks to SciDAC, accelerator design calculations that were once thought impossible are now carried routinely, and new challenging and important calculations are within reach. SciDAC accelerator modeling codes are being used to get the most science out of existing facilities, to produce optimal designs for future facilities, and to explore advanced accelerator concepts that may hold the key to qualitatively new ways of accelerating charged particle beams. In this poster we present highlights from the SciDAC Accelerator Science and Technology (AST) project Beam Dynamics focus area in regard to algorithm development, software development, and applications

COMPUTER TOOLS OF DYNAMIC MATHEMATIC SOFTWARE AND METHODICAL PROBLEMS OF THEIR USE

Directory of Open Access Journals (Sweden)

Olena V. Semenikhina

2014-08-01

Full Text Available The article presents results of analyses of standard computer tools of dynamic mathematic software which are used in solving tasks, and tools on which the teacher can support in the teaching of mathematics. Possibility of the organization of experimental investigating of mathematical objects on the basis of these tools and the wording of new tasks on the basis of the limited number of tools, fast automated check are specified. Some methodological comments on application of computer tools and methodological features of the use of interactive mathematical environments are presented. Problems, which are arising from the use of computer tools, among which rethinking forms and methods of training by teacher, the search for creative problems, the problem of rational choice of environment, check the e-solutions, common mistakes in the use of computer tools are selected.

Cepstrum analysis and applications to computational fluid dynamic solutions

Science.gov (United States)

Meadows, Kristine R.

1990-04-01

A novel approach to the problem of spurious reflections introduced by artificial boundary conditions in computational fluid dynamic (CFD) solutions is proposed. Instead of attempting to derive non-reflecting boundary conditions, the approach is to accept the fact that spurious reflections occur, but to remove these reflections with cepstrum analysis, a signal processing technique which has been successfully used to remove echoes from experimental data. First, the theory of the cepstrum method is presented. This includes presentation of two types of cepstra: The Power Cepstrum and the Complex Cepstrum. The definitions of the cepstrum methods are applied theoretically and numerically to the analytical solution of sinusoidal plane wave propagation in a duct. One-D and 3-D time dependent solutions to the Euler equations are computed, and hard-wall conditions are prescribed at the numerical boundaries. The cepstrum method is applied, and the reflections from the boundaries are removed from the solutions. One-D and 3-D solutions are computed with so called nonreflecting boundary conditions, and these solutions are compared to those obtained by prescribing hard wall conditions and processing with the cepstrum.

Algorithms for computational fluid dynamics n parallel processors

International Nuclear Information System (INIS)

Van de Velde, E.F.

1986-01-01

A study of parallel algorithms for the numerical solution of partial differential equations arising in computational fluid dynamics is presented. The actual implementation on parallel processors of shared and nonshared memory design is discussed. The performance of these algorithms is analyzed in terms of machine efficiency, communication time, bottlenecks and software development costs. For elliptic equations, a parallel preconditioned conjugate gradient method is described, which has been used to solve pressure equations discretized with high order finite elements on irregular grids. A parallel full multigrid method and a parallel fast Poisson solver are also presented. Hyperbolic conservation laws were discretized with parallel versions of finite difference methods like the Lax-Wendroff scheme and with the Random Choice method. Techniques are developed for comparing the behavior of an algorithm on different architectures as a function of problem size and local computational effort. Effective use of these advanced architecture machines requires the use of machine dependent programming. It is shown that the portability problems can be minimized by introducing high level operations on vectors and matrices structured into program libraries

An effective chaos-geometric computational approach to analysis and prediction of evolutionary dynamics of the environmental systems: Atmospheric pollution dynamics

Science.gov (United States)

Buyadzhi, V. V.; Glushkov, A. V.; Khetselius, O. Yu; Bunyakova, Yu Ya; Florko, T. A.; Agayar, E. V.; Solyanikova, E. P.

2017-10-01

The present paper concerns the results of computational studying dynamics of the atmospheric pollutants (dioxide of nitrogen, sulphur etc) concentrations in an atmosphere of the industrial cities (Odessa) by using the dynamical systems and chaos theory methods. A chaotic behaviour in the nitrogen dioxide and sulphurous anhydride concentration time series at several sites of the Odessa city is numerically investigated. As usually, to reconstruct the corresponding attractor, the time delay and embedding dimension are needed. The former is determined by the methods of autocorrelation function and average mutual information, and the latter is calculated by means of a correlation dimension method and algorithm of false nearest neighbours. Further, the Lyapunov’s exponents spectrum, Kaplan-Yorke dimension and Kolmogorov entropy are computed. It has been found an existence of a low-D chaos in the time series of the atmospheric pollutants concentrations.

Linear stability analysis of detonations via numerical computation and dynamic mode decomposition

KAUST Repository

Kabanov, Dmitry I.

2017-12-08

We introduce a new method to investigate linear stability of gaseous detonations that is based on an accurate shock-fitting numerical integration of the linearized reactive Euler equations with a subsequent analysis of the computed solution via the dynamic mode decomposition. The method is applied to the detonation models based on both the standard one-step Arrhenius kinetics and two-step exothermic-endothermic reaction kinetics. Stability spectra for all cases are computed and analyzed. The new approach is shown to be a viable alternative to the traditional normal-mode analysis used in detonation theory.

Linear stability analysis of detonations via numerical computation and dynamic mode decomposition

KAUST Repository

Kabanov, Dmitry; Kasimov, Aslan R.

2018-01-01

We introduce a new method to investigate linear stability of gaseous detonations that is based on an accurate shock-fitting numerical integration of the linearized reactive Euler equations with a subsequent analysis of the computed solution via the dynamic mode decomposition. The method is applied to the detonation models based on both the standard one-step Arrhenius kinetics and two-step exothermic-endothermic reaction kinetics. Stability spectra for all cases are computed and analyzed. The new approach is shown to be a viable alternative to the traditional normal-mode analysis used in detonation theory.

Linear stability analysis of detonations via numerical computation and dynamic mode decomposition

KAUST Repository

Kabanov, Dmitry

2018-03-20

We introduce a new method to investigate linear stability of gaseous detonations that is based on an accurate shock-fitting numerical integration of the linearized reactive Euler equations with a subsequent analysis of the computed solution via the dynamic mode decomposition. The method is applied to the detonation models based on both the standard one-step Arrhenius kinetics and two-step exothermic-endothermic reaction kinetics. Stability spectra for all cases are computed and analyzed. The new approach is shown to be a viable alternative to the traditional normal-mode analysis used in detonation theory.

Dynamic computed tomography for the diagnosis of microadenoma, (2)

International Nuclear Information System (INIS)

Tsuchiya, Toshiaki; Andou, Kazuo; Ito, Jusuke; Kuroki, Sumio; Yokoyama, Motoharu; Tanaka, Ryuichi.

1987-01-01

Dynamic computed tomography was used to study 19 patients with hormone-secreting microadenomas: 10 prolactin-secreting, 5 growth-hormone-secreting, and 4 adrenocorticotropic-hormone-secreting. A distorted and displaced tuft indicates a mass effect mainly on the opposite side. A mid-situated tuft with a disproportionately small size compared with the size of the anterior lobe indicates a mass effect mainly in the midportion. An area into which a high density at the tuft definitely spreads indicates a normal anterior lobe; an area in which less increase in the density than in the former area is observed indicates an abnormal mass. In the time-density curve, the former area represents the vascular pattern or the hypervascular extravasation pattern, while the latter area represents the extravasation of the contrast material in a hypovascular tissue. Only eight microadenomas appeared as a less enhanced mass. The rest of the cases exhibited adenomas isodense to the normal pituitary gland. A dynamic CT scan was particularly useful in the diagnosis of isodense adenomas. In these isodense adenomas, the dynamic CT scan facilitated the identification of an adenoma as a relatively less enhanced area than the normal gland. The extent of a normal pituitary gland could also be identified by means of dynamic CT. In three of the 11 isodense microadenomas, the conventional diagnostic criteria, such as infundibulum displacement, abnormal height and upward convexity of a pituitary-microadenoma complex, and changes in the sellar floor, were not encountered. A dynamic CT scan, however, enabled us to diagnose the localization of microadenomas in two of these three cases. In 18 of the 19 microadenomas, dynamic CT findings as to the localization of a microadenoma and the normal pituitary gland correlated well with the surgical findings. (J.P.N.)

Improving coal flotation recovery using computational fluid dynamics

Energy Technology Data Exchange (ETDEWEB)

Peter Koh [CSIRO Minerals (Australia)

2009-06-15

This work involves using the latest advances in computational fluid dynamics (CFD) to increase understanding of the hydrodynamics in coal flotation and to identify any opportunities to improve design and operation of both the Microcel column and Jameson cell. The CSIRO CFD model incorporates micro-processes from cell hydrodynamics that affect particle-bubble attachments and detachments. CFD simulation results include the liquid velocities, turbulent dissipation rates, gas hold-up, particle-bubble attachment rates and detachment rates. This work has demonstrated that CFD modelling is a cost effective means of developing an understanding of particle-bubble attachments and detachments, and can be used to identify and test potential cell or process modifications.

Fluid dynamic computations of the flue-gas channel in an evaporative gas turbine

Energy Technology Data Exchange (ETDEWEB)

Engdar, Ulf

1999-12-01

A new pilot power plant, based on an advanced thermodynamic cycle, called Evaporative Gas Turbine (EvGT), has been erected at the department for Heat- and Power Engineering, Lund University. The pilot plant is a part of the Evaporative Gas Turbine project, a cooperation between universities and industry in Sweden. The fluid dynamics layout of the plant is not optimized and hence no pressure drop reduction modifications have been made on the plant. A pressure drop will decrease the efficiency of the plant. Temperature measurements have shown that there maybe is a temperature stratification of the flow on the flue-gas side downstream the recuperator. A temperature stratification will influence the measurements and heat exchangers. The objective of this thesis is to investigate pressure drops and temperature stratification in the flue-gas channel between the recuperator and the economizer at the present pilot plant. Further, suggest modifications that can reduce pressure drops and/or a temperature stratification of the flow. The way of dealing with these problems was to utilize computational fluid dynamics (CFD), which makes it possible to compute the flue-gas channel in detail. The CFD-computations were conducted with a commercial computer program, called Star-CD. The pressure drop was calculated as the sum of the static- and the dynamic- pressure drop. No information about the shape of the temperature stratification was available to investigate whether a stratification will sustain or vanish. Therefore, two different temperature profiles was applied at the outlet of the recuperator. To compare modifications with the present plant, concerning the temperature stratification, a temperature rms-value was utilized as a measure of the deviation from a flow with constant temperature over a cross-section. The computations show that the pressure drop in the flue-gas channel is small compared to the pressure drop over the recuperator. Therefore, no pressure drop reducing

LION: A dynamic computer model for the low-latitude ionosphere

Directory of Open Access Journals (Sweden)

J. A. Bittencourt

2007-11-01

Full Text Available A realistic fully time-dependent computer model, denominated LION (Low-latitude Ionospheric model, that simulates the dynamic behavior of the low-latitude ionosphere is presented. The time evolution and spatial distribution of the ionospheric particle densities and velocities are computed by numerically solving the time-dependent, coupled, nonlinear system of continuity and momentum equations for the ions O⁺, O₂⁺, NO⁺, N₂⁺ and N⁺, taking into account photoionization of the atmospheric species by the solar extreme ultraviolet radiation, chemical and ionic production and loss reactions, and plasma transport processes, including the ionospheric effects of thermospheric neutral winds, plasma diffusion and electromagnetic E×B plasma drifts. The Earth's magnetic field is represented by a tilted centered magnetic dipole. This set of coupled nonlinear equations is solved along a given magnetic field line in a Lagrangian frame of reference moving vertically, in the magnetic meridian plane, with the electromagnetic E×B plasma drift velocity. The spatial and time distribution of the thermospheric neutral wind velocities and the pattern of the electromagnetic drifts are taken as known quantities, given through specified analytical or empirical models. The model simulation results are presented in the form of computer-generated color maps and reproduce the typical ionization distribution and time evolution normally observed in the low-latitude ionosphere, including details of the equatorial Appleton anomaly dynamics. The specific effects on the ionosphere due to changes in the thermospheric neutral winds and the electromagnetic plasma drifts can be investigated using different wind and drift models, including the important longitudinal effects associated with magnetic declination dependence and latitudinal separation between geographic and

LION: A dynamic computer model for the low-latitude ionosphere

Directory of Open Access Journals (Sweden)

J. A. Bittencourt

2007-11-01

Full Text Available A realistic fully time-dependent computer model, denominated LION (Low-latitude Ionospheric model, that simulates the dynamic behavior of the low-latitude ionosphere is presented. The time evolution and spatial distribution of the ionospheric particle densities and velocities are computed by numerically solving the time-dependent, coupled, nonlinear system of continuity and momentum equations for the ions O+, O2+, NO+, N2+ and N+, taking into account photoionization of the atmospheric species by the solar extreme ultraviolet radiation, chemical and ionic production and loss reactions, and plasma transport processes, including the ionospheric effects of thermospheric neutral winds, plasma diffusion and electromagnetic E×B plasma drifts. The Earth's magnetic field is represented by a tilted centered magnetic dipole. This set of coupled nonlinear equations is solved along a given magnetic field line in a Lagrangian frame of reference moving vertically, in the magnetic meridian plane, with the electromagnetic E×B plasma drift velocity. The spatial and time distribution of the thermospheric neutral wind velocities and the pattern of the electromagnetic drifts are taken as known quantities, given through specified analytical or empirical models. The model simulation results are presented in the form of computer-generated color maps and reproduce the typical ionization distribution and time evolution normally observed in the low-latitude ionosphere, including details of the equatorial Appleton anomaly dynamics. The specific effects on the ionosphere due to changes in the thermospheric neutral winds and the electromagnetic plasma drifts can be investigated using different wind and drift models, including the important longitudinal effects associated with magnetic declination dependence and latitudinal separation between geographic and geomagnetic equators. The model runs in a normal personal computer (PC and generates color maps illustrating the

Comprehensive validation of computational fluid dynamics simulationsof in-vivo blood flow in patient-specific cerebral aneurysms

NARCIS (Netherlands)

Sun, Q.; Groth, A.; Aach, T.

2012-01-01

Purpose: Recently, image-based computational fluid dynamic (CFD) simulations have been proposed to investigate the local hemodynamics inside human cerebral aneurysms. It is suggested that the knowledge ofthe computed three-dimensional flow fields can be used to assist clinical risk assessment and

An Innovative Improvement of Engineering Learning System Using Computational Fluid Dynamics Concept

Science.gov (United States)

Hung, T. C.; Wang, S. K.; Tai, S. W.; Hung, C. T.

2007-01-01

An innovative concept of an electronic learning system has been established in an attempt to achieve a technology that provides engineering students with an instructive and affordable framework for learning engineering-related courses. This system utilizes an existing Computational Fluid Dynamics (CFD) package, Active Server Pages programming,…

Decoding the Divergent Subcellular Location of Two Highly Similar Paralogous LEA Proteins

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Marie-Hélène Avelange-Macherel

2018-05-01

Full Text Available Many mitochondrial proteins are synthesized as precursors in the cytosol with an N-terminal mitochondrial targeting sequence (MTS which is cleaved off upon import. Although much is known about import mechanisms and MTS structural features, the variability of MTS still hampers robust sub-cellular software predictions. Here, we took advantage of two paralogous late embryogenesis abundant proteins (LEA from Arabidopsis with different subcellular locations to investigate structural determinants of mitochondrial import and gain insight into the evolution of the LEA genes. LEA38 and LEA2 are short proteins of the LEA_3 family, which are very similar along their whole sequence, but LEA38 is targeted to mitochondria while LEA2 is cytosolic. Differences in the N-terminal protein sequences were used to generate a series of mutated LEA2 which were expressed as GFP-fusion proteins in leaf protoplasts. By combining three types of mutation (substitution, charge inversion, and segment replacement, we were able to redirect the mutated LEA2 to mitochondria. Analysis of the effect of the mutations and determination of the LEA38 MTS cleavage site highlighted important structural features within and beyond the MTS. Overall, these results provide an explanation for the likely loss of mitochondrial location after duplication of the ancestral gene.

Computational methods for molecular imaging

CERN Document Server

Shi, Kuangyu; Li, Shuo

2015-01-01

This volume contains original submissions on the development and application of molecular imaging computing. The editors invited authors to submit high-quality contributions on a wide range of topics including, but not limited to: • Image Synthesis & Reconstruction of Emission Tomography (PET, SPECT) and other Molecular Imaging Modalities • Molecular Imaging Enhancement • Data Analysis of Clinical & Pre-clinical Molecular Imaging • Multi-Modal Image Processing (PET/CT, PET/MR, SPECT/CT, etc.) • Machine Learning and Data Mining in Molecular Imaging. Molecular imaging is an evolving clinical and research discipline enabling the visualization, characterization and quantification of biological processes taking place at the cellular and subcellular levels within intact living subjects. Computational methods play an important role in the development of molecular imaging, from image synthesis to data analysis and from clinical diagnosis to therapy individualization. This work will bring readers fro...

Computational Analysis of Static and Dynamic Behaviour of Magnetic Suspensions and Magnetic Bearings

Science.gov (United States)

Britcher, Colin P. (Editor); Groom, Nelson J.

1996-01-01

Static modelling of magnetic bearings is often carried out using magnetic circuit theory. This theory cannot easily include nonlinear effects such as magnetic saturation or the fringing of flux in air-gaps. Modern computational tools are able to accurately model complex magnetic bearing geometries, provided some care is exercised. In magnetic suspension applications, the magnetic fields are highly three-dimensional and require computational tools for the solution of most problems of interest. The dynamics of a magnetic bearing or magnetic suspension system can be strongly affected by eddy currents. Eddy currents are present whenever a time-varying magnetic flux penetrates a conducting medium. The direction of flow of the eddy current is such as to reduce the rate-of-change of flux. Analytic solutions for eddy currents are available for some simplified geometries, but complex geometries must be solved by computation. It is only in recent years that such computations have been considered truly practical. At NASA Langley Research Center, state-of-the-art finite-element computer codes, 'OPERA', 'TOSCA' and 'ELEKTRA' have recently been installed and applied to the magnetostatic and eddy current problems. This paper reviews results of theoretical analyses which suggest general forms of mathematical models for eddy currents, together with computational results. A simplified circuit-based eddy current model proposed appears to predict the observed trends in the case of large eddy current circuits in conducting non-magnetic material. A much more difficult case is seen to be that of eddy currents in magnetic material, or in non-magnetic material at higher frequencies, due to the lower skin depths. Even here, the dissipative behavior has been shown to yield at least somewhat to linear modelling. Magnetostatic and eddy current computations have been carried out relating to the Annular Suspension and Pointing System, a prototype for a space payload pointing and vibration

Computational fluid dynamics principles and applications

CERN Document Server

Blazek, J

2005-01-01

Computational Fluid Dynamics (CFD) is an important design tool in engineering and also a substantial research tool in various physical sciences as well as in biology. The objective of this book is to provide university students with a solid foundation for understanding the numerical methods employed in today's CFD and to familiarise them with modern CFD codes by hands-on experience. It is also intended for engineers and scientists starting to work in the field of CFD or for those who apply CFD codes. Due to the detailed index, the text can serve as a reference handbook too. Each chapter includes an extensive bibliography, which provides an excellent basis for further studies. The accompanying companion website contains the sources of 1-D and 2-D Euler and Navier-Stokes flow solvers (structured and unstructured) as well as of grid generators. Provided are also tools for Von Neumann stability analysis of 1-D model equations. Finally, the companion website includes the source code of a dedicated visualisation so...

MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS

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Paolo Ruggerone

2013-02-01

Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

Directory of Open Access Journals (Sweden)

Paolo Ruggerone

2013-02-01

Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

Specialized computer architectures for computational aerodynamics

Science.gov (United States)

Stevenson, D. K.

1978-01-01

In recent years, computational fluid dynamics has made significant progress in modelling aerodynamic phenomena. Currently, one of the major barriers to future development lies in the compute-intensive nature of the numerical formulations and the relative high cost of performing these computations on commercially available general purpose computers, a cost high with respect to dollar expenditure and/or elapsed time. Today's computing technology will support a program designed to create specialized computing facilities to be dedicated to the important problems of computational aerodynamics. One of the still unresolved questions is the organization of the computing components in such a facility. The characteristics of fluid dynamic problems which will have significant impact on the choice of computer architecture for a specialized facility are reviewed.

FPGA-based distributed computing microarchitecture for complex physical dynamics investigation.

Science.gov (United States)

Borgese, Gianluca; Pace, Calogero; Pantano, Pietro; Bilotta, Eleonora

2013-09-01

In this paper, we present a distributed computing system, called DCMARK, aimed at solving partial differential equations at the basis of many investigation fields, such as solid state physics, nuclear physics, and plasma physics. This distributed architecture is based on the cellular neural network paradigm, which allows us to divide the differential equation system solving into many parallel integration operations to be executed by a custom multiprocessor system. We push the number of processors to the limit of one processor for each equation. In order to test the present idea, we choose to implement DCMARK on a single FPGA, designing the single processor in order to minimize its hardware requirements and to obtain a large number of easily interconnected processors. This approach is particularly suited to study the properties of 1-, 2- and 3-D locally interconnected dynamical systems. In order to test the computing platform, we implement a 200 cells, Korteweg-de Vries (KdV) equation solver and perform a comparison between simulations conducted on a high performance PC and on our system. Since our distributed architecture takes a constant computing time to solve the equation system, independently of the number of dynamical elements (cells) of the CNN array, it allows us to reduce the elaboration time more than other similar systems in the literature. To ensure a high level of reconfigurability, we design a compact system on programmable chip managed by a softcore processor, which controls the fast data/control communication between our system and a PC Host. An intuitively graphical user interface allows us to change the calculation parameters and plot the results.

Perspectives for the application of computer models to forest dynamics forecasting in bieszczadzki national park (Poland

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Kozak Ihor

2014-03-01

Full Text Available This paper presents the perspectives for application of computer models in forecasting the dynamics of forest development on example of Moczarne area, in Bieszczadzki National Park, based on authors’ computer models. First, the possibilities for forecasting the dynamics of forest development in a local scale, i.e. within single rectangular or circular study plot, are presented. For this purpose, a computer prognostic model FORKOM E has been applied, using both general mathematical relationships functioning within a forest ecosystem and empirical ones, characteristic for tree stands at analysed plots. Additionally, a layer of 3D visualisation of a tree stand, which is an integral part of the mentioned model, is also presented. Presented also are the possibilities for forecasting the dynamics of forest development at landscape scale, applying the theory of cellular automata. For this purpose, a prognostic computer model CELLAUT was used in which the whole analysed tree stand is understood as a set of single cells, where stages of landscape development dominating within those cells are considered as also the influence of particular cells upon their neighbours. The paper also describes the perspectives for application of self-learning neural networks in the process of supplementation and verification of some parameters of a tree stand, calculated by the above-mentioned models.

Metabolic Interplay between Peroxisomes and Other Subcellular Organelles Including Mitochondria and the Endoplasmic Reticulum

Science.gov (United States)

Wanders, Ronald J. A.; Waterham, Hans R.; Ferdinandusse, Sacha

2016-01-01

Peroxisomes are unique subcellular organelles which play an indispensable role in several key metabolic pathways which include: (1.) etherphospholipid biosynthesis; (2.) fatty acid beta-oxidation; (3.) bile acid synthesis; (4.) docosahexaenoic acid (DHA) synthesis; (5.) fatty acid alpha-oxidation; (6.) glyoxylate metabolism; (7.) amino acid degradation, and (8.) ROS/RNS metabolism. The importance of peroxisomes for human health and development is exemplified by the existence of a large number of inborn errors of peroxisome metabolism in which there is an impairment in one or more of the metabolic functions of peroxisomes. Although the clinical signs and symptoms of affected patients differ depending upon the enzyme which is deficient and the extent of the deficiency, the disorders involved are usually (very) severe diseases with neurological dysfunction and early death in many of them. With respect to the role of peroxisomes in metabolism it is clear that peroxisomes are dependent on the functional interplay with other subcellular organelles to sustain their role in metabolism. Indeed, whereas mitochondria can oxidize fatty acids all the way to CO2 and H2O, peroxisomes are only able to chain-shorten fatty acids and the end products of peroxisomal beta-oxidation need to be shuttled to mitochondria for full oxidation to CO2 and H2O. Furthermore, NADH is generated during beta-oxidation in peroxisomes and beta-oxidation can only continue if peroxisomes are equipped with a mechanism to reoxidize NADH back to NAD+, which is now known to be mediated by specific NAD(H)-redox shuttles. In this paper we describe the current state of knowledge about the functional interplay between peroxisomes and other subcellular compartments notably the mitochondria and endoplasmic reticulum for each of the metabolic pathways in which peroxisomes are involved. PMID:26858947

Teachers' Use of Computational Tools to Construct and Explore Dynamic Mathematical Models

Science.gov (United States)

Santos-Trigo, Manuel; Reyes-Rodriguez, Aaron

2011-01-01

To what extent does the use of computational tools offer teachers the possibility of constructing dynamic models to identify and explore diverse mathematical relations? What ways of reasoning or thinking about the problems emerge during the model construction process that involves the use of the tools? These research questions guided the…

The cellular and subcellular localization of zinc transporter 7 in the mouse spinal cord

Science.gov (United States)

The present work addresses the cellular and subcellular localization of the zinc transporter 7 (ZNT7, SLC30a7) protein and the distribution of zinc ions (Zn2+) in the mouse spinal cord. Our results indicated that the ZNT7 immunoreactive neurons were widely distributed in the Rexed’s laminae of the g...

INTRODUCING CAFein, A NEW COMPUTATIONAL TOOL FOR STELLAR PULSATIONS AND DYNAMIC TIDES

International Nuclear Information System (INIS)

Valsecchi, F.; Farr, W. M.; Willems, B.; Rasio, F. A.; Kalogera, V.

2013-01-01

Here we present CAFein, a new computational tool for investigating radiative dissipation of dynamic tides in close binaries and of non-adiabatic, non-radial stellar oscillations in isolated stars in the linear regime. For the latter, CAFein computes the non-adiabatic eigenfrequencies and eigenfunctions of detailed stellar models. The code is based on the so-called Riccati method, a numerical algorithm that has been successfully applied to a variety of stellar pulsators, and which does not suffer from the major drawbacks of commonly used shooting and relaxation schemes. Here we present an extension of the Riccati method to investigate dynamic tides in close binaries. We demonstrate CAFein's capabilities as a stellar pulsation code both in the adiabatic and non-adiabatic regimes, by reproducing previously published eigenfrequencies of a polytrope, and by successfully identifying the unstable modes of a stellar model in the β Cephei/SPB region of the Hertzsprung-Russell diagram. Finally, we verify CAFein's behavior in the dynamic tides regime by investigating the effects of dynamic tides on the eigenfunctions and orbital and spin evolution of massive main sequence stars in eccentric binaries, and of hot Jupiter host stars. The plethora of asteroseismic data provided by NASA's Kepler satellite, some of which include the direct detection of tidally excited stellar oscillations, make CAFein quite timely. Furthermore, the increasing number of observed short-period detached double white dwarfs (WDs) and the observed orbital decay in the tightest of such binaries open up a new possibility of investigating WD interiors through the effects of tides on their orbital evolution

A survey of computational physics introductory computational science

CERN Document Server

Landau, Rubin H; Bordeianu, Cristian C

2008-01-01

Computational physics is a rapidly growing subfield of computational science, in large part because computers can solve previously intractable problems or simulate natural processes that do not have analytic solutions. The next step beyond Landau's First Course in Scientific Computing and a follow-up to Landau and Páez's Computational Physics, this text presents a broad survey of key topics in computational physics for advanced undergraduates and beginning graduate students, including new discussions of visualization tools, wavelet analysis, molecular dynamics, and computational fluid dynamics

Using computer simulations to probe the structure and dynamics of biopolymers

International Nuclear Information System (INIS)

Levy, R.M.; Hirata, F.; Kim, K.; Zhang, P.

1987-01-01

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper the authors review recent work in their laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized: (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper the authors review a more analytical approach they developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations

Vascular dynamics aid a coupled neurovascular network learn sparse independent features: A computational model

Directory of Open Access Journals (Sweden)

Ryan Thomas Philips

2016-02-01

Full Text Available Cerebral vascular dynamics are generally thought to be controlled by neural activity in a unidirectional fashion. However, both computational modeling and experimental evidence point to the feedback effects of vascular dynamics on neural activity. Vascular feedback in the form of glucose and oxygen controls neuronal ATP, either directly or via the agency of astrocytes, which in turn modulates neural firing. Recently, a detailed model of the neuron-astrocyte-vessel system has shown how vasomotion can modulate neural firing. Similarly, arguing from known cerebrovascular physiology, an approach known as `hemoneural hypothesis' postulates functional modulation of neural activity by vascular feedback. To instantiate this perspective, we present a computational model in which a network of `vascular units' supplies energy to a neural network. The complex dynamics of the vascular network, modeled by a network of oscillators, turns neurons ON and OFF randomly. The informational consequence of such dynamics is explored in the context of an auto-encoder network. In the proposed model, each vascular unit supplies energy to a subset of hidden neurons of an autoencoder network, which constitutes its `projective field'. Neurons that receive adequate energy in a given trial have reduced threshold, and thus are prone to fire. Dynamics of the vascular network are governed by changes in the reconstruction error of the auto-encoder network, interpreted as the neuronal demand. Vascular feedback causes random inactivation of a subset of hidden neurons in every trial. We observe that, under conditions of desynchronized vascular dynamics, the output reconstruction error is low and the feature vectors learnt are sparse and independent. Our earlier modeling study highlighted the link between desynchronized vascular dynamics and efficient energy delivery in skeletal muscle. We now show that desynchronized vascular dynamics leads to efficient training in an auto

Subcellular partitioning profiles and metallothionein levels in indigenous clams Moerella iridescens from a metal-impacted coastal bay

Energy Technology Data Exchange (ETDEWEB)

Wang, Zaosheng, E-mail: zswang@iue.ac.cn [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Boulevard, Xiamen 361021 (China); State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Feng, Chenglian; Ye, Chun [State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Wang, Youshao [State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301 (China); Yan, Changzhou, E-mail: czyan@iue.ac.cn [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Boulevard, Xiamen 361021 (China); Li, Rui; Yan, Yijun; Chi, Qiaoqiao [Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Boulevard, Xiamen 361021 (China)

2016-07-15

Highlights: • Subcellular partitioning profile of metals were investigated in biomonitor organism. • Cu, Zn and Cd levels in main fraction of HSP increase along accumulation gradients. • Despite MTs as the major binding pool, detoxification of Cd and Pb was incomplete. • Induced MTs were sequentially correlated with Cu, Zn and Cd levels in HSP fraction. • Intracellular metal fates highlighted the metabolic availability within organism. - Abstract: In this study, the effect of environmental metal exposure on the accumulation and subcellular distribution of metals in the digestive gland of clams with special emphasis on metallothioneins (MTs) was investigated. Specimens of indigenous Moerella iridescens were collected from different natural habitats in Maluan Bay (China), characterized by varying levels of metal contamination. The digestive glands were excised, homogenized and six subcellular fractions were separated by differential centrifugation procedures and analyzed for their Cu, Zn, Cd and Pb contents. MTs were quantified independently by spectrophotometric measurements of thiols. Site-specific differences were observed in total metal concentrations in the tissues, correlating well with variable environmental metal concentrations and reflecting the gradient trends in metal contamination. Concentrations of the non-essential Cd and Pb were more responsive to environmental exposure gradients than were tissue concentrations of the essential metals, Cu and Zn. Subcellular partitioning profiles for Cu, Zn and Cd were relatively similar, with the heat-stable protein (HSP) fraction as the dominant metal-binding compartment, whereas for Pb this fraction was much less important. The variations in proportions and concentrations of metals in this fraction along with the metal bioaccumulation gradients suggested that the induced MTs play an important role in metal homeostasis and detoxification for M. iridescens in the metal-contaminated bay. Nevertheless

Energy Conservation Using Dynamic Voltage Frequency Scaling for Computational Cloud

Directory of Open Access Journals (Sweden)

A. Paulin Florence

2016-01-01

Full Text Available Cloud computing is a new technology which supports resource sharing on a “Pay as you go” basis around the world. It provides various services such as SaaS, IaaS, and PaaS. Computation is a part of IaaS and the entire computational requests are to be served efficiently with optimal power utilization in the cloud. Recently, various algorithms are developed to reduce power consumption and even Dynamic Voltage and Frequency Scaling (DVFS scheme is also used in this perspective. In this paper we have devised methodology which analyzes the behavior of the given cloud request and identifies the associated type of algorithm. Once the type of algorithm is identified, using their asymptotic notations, its time complexity is calculated. Using best fit strategy the appropriate host is identified and the incoming job is allocated to the victimized host. Using the measured time complexity the required clock frequency of the host is measured. According to that CPU frequency is scaled up or down using DVFS scheme, enabling energy to be saved up to 55% of total Watts consumption.

A computational fluid dynamics simulation framework for ventricular catheter design optimization.

Science.gov (United States)

Weisenberg, Sofy H; TerMaath, Stephanie C; Barbier, Charlotte N; Hill, Judith C; Killeffer, James A

2017-11-10

OBJECTIVE Cerebrospinal fluid (CSF) shunts are the primary treatment for patients suffering from hydrocephalus. While proven effective in symptom relief, these shunt systems are plagued by high failure rates and often require repeated revision surgeries to replace malfunctioning components. One of the leading causes of CSF shunt failure is obstruction of the ventricular catheter by aggregations of cells, proteins, blood clots, or fronds of choroid plexus that occlude the catheter's small inlet holes or even the full internal catheter lumen. Such obstructions can disrupt CSF diversion out of the ventricular system or impede it entirely. Previous studies have suggested that altering the catheter's fluid dynamics may help to reduce the likelihood of complete ventricular catheter failure caused by obstruction. However, systematic correlation between a ventricular catheter's design parameters and its performance, specifically its likelihood to become occluded, still remains unknown. Therefore, an automated, open-source computational fluid dynamics (CFD) simulation framework was developed for use in the medical community to determine optimized ventricular catheter designs and to rapidly explore parameter influence for a given flow objective. METHODS The computational framework was developed by coupling a 3D CFD solver and an iterative optimization algorithm and was implemented in a high-performance computing environment. The capabilities of the framework were demonstrated by computing an optimized ventricular catheter design that provides uniform flow rates through the catheter's inlet holes, a common design objective in the literature. The baseline computational model was validated using 3D nuclear imaging to provide flow velocities at the inlet holes and through the catheter. RESULTS The optimized catheter design achieved through use of the automated simulation framework improved significantly on previous attempts to reach a uniform inlet flow rate distribution using

Skeletal muscle glycogen content and particle size of distinct subcellular localizations in the recovery period after a high-level soccer match

DEFF Research Database (Denmark)

Nielsen, Joachim; Krustrup, Peter; Nybo, Lars

2012-01-01

Whole muscle glycogen levels remain low for a prolonged period following a soccer match. The present study was conducted to investigate how this relates to glycogen content and particle size in distinct subcellular localizations. Seven high-level male soccer players had a vastus lateralis muscle...... biopsy collected immediately after and 24, 48, 72 and 120 h after a competitive soccer match. Transmission electron microscopy was used to estimate the subcellular distribution of glycogen and individual particle size. During the first day of recovery, glycogen content increased by ~60% in all...

Dynamic optimization of CELSS crop photosynthetic rate by computer-assisted feedback control

Science.gov (United States)

Chun, C.; Mitchell, C. A.

1997-01-01

A procedure for dynamic optimization of net photosynthetic rate (Pn) for crop production in Controlled Ecological Life-Support Systems (CELSS) was developed using leaf lettuce as a model crop. Canopy Pn was measured in real time and fed back for environmental control. Setpoints of photosynthetic photon flux (PPF) and CO_2 concentration for each hour of the crop-growth cycle were decided by computer to reach a targeted Pn each day. Decision making was based on empirical mathematical models combined with rule sets developed from recent experimental data. Comparisons showed that dynamic control resulted in better yield per unit energy input to the growth system than did static control. With comparable productivity parameters and potential for significant energy savings, dynamic control strategies will contribute greatly to the sustainability of space-deployed CELSS.

Demonstration of arterioportal shunt by dynamic computed tomography and its diagnostic value

International Nuclear Information System (INIS)

Nakayama, Takatsune; Hiyama, Yoshiaki; Saitoh, Masayuki

1983-01-01

Sixty-one patients, 41 with hepatocellular carcinoma and 20 with liver cirrhosis, were examined by dynamic computed tomography (CT) and all but one with hepatocellular carcinoma were examined by celiac angiography. Dynamic CT disclosed arterioportal shunting in eleven cases of hepatocellular carcinima and in one of cirrhotics. All of them were confirmed by angiography except one case in which angiography could not be performed. In ten of these eleven cases arterioportal shunt was adjacent to a mass lesion on dynamic CT, suggesting tumor invasion into the portal branch. In one with hepatocellular carcinoma, the shunt was remote from the mass. In one with cirrhosis, there was no mass. In these last two cases, the shunt might have been caused by prior percutaneus needle puncture. In another case of hepatocellular carcinoma, celiac angiography but not CT demonstrated an arterioportal shunt. Thus dynamic CT was nearly as diagnostic as celiac arterigraphy for the demonstration of arterioportal shunt due to portal invasion of hepatocellular carcinoma and percutaneus needle puncture. (author)

Demonstration of arterioportal shunt by dynamic computed tomography and its diagnostic value

Energy Technology Data Exchange (ETDEWEB)

Nakayama, Takatsune; Hiyama, Yoshiaki; Saitoh, Masayuki

1983-11-01

Sixty-one patients, 41 with hepatocellular carcinoma and 20 with liver cirrhosis, were examined by dynamic computed tomography (CT) and all but one with hepatocellular carcinoma were examined by celiac angiography. Dynamic CT disclosed arterioportal shunting in eleven cases of hepatocellular carcinoma and in one of cirrhotics. All of them were confirmed by angiography except one case in which angiography could not be performed. In ten of these eleven cases arterooportal shunt was adjacent to a mass lesion on dynamic CT, suggesting tumor invasion into the portal branch. In one with hepatocellular carcinoma, the shunt was remote from the mass. In one with cirrhosis, there was no mass. In these last two cases, the shunt might have been caused by prior percutaneus needle puncture. In another case of hepatocellular carcinoma, celiac angiography but not CT demonstrated an arterioportal shunt. Thus dynamic CT was nearly as diagnostic as celiac arterigraphy for the demonstration of arterioportal shunt due to portal invasion of hepatocellular carcinoma and percutaneus needle puncture.

Tissue and subcellular localizations of 3H-cyclosporine A in mice

International Nuclear Information System (INIS)

Baeckman, L.; Brandt, I.; Appelkvist, E.-L.; Dallner, G.

1988-01-01

The tissue and subcellular localizations of 3 H-cyclosporine A after administration to mice were determined with whole-body autoradiography and scintillation counting of lipid extracts of tissues and subcellular fractions. The radioactivity was widely distributed in the body and the pattern of distribution after oral or parenteral administration was the same, except that tissue levels were generatlly lower after oral administration. Pretreatment of the animals with a diet containing cyclosporine A for 30 days before the injection of radioactive cyclosporine A did not change the pattern of distribution substantially. No significant radioactivity was found in the central nervous system, except for the choroidal plexus and the area postrema region of the brain. In pregnant mice no passage of radioactivity from the placentas to fetuses was observed after a single injection. 3 H-cyclosporine A and/or its metabolites showed a high affinity for the lympho-myeloid tissues, with a marked long-term retention in bone marrow and lymph nodes. There was massive excretion in the intestinal tract after parenteral administration, and the liver, bile, pancreas and salivary glands contained high levels of radioactivity. In the kidney radioactivity was confined to the outer zone of the outer kidney medulla. In liver homogenates no quantitatively significant binding of 3 H-cyclosporine A and/or its metabolites to cellular molecules such as proteins, DNA, phospho- or neutral lipids was found. After lipid extraction with organic solvents, almost all radioactivity was recovered in the organic phase. (author)

Synthesis, characterization, and subcellular localization studies of amino acid-substituted porphyrinic pigments

Science.gov (United States)

van Diggelen, Lisa; Khin, Hnin; Conner, Kip; Shao, Jenny; Sweezy, Margaretta; Jung, Anna H.; Isaac, Meden; Simonis, Ursula

2009-06-01

Stopping cancer in its path occurs when photosensitizers (PSs) induce apoptotic cell death after their exposure to light and the subsequent formation of reactive oxygen species. In pursuit of our hypothesis that mitochondrial localizing PSs will enhance the efficacy of the photosensitizing process in photodynamic therapy, since they provoke cell death by inducing apoptosis, we synthesized and characterized tetraphenylporphyrins (TPPs) that are substituted at the paraphenyl positions by two amino acids and two fluoro or hydroxyl groups, respectively. They were prepared according to the Lindsey-modified Adler-Longo methodology using trifluoromethanesulfonylchloride (CF3SO2Cl) as a catalyst instead of trifluoroacetic acid. The use of CF3SO2Cl yielded cleaner products in significantly higher yields. During the synthesis, not only the yields and work-up procedure of the TPPs were improved by using CF3SO2Cl as a catalyst, but also a better means of synthesizing the precursor dipyrromethanes was tested by using indium(III) chloride. Column chromatography, HPLC, and NMR spectroscopy were used to separate and characterize the di-amino acid-dihydroxy, or difluoro-substituted porphyrins and to ascertain their purity before subcellular localization studies were carried out. Studies using androgen-sensitive human prostate adenocarcinoma cells LNCaP revealed that certain amino acid substituted porphyrins that are positively charged in the slightly acidic medium of cancer cells are very useful in shedding light on the targets of TPPs in subcellular organelles of cancer cells. Although some of these compounds have properties of promising photosensitizers by revealing increased water solubility, acidic properties, and innate ability to provoke cell death by apoptosis, the cell killing efficacy of these TPPs is low. This correlates with their subcellular localization. The di-amino acid, di-hydroxy substituted TPPs localize mainly to the lysosomes, whereas the di

Dynamic single photon emission computed tomography-basic principles and cardiac applications

Energy Technology Data Exchange (ETDEWEB)

Gullberg, Grant T; Reutter, Bryan W; Maltz, Jonathan S; Budinger, Thomas F [E O Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Sitek, Arkadiusz, E-mail: gtgullberg@lbl.go [Brigham and Women' s Hospital and Harvard Medical School, Boston, MA (United States)

2010-10-21

The very nature of nuclear medicine, the visual representation of injected radiopharmaceuticals, implies imaging of dynamic processes such as the uptake and wash-out of radiotracers from body organs. For years, nuclear medicine has been touted as the modality of choice for evaluating function in health and disease. This evaluation is greatly enhanced using single photon emission computed tomography (SPECT), which permits three-dimensional (3D) visualization of tracer distributions in the body. However, to fully realize the potential of the technique requires the imaging of in vivo dynamic processes of flow and metabolism. Tissue motion and deformation must also be addressed. Absolute quantification of these dynamic processes in the body has the potential to improve diagnosis. This paper presents a review of advancements toward the realization of the potential of dynamic SPECT imaging and a brief history of the development of the instrumentation. A major portion of the paper is devoted to the review of special data processing methods that have been developed for extracting kinetics from dynamic cardiac SPECT data acquired using rotating detector heads that move as radiopharmaceuticals exchange between biological compartments. Recent developments in multi-resolution spatiotemporal methods enable one to estimate kinetic parameters of compartment models of dynamic processes using data acquired from a single camera head with slow gantry rotation. The estimation of kinetic parameters directly from projection measurements improves bias and variance over the conventional method of first reconstructing 3D dynamic images, generating time-activity curves from selected regions of interest and then estimating the kinetic parameters from the generated time-activity curves. Although the potential applications of SPECT for imaging dynamic processes have not been fully realized in the clinic, it is hoped that this review illuminates the potential of SPECT for dynamic imaging

Dynamic single photon emission computed tomography-basic principles and cardiac applications

International Nuclear Information System (INIS)

Gullberg, Grant T; Reutter, Bryan W; Maltz, Jonathan S; Budinger, Thomas F; Sitek, Arkadiusz

2010-01-01