Predictive modelling of complex agronomic and biological systems.

Science.gov (United States)

Keurentjes, Joost J B; Molenaar, Jaap; Zwaan, Bas J

2013-09-01

Biological systems are tremendously complex in their functioning and regulation. Studying the multifaceted behaviour and describing the performance of such complexity has challenged the scientific community for years. The reduction of real-world intricacy into simple descriptive models has therefore convinced many researchers of the usefulness of introducing mathematics into biological sciences. Predictive modelling takes such an approach another step further in that it takes advantage of existing knowledge to project the performance of a system in alternating scenarios. The ever growing amounts of available data generated by assessing biological systems at increasingly higher detail provide unique opportunities for future modelling and experiment design. Here we aim to provide an overview of the progress made in modelling over time and the currently prevalent approaches for iterative modelling cycles in modern biology. We will further argue for the importance of versatility in modelling approaches, including parameter estimation, model reduction and network reconstruction. Finally, we will discuss the difficulties in overcoming the mathematical interpretation of in vivo complexity and address some of the future challenges lying ahead. © 2013 John Wiley & Sons Ltd.

Quantifying biologically and physically induced flow and tracer dynamics in permeable sediments

Directory of Open Access Journals (Sweden)

F. J. R. Meysman

2007-08-01

Full Text Available Insight in the biogeochemistry and ecology of sandy sediments crucially depends on a quantitative description of pore water flow and the associated transport of various solutes and particles. We show that widely different problems can be modelled by the same flow and tracer equations. The principal difference between model applications concerns the geometry of the sediment-water interface and the pressure conditions that are specified along this boundary. We illustrate this commonality with four different case studies. These include biologically and physically induced pore water flows, as well as simplified laboratory set-ups versus more complex field-like conditions: [1] lugworm bio-irrigation in laboratory set-up, [2] interaction of bio-irrigation and groundwater seepage on a tidal flat, [3] pore water flow induced by rotational stirring in benthic chambers, and [4] pore water flow induced by unidirectional flow over a ripple sequence. The same two example simulations are performed in all four cases: (a the time-dependent spreading of an inert tracer in the pore water, and (b the computation of the steady-state distribution of oxygen in the sediment. Overall, our model comparison indicates that model development for sandy sediments is promising, but within an early stage. Clear challenges remain in terms of model development, model validation, and model implementation.

Network Analyses in Systems Biology: New Strategies for Dealing with Biological Complexity

DEFF Research Database (Denmark)

Green, Sara; Serban, Maria; Scholl, Raphael

2018-01-01

of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological...... strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties...

Modeling two-phase flow in three-dimensional complex flow-fields of proton exchange membrane fuel cells

Science.gov (United States)

Kim, Jinyong; Luo, Gang; Wang, Chao-Yang

2017-10-01

3D fine-mesh flow-fields recently developed by Toyota Mirai improved water management and mass transport in proton exchange membrane (PEM) fuel cell stacks, suggesting their potential value for robust and high-power PEM fuel cell stack performance. In such complex flow-fields, Forchheimer's inertial effect is dominant at high current density. In this work, a two-phase flow model of 3D complex flow-fields of PEMFCs is developed by accounting for Forchheimer's inertial effect, for the first time, to elucidate the underlying mechanism of liquid water behavior and mass transport inside 3D complex flow-fields and their adjacent gas diffusion layers (GDL). It is found that Forchheimer's inertial effect enhances liquid water removal from flow-fields and adds additional flow resistance around baffles, which improves interfacial liquid water and mass transport. As a result, substantial improvements in high current density cell performance and operational stability are expected in PEMFCs with 3D complex flow-fields, compared to PEMFCs with conventional flow-fields. Higher current density operation required to further reduce PEMFC stack cost per kW in the future will necessitate optimizing complex flow-field designs using the present model, in order to efficiently remove a large amount of product water and hence minimize the mass transport voltage loss.

Complex biological and bio-inspired systems

Energy Technology Data Exchange (ETDEWEB)

Ecke, Robert E [Los Alamos National Laboratory

2009-01-01

The understanding and characterization ofthe fundamental processes of the function of biological systems underpins many of the important challenges facing American society, from the pathology of infectious disease and the efficacy ofvaccines, to the development of materials that mimic biological functionality and deliver exceptional and novel structural and dynamic properties. These problems are fundamentally complex, involving many interacting components and poorly understood bio-chemical kinetics. We use the basic science of statistical physics, kinetic theory, cellular bio-chemistry, soft-matter physics, and information science to develop cell level models and explore the use ofbiomimetic materials. This project seeks to determine how cell level processes, such as response to mechanical stresses, chemical constituents and related gradients, and other cell signaling mechanisms, integrate and combine to create a functioning organism. The research focuses on the basic physical processes that take place at different levels ofthe biological organism: the basic role of molecular and chemical interactions are investigated, the dynamics of the DNA-molecule and its phylogenetic role are examined and the regulatory networks of complex biochemical processes are modeled. These efforts may lead to early warning algorithms ofpathogen outbreaks, new bio-sensors to detect hazards from pathomic viruses to chemical contaminants. Other potential applications include the development of efficient bio-fuel alternative-energy processes and the exploration ofnovel materials for energy usages. Finally, we use the notion of 'coarse-graining,' which is a method for averaging over less important degrees of freedom to develop computational models to predict cell function and systems-level response to disease, chemical stress, or biological pathomic agents. This project supports Energy Security, Threat Reduction, and the missions of the DOE Office of Science through its efforts to

Inertial objects in complex flows

Science.gov (United States)

Syed, Rayhan; Ho, George; Cavas, Samuel; Bao, Jialun; Yecko, Philip

2017-11-01

Chaotic Advection and Finite Time Lyapunov Exponents both describe stirring and transport in complex and time-dependent flows, but FTLE analysis has been largely limited to either purely kinematic flow models or high Reynolds number flow field data. The neglect of dynamic effects in FTLE and Lagrangian Coherent Structure studies has stymied detailed information about the role of pressure, Coriolis effects and object inertia. We present results of laboratory and numerical experiments on time-dependent and multi-gyre Stokes flows. In the lab, a time-dependent effectively two-dimensional low Re flow is used to distinguish transport properties of passive tracer from those of small paramagnetic spheres. Companion results of FTLE calculations for inertial particles in a time-dependent multi-gyre flow are presented, illustrating the critical roles of density, Stokes number and Coriolis forces on their transport. Results of Direct Numerical Simulations of fully resolved inertial objects (spheroids) immersed in a three dimensional (ABC) flow show the role of shape and finite size in inertial transport at small finite Re. We acknowledge support of NSF DMS-1418956.

Fish and invertebrate flow-biology relationships to support the determination of ecological flows for North Carolina

Science.gov (United States)

Phelan, Jennifer; Cuffney, Thomas F.; Patterson, Lauren A.; Eddy, Michele; Dykes, Robert; Pearsall, Sam; Goudreau, Chris; Mead, Jim; Tarver, Fred

2017-01-01

A method was developed to characterize fish and invertebrate responses to flow alteration in the state of North Carolina. This method involved using 80th percentile linear quantile regressions to relate six flow metrics to the diversity of riffle-run fish and benthic Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness. All twelve flow-biology relationships were found to be significant, with both benthos and fish showing negative responses to ecodeficits and reductions in flow. The responses of benthic richness to reduced flows were consistent and generally greater than that of fish diversity. However, the riffle-run fish guild showed the greatest reductions in diversity in response to summer ecodeficits. The directional consistency and differential seasonal sensitivities of fish and invertebrates to reductions in flow highlight the need to consider seasonality when managing flows. In addition, all relationships were linear, and therefore do not provide clear thresholds to support ecological flow determinations and flow prescriptions to prevent the degradation of fish and invertebrate communities in North Carolina rivers and streams. A method of setting ecological flows based on the magnitude of change in biological condition that is acceptable to society is explored.

Complex blood flow quantification using real-time in vivo vector flow ultrasound

DEFF Research Database (Denmark)

Pedersen, Mads Møller; Pihl, Michael Johannes; Per, Haugaard

A new method to define and quantify complex blood flow is presented. The standard deviations of real-time in vivo vector flow angle estimates are used. Using vector flow ultrasound imaging both carotid bifurcations of two healthy volunteers were scanned. Scanning was performed with a 7.6 MHz linear...... transducer (8670, B-K Medical, Denmark) and a commercial vector flow ultrasound scanner (ProFocus 2202, B-K Medical). Eight video sequences of one cardiac cycle were obtained. In every frame boxes were placed to define the common carotid artery(box1) and the carotid bulb(box2). The standard deviation...... for the vector angle estimates was calculated for each box in every frame. For comparison three ultrasound experts evaluated the presence of complex flow in every box. The trial was blinded. For every sequence the mean standard deviation of the vector angle estimates were calculated for box1 {39...

Synthesis, characterization, and biological activity of a new palladium(II) complex with deoxyalliin

Energy Technology Data Exchange (ETDEWEB)

Corbi, P.P.; Massabni, A.C. [Inst. de Quimica - UNESP, Dept., Dept. de Quimica Geral e Inoganica, Araraquara (Brazil)]. E-mail: pedrocorbi@yahoo.com; Moreira, A.G. [Inst. de Quimica - UNESP, Dept. de Quimica Geral e Inoganica, Araraquara (Brazil); Faculdade de Medicina de Ribeirao Preto - USP, Dept. de Bioquimica e Imunologia, Ribeirao Preto (Brazil); Medrano, F.J. [Laboratorio Nacional de Luz Sincrotron - LNLS, Campinas (Brazil); Jasiulionis, M.G. [Escola Paulista de Medicina - UNIFESP, Dept. de Micro-Imuno-Parasitologia, Sao Paulo (Brazil); Costa-Neto, C.M. [Faculdade de Medicina de Ribeirao Preto - USP, Dept. de Bioquimica e Imunologia, Ribeirao Preto (Brazil)

2005-02-15

Synthesis, characterization, and biological activity of a new water-soluble Pd(II)-deoxyalliin (S-allyl-L-cysteine) complex are described in this article. Elemental and thermal analysis for the complex are consistent with the formula [Pd(C{sub 6}H{sub 10}NO{sub 2}S){sub 2}]. {sup 13}C NMR, {sup 1}H NMR, and IR spectroscopy show coordination of the ligand to Pd(II) through S and N atoms in a square planar geometry. Final residue of the thermal treatment was identified as a mixture of PdO and metallic Pd. Antiproliferative assays using aqueous solutions of the complex against HeLa and TM5 tumor cells showed a pronounced activity of the complex even at low concentrations. After incubation for 24 h, the complex induced cytotoxic effect over HeLa cells when used at concentrations higher than 0.40 mmol/L. At lower concentrations, the complex was nontoxic, indicating its action is probably due to cell cycle arrest, rather than cell death. In agreement with these results, the flow cytometric analysis indicated that after incubation for 24 h at low concentrations of the complex cells are arrested in G0/G1. (author)

Some applications of magnetic resonance imaging in fluid mechanics: Complex flows and complex fluids

NARCIS (Netherlands)

Bonn, Daniel; Rodts, Stephane; Groenink, Maarten; Rafai, Salima; Shahidzadeh-Bonn, Noushine; Coussot, Philippe

2008-01-01

The review deals with applications of magnetic resonance imaging (MRI) techniques to study flow. We first briefly discuss the principles of flow measurement by MRI and give examples of some applications, such as multiphase flows, the MRI rheology of complex fluid flows, and blood flows in the human

Mössbauer study of some biological iron complexes

Indian Academy of Sciences (India)

Abstract. Some biological complexes containing iron are investigated experimentally at room temperature using the Mössbauer resonance. The complexes show quadrupole doublet and Kramer's degeneracy is found to exist. The electric field gradient, difference in s-electron densities and quadrupole coupling constant ...

Complex analysis with applications to flows and fields

CERN Document Server

Braga da Costa Campos, Luis Manuel

2012-01-01

Complex Analysis with Applications to Flows and Fields presents the theory of functions of a complex variable, from the complex plane to the calculus of residues to power series to conformal mapping. The book explores numerous physical and engineering applications concerning potential flows, the gravity field, electro- and magnetostatics, steady heat conduction, and other problems. It provides the mathematical results to sufficiently justify the solution of these problems, eliminating the need to consult external references.The book is conveniently divided into four parts. In each part, the ma

Finding optimal interaction interface alignments between biological complexes

KAUST Repository

Cui, Xuefeng

2015-06-13

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

Biological properties of novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles

KAUST Repository

Novak, Maria S.; Bü chel, Gabriel E.; Keppler, Bernhard K.; Jakupec, Michael A.

2016-01-01

Since the discovery that nitric oxide (NO) is a physiologically relevant molecule, there has been great interest in the use of metal nitrosyl compounds as antitumor pharmaceuticals. Particularly interesting are those complexes which can deliver NO to biological targets. Ruthenium- and osmium-based compounds offer lower toxicity compared to other metals and show different mechanisms of action as well as different spectra of activity compared to platinum-based drugs. Novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles were studied to elucidate their cytotoxicity and possible interactions with DNA. Apoptosis induction, changes of mitochondrial transmembrane potential and possible formation of reactive oxygen species were investigated as indicators of NO-mediated damage by flow cytometry. Results suggest that ruthenium- and osmium-nitrosyl complexes with the general formula (indazolium)[cis/trans-MCl4(NO)(1H-indazole)] have pronounced cytotoxic potency in cancer cell lines. Especially the more potent ruthenium complexes strongly induce apoptosis associated with depolarization of mitochondrial membranes, and elevated reactive oxygen species levels. Furthermore, a slight yet not unequivocal trend to accumulation of intracellular cyclic guanosine monophosphate attributable to NO-mediated effects was observed.

Biological properties of novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles

KAUST Repository

Novak, Maria S.

2016-03-09

Since the discovery that nitric oxide (NO) is a physiologically relevant molecule, there has been great interest in the use of metal nitrosyl compounds as antitumor pharmaceuticals. Particularly interesting are those complexes which can deliver NO to biological targets. Ruthenium- and osmium-based compounds offer lower toxicity compared to other metals and show different mechanisms of action as well as different spectra of activity compared to platinum-based drugs. Novel ruthenium- and osmium-nitrosyl complexes with azole heterocycles were studied to elucidate their cytotoxicity and possible interactions with DNA. Apoptosis induction, changes of mitochondrial transmembrane potential and possible formation of reactive oxygen species were investigated as indicators of NO-mediated damage by flow cytometry. Results suggest that ruthenium- and osmium-nitrosyl complexes with the general formula (indazolium)[cis/trans-MCl4(NO)(1H-indazole)] have pronounced cytotoxic potency in cancer cell lines. Especially the more potent ruthenium complexes strongly induce apoptosis associated with depolarization of mitochondrial membranes, and elevated reactive oxygen species levels. Furthermore, a slight yet not unequivocal trend to accumulation of intracellular cyclic guanosine monophosphate attributable to NO-mediated effects was observed.

Numerical simulations and mathematical models of flows in complex geometries

DEFF Research Database (Denmark)

Hernandez Garcia, Anier

The research work of the present thesis was mainly aimed at exploiting one of the strengths of the Lattice Boltzmann methods, namely, the ability to handle complicated geometries to accurately simulate flows in complex geometries. In this thesis, we perform a very detailed theoretical analysis...... and through the Chapman-Enskog multi-scale expansion technique the dependence of the kinetic viscosity on each scheme is investigated. Seeking for optimal numerical schemes to eciently simulate a wide range of complex flows a variant of the finite element, off-lattice Boltzmann method [5], which uses...... the characteristic based integration is also implemented. Using the latter scheme, numerical simulations are conducted in flows of different complexities: flow in a (real) porous network and turbulent flows in ducts with wall irregularities. From the simulations of flows in porous media driven by pressure gradients...

Complex fluids in biological systems experiment, theory, and computation

CERN Document Server

2015-01-01

This book serves as an introduction to the continuum mechanics and mathematical modeling of complex fluids in living systems. The form and function of living systems are intimately tied to the nature of surrounding fluid environments, which commonly exhibit nonlinear and history dependent responses to forces and displacements. With ever-increasing capabilities in the visualization and manipulation of biological systems, research on the fundamental phenomena, models, measurements, and analysis of complex fluids has taken a number of exciting directions. In this book, many of the world’s foremost experts explore key topics such as: Macro- and micro-rheological techniques for measuring the material properties of complex biofluids and the subtleties of data interpretation Experimental observations and rheology of complex biological materials, including mucus, cell membranes, the cytoskeleton, and blood The motility of microorganisms in complex fluids and the dynamics of active suspensions Challenges and solut...

Two problems in multiphase biological flows: Blood flow and particulate transport in microvascular network, and pseudopod-driven motility of amoeboid cells

Science.gov (United States)

Bagchi, Prosenjit

2016-11-01

In this talk, two problems in multiphase biological flows will be discussed. The first is the direct numerical simulation of whole blood and drug particulates in microvascular networks. Blood in microcirculation behaves as a dense suspension of heterogeneous cells. The erythrocytes are extremely deformable, while inactivated platelets and leukocytes are nearly rigid. A significant progress has been made in recent years in modeling blood as a dense cellular suspension. However, many of these studies considered the blood flow in simple geometry, e.g., straight tubes of uniform cross-section. In contrast, the architecture of a microvascular network is very complex with bifurcating, merging and winding vessels, posing a further challenge to numerical modeling. We have developed an immersed-boundary-based method that can consider blood cell flow in physiologically realistic and complex microvascular network. In addition to addressing many physiological issues related to network hemodynamics, this tool can be used to optimize the transport properties of drug particulates for effective organ-specific delivery. Our second problem is pseudopod-driven motility as often observed in metastatic cancer cells and other amoeboid cells. We have developed a multiscale hydrodynamic model to simulate such motility. We study the effect of cell stiffness on motility as the former has been considered as a biomarker for metastatic potential. Funded by the National Science Foundation.

Complex groundwater flow systems as traveling agent models

Directory of Open Access Journals (Sweden)

Oliver López Corona

2014-10-01

Full Text Available Analyzing field data from pumping tests, we show that as with many other natural phenomena, groundwater flow exhibits complex dynamics described by 1/f power spectrum. This result is theoretically studied within an agent perspective. Using a traveling agent model, we prove that this statistical behavior emerges when the medium is complex. Some heuristic reasoning is provided to justify both spatial and dynamic complexity, as the result of the superposition of an infinite number of stochastic processes. Even more, we show that this implies that non-Kolmogorovian probability is needed for its study, and provide a set of new partial differential equations for groundwater flow.

Mesoscale meteorological measurements characterizing complex flows

International Nuclear Information System (INIS)

Hubbe, J.M.; Allwine, K.J.

1993-09-01

Meteorological measurements are an integral and essential component of any emergency response system for addressing accidental releases from nuclear facilities. An important element of the US Department of Energy's (DOE's) Atmospheric Studies in Complex Terrain (ASCOT) program is the refinement and use of state-of-the-art meteorological instrumentation. ASCOT is currently making use of ground-based remote wind sensing instruments such as doppler acoustic sounders (sodars). These instruments are capable of continuously and reliably measuring winds up to several hundred meters above the ground, unattended. Two sodars are currently measuring the winds, as part of ASCOT's Front Range Study, in the vicinity of DOE's Rocky Flats Plant (RFP) near Boulder, Colorado. A brief description of ASCOT's ongoing Front Range Study is given followed by a case study analysis that demonstrates the utility of the meteorological measurement equipment and the complexity of flow phenomena that are experienced near RFP. These complex flow phenomena can significantly influence the transport of the released material and consequently need to be identified for accurate assessments of the consequences of a release

Circulating immune complexes – reviewing the biological roles in ...

African Journals Online (AJOL)

Circulating immune complexes – reviewing the biological roles in human immune function and exercise. ... studies that have investigated CIC's following exercise and proposes that a comprehensive understanding and interpretation of immune system responses to exercise should take these complexes into consideration.

Nonlinear analysis of gas-water/oil-water two-phase flow in complex networks

CERN Document Server

Gao, Zhong-Ke; Wang, Wen-Xu

2014-01-01

Understanding the dynamics of multi-phase flows has been a challenge in the fields of nonlinear dynamics and fluid mechanics. This chapter reviews our work on two-phase flow dynamics in combination with complex network theory. We systematically carried out gas-water/oil-water two-phase flow experiments for measuring the time series of flow signals which is studied in terms of the mapping from time series to complex networks. Three network mapping methods were proposed for the analysis and identification of flow patterns, i.e. Flow Pattern Complex Network (FPCN), Fluid Dynamic Complex Network (FDCN) and Fluid Structure Complex Network (FSCN). Through detecting the community structure of FPCN based on K-means clustering, distinct flow patterns can be successfully distinguished and identified. A number of FDCN’s under different flow conditions were constructed in order to reveal the dynamical characteristics of two-phase flows. The FDCNs exhibit universal power-law degree distributions. The power-law exponent ...

GenFlow: generic flow for integration, management and analysis of molecular biology data

Directory of Open Access Journals (Sweden)

Marcio Katsumi Oikawa

2004-01-01

Full Text Available A large number of DNA sequencing projects all over the world have yielded a fantastic amount of data, whose analysis is, currently, a big challenge for computational biology. The limiting step in this task is the integration of large volumes of data stored in highly heterogeneous repositories of genomic and cDNA sequences, as well as gene expression results. Solving this problem requires automated analytical tools to optimize operations and efficiently generate knowledge. This paper presents an information flow model , called GenFlow, that can tackle this analytical task.

Large-Eddy Simulations of Flows in Complex Terrain

Science.gov (United States)

Kosovic, B.; Lundquist, K. A.

2011-12-01

Large-eddy simulation as a methodology for numerical simulation of turbulent flows was first developed to study turbulent flows in atmospheric by Lilly (1967). The first LES were carried by Deardorff (1970) who used these simulations to study atmospheric boundary layers. Ever since, LES has been extensively used to study canonical atmospheric boundary layers, in most cases flat plate boundary layers under the assumption of horizontal homogeneity. Carefully designed LES of canonical convective and neutrally stratified and more recently stably stratified atmospheric boundary layers have contributed significantly to development of better understanding of these flows and their parameterizations in large scale models. These simulations were often carried out using codes specifically designed and developed for large-eddy simulations of horizontally homogeneous flows with periodic lateral boundary conditions. Recent developments in multi-scale numerical simulations of atmospheric flows enable numerical weather prediction (NWP) codes such as ARPS (Chow and Street, 2009), COAMPS (Golaz et al., 2009) and Weather Research and Forecasting model, to be used nearly seamlessly across a wide range of atmospheric scales from synoptic down to turbulent scales in atmospheric boundary layers. Before we can with confidence carry out multi-scale simulations of atmospheric flows, NWP codes must be validated for accurate performance in simulating flows over complex or inhomogeneous terrain. We therefore carry out validation of WRF-LES for simulations of flows over complex terrain using data from Askervein Hill (Taylor and Teunissen, 1985, 1987) and METCRAX (Whiteman et al., 2008) field experiments. WRF's nesting capability is employed with a one-way nested inner domain that includes complex terrain representation while the coarser outer nest is used to spin up fully developed atmospheric boundary layer turbulence and thus represent accurately inflow to the inner domain. LES of a

Renal blood flow in sepsis: a complex issue

OpenAIRE

Molitoris, Bruce A

2005-01-01

The clinical complexity of sepsis and the regional variability in renal blood flow present a difficult challenge for the clinician or investigator in understanding the role and clinical importance of reduced blood flow in the pathophysiology of sepsis-induced acute renal failure. Understanding the role of regional microvasculature flow and interactions between endothelium and white blood cells in the local delivery of oxygen and substrates is of critical importance. Therefore, measuring total...

Synthesis, Physical Characterization and Biological Activity of Some Schiff Base Complexes

Directory of Open Access Journals (Sweden)

R. Rajavel

2008-01-01

Full Text Available Structural modification of organic molecule has considerable biological relevance. Further, coordination of a biomolecules to the metal ions significantly alters the effectiveness of the biomolecules. In view of the antimicrobial activity ligand [bis-(2-aminobenzaldehyde] malonoyl dihydrazone], metal complexes with Cu(II, Ni(II, Zn(II and oxovanadium(IV have been synthesized and found to be potential antimicrobial agents. An attempt is also made to correlate the biological activities with geometry of the complexes. The complexes have been characterized by elemental analysis, molar conductance, spectra and cyclicvoltammetric measurements. The structural assessment of the complexes has been carried out based on electronic, infrared and molar conductivity values.

EPR spectroscopy of complex biological iron-sulfur systems.

Science.gov (United States)

Hagen, Wilfred R

2018-02-21

From the very first discovery of biological iron-sulfur clusters with EPR, the spectroscopy has been used to study not only purified proteins but also complex systems such as respiratory complexes, membrane particles and, later, whole cells. In recent times, the emphasis of iron-sulfur biochemistry has moved from characterization of individual proteins to the systems biology of iron-sulfur biosynthesis, regulation, degradation, and implications for human health. Although this move would suggest a blossoming of System-EPR as a specific, non-invasive monitor of Fe/S (dys)homeostasis in whole cells, a review of the literature reveals limited success possibly due to technical difficulties in adherence to EPR spectroscopic and biochemical standards. In an attempt to boost application of System-EPR the required boundary conditions and their practical applications are explicitly and comprehensively formulated.

Multi-frequency complex network from time series for uncovering oil-water flow structure.

Science.gov (United States)

Gao, Zhong-Ke; Yang, Yu-Xuan; Fang, Peng-Cheng; Jin, Ning-De; Xia, Cheng-Yi; Hu, Li-Dan

2015-02-04

Uncovering complex oil-water flow structure represents a challenge in diverse scientific disciplines. This challenge stimulates us to develop a new distributed conductance sensor for measuring local flow signals at different positions and then propose a novel approach based on multi-frequency complex network to uncover the flow structures from experimental multivariate measurements. In particular, based on the Fast Fourier transform, we demonstrate how to derive multi-frequency complex network from multivariate time series. We construct complex networks at different frequencies and then detect community structures. Our results indicate that the community structures faithfully represent the structural features of oil-water flow patterns. Furthermore, we investigate the network statistic at different frequencies for each derived network and find that the frequency clustering coefficient enables to uncover the evolution of flow patterns and yield deep insights into the formation of flow structures. Current results present a first step towards a network visualization of complex flow patterns from a community structure perspective.

Modified laminar flow biological safety cabinet.

Science.gov (United States)

McGarrity, G J; Coriell, L L

1974-10-01

Tests are reported on a modified laminar flow biological safety cabinet in which the return air plenum that conducts air from the work area to the high efficiency particulate air filters is under negative pressure. Freon gas released inside the cabinet could not be detected outside by a freon gas detection method capable of detecting 10(-6) cc/s. When T3 bacteriophage was aerosolized 5 cm outside the front opening in 11 tests, no phage could be detected inside the cabinet with the motor-filter unit in operation. An average of 2.8 x 10(5) plaque-forming units (PFU)/ft(3) (ca. 0.028 m(3)) were detected with the motor-filter unit not in operation, a penetration of 0.0%. Aerosolization 5 cm inside the cabinet yielded an average of 10 PFU/ft(3) outside the cabinet with the motor-filter unit in operation and an average of 4.1 x 10(5) PFU/ft(3) with the motor-filter unit not in operation, a penetration of 0.002%. These values are the same order of effectiveness as the positive-pressure laminar flow biological safety cabinets previously tested. The advantages of the negative-pressure return plenum design include: (i) assurance that if cracks or leaks develop in the plenum it will not lead to discharge of contaminated air into the laboratory; and (ii) the price is lower due to reduced manufacturing costs.

Physics and biology

International Nuclear Information System (INIS)

Frauenfelder, H.

1988-01-01

The author points out that the coupling between physics and biology is becoming closer as time goes on. He tries to show that physical studies on biological systems not only yield insight into biology but also provide results of interest to physics. Biological systems are extremly complex system. Ideally one would like to understand the behavior of such systems in terms of the behavior of its constituent atoms. Since in small organisms this may be 10 20 atoms, it is clear these are not simple many-body systems. He reviews the basic elements of cells and then considers the broader questions of structure, complexity, and function, which must be looked at on levels from the cell to the organism. Despite the vast amount of observational material already in existence, biophysics and biological physics are only at a beginning. We can expect that physics will continue to interact strongly with biology. Actually, the connection also includes chemistry and mathematics. New tools that become available in physics will continue to be applied to biological problems. We can expect that the flow of information will not be one way; biological systems will provide new information on many old and new parts of physics, from reaction theory and transport phenomena to complexity, cooperativity, and nonlinear processes

How do precision medicine and system biology response to human body's complex adaptability?

Science.gov (United States)

Yuan, Bing

2016-12-01

In the field of life sciences, although system biology and "precision medicine" introduce some complex scientifific methods and techniques, it is still based on the "analysis-reconstruction" of reductionist theory as a whole. Adaptability of complex system increase system behaviour uncertainty as well as the difficulties of precise identifification and control. It also put systems biology research into trouble. To grasp the behaviour and characteristics of organism fundamentally, systems biology has to abandon the "analysis-reconstruction" concept. In accordance with the guidelines of complexity science, systems biology should build organism model from holistic level, just like the Chinese medicine did in dealing with human body and disease. When we study the living body from the holistic level, we will fifind the adaptability of complex system is not the obstacle that increases the diffificulty of problem solving. It is the "exceptional", "right-hand man" that helping us to deal with the complexity of life more effectively.

Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

DEFF Research Database (Denmark)

Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

2004-01-01

for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......  FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

Interaction of Air Flow in Complex Ventilation Systems

Directory of Open Access Journals (Sweden)

Zhorzh G. Levitskiy

2013-01-01

Full Text Available The article presents the results of study of interaction of air flow in complex ventilation systems. The study used Taylor and Maclaurin’s series and Lagrange formula to create the functional connections on estimation of the impact of changing aerodynamic parameters of one or several simultaneously working regulators on the air flow distribution in mines

Regularizing properties of Complex Monge-Amp\\`ere flows

OpenAIRE

Tô, Tat Dat

2016-01-01

We study the regularizing properties of complex Monge-Amp\\`ere flows on a K\\"ahler manifold $(X,\\omega)$ when the initial data are $\\omega$-psh functions with zero Lelong number at all points. We prove that the general Monge-Amp\\`ere flow has a solution which is immediately smooth. We also prove the uniqueness and stability of solution.

Simulation and Analysis of Complex Biological Processes: an Organisation Modelling Perspective

NARCIS (Netherlands)

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

2005-01-01

This paper explores how the dynamics of complex biological processes can be modelled and simulated as an organisation of multiple agents. This modelling perspective identifies organisational structure occurring in complex decentralised processes and handles complexity of the analysis of the dynamics

Exploitation of complex network topology for link prediction in biological interactomes

KAUST Repository

Alanis Lobato, Gregorio

2014-06-01

The network representation of the interactions between proteins and genes allows for a holistic perspective of the complex machinery underlying the living cell. However, the large number of interacting entities within the cell makes network construction a daunting and arduous task, prone to errors and missing information. Fortunately, the structure of biological networks is not different from that of other complex systems, such as social networks, the world-wide web or power grids, for which growth models have been proposed to better understand their structure and function. This means that we can design tools based on these models in order to exploit the topology of biological interactomes with the aim to construct more complete and reliable maps of the cell. In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable and biologically meaningful information that enriches the datasets to which we have access today.

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

Directory of Open Access Journals (Sweden)

Mi Huaiyu

2015-06-01

Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

Science.gov (United States)

Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

A biological tool to assess flow connectivity in reference temporary streams from the Mediterranean Basin

Energy Technology Data Exchange (ETDEWEB)

Cid, N., E-mail: ncid@ub.edu [Grup de Recerca “Freshwater Ecology and Management (FEM)”, Departament d' Ecologia, Universitat de Barcelona, Catalonia (Spain); Verkaik, I. [Grup de Recerca “Freshwater Ecology and Management (FEM)”, Departament d' Ecologia, Universitat de Barcelona, Catalonia (Spain); García-Roger, E.M. [Grup de Recerca “Freshwater Ecology and Management (FEM)”, Departament d' Ecologia, Universitat de Barcelona, Catalonia (Spain); Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València (Spain); Rieradevall, M.; Bonada, N. [Grup de Recerca “Freshwater Ecology and Management (FEM)”, Departament d' Ecologia, Universitat de Barcelona, Catalonia (Spain); Sánchez-Montoya, M.M. [Department of Ecology and Hydrology, Regional Campus of International Excellence “Campus Mare Nostrum”—University of Murcia (Spain); Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin (Germany); Gómez, R.; Suárez, M.L.; Vidal-Abarca, M.R. [Department of Ecology and Hydrology, Regional Campus of International Excellence “Campus Mare Nostrum”—University of Murcia (Spain); Demartini, D.; Buffagni, A.; Erba, S. [Instituto di Ricerca Sulle Acque (CNR-IRSA) (Italy); Karaouzas, I.; Skoulikidis, N. [Hellenic Center for Marine Research (HCMR) (Greece); Prat, N. [Grup de Recerca “Freshwater Ecology and Management (FEM)”, Departament d' Ecologia, Universitat de Barcelona, Catalonia (Spain)

2016-01-01

Many streams in the Mediterranean Basin have temporary flow regimes. While timing for seasonal drought is predictable, they undergo strong inter-annual variability in flow intensity. This high hydrological variability and associated ecological responses challenge the ecological status assessment of temporary streams, particularly when setting reference conditions. This study examined the effects of flow connectivity in aquatic macroinvertebrates from seven reference temporary streams across the Mediterranean Basin where hydrological variability and flow conditions are well studied. We tested for the effect of flow cessation on two streamflow indices and on community composition, and, by performing random forest and classification tree analyses we identified important biological predictors for classifying the aquatic state either as flowing or disconnected pools. Flow cessation was critical for one of the streamflow indices studied and for community composition. Macroinvertebrate families found to be important for classifying the aquatic state were Hydrophilidae, Simuliidae, Hydropsychidae, Planorbiidae, Heptageniidae and Gerridae. For biological traits, trait categories associated to feeding habits, food, locomotion and substrate relation were the most important and provided more accurate predictions compared to taxonomy. A combination of selected metrics and associated thresholds based on the most important biological predictors (i.e. Bio-AS Tool) were proposed in order to assess the aquatic state in reference temporary streams, especially in the absence of hydrological data. Although further development is needed, the tool can be of particular interest for monitoring, restoration, and conservation purposes, representing an important step towards an adequate management of temporary rivers not only in the Mediterranean Basin but also in other regions vulnerable to the effects of climate change. - Highlights: • The effect of flow connectivity on macroinvertebrate

Complexity analysis of the turbulent environmental fluid flow time series

Science.gov (United States)

Mihailović, D. T.; Nikolić-Đorić, E.; Drešković, N.; Mimić, G.

2014-02-01

We have used the Kolmogorov complexities, sample and permutation entropies to quantify the randomness degree in river flow time series of two mountain rivers in Bosnia and Herzegovina, representing the turbulent environmental fluid, for the period 1926-1990. In particular, we have examined the monthly river flow time series from two rivers (the Miljacka and the Bosnia) in the mountain part of their flow and then calculated the Kolmogorov complexity (KL) based on the Lempel-Ziv Algorithm (LZA) (lower-KLL and upper-KLU), sample entropy (SE) and permutation entropy (PE) values for each time series. The results indicate that the KLL, KLU, SE and PE values in two rivers are close to each other regardless of the amplitude differences in their monthly flow rates. We have illustrated the changes in mountain river flow complexity by experiments using (i) the data set for the Bosnia River and (ii) anticipated human activities and projected climate changes. We have explored the sensitivity of considered measures in dependence on the length of time series. In addition, we have divided the period 1926-1990 into three subintervals: (a) 1926-1945, (b) 1946-1965, (c) 1966-1990, and calculated the KLL, KLU, SE, PE values for the various time series in these subintervals. It is found that during the period 1946-1965, there is a decrease in their complexities, and corresponding changes in the SE and PE, in comparison to the period 1926-1990. This complexity loss may be primarily attributed to (i) human interventions, after the Second World War, on these two rivers because of their use for water consumption and (ii) climate change in recent times.

Flow-through biological conversion of lignocellulosic biomass

Science.gov (United States)

Herring, Christopher D.; Liu, Chaogang; Bardsley, John

2014-07-01

The present invention is directed to a process for biologically converting carbohydrates from lignocellulosic biomass comprising the steps of: suspending lignocellulosic biomass in a flow-through reactor, passing a reaction solution into the reactor, wherein the solution is absorbed into the biomass substrate and at least a portion of the solution migrates through said biomass substrate to a liquid reservoir, recirculating the reaction solution in the liquid reservoir at least once to be absorbed into and migrate through the biomass substrate again. The biological converting of the may involve hydrolyzing cellulose, hemicellulose, or a combination thereof to form oligosaccharides, monomelic sugars, or a combination thereof; fermenting oligosaccharides, monomelic sugars, or a combination thereof to produce ethanol, or a combination thereof. The process can further comprise removing the reaction solution and processing the solution to separate the ethanol produced from non-fermented solids.

Tackling complex turbulent flows with transient RANS

NARCIS (Netherlands)

Kenjeres, S.; Hanjalic, K.

2009-01-01

This article reviews some recent applications of the transient-Reynoldsaveraged Navier–Stokes (T-RANS) approach in simulating complex turbulent flows dominated by externally imposed body forces, primarily by thermal buoyancy and the Lorentz force. The T-RANS aims at numerical resolving unsteady

Visualization and simulation of complex flows in biomedical engineering

CERN Document Server

Imai, Yohsuke; Ishikawa, Takuji; Oliveira, Mónica

2014-01-01

This book focuses on the most recent advances in the application of visualization and simulation methods to understand the flow behavior of complex fluids used in biomedical engineering and other related fields. It shows the physiological flow behavior in large arteries, microcirculation, respiratory systems and in biomedical microdevices.

Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

Science.gov (United States)

Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

2017-07-05

Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

Introduction to Focus Issue: Complex network perspectives on flow systems.

Science.gov (United States)

Donner, Reik V; Hernández-García, Emilio; Ser-Giacomi, Enrico

2017-03-01

During the last few years, complex network approaches have demonstrated their great potentials as versatile tools for exploring the structural as well as dynamical properties of dynamical systems from a variety of different fields. Among others, recent successful examples include (i) functional (correlation) network approaches to infer hidden statistical interrelationships between macroscopic regions of the human brain or the Earth's climate system, (ii) Lagrangian flow networks allowing to trace dynamically relevant fluid-flow structures in atmosphere, ocean or, more general, the phase space of complex systems, and (iii) time series networks unveiling fundamental organization principles of dynamical systems. In this spirit, complex network approaches have proven useful for data-driven learning of dynamical processes (like those acting within and between sub-components of the Earth's climate system) that are hidden to other analysis techniques. This Focus Issue presents a collection of contributions addressing the description of flows and associated transport processes from the network point of view and its relationship to other approaches which deal with fluid transport and mixing and/or use complex network techniques.

From globally coupled maps to complex-systems biology

Energy Technology Data Exchange (ETDEWEB)

Kaneko, Kunihiko, E-mail: kaneko@complex.c.u-tokyo.ac.jp [Research Center for Complex Systems Biology, Graduate School of Arts and Sciences, The University of Tokyo 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

2015-09-15

Studies of globally coupled maps, introduced as a network of chaotic dynamics, are briefly reviewed with an emphasis on novel concepts therein, which are universal in high-dimensional dynamical systems. They include clustering of synchronized oscillations, hierarchical clustering, chimera of synchronization and desynchronization, partition complexity, prevalence of Milnor attractors, chaotic itinerancy, and collective chaos. The degrees of freedom necessary for high dimensionality are proposed to equal the number in which the combinatorial exceeds the exponential. Future analysis of high-dimensional dynamical systems with regard to complex-systems biology is briefly discussed.

Modelling complex draft-tube flows using near-wall turbulence closures

Energy Technology Data Exchange (ETDEWEB)

Ventikos, Y.; Sotiropoulos, F. [Georgia Institute of Technology, Atlanta, GA (United States). School of Civil and Environmental Engineering; Patel, V.C. [Univ. of Iowa, Iowa City, IA (United States). Iowa Institute of Hydraulic Research

1996-12-31

This paper presents a finite-volume method for simulating flows through complex hydroturbine draft-tube configurations using near-wall turbulence closures. The method employs the artificial-compressibility pressure-velocity coupling approach in conjunction with multigrid acceleration for fast convergence on very fine grids. Calculations are carried out for a draft tube with two downstream piers on a computational mesh consisting of 1.2x10{sup 6} nodes. Comparisons of the computed results with measurements demonstrate the ability of the method to capture most experimental trends with reasonable accuracy. Calculated three-dimensional particle traces reveal very complex flow features in the vicinity of the piers, including horse-shoe longitudinal vortices and and regions of flow reversal.

Biology and flow cytometry of proangiogenic hematopoietic progenitors cells.

Science.gov (United States)

Rose, Jonathan A; Erzurum, Serpil; Asosingh, Kewal

2015-01-01

During development, hematopoiesis and neovascularization are closely linked to each other via a common bipotent stem cell called the hemangioblast that gives rise to both hematopoietic cells and endothelial cells. In postnatal life, this functional connection between the vasculature and hematopoiesis is maintained by a subset of hematopoietic progenitor cells endowed with the capacity to differentiate into potent proangiogenic cells. These proangiogenic hematopoietic progenitors comprise a specific subset of bone marrow (BM)-derived cells that homes to sites of neovascularization and possess potent paracrine angiogenic activity. There is emerging evidence that this subpopulation of hematopoietic progenitors plays a critical role in vascular health and disease. Their angiogenic activity is distinct from putative "endothelial progenitor cells" that become structural cells of the endothelium by differentiation into endothelial cells. Proangiogenic hematopoietic progenitor cell research requires multidisciplinary expertise in flow cytometry, hematology, and vascular biology. This review provides a comprehensive overview of proangiogenic hematopoietic progenitor cell biology and flow cytometric methods to detect these cells in the peripheral blood circulation and BM. © 2014 International Society for Advancement of Cytometry.

Stochastic cycle selection in active flow networks

Science.gov (United States)

Woodhouse, Francis; Forrow, Aden; Fawcett, Joanna; Dunkel, Jorn

2016-11-01

Active biological flow networks pervade nature and span a wide range of scales, from arterial blood vessels and bronchial mucus transport in humans to bacterial flow through porous media or plasmodial shuttle streaming in slime molds. Despite their ubiquity, little is known about the self-organization principles that govern flow statistics in such non-equilibrium networks. By connecting concepts from lattice field theory, graph theory and transition rate theory, we show how topology controls dynamics in a generic model for actively driven flow on a network. Through theoretical and numerical analysis we identify symmetry-based rules to classify and predict the selection statistics of complex flow cycles from the network topology. Our conceptual framework is applicable to a broad class of biological and non-biological far-from-equilibrium networks, including actively controlled information flows, and establishes a new correspondence between active flow networks and generalized ice-type models.

Linking structural features of protein complexes and biological function.

Science.gov (United States)

Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

2015-09-01

Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. © 2015 The Protein Society.

Physics of flow in weighted complex networks

Science.gov (United States)

Wu, Zhenhua

This thesis uses concepts from statistical physics to understand the physics of flow in weighted complex networks. The traditional model for random networks is the Erdoḧs-Renyi (ER.) network, where a network of N nodes is created by connecting each of the N(N - 1)/2 pairs of nodes with a probability p. The degree distribution, which is the probability distribution of the number of links per node, is a Poisson distribution. Recent studies of the topology in many networks such as the Internet and the world-wide airport network (WAN) reveal a power law degree distribution, known as a scale-free (SF) distribution. To yield a better description of network dynamics, we study weighted networks, where each link or node is given a number. One asks how the weights affect the static and the dynamic properties of the network. In this thesis, two important dynamic problems are studied: the current flow problem, described by Kirchhoff's laws, and the maximum flow problem, which maximizes the flow between two nodes. Percolation theory is applied to these studies of the dynamics in complex networks. We find that the current flow in disordered media belongs to the same universality class as the optimal path. In a randomly weighted network, we identify the infinite incipient percolation cluster as the "superhighway", which contains most of the traffic in a network. We propose an efficient strategy to improve significantly the global transport by improving the superhighways, which comprise a small fraction of the network. We also propose a network model with correlated weights to describe weighted networks such as the WAN. Our model agrees with WAN data, and provides insight into the advantages of correlated weights in networks. Lastly, the upper critical dimension is evaluated using two different numerical methods, and the result is consistent with the theoretical prediction.

Assessment of salivary flow rate: biologic variation and measure error.

NARCIS (Netherlands)

Jongerius, P.H.; Limbeek, J. van; Rotteveel, J.J.

2004-01-01

OBJECTIVE: To investigate the applicability of the swab method in the measurement of salivary flow rate in multiple-handicap drooling children. To quantify the measurement error of the procedure and the biologic variation in the population. STUDY DESIGN: Cohort study. METHODS: In a repeated

Accuracy and Precision of Plane Wave Vector Flow Imaging for Laminar and Complex Flow In Vivo

DEFF Research Database (Denmark)

Jensen, Jonas; Traberg, Marie Sand; Villagómez Hoyos, Carlos Armando

2017-01-01

In this study, a comparison between velocity fields for a plane wave 2-D vector flow imaging (VFI) method and a computational fluid dynamics (CFD) simulation is made. VFI estimates are obtained from the scan of a flow phantom, which mimics the complex flow conditions in the carotid artery....... Furthermore, the precision of the VFI method is investigated under laminar and complex flow conditions in vivo. The carotid bifurcation of a healthy volunteer was scanned using both fast plane wave ultrasound and magnetic resonance imaging (MRI). The acquired MRI geometry of the bifurcation was used...... difference within 15 %, however, it was 23 % in the external branch. For the in vivo scan, the precision in terms of mean standard deviation (SD) of estimates aligned to the cardiac cycle was highest in the center of the common carotid artery (SD 4.7◦ for angles) and lowest in the external branch and close...

A parallel overset-curvilinear-immersed boundary framework for simulating complex 3D incompressible flows

Science.gov (United States)

Borazjani, Iman; Ge, Liang; Le, Trung; Sotiropoulos, Fotis

2013-01-01

We develop an overset-curvilinear immersed boundary (overset-CURVIB) method in a general non-inertial frame of reference to simulate a wide range of challenging biological flow problems. The method incorporates overset-curvilinear grids to efficiently handle multi-connected geometries and increase the resolution locally near immersed boundaries. Complex bodies undergoing arbitrarily large deformations may be embedded within the overset-curvilinear background grid and treated as sharp interfaces using the curvilinear immersed boundary (CURVIB) method (Ge and Sotiropoulos, Journal of Computational Physics, 2007). The incompressible flow equations are formulated in a general non-inertial frame of reference to enhance the overall versatility and efficiency of the numerical approach. Efficient search algorithms to identify areas requiring blanking, donor cells, and interpolation coefficients for constructing the boundary conditions at grid interfaces of the overset grid are developed and implemented using efficient parallel computing communication strategies to transfer information among sub-domains. The governing equations are discretized using a second-order accurate finite-volume approach and integrated in time via an efficient fractional-step method. Various strategies for ensuring globally conservative interpolation at grid interfaces suitable for incompressible flow fractional step methods are implemented and evaluated. The method is verified and validated against experimental data, and its capabilities are demonstrated by simulating the flow past multiple aquatic swimmers and the systolic flow in an anatomic left ventricle with a mechanical heart valve implanted in the aortic position. PMID:23833331

Screening the efficient biological prospects of triazole allied mixed ligand metal complexes

Science.gov (United States)

Utthra, Ponnukalai Ponya; Kumaravel, Ganesan; Raman, Natarajan

2017-12-01

Triazole appended mixed ligand complexes (1-8) of the general formula [ML (bpy/phen)2]Cl2, where M = Cu(II), Co(II), Ni(II) and Zn(II), L = triazole appended Schiff base (E)sbnd N-(4-nitrobenzylidene)-1H-1,2,4-triazol-3-amine and bpy/phen = 2,2‧-bipyridine/1,10-phenanthroline, have been synthesized. The design and synthesis of this elaborate ligand has been performed with the aim of increasing stability and conjugation of 1,2,4 triazole, whose Schiff base derivatives are known as biologically active compounds thereby exploring their DNA binding affinity and other biological applications. The compounds have been comprehensively characterized by elemental analysis, spectroscopic methods (IR, UV-Vis, EPR, 1H and 13C NMR spectroscopy), ESI mass spectrometry and magnetic susceptibility measurements. The complexes were found to exhibit octahedral geometry. The complexes 1-8 were subjected to DNA binding techniques evaluated using UV-Vis absorption, CV, CD, Fluorescence spectroscopy and hydrodynamic measurements. Complex 5 showed a Kb value of 3.9 × 105 M-1. The DNA damaging efficacy for the complexes was observed to be high compared to the ligand. The antimicrobial screening of the compounds against bacterial and fungal strains indicates that the complexes possess excellent antimicrobial activity than the ligand. The overall biological activity of the complexes with phen as a co-ligand possessed superior potential than the ligand.

High performance parallel computing of flows in complex geometries: II. Applications

International Nuclear Information System (INIS)

Gourdain, N; Gicquel, L; Staffelbach, G; Vermorel, O; Duchaine, F; Boussuge, J-F; Poinsot, T

2009-01-01

Present regulations in terms of pollutant emissions, noise and economical constraints, require new approaches and designs in the fields of energy supply and transportation. It is now well established that the next breakthrough will come from a better understanding of unsteady flow effects and by considering the entire system and not only isolated components. However, these aspects are still not well taken into account by the numerical approaches or understood whatever the design stage considered. The main challenge is essentially due to the computational requirements inferred by such complex systems if it is to be simulated by use of supercomputers. This paper shows how new challenges can be addressed by using parallel computing platforms for distinct elements of a more complex systems as encountered in aeronautical applications. Based on numerical simulations performed with modern aerodynamic and reactive flow solvers, this work underlines the interest of high-performance computing for solving flow in complex industrial configurations such as aircrafts, combustion chambers and turbomachines. Performance indicators related to parallel computing efficiency are presented, showing that establishing fair criterions is a difficult task for complex industrial applications. Examples of numerical simulations performed in industrial systems are also described with a particular interest for the computational time and the potential design improvements obtained with high-fidelity and multi-physics computing methods. These simulations use either unsteady Reynolds-averaged Navier-Stokes methods or large eddy simulation and deal with turbulent unsteady flows, such as coupled flow phenomena (thermo-acoustic instabilities, buffet, etc). Some examples of the difficulties with grid generation and data analysis are also presented when dealing with these complex industrial applications.

Micro-segmented flow applications in chemistry and biology

CERN Document Server

Cahill, Brian

2014-01-01

The book is dedicated to the method and application potential of micro segmented flow. The recent state of development of this powerful technique is presented in 12 chapters by leading researchers from different countries. In the first section, the principles of generation and manipulation of micro-fluidic segments are explained. In the second section, the micro continuous-flow synthesis of different types of nanomaterials is shown as a typical example for the use of advantages of the technique in chemistry. In the third part, the particular importance of the technique in biotechnical applications is presented demonstrating the progress for miniaturized cell-free processes, for molecular biology and DNA-based diagnostis and sequencing as well as for the development of antibiotics and the evaluation of toxic effects in medicine and environment.

A computational approach to modeling cellular-scale blood flow in complex geometry

Science.gov (United States)

Balogh, Peter; Bagchi, Prosenjit

2017-04-01

We present a computational methodology for modeling cellular-scale blood flow in arbitrary and highly complex geometry. Our approach is based on immersed-boundary methods, which allow modeling flows in arbitrary geometry while resolving the large deformation and dynamics of every blood cell with high fidelity. The present methodology seamlessly integrates different modeling components dealing with stationary rigid boundaries of complex shape, moving rigid bodies, and highly deformable interfaces governed by nonlinear elasticity. Thus it enables us to simulate 'whole' blood suspensions flowing through physiologically realistic microvascular networks that are characterized by multiple bifurcating and merging vessels, as well as geometrically complex lab-on-chip devices. The focus of the present work is on the development of a versatile numerical technique that is able to consider deformable cells and rigid bodies flowing in three-dimensional arbitrarily complex geometries over a diverse range of scenarios. After describing the methodology, a series of validation studies are presented against analytical theory, experimental data, and previous numerical results. Then, the capability of the methodology is demonstrated by simulating flows of deformable blood cells and heterogeneous cell suspensions in both physiologically realistic microvascular networks and geometrically intricate microfluidic devices. It is shown that the methodology can predict several complex microhemodynamic phenomena observed in vascular networks and microfluidic devices. The present methodology is robust and versatile, and has the potential to scale up to very large microvascular networks at organ levels.

A Constitutive Model for Flow-Induced Anisotropic Behavior of Viscoelastic Complex Fluids

International Nuclear Information System (INIS)

Zhu, H.; De Kee, D.

2008-01-01

Flow-induced structural anisotropy could result when a complex fluid system is removed from equilibrium by means of hydrodynamic forces. In this paper, a general theory is developed to model flow induced anisotropic behavior of complex viscoelastic systems, e.g. polymer solutions/melts and suspensions. The rheological properties are characterized by viscosity and relaxation time tensors. We consider a second-rank tensor as a measure of the microstructure. We consider the effect of the flow on the structural changes: i.e. the evolution of the microstructure tensor is governed by a relaxation-type differential equation. We also propose that the viscosity and the relaxation time tensors depend on the second-rank microstructure tensor. That is as the microstructure tensor changes with the applied rate of deformation, the viscosity and relaxation time tensors evolve accordingly. As an example we consider elongational flow of two complex fluids

Geometric triangular chiral hexagon crystal-like complexes organization in pathological tissues biological collision order.

Directory of Open Access Journals (Sweden)

Jairo A Díaz

Full Text Available The present study describes and documents self-assembly of geometric triangular chiral hexagon crystal like complex organizations (GTCHC in human pathological tissues. The authors have found this architectural geometric expression at macroscopic and microscopic levels mainly in cancer processes. This study is based essentially on macroscopic and histopathologic analyses of 3000 surgical specimens: 2600 inflammatory lesions and 400 malignant tumours. Geometric complexes identified photographically at macroscopic level were located in the gross surgical specimen, and these areas were carefully dissected. Samples were taken to carry out histologic analysis. Based on the hypothesis of a collision genesis mechanism and because it is difficult to carry out an appropriate methodological observation in biological systems, the authors designed a model base on other dynamic systems to obtain indirect information in which a strong white flash wave light discharge, generated by an electronic device, hits over the lines of electrical conductance structured in helicoidal pattern. In their experimental model, the authors were able to reproduce and to predict polarity, chirality, helicoid geometry, triangular and hexagonal clusters through electromagnetic sequential collisions. They determined that similar events among constituents of extracelular matrix which drive and produce piezoelectric activity are responsible for the genesis of GTCHC complexes in pathological tissues. This research suggests that molecular crystals represented by triangular chiral hexagons derived from a collision-attraction event against collagen type I fibrils emerge at microscopic and macroscopic scales presenting a lateral assembly of each side of hypertrophy helicoid fibers, that represent energy flow in cooperative hierarchically chiral electromagnetic interaction in pathological tissues and arises as a geometry of the equilibrium in perturbed biological systems. Further

Geometric triangular chiral hexagon crystal-like complexes organization in pathological tissues biological collision order.

Science.gov (United States)

Díaz, Jairo A; Jaramillo, Natalia A; Murillo, Mauricio F

2007-12-12

The present study describes and documents self-assembly of geometric triangular chiral hexagon crystal like complex organizations (GTCHC) in human pathological tissues. The authors have found this architectural geometric expression at macroscopic and microscopic levels mainly in cancer processes. This study is based essentially on macroscopic and histopathologic analyses of 3000 surgical specimens: 2600 inflammatory lesions and 400 malignant tumours. Geometric complexes identified photographically at macroscopic level were located in the gross surgical specimen, and these areas were carefully dissected. Samples were taken to carry out histologic analysis. Based on the hypothesis of a collision genesis mechanism and because it is difficult to carry out an appropriate methodological observation in biological systems, the authors designed a model base on other dynamic systems to obtain indirect information in which a strong white flash wave light discharge, generated by an electronic device, hits over the lines of electrical conductance structured in helicoidal pattern. In their experimental model, the authors were able to reproduce and to predict polarity, chirality, helicoid geometry, triangular and hexagonal clusters through electromagnetic sequential collisions. They determined that similar events among constituents of extracelular matrix which drive and produce piezoelectric activity are responsible for the genesis of GTCHC complexes in pathological tissues. This research suggests that molecular crystals represented by triangular chiral hexagons derived from a collision-attraction event against collagen type I fibrils emerge at microscopic and macroscopic scales presenting a lateral assembly of each side of hypertrophy helicoid fibers, that represent energy flow in cooperative hierarchically chiral electromagnetic interaction in pathological tissues and arises as a geometry of the equilibrium in perturbed biological systems. Further interdisciplinary studies must

A microfluidic dialysis device for complex biological mixture SERS analysis

KAUST Repository

Perozziello, Gerardo; Candeloro, Patrizio; Gentile, Francesco T.; Coluccio, Maria Laura; Tallerico, Marco; De Grazia, Antonio; Nicastri, Annalisa; Perri, Angela Mena; Parrotta, Elvira; Pardeo, Francesca; Catalano, Rossella; Cuda, Giovanni; Di Fabrizio, Enzo M.

2015-01-01

In this paper, we present a microfluidic device fabricated with a simple and inexpensive process allowing rapid filtering of peptides from a complex mixture. The polymer microfluidic device can be used for sample preparation in biological

Evolution of weighted complex bus transit networks with flow

Science.gov (United States)

Huang, Ailing; Xiong, Jie; Shen, Jinsheng; Guan, Wei

2016-02-01

Study on the intrinsic properties and evolutional mechanism of urban public transit networks (PTNs) has great significance for transit planning and control, particularly considering passengers’ dynamic behaviors. This paper presents an empirical analysis for exploring the complex properties of Beijing’s weighted bus transit network (BTN) based on passenger flow in L-space, and proposes a bi-level evolution model to simulate the development of transit routes from the view of complex network. The model is an iterative process that is driven by passengers’ travel demands and dual-controlled interest mechanism, which is composed of passengers’ spatio-temporal requirements and cost constraint of transit agencies. Also, the flow’s dynamic behaviors, including the evolutions of travel demand, sectional flow attracted by a new link and flow perturbation triggered in nearby routes, are taken into consideration in the evolutional process. We present the numerical experiment to validate the model, where the main parameters are estimated by using distribution functions that are deduced from real-world data. The results obtained have proven that our model can generate a BTN with complex properties, such as the scale-free behavior or small-world phenomenon, which shows an agreement with our empirical results. Our study’s results can be exploited to optimize the real BTN’s structure and improve the network’s robustness.

Degeneracy: a link between evolvability, robustness and complexity in biological systems

Directory of Open Access Journals (Sweden)

Whitacre James M

2010-02-01

Full Text Available Abstract A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as ecosystem services and resilience is well recognized, the broader relationship between robustness and evolution is only starting to be fully appreciated. A renewed interest in this relationship has been prompted by evidence that mutational robustness can play a positive role in the discovery of adaptive innovations (evolvability and evidence of an intimate relationship between robustness and complexity in biology. This paper offers a new perspective on the mechanics of evolution and the origins of complexity, robustness, and evolvability. Here we explore the hypothesis that degeneracy, a partial overlap in the functioning of multi-functional components, plays a central role in the evolution and robustness of complex forms. In support of this hypothesis, we present evidence that degeneracy is a fundamental source of robustness, it is intimately tied to multi-scaled complexity, and it establishes conditions that are necessary for system evolvability.

Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

Science.gov (United States)

Jalili, Mahdi

2018-03-01

I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

Lattice Boltzmann methods for complex micro-flows: applicability and limitations for practical applications

Energy Technology Data Exchange (ETDEWEB)

Suga, K, E-mail: suga@me.osakafu-u.ac.jp [Department of Mechanical Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531 (Japan)

2013-06-15

The extensive evaluation studies of the lattice Boltzmann method for micro-scale flows ({mu}-flow LBM) by the author's group are summarized. For the two-dimensional test cases, force-driven Poiseuille flows, Couette flows, a combined nanochannel flow, and flows in a nanochannel with a square- or triangular cylinder are discussed. The three-dimensional (3D) test cases are nano-mesh flows and a flow between 3D bumpy walls. The reference data for the complex test flow geometries are from the molecular dynamics simulations of the Lennard-Jones fluid by the author's group. The focused flows are mainly in the slip and a part of the transitional flow regimes at Kn < 1. The evaluated schemes of the {mu}-flow LBMs are the lattice Bhatnagar-Gross-Krook and the multiple-relaxation time LBMs with several boundary conditions and discrete velocity models. The effects of the discrete velocity models, the wall boundary conditions, the near-wall correction models of the molecular mean free path and the regularization process are discussed to confirm the applicability and the limitations of the {mu}-flow LBMs for complex flow geometries. (invited review)

Lattice Boltzmann methods for complex micro-flows: applicability and limitations for practical applications

International Nuclear Information System (INIS)

Suga, K

2013-01-01

The extensive evaluation studies of the lattice Boltzmann method for micro-scale flows (μ-flow LBM) by the author's group are summarized. For the two-dimensional test cases, force-driven Poiseuille flows, Couette flows, a combined nanochannel flow, and flows in a nanochannel with a square- or triangular cylinder are discussed. The three-dimensional (3D) test cases are nano-mesh flows and a flow between 3D bumpy walls. The reference data for the complex test flow geometries are from the molecular dynamics simulations of the Lennard-Jones fluid by the author's group. The focused flows are mainly in the slip and a part of the transitional flow regimes at Kn < 1. The evaluated schemes of the μ-flow LBMs are the lattice Bhatnagar–Gross–Krook and the multiple-relaxation time LBMs with several boundary conditions and discrete velocity models. The effects of the discrete velocity models, the wall boundary conditions, the near-wall correction models of the molecular mean free path and the regularization process are discussed to confirm the applicability and the limitations of the μ-flow LBMs for complex flow geometries. (invited review)

CFD Numerical Simulation of the Complex Turbulent Flow Field in an Axial-Flow Water Pump

Directory of Open Access Journals (Sweden)

Wan-You Li

2014-09-01

Full Text Available Further optimal design of an axial-flow water pump calls for a thorough recognition of the characteristics of the complex turbulent flow field in the pump, which is however extremely difficult to be measured using the up-to-date experimental techniques. In this study, a numerical simulation procedure based on computational fluid dynamics (CFD was elaborated in order to obtain the fully three-dimensional unsteady turbulent flow field in an axial-flow water pump. The shear stress transport (SST k-ω model was employed in the CFD calculation to study the unsteady internal flow of the axial-flow pump. Upon the numerical simulation results, the characteristics of the velocity field and pressure field inside the impeller region were discussed in detail. The established model procedure in this study may provide guidance to the numerical simulations of turbomachines during the design phase or the investigation of flow and pressure field characteristics and performance. The presented information can be of reference value in further optimal design of the axial-flow pump.

Long ligands reinforce biological adhesion under shear flow

Science.gov (United States)

Belyaev, Aleksey V.

2018-04-01

In this work, computer modeling has been used to show that longer ligands allow biological cells (e.g., blood platelets) to withstand stronger flows after their adhesion to solid walls. A mechanistic model of polymer-mediated ligand-receptor adhesion between a microparticle (cell) and a flat wall has been developed. The theoretical threshold between adherent and non-adherent regimes has been derived analytically and confirmed by simulations. These results lead to a deeper understanding of numerous biophysical processes, e.g., arterial thrombosis, and to the design of new biomimetic colloid-polymer systems.

Surface obstacles in pulsatile flow

Science.gov (United States)

Carr, Ian A.; Plesniak, Michael W.

2017-11-01

Flows past obstacles mounted on flat surfaces have been widely studied due to their ubiquity in nature and engineering. For nearly all of these studies, the freestream flow over the obstacle was steady, i.e., constant velocity, unidirectional flow. Unsteady, pulsatile flows occur frequently in biology, geophysics, biomedical engineering, etc. Our study is aimed at extending the comprehensive knowledge base that exists for steady flows to considerably more complex pulsatile flows. Characterizing the vortex and wake dynamics of flows around surface obstacles embedded in pulsatile flows can provide insights into the underlying physics in all wake and junction flows. In this study, we experimentally investigate the wake of two canonical obstacles: a cube and a circular cylinder with an aspect ratio of unity. Our previous studies of a surface-mounted hemisphere in pulsatile flow are used as a baseline for these two new, more complex geometries. Phase-averaged PIV and hot-wire anemometry are used to characterize the dynamics of coherent structures in the wake and at the windward junction of the obstacles. Complex physics occur during the deceleration phase of the pulsatile inflow. We propose a framework for understanding these physics based on self-induced vortex propagation, similar to the phenomena exhibited by vortex rings.

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology.

Science.gov (United States)

Sudhir, Putty-Reddy; Chen, Chung-Hsuan

2016-03-22

A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.

Complex network problems in physics, computer science and biology

Science.gov (United States)

Cojocaru, Radu Ionut

lattice at zero temperature and then we apply this formalism to the K-SAT problem defined in Chapter 1. The phase transition which physicists study often corresponds to a change in the computational complexity of the corresponding computer science problem. Chapter 3 presents phase transitions which are specific to the problems discussed in Chapter 1 and also known results for the K-SAT problem. We discuss the replica method and experimental evidences of replica symmetry breaking. The physics approach to hard problems is based on replica methods which are difficult to understand. In Chapter 4 we develop novel methods for studying hard problems using methods similar to the message passing techniques that were discussed in Chapter 2. Although we concentrated on the symmetric case, cavity methods show promise for generalizing our methods to the un-symmetric case. As has been highlighted by John Hopfield, several key features of biological systems are not shared by physical systems. Although living entities follow the laws of physics and chemistry, the fact that organisms adapt and reproduce introduces an essential ingredient that is missing in the physical sciences. In order to extract information from networks many algorithm have been developed. In Chapter 5 we apply polynomial algorithms like minimum spanning tree in order to study and construct gene regulatory networks from experimental data. As future work we propose the use of algorithms like min-cut/max-flow and Dijkstra for understanding key properties of these networks.

Turbulence modeling needs of commercial CFD codes: Complex flows in the aerospace and automotive industries

Science.gov (United States)

Befrui, Bizhan A.

1995-01-01

This viewgraph presentation discusses the following: STAR-CD computational features; STAR-CD turbulence models; common features of industrial complex flows; industry-specific CFD development requirements; applications and experiences of industrial complex flows, including flow in rotating disc cavities, diffusion hole film cooling, internal blade cooling, and external car aerodynamics; and conclusions on turbulence modeling needs.

Flow cytometric applications of tumor biology: prospects and pitfalls

International Nuclear Information System (INIS)

Raju, M.R.; Johnson, T.S.; Tokita, N.; Gillette, E.L.

1979-01-01

A brief review of cytometry instrumentation and its potential applications in tumor biology is presented using our recent data. Age-distribution measurements of cells from spontaneous dog tumors and cultured cells after exposure to x rays, alpha particles, or adriamycin are shown. The data show that DNA fluorescence measurements have application in the study of cell kinetics after either radiation or drug treatment. Extensive and careful experimentation is needed to utilize the sophisticated developments in flow cytometry instrumentation

Flow cytometric applications to tumour biology: prospects and pitfalls

International Nuclear Information System (INIS)

Raju, M.R.; Johnson, T.S.; Tokita, N.; Gillette, E.L.

1980-01-01

A brief review of cytometry instrumentation and its potential applications in tumour biology is presented. DNA distribution measurements of cells from spontaneous dog tumours and cultured cells after exposure to X-rays, alpha particles or adriamycin are shown. The data show that DNA fluorescence measurements have application in the study of cell kinetics after either radiation or drug treatment. Extensive and careful experimentation is needed, however, to utilize the sophisticated developments in flow cytometry instrumentation. (author)

A biological tool to assess flow connectivity in reference temporary streams from the Mediterranean Basin.

Science.gov (United States)

Cid, N; Verkaik, I; García-Roger, E M; Rieradevall, M; Bonada, N; Sánchez-Montoya, M M; Gómez, R; Suárez, M L; Vidal-Abarca, M R; Demartini, D; Buffagni, A; Erba, S; Karaouzas, I; Skoulikidis, N; Prat, N

2016-01-01

Many streams in the Mediterranean Basin have temporary flow regimes. While timing for seasonal drought is predictable, they undergo strong inter-annual variability in flow intensity. This high hydrological variability and associated ecological responses challenge the ecological status assessment of temporary streams, particularly when setting reference conditions. This study examined the effects of flow connectivity in aquatic macroinvertebrates from seven reference temporary streams across the Mediterranean Basin where hydrological variability and flow conditions are well studied. We tested for the effect of flow cessation on two streamflow indices and on community composition, and, by performing random forest and classification tree analyses we identified important biological predictors for classifying the aquatic state either as flowing or disconnected pools. Flow cessation was critical for one of the streamflow indices studied and for community composition. Macroinvertebrate families found to be important for classifying the aquatic state were Hydrophilidae, Simuliidae, Hydropsychidae, Planorbiidae, Heptageniidae and Gerridae. For biological traits, trait categories associated to feeding habits, food, locomotion and substrate relation were the most important and provided more accurate predictions compared to taxonomy. A combination of selected metrics and associated thresholds based on the most important biological predictors (i.e. Bio-AS Tool) were proposed in order to assess the aquatic state in reference temporary streams, especially in the absence of hydrological data. Although further development is needed, the tool can be of particular interest for monitoring, restoration, and conservation purposes, representing an important step towards an adequate management of temporary rivers not only in the Mediterranean Basin but also in other regions vulnerable to the effects of climate change. Copyright © 2015 Elsevier B.V. All rights reserved.

Reflecting on complexity of biological systems: Kant and beyond?

Science.gov (United States)

Van de Vijver, Gertrudis; Van Speybroeck, Linda; Vandevyvere, Windy

2003-01-01

Living organisms are currently most often seen as complex dynamical systems that develop and evolve in relation to complex environments. Reflections on the meaning of the complex dynamical nature of living systems show an overwhelming multiplicity in approaches, descriptions, definitions and methodologies. Instead of sustaining an epistemic pluralism, which often functions as a philosophical armistice in which tolerance and so-called neutrality discharge proponents of the burden to clarify the sources and conditions of agreement and disagreement, this paper aims at analysing: (i) what has been Kant's original conceptualisation of living organisms as natural purposes; (ii) how the current perspectives are to be related to Kant's viewpoint; (iii) what are the main trends in current complexity thinking. One of the basic ideas is that the attention for structure and its epistemological consequences witness to a great extent of Kant's viewpoint, and that the idea of organisational stratification today constitutes a different breeding ground within which complexity issues are raised. The various approaches of complexity in biological systems are captured in terms of two different styles, universalism and (weak and strong) constructivism, between which hybrid forms exist.

Life: An Introduction to Complex Systems Biology

CERN Document Server

Kaneko, Kunihiko

2006-01-01

What is life? Has molecular biology given us a satisfactory answer to this question? And if not, why, and how to carry on from there? This book examines life not from the reductionist point of view, but rather asks the question: what are the universal properties of living systems and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation has been deliberately kept fairly non-technical so as to address a broad spectrum of students and researchers from the natural sciences and informatics.

Exploitation of complex network topology for link prediction in biological interactomes

KAUST Repository

Alanis Lobato, Gregorio

2014-01-01

In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable

Complexity: the organizing principle at the interface of biological (dis ...

Indian Academy of Sciences (India)

RAMRAY BHAT

2017-07-05

Jul 5, 2017 ... opment of complexity theory in the context of biological systems. ... (DST), a mathematical enterprise that deals with the behaviour of ... and application of programming to trace the dynamical .... with the resultant organization being regulated by the ... more regular the pattern, the smaller the program needed.

The complexity of DNA damage: relevance to biological consequences

International Nuclear Information System (INIS)

Ward, J.F.

1994-01-01

Ionizing radiation causes both singly and multiply damaged sites in DNA when the range of radical migration is limited by the presence of hydroxyl radical scavengers (e.g. within cells). Multiply damaged sites are considered to be more biologically relevant because of the challenges they present to cellular repair mechanisms. These sites occur in the form of DNA double-strand breaks (dsb) but also as other multiple damages that can be converted to dsb during attempted repair. The presence of a dsb can lead to loss of base sequence information and/or can permit the two ends of a break to separate and rejoin with the wrong partner. (Multiply damaged sites may also be the biologically relevant type of damage caused by other agents, such as UVA, B and/or C light, and some antitumour antibiotics). The quantitative data available from radiation studies of DNA are shown to support the proposed mechanisms for the production of complex damage in cellular DNA, i.e. via scavengable and non-scavengable mechanisms. The yields of complex damages can in turn be used to support the conclusion that cellular mutations are a consequence of the presence of these damages within a gene. (Author)

An Assessment of Wind Plant Complex Flows Using Advanced Doppler Radar Measurements

Science.gov (United States)

Gunter, W. S.; Schroeder, J.; Hirth, B.; Duncan, J.; Guynes, J.

2015-12-01

As installed wind energy capacity continues to steadily increase, the need for comprehensive measurements of wind plant complex flows to further reduce the cost of wind energy has been well advertised by the industry as a whole. Such measurements serve diverse perspectives including resource assessment, turbine inflow and power curve validation, wake and wind plant layout model verification, operations and maintenance, and the development of future advanced wind plant control schemes. While various measurement devices have been matured for wind energy applications (e.g. meteorological towers, LIDAR, SODAR), this presentation will focus on the use of advanced Doppler radar systems to observe the complex wind flows within and surrounding wind plants. Advanced Doppler radars can provide the combined advantage of a large analysis footprint (tens of square kilometers) with rapid data analysis updates (a few seconds to one minute) using both single- and dual-Doppler data collection methods. This presentation demonstrates the utility of measurements collected by the Texas Tech University Ka-band (TTUKa) radars to identify complex wind flows occurring within and nearby operational wind plants, and provide reliable forecasts of wind speeds and directions at given locations (i.e. turbine or instrumented tower sites) 45+ seconds in advance. Radar-derived wind maps reveal commonly observed features such as turbine wakes and turbine-to-turbine interaction, high momentum wind speed channels between turbine wakes, turbine array edge effects, transient boundary layer flow structures (such as wind streaks, frontal boundaries, etc.), and the impact of local terrain. Operational turbine or instrumented tower data are merged with the radar analysis to link the observed complex flow features to turbine and wind plant performance.

Simulating Engineering Flows through Complex Porous Media via the Lattice Boltzmann Method

Directory of Open Access Journals (Sweden)

Vesselin Krassimirov Krastev

2018-03-01

Full Text Available In this paper, recent achievements in the application of the lattice Boltzmann method (LBM to complex fluid flows are reported. More specifically, we focus on flows through reactive porous media, such as the flow through the substrate of a selective catalytic reactor (SCR for the reduction of gaseous pollutants in the automotive field; pulsed-flow analysis through heterogeneous catalyst architectures; and transport and electro-chemical phenomena in microbial fuel cells (MFC for novel waste-to-energy applications. To the authors’ knowledge, this is the first known application of LBM modeling to the study of MFCs, which represents by itself a highly innovative and challenging research area. The results discussed here essentially confirm the capabilities of the LBM approach as a flexible and accurate computational tool for the simulation of complex multi-physics phenomena of scientific and technological interest, across physical scales.

Directed weighted network structure analysis of complex impedance measurements for characterizing oil-in-water bubbly flow.

Science.gov (United States)

Gao, Zhong-Ke; Dang, Wei-Dong; Xue, Le; Zhang, Shan-Shan

2017-03-01

Characterizing the flow structure underlying the evolution of oil-in-water bubbly flow remains a contemporary challenge of great interests and complexity. In particular, the oil droplets dispersing in a water continuum with diverse size make the study of oil-in-water bubbly flow really difficult. To study this issue, we first design a novel complex impedance sensor and systematically conduct vertical oil-water flow experiments. Based on the multivariate complex impedance measurements, we define modalities associated with the spatial transient flow structures and construct modality transition-based network for each flow condition to study the evolution of flow structures. In order to reveal the unique flow structures underlying the oil-in-water bubbly flow, we filter the inferred modality transition-based network by removing the edges with small weight and resulting isolated nodes. Then, the weighted clustering coefficient entropy and weighted average path length are employed for quantitatively assessing the original network and filtered network. The differences in network measures enable to efficiently characterize the evolution of the oil-in-water bubbly flow structures.

Comparative exploration of multidimensional flow cytometry software: a model approach evaluating T cell polyfunctional behavior.

Science.gov (United States)

Spear, Timothy T; Nishimura, Michael I; Simms, Patricia E

2017-08-01

Advancement in flow cytometry reagents and instrumentation has allowed for simultaneous analysis of large numbers of lineage/functional immune cell markers. Highly complex datasets generated by polychromatic flow cytometry require proper analytical software to answer investigators' questions. A problem among many investigators and flow cytometry Shared Resource Laboratories (SRLs), including our own, is a lack of access to a flow cytometry-knowledgeable bioinformatics team, making it difficult to learn and choose appropriate analysis tool(s). Here, we comparatively assess various multidimensional flow cytometry software packages for their ability to answer a specific biologic question and provide graphical representation output suitable for publication, as well as their ease of use and cost. We assessed polyfunctional potential of TCR-transduced T cells, serving as a model evaluation, using multidimensional flow cytometry to analyze 6 intracellular cytokines and degranulation on a per-cell basis. Analysis of 7 parameters resulted in 128 possible combinations of positivity/negativity, far too complex for basic flow cytometry software to analyze fully. Various software packages were used, analysis methods used in each described, and representative output displayed. Of the tools investigated, automated classification of cellular expression by nonlinear stochastic embedding (ACCENSE) and coupled analysis in Pestle/simplified presentation of incredibly complex evaluations (SPICE) provided the most user-friendly manipulations and readable output, evaluating effects of altered antigen-specific stimulation on T cell polyfunctionality. This detailed approach may serve as a model for other investigators/SRLs in selecting the most appropriate software to analyze complex flow cytometry datasets. Further development and awareness of available tools will help guide proper data analysis to answer difficult biologic questions arising from incredibly complex datasets. © Society

Understanding characteristics in multivariate traffic flow time series from complex network structure

Science.gov (United States)

Yan, Ying; Zhang, Shen; Tang, Jinjun; Wang, Xiaofei

2017-07-01

Discovering dynamic characteristics in traffic flow is the significant step to design effective traffic managing and controlling strategy for relieving traffic congestion in urban cities. A new method based on complex network theory is proposed to study multivariate traffic flow time series. The data were collected from loop detectors on freeway during a year. In order to construct complex network from original traffic flow, a weighted Froenius norm is adopt to estimate similarity between multivariate time series, and Principal Component Analysis is implemented to determine the weights. We discuss how to select optimal critical threshold for networks at different hour in term of cumulative probability distribution of degree. Furthermore, two statistical properties of networks: normalized network structure entropy and cumulative probability of degree, are utilized to explore hourly variation in traffic flow. The results demonstrate these two statistical quantities express similar pattern to traffic flow parameters with morning and evening peak hours. Accordingly, we detect three traffic states: trough, peak and transitional hours, according to the correlation between two aforementioned properties. The classifying results of states can actually represent hourly fluctuation in traffic flow by analyzing annual average hourly values of traffic volume, occupancy and speed in corresponding hours.

Effect of flow rate and disc area increment on the efficiency of rotating biological contactor for treating greywater

International Nuclear Information System (INIS)

Pathan, A.A.

2015-01-01

The performance of greywater treatment through RBC (Rotating Biological Contactor) is related to many factors including rotational speed of disc, surface area of the media, thickness of biological film; quality and flow rate of influent. The plastic media provides surface for biological slime. The slime is rotated alternatively into the settled wastewater and then into atmosphere to provide aerobic conditions for the microorganisms. In this study the performance of RBC is investigated at different flow rates and disk areas of media by introducing additional discs on the shaft of RBC. Initially efficiency of the RBC was observed on six flow rates at the disc area of 9.78m/sup 2/. Furthermore optimized three flow rates were used to augment the disk area. The efficiency of RBC system was improved significantly at disk area of 11.76m/sup 2/ and flow rate of 20 L/h. Under these conditions the removal of BOD5 (Biochemical Oxygen Demand) COD (Chemical Oxygen Demand) and TSS (Total Suspended Solid) was observed 83, 57 and 90% respectively. (author)

A comparison of the application of a biological and phenetic species concept in the Hebeloma crustuliniforme complex within a phylogenetic framework

DEFF Research Database (Denmark)

Aanen, Duur Kornelis; Kuyper, T.W.

2004-01-01

a major factor. Intercompatibility tests and DNA based phylogenies indicate that most biological species are very closely related and hence provide support for the claim that correspondence between a biological species concept and a phenetic species concept in the H. crustuliniforme complex is not likely...... biological species in that complex. Based on two nuclear sequences, we present a best estimate of the phylogeny of biological species within the complex. Using this phylogeny, on the basis of strict monophyly only two species can be morphologically recognised among 22 biological species. Relaxing......A method is presented to derive an operational phenetic species concept for the Hebeloma crustuliniforme complex in northwestern Europe. The complex was found to consist of at least 22 biological species (intercompatibility groups; ICGs). Almost none of these biological species could be recognised...

Kirigami artificial muscles with complex biologically inspired morphologies

International Nuclear Information System (INIS)

Sareh, Sina; Rossiter, Jonathan

2013-01-01

In this paper we present bio-inspired smart structures which exploit the actuation of flexible ionic polymer composites and the kirigami design principle. Kirigami design is used to convert planar actuators into active 3D structures capable of large out-of-plane displacement and that replicate biological mechanisms. Here we present the burstbot, a fluid control and propulsion mechanism based on the atrioventricular cuspid valve, and the vortibot, a spiral actuator based on Vorticella campanula, a ciliate protozoa. Models derived from biological counterparts are used as a platform for design optimization and actuator performance measurement. The symmetric and asymmetric fluid interactions of the burstbot are investigated and the effectiveness in fluid transport applications is demonstrated. The vortibot actuator is geometrically optimized as a camera positioner capable of 360° scanning. Experimental results for a one-turn spiral actuator show complex actuation derived from a single degree of freedom control signal. (paper)

Multivariate multiscale complex network analysis of vertical upward oil-water two-phase flow in a small diameter pipe.

Science.gov (United States)

Gao, Zhong-Ke; Yang, Yu-Xuan; Zhai, Lu-Sheng; Dang, Wei-Dong; Yu, Jia-Liang; Jin, Ning-De

2016-02-02

High water cut and low velocity vertical upward oil-water two-phase flow is a typical complex system with the features of multiscale, unstable and non-homogenous. We first measure local flow information by using distributed conductance sensor and then develop a multivariate multiscale complex network (MMCN) to reveal the dispersed oil-in-water local flow behavior. Specifically, we infer complex networks at different scales from multi-channel measurements for three typical vertical oil-in-water flow patterns. Then we characterize the generated multiscale complex networks in terms of network clustering measure. The results suggest that the clustering coefficient entropy from the MMCN not only allows indicating the oil-in-water flow pattern transition but also enables to probe the dynamical flow behavior governing the transitions of vertical oil-water two-phase flow.

Complex and biofluids: From Maxwell to nowadays

Science.gov (United States)

Misbah, Chaouqi

2009-11-01

Complex fluids are the rule in biology and in many industrial applications. Typical examples are blood, cartilage, and polymer solutions. Unlike water (as well as domestic oils, soft clear drinks, and so on), the law(s) describing the behavior of complex fluids are not yet fully established. The complexity arises from strong coupling between microscopic scales (like the motion of a red blood cell in the case of blood, or a polymer molecule for a polymer solution) and the global scale of the flow (say at the scale of a blood artery, or a channel in laboratory experiments). In this issue entitled Complex and Biofluids a large panel of experimental and theoretical problems of complex fluids is exposed. The topics range from dilute polymer solutions, food products, to biology (blood flow, cell and tissue mechanics). One of the earliest model put forward as an attempt to describe a complex fluid was suggested a long time ago by James Clerk Maxwell (in 1867). Other famous scientists, like Einstein (in 1906), and Taylor (in 1932) have made important contributions to the field, but the topic of complex fluids still continues to pose a formidable challenge to science. This field has known during the past decade an unbelievable upsurge of interest in many branches of science (physics, mechanics, chemistry, biology, medical science, mathematics, and so on). Understanding complex fluids is viewed as one of the biggest challenge of the present century. This synthesis will provide a simple introduction to the topic, summarize the main contribution of this issue, and list major open questions in this field. To cite this article: C. Misbah, C. R. Physique 10 (2009).

Large, dynamic, multi-protein complexes: a challenge for structural biology

Czech Academy of Sciences Publication Activity Database

Rozycki, B.; Bouřa, Evžen

2014-01-01

Roč. 26, č. 46 (2014), 463103/1-463103/11 ISSN 0953-8984 R&D Projects: GA MŠk LO1302 EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : protein structure * multi-protein complexes * hybrid methods of structural biology Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.346, year: 2014

Physical modelling of flow and dispersion over complex terrain

Science.gov (United States)

Cermak, J. E.

1984-09-01

Atmospheric motion and dispersion over topography characterized by irregular (or regular) hill-valley or mountain-valley distributions are strongly dependent upon three general sets of variables. These are variables that describe topographic geometry, synoptic-scale winds and surface-air temperature distributions. In addition, pollutant concentration distributions also depend upon location and physical characteristics of the pollutant source. Overall fluid-flow complexity and variability from site to site have stimulated the development and use of physical modelling for determination of flow and dispersion in many wind-engineering applications. Models with length scales as small as 1:12,000 have been placed in boundary-layer wind tunnels to study flows in which forced convection by synoptic winds is of primary significance. Flows driven primarily by forces arising from temperature differences (gravitational or free convection) have been investigated by small-scale physical models placed in an isolated space (gravitational convection chamber). Similarity criteria and facilities for both forced and gravitational-convection flow studies are discussed. Forced-convection modelling is illustrated by application to dispersion of air pollutants by unstable flow near a paper mill in the state of Maryland and by stable flow over Point Arguello, California. Gravitational-convection modelling is demonstrated by a study of drainage flow and pollutant transport from a proposed mining operation in the Rocky Mountains of Colorado. Other studies in which field data are available for comparison with model data are reviewed.

Filtration device for rapid separation of biological particles from complex matrices

Science.gov (United States)

Kim, Sangil; Naraghi-Arani, Pejman; Liou, Megan

2018-01-09

Methods and systems for filtering of biological particles are disclosed. Filtering membranes separate adjacent chambers. Through osmotic or electrokinetic processes, flow of particles is carried out through the filtering membranes. Cells, viruses and cell waste can be filtered depending on the size of the pores of the membrane. A polymer brush can be applied to a surface of the membrane to enhance filtering and prevent fouling.

Chemometric and Statistical Analyses of ToF-SIMS Spectra of Increasingly Complex Biological Samples

Energy Technology Data Exchange (ETDEWEB)

Berman, E S; Wu, L; Fortson, S L; Nelson, D O; Kulp, K S; Wu, K J

2007-10-24

Characterizing and classifying molecular variation within biological samples is critical for determining fundamental mechanisms of biological processes that will lead to new insights including improved disease understanding. Towards these ends, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to examine increasingly complex samples of biological relevance, including monosaccharide isomers, pure proteins, complex protein mixtures, and mouse embryo tissues. The complex mass spectral data sets produced were analyzed using five common statistical and chemometric multivariate analysis techniques: principal component analysis (PCA), linear discriminant analysis (LDA), partial least squares discriminant analysis (PLSDA), soft independent modeling of class analogy (SIMCA), and decision tree analysis by recursive partitioning. PCA was found to be a valuable first step in multivariate analysis, providing insight both into the relative groupings of samples and into the molecular basis for those groupings. For the monosaccharides, pure proteins and protein mixture samples, all of LDA, PLSDA, and SIMCA were found to produce excellent classification given a sufficient number of compound variables calculated. For the mouse embryo tissues, however, SIMCA did not produce as accurate a classification. The decision tree analysis was found to be the least successful for all the data sets, providing neither as accurate a classification nor chemical insight for any of the tested samples. Based on these results we conclude that as the complexity of the sample increases, so must the sophistication of the multivariate technique used to classify the samples. PCA is a preferred first step for understanding ToF-SIMS data that can be followed by either LDA or PLSDA for effective classification analysis. This study demonstrates the strength of ToF-SIMS combined with multivariate statistical and chemometric techniques to classify increasingly complex biological samples

Using Simple Manipulatives to Improve Student Comprehension of a Complex Biological Process: Protein Synthesis

Science.gov (United States)

Guzman, Karen; Bartlett, John

2012-01-01

Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article…

Preparative divergent flow IEF without carrier ampholytes for separation of complex biological samples

Czech Academy of Sciences Publication Activity Database

Šťastná, Miroslava; Šlais, Karel

2010-01-01

Roč. 31, č. 3 (2010), s. 433-439 ISSN 0173-0835 R&D Projects: GA AV ČR IAAX00310701 Institutional research plan: CEZ:AV0Z40310501 Keywords : carrier-free divergent flow IEF * proteins * yeast lysate Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.569, year: 2010

A study of ruthenium complexes of some biologically relevant a-N ...

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences; Volume 112; Issue 3. A study of ruthenium complexes of some biologically relevant ∙ -N-heterocyclic ... Author Affiliations. P Sengupta1 S Ghosh1. Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700 032, India ...

Development of axisymmetric lattice Boltzmann flux solver for complex multiphase flows

Science.gov (United States)

Wang, Yan; Shu, Chang; Yang, Li-Ming; Yuan, Hai-Zhuan

2018-05-01

This paper presents an axisymmetric lattice Boltzmann flux solver (LBFS) for simulating axisymmetric multiphase flows. In the solver, the two-dimensional (2D) multiphase LBFS is applied to reconstruct macroscopic fluxes excluding axisymmetric effects. Source terms accounting for axisymmetric effects are introduced directly into the governing equations. As compared to conventional axisymmetric multiphase lattice Boltzmann (LB) method, the present solver has the kinetic feature for flux evaluation and avoids complex derivations of external forcing terms. In addition, the present solver also saves considerable computational efforts in comparison with three-dimensional (3D) computations. The capability of the proposed solver in simulating complex multiphase flows is demonstrated by studying single bubble rising in a circular tube. The obtained results compare well with the published data.

Oscillations and Multiple Equilibria in Microvascular Blood Flow.

Science.gov (United States)

Karst, Nathaniel J; Storey, Brian D; Geddes, John B

2015-07-01

We investigate the existence of oscillatory dynamics and multiple steady-state flow rates in a network with a simple topology and in vivo microvascular blood flow constitutive laws. Unlike many previous analytic studies, we employ the most biologically relevant models of the physical properties of whole blood. Through a combination of analytic and numeric techniques, we predict in a series of two-parameter bifurcation diagrams a range of dynamical behaviors, including multiple equilibria flow configurations, simple oscillations in volumetric flow rate, and multiple coexistent limit cycles at physically realizable parameters. We show that complexity in network topology is not necessary for complex behaviors to arise and that nonlinear rheology, in particular the plasma skimming effect, is sufficient to support oscillatory dynamics similar to those observed in vivo.

[Physico-chemical features of dinitrosyl iron complexes with natural thiol-containing ligands underlying biological activities of these complexes].

Science.gov (United States)

Vanin, A F; Borodulin, R R; Kubrina, L N; Mikoian, V D; Burbaev, D Sh

2013-01-01

Current notions and new experimental data of the authors on physico-chemical features of dinitrosyl iron complexes with natural thiol-containing ligands (glutathione or cysteine), underlying the ability of the complexes to act as NO molecule and nitrosonium ion donors, are considered. This ability determines various biological activities of dinitrosyl iron complexes--inducing long-lasting vasodilation and thereby long-lasting hypotension in human and animals, inhibiting pellet aggregation, increasing red blood cell elasticity, thereby stimulating microcirculation, and reducing necrotic zone in animals with myocardial infarction. Moreover, dinitrosyl iron complexes are capable of accelerating skin wound healing, improving the function of penile cavernous tissue, blocking apoptosis development in cell cultures. When decomposed dinitrosyl iron complexes can exert cytotoxic effect that can be used for curing infectious and carcinogenic pathologies.

Hybrid RANS/LES method for wind flow over complex terrain

DEFF Research Database (Denmark)

Bechmann, Andreas; Sørensen, Niels N.

2010-01-01

for flows at high Reynolds numbers. To reduce the computational cost of traditional LES, a hybrid method is proposed in which the near-wall eddies are modelled in a Reynolds-averaged sense. Close to walls, the flow is treated with the Reynolds-averaged Navier-Stokes (RANS) equations (unsteady RANS...... rough walls. Previous attempts of combining RANS and LES has resulted in unphysical transition regions between the two layers, but the present work improves this region by using a stochastic backscatter model. To demonstrate the ability of the proposed hybrid method, simulations are presented for wind...... the turbulent kinetic energy, whereas the new method captures the high turbulence levels well but underestimates the mean velocity. The presented results are for a relative mild configuration of complex terrain, but the proposed method can also be used for highly complex terrain where the benefits of the new...

A network-flow based valve-switching aware binding algorithm for flow-based microfluidic biochips

DEFF Research Database (Denmark)

Tseng, Kai-Han; You, Sheng-Chi; Minhass, Wajid Hassan

2013-01-01

-flow based resource binding algorithm based on breadth-first search (BFS) and minimum cost maximum flow (MCMF) in architectural-level synthesis. The experimental results show that our methodology not only makes significant reduction of valve-switching activities but also diminishes the application completion......Designs of flow-based microfluidic biochips are receiving much attention recently because they replace conventional biological automation paradigm and are able to integrate different biochemical analysis functions on a chip. However, as the design complexity increases, a flow-based microfluidic...... biochip needs more chip-integrated micro-valves, i.e., the basic unit of fluid-handling functionality, to manipulate the fluid flow for biochemical applications. Moreover, frequent switching of micro-valves results in decreased reliability. To minimize the valve-switching activities, we develop a network...

Flow MRI simulation in complex 3D geometries: Application to the cerebral venous network.

Science.gov (United States)

Fortin, Alexandre; Salmon, Stéphanie; Baruthio, Joseph; Delbany, Maya; Durand, Emmanuel

2018-02-05

Develop and evaluate a complete tool to include 3D fluid flows in MRI simulation, leveraging from existing software. Simulation of MR spin flow motion is of high interest in the study of flow artifacts and angiography. However, at present, only a few simulators include this option and most are restricted to static tissue imaging. An extension of JEMRIS, one of the most advanced high performance open-source simulation platforms to date, was developed. The implementation of a Lagrangian description of the flow allows simulating any MR experiment, including both static tissues and complex flow data from computational fluid dynamics. Simulations of simple flow models are compared with real experiments on a physical flow phantom. A realistic simulation of 3D flow MRI on the cerebral venous network is also carried out. Simulations and real experiments are in good agreement. The generality of the framework is illustrated in 2D and 3D with some common flow artifacts (misregistration and inflow enhancement) and with the three main angiographic techniques: phase contrast velocimetry (PC), time-of-flight, and contrast-enhanced imaging MRA. The framework provides a versatile and reusable tool for the simulation of any MRI experiment including physiological fluids and arbitrarily complex flow motion. © 2018 International Society for Magnetic Resonance in Medicine.

Transition metal complexes of some biologically active ligands; synthesis characterization and bioactivities

International Nuclear Information System (INIS)

Rehman, S.; Ali, N.; Nisar, M.

2009-01-01

Transition/representative transition metals complexes of biologically active chelating agent 1,2-dipyrolodinoethane were synthesized and characterized through spectral and analytical data. The complexes are of the formula (M(L)X/sub 2/). Where (M = Co (II), Ni (II), Cu (II), Zn (II), Hg (II) and Cd (II) and X = CI, Br, NO/sub 3/). Tetrahedral geometry has been proposed to these-metal complexes with the help of magnetic measurements, elemental analysis, chemical stoichiometry and spectroscopic data Antibacterial activity of the ligand and its metal complexes were screened against Eschereschi coli, Klebsiello pneumonia, Proteus mirabilis, Proteus vulhari, Streptococcus pneumonia, Salmonella Iyphi, Bacilh,s anthrax, Streptococcus fecalis and Staphylococcus aureus. Complexes were found to be active against Eschereschi coli, Klebsiella pneumonia, Proteus mirabilis and Proteus vulharis. (author)

Evaluating the biological activity of oil-polluted soils using a complex index

Science.gov (United States)

Kabirov, R. R.; Kireeva, N. A.; Kabirov, T. R.; Dubovik, I. Ye.; Yakupova, A. B.; Safiullina, L. M.

2012-02-01

A complex index characterizing the biological activity of soils (BAS) is suggested. It is based on an estimate of the level of activity of catalase; the number of heterotrophic and hydrocarbon oxidizing microorganisms, microscopic fungi, algae, and cyanobacteria; and the degree of development of higher plants and insects in the studied soil. The data on using the BAS coefficient for evaluating the efficiency of rehabilitation measures for oil-polluted soils are given. Such measures included introducing the following biological preparations: Lenoil based on a natural consortium of microorganisms Bacillus brevis and Arthrobacter sp.; the Azolen biofertilizer with complex action based on Azotobacter vinelandii; the Belvitamil biopreparation, which is the active silt of pulp and paper production; and a ready-mixed industrial association of aerobic and anaerobic microorganisms that contains hydrocarbon oxidizing microorganisms of the Arthrobacter, Bacillus, Candida, Desulfovibrio, and Pseudomonas genera.

Biological evaluation of transdichloridoplatinum(II) complexes with 3- and 4-acetylpyridine in comparison to cisplatin

International Nuclear Information System (INIS)

Filipovic, Lana; Arandelovic, Sandra; Gligorijevic, Nevenka; Krivokuca, Ana; Jankovic, Radmila; Srdic-Rajic, Tatjana; Rakic, Gordana; Tesic, Zivoslav; Radulovic, Sinisa

2013-01-01

In our previous study we reported the synthesis and cytotoxicity of two trans-platinum(II) complexes: trans-[PtCl 2 (3-acetylpyridine) 2 ] (1) and trans-[PtCl 2 (4-acetylpyridine) 2 ] (2), revealing significant cytotoxic potential of 2. In order to evaluate the mechanism underlying biological activity of both trans-Pt(II) isomers, comparative studies versus cisplatin were performed in HeLa, MRC-5 and MS1 cells. The cytotoxic activity of the investigated complexes was determined using SRB assay. The colagenolytic activity was determined using gelatin zymography, while the effect of platinum complexes on matrix metalloproteinases 2 and 9 mRNA expression was evaluated by quantitative real-time PCR. Apoptotic potential and cell cycle alterations were determined by FACS analyses. Western blot analysis was used to evaluate the effect on expression of DNA-repair enzyme ERCC1, and quantitative real-time PCR was used for the ERCC1 mRNA expression analysis. In vitro antiangiogenic potential was determined by tube formation assay. Platinum content in intracellular DNA and proteins was determined by inductively coupled plasma-optical emission spectrometry. Compound 2 displayed an apparent cytoselective profile, and flow cytometry analysis in HeLa cells indicated that 2 exerted antiproliferative effect through apoptosis induction, while 1 induced both apoptosis and necrosis. Action of 1 and 2, as analyzed by quantitative real-time PCR and Western blot, was associated with down-regulation of ERCC1. Both trans-complexes inhibited MMP-9 mRNA expression in HeLa, while 2 significantly abrogated in vitro tubulogenesis in MS1 cells. The ability of 2 to induce multiple and selective in vitro cytotoxic effects encourages further investigations of trans-platinum(II) complexes with substituted pyridines

RECOVERY ACT - Robust Optimization for Connectivity and Flows in Dynamic Complex Networks

Energy Technology Data Exchange (ETDEWEB)

Balasundaram, Balabhaskar [Oklahoma State Univ., Stillwater, OK (United States); Butenko, Sergiy [Texas A & M Univ., College Station, TX (United States); Boginski, Vladimir [Univ. of Florida, Gainesville, FL (United States); Uryasev, Stan [Univ. of Florida, Gainesville, FL (United States)

2013-12-25

The goal of this project was to study robust connectivity and flow patterns of complex multi-scale systems modeled as networks. Networks provide effective ways to study global, system level properties, as well as local, multi-scale interactions at a component level. Numerous applications from power systems, telecommunication, transportation, biology, social science, and other areas have benefited from novel network-based models and their analysis. Modeling and optimization techniques that employ appropriate measures of risk for identifying robust clusters and resilient network designs in networks subject to uncertain failures were investigated in this collaborative multi-university project. In many practical situations one has to deal with uncertainties associated with possible failures of network components, thereby affecting the overall efficiency and performance of the system (e.g., every node/connection has a probability of partial or complete failure). Some extreme examples include power grid component failures, airline hub failures due to weather, or freeway closures due to emergencies. These are also situations in which people, materials, or other resources need to be managed efficiently. Important practical examples include rerouting flow through power grids, adjusting flight plans, and identifying routes for emergency services and supplies, in the event network elements fail unexpectedly. Solutions that are robust under uncertainty, in addition to being economically efficient, are needed. This project has led to the development of novel models and methodologies that can tackle the optimization problems arising in such situations. A number of new concepts, which have not been previously applied in this setting, were investigated in the framework of the project. The results can potentially help decision-makers to better control and identify robust or risk-averse decisions in such situations. Formulations and optimal solutions of the considered problems need

Leveraging Understanding of Flow of Variable Complex Fluid to Design Better Absorbent Hygiene Products

Science.gov (United States)

Krautkramer, C.; Rend, R. R.

2014-12-01

Menstrual flow, which is a result of shedding of uterus endometrium, occurs periodically in sync with a women's hormonal cycle. Management of this flow while allowing women to pursue their normal daily lives is the purpose of many commercial products. Some of these products, e.g. feminine hygiene pads and tampons, utilize porous materials in achieving their goal. In this paper we will demonstrate different phenomena that have been observed in flow of menstrual fluid through these porous materials, share some of the advances made in experimental and analytical study of these phenomena, and also present some of the unsolved challenges and difficulties encountered while studying this kind of flow. Menstrual fluid is generally composed of four main components: blood plasma, blood cells, cervical mucus, and tissue debris. This non-homogeneous, multiphase fluid displays very complex rheological behavior, e. g., yield stress, thixotropy, and visco-elasticity, that varies throughout and between menstrual cycles and among women due to various factors. Flow rates are also highly variable during menstruation and across the population and the rheological properties of the fluid change during the flow into and through the product. In addition to these phenomena, changes to the structure of the porous medium within the product can also be seen due to fouling and/or swelling of the material. This paper will, also, share how the fluid components impact the flow and the consequences for computer simulation, the creation of a simulant fluid and testing methods, and for designing products that best meet consumer needs. We hope to bring to light the challenges of managing this complex flow to meet a basic need of women all over the world. An opportunity exists to apply learnings from research in other disciplines to improve the scientific knowledge related to the flow of this complex fluid through the porous medium that is a sanitary product.

Randomness Representation of Turbulence in Canopy Flows Using Kolmogorov Complexity Measures

Directory of Open Access Journals (Sweden)

Dragutin Mihailović

2017-09-01

Full Text Available Turbulence is often expressed in terms of either irregular or random fluid flows, without quantification. In this paper, a methodology to evaluate the randomness of the turbulence using measures based on the Kolmogorov complexity (KC is proposed. This methodology is applied to experimental data from a turbulent flow developing in a laboratory channel with canopy of three different densities. The methodology is even compared with the traditional approach based on classical turbulence statistics.

Integrating systems biology models and biomedical ontologies.

Science.gov (United States)

Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

2011-08-11

Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

Multiphase flows in complex geometries: a UQ perspective

KAUST Repository

Icardi, Matteo

2015-01-01

Nowadays computer simulations are widely used in many multiphase flow applications involving interphases, dispersed particles, and complex geometries. Most of these problems are solved with mixed models composed of fundamental physical laws, rigorous mathematical upscaling, and empirical correlations/closures. This means that classical inference techniques or forward parametric studies, for example, becomes computationally prohibitive and must take into account the physical meaning and constraints of the equations. However mathematical techniques commonly used in Uncertainty Quantification can come to the aid for the (i) modeling, (ii) simulation, and (iii) validation steps. Two relevant applications for environmental, petroleum, and chemical engineering will be presented to highlight these aspects and the importance of bridging the gaps between engineering applications, computational physics and mathematical methods. The first example is related to the mathematical modeling of sub-grid/sub-scale information with Probability Density Function (PDF) models in problems involving flow, mixing, and reaction in random environment. After a short overview of the research field, some connections and similarities with Polynomial Chaos techniques, will be investigated. In the second example, averaged correlations laws and effective parameters for multiphase flow and their statistical fluctuations, will be considered and efficient computational techniques, borrowed from high-dimensional stochastic PDE problems, will be applied. In presence of interfacial flow, where small spatial scales and fast time scales are neglected, the assessment of robustness and predictive capabilities are studied. These illustrative examples are inspired by common problems arising, for example, from the modeling and simulation of turbulent and porous media flows.

Multiphase flows in complex geometries: a UQ perspective

KAUST Repository

Icardi, Matteo

2015-01-07

Nowadays computer simulations are widely used in many multiphase flow applications involving interphases, dispersed particles, and complex geometries. Most of these problems are solved with mixed models composed of fundamental physical laws, rigorous mathematical upscaling, and empirical correlations/closures. This means that classical inference techniques or forward parametric studies, for example, becomes computationally prohibitive and must take into account the physical meaning and constraints of the equations. However mathematical techniques commonly used in Uncertainty Quantification can come to the aid for the (i) modeling, (ii) simulation, and (iii) validation steps. Two relevant applications for environmental, petroleum, and chemical engineering will be presented to highlight these aspects and the importance of bridging the gaps between engineering applications, computational physics and mathematical methods. The first example is related to the mathematical modeling of sub-grid/sub-scale information with Probability Density Function (PDF) models in problems involving flow, mixing, and reaction in random environment. After a short overview of the research field, some connections and similarities with Polynomial Chaos techniques, will be investigated. In the second example, averaged correlations laws and effective parameters for multiphase flow and their statistical fluctuations, will be considered and efficient computational techniques, borrowed from high-dimensional stochastic PDE problems, will be applied. In presence of interfacial flow, where small spatial scales and fast time scales are neglected, the assessment of robustness and predictive capabilities are studied. These illustrative examples are inspired by common problems arising, for example, from the modeling and simulation of turbulent and porous media flows.

Novel synthesis on poly (vinyl alcohol): characterization, complexation a biological activity

International Nuclear Information System (INIS)

El-Sawy, N.M.; Elassar, A.Z.; Al-Fulaij, O.

2002-01-01

Poly(vinyl alcohol), PVA, readily condensed with phenyl hydrazine and malononitrile in basic medium to give the hydrazone and pyran derivatives, respectively. PVA reacted with chloroacetonitrile, biuet and thiophene carbonyl chloride to give modified polymeric materials. While addition of PVA to acrylonitrile and phenyl isothiocyanate gives the ether and thiocarbamate ester derivatives, respectively. Hydroxylamine hydrochloride reacted with the modified, carbonitrile containing, polymer to give the amidoxime derivative. The amidoximated products of PVA and carbamate ester of polymeric material were complexed with CUCL2 solution. The complex materials were confirmed by using UV and ESDS measurements. The morphology of PVA and complex with CUII was observed by SEM. Biological activity of some of the prepared compounds was investigated toward bacteria and fungi

Complex network analysis of phase dynamics underlying oil-water two-phase flows

Science.gov (United States)

Gao, Zhong-Ke; Zhang, Shan-Shan; Cai, Qing; Yang, Yu-Xuan; Jin, Ning-De

2016-01-01

Characterizing the complicated flow behaviors arising from high water cut and low velocity oil-water flows is an important problem of significant challenge. We design a high-speed cycle motivation conductance sensor and carry out experiments for measuring the local flow information from different oil-in-water flow patterns. We first use multivariate time-frequency analysis to probe the typical features of three flow patterns from the perspective of energy and frequency. Then we infer complex networks from multi-channel measurements in terms of phase lag index, aiming to uncovering the phase dynamics governing the transition and evolution of different oil-in-water flow patterns. In particular, we employ spectral radius and weighted clustering coefficient entropy to characterize the derived unweighted and weighted networks and the results indicate that our approach yields quantitative insights into the phase dynamics underlying the high water cut and low velocity oil-water flows. PMID:27306101

Variable speed limit strategies analysis with mesoscopic traffic flow model based on complex networks

Science.gov (United States)

Li, Shu-Bin; Cao, Dan-Ni; Dang, Wen-Xiu; Zhang, Lin

As a new cross-discipline, the complexity science has penetrated into every field of economy and society. With the arrival of big data, the research of the complexity science has reached its summit again. In recent years, it offers a new perspective for traffic control by using complex networks theory. The interaction course of various kinds of information in traffic system forms a huge complex system. A new mesoscopic traffic flow model is improved with variable speed limit (VSL), and the simulation process is designed, which is based on the complex networks theory combined with the proposed model. This paper studies effect of VSL on the dynamic traffic flow, and then analyzes the optimal control strategy of VSL in different network topologies. The conclusion of this research is meaningful to put forward some reasonable transportation plan and develop effective traffic management and control measures to help the department of traffic management.

Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

Directory of Open Access Journals (Sweden)

Schwieger Michael

2005-01-01

Full Text Available Abstract Background Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships. Results Using this system as an example, we perform a critical evaluation of current JDO technology; discuss the suitability of the JDO standard to achieve portability, scalability and performance. We show that JDO supports portability of the SigPath system from a relational database backend to an object database backend and achieves acceptable scalability. To answer the performance question, we have created the SigPath JDO application benchmark that we distribute under the Gnu General Public License. This benchmark can be used as an example of using JDO technology to create a complex biological database and makes it possible for vendors and users of the technology to evaluate the performance of other JDO implementations for similar applications. Conclusions The SigPath JDO benchmark and our discussion of JDO technology in the context of biological databases will be useful to bioinformaticians who design new complex biological databases and aim to create systems that can be ported easily to a variety of database backends.

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

Science.gov (United States)

Urrios, Arturo; de Nadal, Eulàlia; Solé, Ricard; Posas, Francesc

2016-01-01

Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space as key computational elements. This spatial modular design grants scalability since its general architecture is independent of the circuit’s complexity, minimizes wiring requirements and allows component reusability with minimal genetic engineering. The potential use of this approach is demonstrated by implementation of complex logical functions with up to six inputs, thus demonstrating the scalability and flexibility of this method. The potential implications of our results are outlined. PMID:26829588

Seeking simplicity for the understanding of multiphase flows

Science.gov (United States)

Stone, Howard A.

2017-10-01

Fluid mechanics is a discipline with rich phenomena, with motions occurring over an enormous range of length scales, and spanning a wide range of laminar and turbulent flows, instabilities, and applications in industry, nature, biology, and medicine. The subfield of complex fluids typically refers to those flows where the complexity is introduced, for example, by the presence of suspended particles, multiple phases, soft boundaries, and electrokinetic effects; several distinct multiphase flows of Newtonian fluids make up the examples in this article. Interfaces play a significant role and modify the flow with feedback that further changes the shapes of the interfaces. I will provide examples of our work highlighting (i) new features of classical instabilities triggered by changes in geometry, (ii) multiphase flows relevant to the design of liquid-infused substrates exhibiting effective slip while retaining the trapped liquid, and (iii) unexpected dynamics in flow at a T-junction. The interplay of experiments and mathematical models and/or simulations is critical to the new understanding developed.

Modelling of the flow of stable air over a complex region

CSIR Research Space (South Africa)

Scholtz, MT

1976-01-01

Full Text Available The flow of stable air over a general region of complex topography and non-uniform surface temperature has been investigated. In order to gain further understanding of the motion of surface air, it was necessary to study the vertical structure...

Biological 12C-13C fractionation increases with increasing community-complexity in soil microcosms

DEFF Research Database (Denmark)

Yang, Weijun; Magid, Jakob; Christensen, Søren

2014-01-01

-rates and determine the trophic level of organisms in biological systems. While it is widely accepted that 15N-accumulates in natural food-chains, it is disputed to which extent this is the case for C-13. We constructed sand-microcosms inoculated with a dilution series of soil organisms and amended with glucose......Isotope fractionation is a ubiquitous phenomenon in natural ecosystems. When chemical elements move through food chains, natural isotope ratios change because biological processes tend to discriminate against heavier isotopes. This effect can be used to trace flows of matter, estimate process...

LES of the interaction between a premixed flame and complex turbulent swirling flow

International Nuclear Information System (INIS)

Iudiciani, P; Duwig, C; Szasz, R Z; Fuchs, L; Gutmark, E

2011-01-01

In this paper the Triple Annular Research Swirler, a fuel injector characterized by complex design with three concentric air passages, has been studied numerically. A swirl-stabilized lean premixed flame has been simulated by means of Large Eddy Simulation. The computations characterize successfully the dynamics of the flame and their interactions with the complex swirling flow. The flame is stabilized upstream the fuel injector exit, and the dynamics are led by a Precessing Vortex Core which seems to originate in the inner air passage. The results obtained by Proper Orthogonal Decomposition analysis are in agreement with previous findings in the context of swirling flows/flames.

Synthesis, characterization and biological activities of semicarbazones and their copper complexes.

Science.gov (United States)

Venkatachalam, Taracad K; Bernhardt, Paul V; Noble, Chris J; Fletcher, Nicholas; Pierens, Gregory K; Thurecht, Kris J; Reutens, David C

2016-09-01

Substituted semicarbazones/thiosemicarbazones and their copper complexes have been prepared and several single crystal structures examined. The copper complexes of these semicarbazone/thiosemicarbazones were prepared and several crystal structures examined. The single crystal X-ray structure of the pyridyl-substituted semicarbazone showed two types of copper complexes, a monomer and a dimer. We also found that the p-nitrophenyl semicarbazone formed a conventional 'magic lantern' acetate-bridged dimer. Electron Paramagnetic Resonance (EPR) of several of the copper complexes was consistent with the results of single crystal X-ray crystallography. The EPR spectra of the p-nitrophenyl semicarbazone copper complex in dimethylsulfoxide (DMSO) showed the presence of two species, confirming the structural information. Since thiosemicarbazones and semicarbazones have been reported to exhibit anticancer activity, we examined the anticancer activity of several of the derivatives reported in the present study and interestingly only the thiosemicarbazone showed activity while the semicarbazones were not active indicating that introduction of sulphur atom alters the biological profile of these thiosemicarbazones. Copyright © 2016 Elsevier Inc. All rights reserved.

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Science.gov (United States)

Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Effect of sub-pore scale morphology of biological deposits on porous media flow properties

Science.gov (United States)

Ghezzehei, T. A.

2012-12-01

Biological deposits often influence fluid flow by altering the pore space morphology and related hydrologic properties such as porosity, water retention characteristics, and permeability. In most coupled-processes models changes in porosity are inferred from biological process models using mass-balance. The corresponding evolution of permeability is estimated using (semi-) empirical porosity-permeability functions such as the Kozeny-Carman equation or power-law functions. These equations typically do not account for the heterogeneous spatial distribution and morphological irregularities of the deposits. As a result, predictions of permeability evolution are generally unsatisfactory. In this presentation, we demonstrate the significance of pore-scale deposit distribution on porosity-permeability relations using high resolution simulations of fluid flow through a single pore interspersed with deposits of varying morphologies. Based on these simulations, we present a modification to the Kozeny-Carman model that accounts for the shape of the deposits. Limited comparison with published experimental data suggests the plausibility of the proposed conceptual model.

Progress in Computational Physics (PiCP) Vol 2 Coupled Fluid Flow in Energy, Biology and Environmental Research

CERN Document Server

Ehrhardt, Matthias

2012-01-01

This second volume contains both, the mathematical analysis of the coupling between fluid flow and porous media flow and state-of-the art numerical techniques, like tailor-made finite element and finite volume methods. Readers will come across articles devoted to concrete applications of these models in the field of energy, biology and environmental research.

Biological significance of complex N-glycans in plants and their impact on plant physiology.

Science.gov (United States)

Strasser, Richard

2014-01-01

Asparagine (N)-linked protein glycosylation is a ubiquitous co- and post-translational modification which can alter the biological function of proteins and consequently affects the development, growth, and physiology of organisms. Despite an increasing knowledge of N-glycan biosynthesis and processing, we still understand very little about the biological function of individual N-glycan structures in plants. In particular, the N-glycan-processing steps mediated by Golgi-resident enzymes create a structurally diverse set of protein-linked carbohydrate structures. Some of these complex N-glycan modifications like the presence of β1,2-xylose, core α1,3-fucose or the Lewis a-epitope are characteristic for plants and are evolutionary highly conserved. In mammals, complex N-glycans are involved in different cellular processes including molecular recognition and signaling events. In contrast, the complex N-glycan function is still largely unknown in plants. Here, in this short review, I focus on important recent developments and discuss their implications for future research in plant glycobiology and plant biotechnology.

Molecular Cloning Designer Simulator (MCDS: All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects

Directory of Open Access Journals (Sweden)

Zhenyu Shi

2016-12-01

Full Text Available Molecular Cloning Designer Simulator (MCDS is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1 it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2 it can perform a user-defined workflow of cloning steps in a single execution of the software; (3 it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4 it includes experimental information to conveniently guide wet lab work; and (5 it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. Keywords: BioCAD, Genetic engineering software, Molecular cloning software, Synthetic biology, Workflow simulation and management

A ghost-cell immersed boundary method for flow in complex geometry

International Nuclear Information System (INIS)

Tseng, Y.-H.; Ferziger, Joel H.

2003-01-01

An efficient ghost-cell immersed boundary method (GCIBM) for simulating turbulent flows in complex geometries is presented. A boundary condition is enforced through a ghost cell method. The reconstruction procedure allows systematic development of numerical schemes for treating the immersed boundary while preserving the overall second-order accuracy of the base solver. Both Dirichlet and Neumann boundary conditions can be treated. The current ghost cell treatment is both suitable for staggered and non-staggered Cartesian grids. The accuracy of the current method is validated using flow past a circular cylinder and large eddy simulation of turbulent flow over a wavy surface. Numerical results are compared with experimental data and boundary-fitted grid results. The method is further extended to an existing ocean model (MITGCM) to simulate geophysical flow over a three-dimensional bump. The method is easily implemented as evidenced by our use of several existing codes

Entropy as a method to investigate complex biological systems. An alternative view on the biological transition from healthy aging to frailty

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Roberto Siciliano

2017-07-01

Full Text Available Everyone is subject to a process of progressive deterioration of control mechanisms, which supervise the complex network of human physiological functions, reducing the individual ability to adapt to emerging situations of stress or change. In the light of results obtained during the last years, it appears that some of the tools of nonlinear dynamics, first developed for the physical sciences are well suited for studies of biological systems. We believe that, considering the level of order or complexity of the anatomical apparatus by measuring a physical quantity, which is the entropy, we can evaluate the health status or vice versa fragility of a biological system. In particular, a reduction in the entropy value, indicates modification of the structural order with a progressive reduction of functional reserve of the individual, which is associated with a failure to adapt to stress conditions, difficult to be analyzed and documented with a unique traditional biochemical or biomolecular vision. Therefore, in this paper, we present a method that, conceptually combines complexity, disease and aging, alloys Poisson statistics, predictive of the personal level of health, to the entropy value indicating the status of bio-dynamic and functional body, seen as a complex and open thermodynamic system.

Complex research of acoustic impact on gas-dust flow in vortex ...

African Journals Online (AJOL)

Complex research of acoustic impact on gas-dust flow in vortex-acoustic dispenser. ... PROMOTING ACCESS TO AFRICAN RESEARCH ... Introduction The processing of wastes from mining operations is usually related to the needs of related industries in raw materials. ... EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

When physics is not "just physics": complexity science invites new measurement frames for exploring the physics of cognitive and biological development.

Science.gov (United States)

Kelty-Stephen, Damian; Dixon, James A

2012-01-01

The neurobiological sciences have struggled to resolve the physical foundations for biological and cognitive phenomena with a suspicion that biological and cognitive systems, capable of exhibiting and contributing to structure within themselves and through their contexts, are fundamentally distinct or autonomous from purely physical systems. Complexity science offers new physics-based approaches to explaining biological and cognitive phenomena. In response to controversy over whether complexity science might seek to "explain away" biology and cognition as "just physics," we propose that complexity science serves as an application of recent advances in physics to phenomena in biology and cognition without reducing or undermining the integrity of the phenomena to be explained. We highlight that physics is, like the neurobiological sciences, an evolving field and that the threat of reduction is overstated. We propose that distinctions between biological and cognitive systems from physical systems are pretheoretical and thus optional. We review our own work applying insights from post-classical physics regarding turbulence and fractal fluctuations to the problems of developing cognitive structure. Far from hoping to reduce biology and cognition to "nothing but" physics, we present our view that complexity science offers new explanatory frameworks for considering physical foundations of biological and cognitive phenomena.

Using multi-criteria analysis of simulation models to understand complex biological systems

Science.gov (United States)

Maureen C. Kennedy; E. David. Ford

2011-01-01

Scientists frequently use computer-simulation models to help solve complex biological problems. Typically, such models are highly integrated, they produce multiple outputs, and standard methods of model analysis are ill suited for evaluating them. We show how multi-criteria optimization with Pareto optimality allows for model outputs to be compared to multiple system...

Metal-containing Complexes of Lactams, Imidazoles, and Benzimidazoles and Their Biological Activity

Science.gov (United States)

Kukalenko, S. S.; Bovykin, B. A.; Shestakova, S. I.; Omel'chenko, A. M.

1985-07-01

The results of the latest investigations of the problem of the synthesis of metal-containing complexes of lactams, imidazoles, and benzimidazoles, their structure, and their stability in solutions are surveyed. Some data on their biological activity (pesticide and pharmacological) and the mechanism of their physiological action are presented. The bibliography includes 190 references.

Synthesis, spectroscopic and biological studies of transition metal complexes of novel schiff bases derived from amoxicillin and sugars

International Nuclear Information System (INIS)

Naz, N.

2009-01-01

Fe (II), Co (II) and Ni (II) metal complexes of new Schiff bases derived from amoxicillin with sugars (D-Glucose, D-Galactose and D-Mannose) have been synthesized and characterized by elemental analysis, FTIR, electronic absorption, and atomic absorption spectroscopy, magnetic moment measurements and thermal analysis. It has been found that Schiff bases behave as bi-dentate ligands forming complexes with 1:2 (metal:ligand) stoichiometry. The complexes were neutral as confirmed by their low conductance values. The biological applications of complexes have been studied on two gram negative (Escherichia coli and Pseudomonas aeruginosa) and two gram positive (Bacillus subtilis and Staphylococcus aureus) microorganisms by Agar diffusion disc method. It has been found that all the complexes have higher biological activities than the pure amoxicillin. (author)

Biologic activity of porphyromonas endodontalis complex lipids.

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Mirucki, Christopher S; Abedi, Mehran; Jiang, Jin; Zhu, Qiang; Wang, Yu-Hsiung; Safavi, Kamran E; Clark, Robert B; Nichols, Frank C

2014-09-01

Periapical infections secondary to pulpal necrosis are associated with bacterial contamination of the pulp. Porphyromonas endodontalis, a gram-negative organism, is considered to be a pulpal pathogen. P. gingivalis is phylogenetically related to P. endodontalis and synthesizes several classes of novel complex lipids that possess biological activity, including the capacity to promote osteoclastogenesis and osteoclast activation. The purpose of this study was to extract and characterize constituent lipids of P. endodontalis and evaluate their capacity to promote proinflammatory secretory responses in the macrophage cell line, RAW 264.7, as well as their capacity to promote osteoclastogenesis and inhibit osteoblast activity. Constituent lipids of both organisms were fractionated by high-performance liquid chromatography and were structurally characterized using electrospray mass spectrometry or electrospray-mass spectrometry/mass spectrometry. The virulence potential of P. endodontalis lipids was then compared with known biologically active lipids isolated from P. gingivalis. P. endodontalis total lipids were shown to promote tumor necrosis factor alpha secretion from RAW 264.7 cells, and the serine lipid fraction appeared to account for the majority of this effect. P. endodontalis lipid preparations also increased osteoclast formation from RAW 264.7 cells, but osteoblast differentiation in culture was inhibited and appeared to be dependent on Toll-like receptor 2 expression. These effects underscore the importance of P. endodontalis lipids in promoting inflammatory and bone cell activation processes that could lead to periapical pathology. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Analysis of undergraduate students' conceptual models of a complex biological system across a diverse body of learners

Science.gov (United States)

Dirnbeck, Matthew R.

Biological systems pose a challenge both for learners and teachers because they are complex systems mediated by feedback loops; networks of cause-effect relationships; and non-linear, hierarchical, and emergent properties. Teachers and scientists routinely use models to communicate ideas about complex systems. Model-based pedagogies engage students in model construction as a means of practicing higher-order reasoning skills. One such modeling paradigm describes systems in terms of their structures, behaviors, and functions (SBF). The SBF framework is a simple modeling language that has been used to teach about complex biological systems. Here, we used student-generated SBF models to assess students' causal reasoning in the context of a novel biological problem on an exam. We compared students' performance on the modeling problem, their performance on a set of knowledge/comprehension questions, and their performance on a set of scientific reasoning questions. We found that students who performed well on knowledge and understanding questions also constructed more networked, higher quality models. Previous studies have shown that learners' mental maps increase in complexity with increased expertise. We wanted to investigate if biology students with varying levels of training in biology showed a similar pattern when constructing system models. In a pilot study, we administered the same modeling problem to two additional groups of students: 1) an animal physiology course for students pursuing a major in biology (n=37) and 2) an exercise physiology course for non-majors (n=27). We found that there was no significant difference in model organization across the three student populations, but there was a significant difference in the ability to represent function between the three populations. Between the three groups the non-majors had the lowest function scores, the introductory majors had the middle function scores, and the upper division majors had the highest function

A Friendly-Biological Reactor SIMulator (BioReSIM for studying biological processes in wastewater treatment processes

Directory of Open Access Journals (Sweden)

Raul Molina

2014-12-01

Full Text Available Biological processes for wastewater treatments are inherently dynamic systems because of the large variations in the influent wastewater flow rate, concentration composition and the adaptive behavior of the involved microorganisms. Moreover, the sludge retention time (SRT is a critical factor to understand the bioreactor performances when changes in the influent or in the operation conditions take place. Since SRT are usually in the range of 10-30 days, the performance of biological reactors needs a long time to be monitored in a regular laboratory demonstration, limiting the knowledge that can be obtained in the experimental lab practice. In order to overcome this lack, mathematical models and computer simulations are useful tools to describe biochemical processes and predict the overall performance of bioreactors under different working operation conditions and variations of the inlet wastewater composition. The mathematical solution of the model could be difficult as numerous biochemical processes can be considered. Additionally, biological reactors description (mass balance, etc. needs models represented by partial or/and ordinary differential equations associated to algebraic expressions, that require complex computational codes to obtain the numerical solutions. Different kind of software for mathematical modeling can be used, from large degree of freedom simulators capable of free models definition (as AQUASIM, to closed predefined model structure programs (as BIOWIN. The first ones usually require long learning curves, whereas the second ones could be excessively rigid for specific wastewater treatment systems. As alternative, we present Biological Reactor SIMulator (BioReSIM, a MATLAB code for the simulation of sequencing batch reactors (SBR and rotating biological contactors (RBC as biological systems of suspended and attached biomass for wastewater treatment, respectively. This BioReSIM allows the evaluation of simple and complex

Modelling and Simulating Complex Systems in Biology: introducing NetBioDyn : A Pedagogical and Intuitive Agent-Based Software

OpenAIRE

Ballet, Pascal; Rivière, Jérémy; Pothet, Alain; Théron, Michaël; Pichavant, Karine; Abautret, Frank; Fronville, Alexandra; Rodin, Vincent

2017-01-01

International audience; Modelling and teaching complex biological systems is a difficult process. Multi-Agent Based Simulations (MABS) have proved to be an appropriate approach both in research and education when dealing with such systems including emergent, self-organizing phenomena. This chapter presents NetBioDyn, an original software aimed at biologists (students, teachers, researchers) to easily build and simulate complex biological mechanisms observed in multicellular and molecular syst...

Removal of iron and manganese using biological roughing up flow filtration technology.

Science.gov (United States)

Pacini, Virginia Alejandra; María Ingallinella, Ana; Sanguinetti, Graciela

2005-11-01

The removal of iron and manganese from groundwater using biological treatment methods is almost unknown in Latin America. Biological systems used in Europe are based on the process of double rapid biofiltration during which dissolved oxygen and pH need to be strictly controlled in order to limit abiotic iron oxidation. The performance of roughing filter technology in a biological treatment process for the removal of iron and manganese, without the use of chemical agents and under natural pH conditions was studied. Two pilot plants, using two different natural groundwaters, were operated with the following treatment line: aeration, up flow roughing filtration and final filtration (either slow or rapid). Iron and manganese removal efficiencies were found to be between 85% and 95%. The high solid retention capability of the roughing filter means that it is possible to remove iron and manganese simultaneously by biotic and abiotic mechanisms. This system combines simple, low-cost operation and maintenance with high iron and manganese removal efficiencies, thus constituting a technology which is particularly suited to small waterworks.

Diagnosis at a glance of biological non-Newtonian fluids with Film Interference Flow Imaging (FIFI)

Science.gov (United States)

Hidema, R.; Yamada, N.; Furukawa, H.

2012-04-01

In the human body, full of biological non-Newtonian fluids exist. For example, synovial fluids exist in our joints, which contain full of biopolymers, such as hyaluronan and mucin. It is thought that these polymers play critical roles on the smooth motion of the joint. Indeed, luck of biopolymers in synovial fluid cause joint pain. Here we study the effects of polymer in thin liquid layer by using an original experimental method called Film Interference Flow Imaging (FIFI). A vertically flowing soap film containing polymers is made as two-dimensional flow to observe turbulence. The thickness of water layer is about 4 μm sandwiched between surfactant mono-layers. The interference pattern of the soap film is linearly related to the flow velocity in the water layer through the change in the thickness of the film. Thus the flow velocity is possibly analyzed by the single image analysis of the interference pattern, that is, FIFI. The grid turbulence was made in the flowing soap films containing the long flexible polymer polyethyleneoxide (PEO, Mw=3.5x106), and rigid polymer hydroxypropyl cellulose (HPC, Mw > 1.0 x106). The decaying process of the turbulence is affected by PEO and HPC at several concentrations. The effects of PEO are sharply seen even at low concentrations, while the effects of HPC are gradually occurred at much higher concentration compared to the PEO. It is assumed that such a difference between PEO and HPC is due to the polymer stretching or polymer orientation under turbulence, which is observed and analyzed by FIFI. We believe the FIFI will be applied in the future to examine biological fluids such as synovial fluids quickly and quantitatively.

Flow and Transport in Complex Microporous Carbonates as a Consequence of Separation of Scales

Science.gov (United States)

Bijeljic, B.; Raeini, A. Q.; Lin, Q.; Blunt, M. J.

2017-12-01

Some of the most important examples of flow and transport in complex pore structures are found in subsurface applications such as contaminant hydrology, carbon storage and enhanced oil recovery. Carbonate rock structures contain most of the world's oil reserves, considerable amount of water reserves, and potentially hold a storage capacity for carbon dioxide. However, this type of pore space is difficult to represent due to complexities associated with a wide range of pore sizes and variation in connectivity which poses a considerable challenge for quantitative predictions of transport across multiple scales.A new concept unifying X-ray tomography experiment and direct numerical simulation has been developed that relies on full description flow and solute transport at the pore scale. Differential imaging method (Lin et al. 2016) provides rich information in microporous space, while advective and diffusive mass transport are simulated on micro-CT images of pore-space: Navier-Stokes equations are solved for flow in the image voxels comprising the pore space, streamline-based simulation is used to account for advection, and diffusion is superimposed by random walk.Quantitative validation has been done on analytical solutions for diffusion and by comparing the model predictions versus the experimental NMR measurements in the dual porosity beadpack. Furthermore, we discriminate signatures of multi-scale transport behaviour for a range of carbonate rock (Figure 1), dependent on the heterogeneity of the inter- and intra-grain pore space, heterogeneity in the flow field, and the mass transfer characteristics of the porous media. Finally, we demonstrate the predictive capabilities of the model through an analysis that includes a number of probability density functions flow and transport (PDFs) measures of non-Fickian transport on the micro-CT i935mages. In complex porous media separation of scales exists, leading to flow and transport signatures that need to be described by

Fan array wind tunnel: a multifunctional, complex environmental flow manipulator

Science.gov (United States)

Dougherty, Christopher; Veismann, Marcel; Gharib, Morteza

2017-11-01

The recent emergence of small unmanned aerial vehicles (UAVs) has reshaped the aerospace testing environment. Traditional closed-loop wind tunnels are not particularly suited nor easily retrofit to take advantage of these coordinated, controls-based rotorcraft. As such, a highly configurable, novel wind tunnel aimed at addressing the unmet technical challenges associated with single or formation flight performance of autonomous drone systems is presented. The open-loop fan array wind tunnel features 1296 individually controllable DC fans arranged in a 2.88m x 2.88m array. The fan array can operate with and without a tunnel enclosure and is able to rotate between horizontal and vertical testing configurations. In addition to standard variable speed uniform flow, the fan array can generate both unsteady and shear flows. Through the aid of smaller side fan array units, vortex flows are also possible. Conceptual design, fabrication, and validation of the tunnel performance will be presented, including theoretical and computational predictions of flow speed and turbulence intensity. Validation of these parameters is accomplished through standard pitot-static and hot-wire techniques. Particle image velocimetry (PIV) of various complex flows will also be shown. This material is based upon work supported by the Center for Autonomous Systems and Technologies (CAST) at the Graduate Aerospace Laboratories of the California Institute of Technology (GALCIT).

A dynamic globalization model for large eddy simulation of complex turbulent flow

Energy Technology Data Exchange (ETDEWEB)

Choi, Hae Cheon; Park, No Ma; Kim, Jin Seok [Seoul National Univ., Seoul (Korea, Republic of)

2005-07-01

A dynamic subgrid-scale model is proposed for large eddy simulation of turbulent flows in complex geometry. The eddy viscosity model by Vreman [Phys. Fluids, 16, 3670 (2004)] is considered as a base model. A priori tests with the original Vreman model show that it predicts the correct profile of subgrid-scale dissipation in turbulent channel flow but the optimal model coefficient is far from universal. Dynamic procedures of determining the model coefficient are proposed based on the 'global equilibrium' between the subgrid-scale dissipation and viscous dissipation. An important feature of the proposed procedures is that the model coefficient determined is globally constant in space but varies only in time. Large eddy simulations with the present dynamic model are conducted for forced isotropic turbulence, turbulent channel flow and flow over a sphere, showing excellent agreements with previous results.

Slip-flow in complex porous media as determined by a multi-relaxation-time lattice Boltzmann model

Science.gov (United States)

Landry, C. J.; Prodanovic, M.; Eichhubl, P.

2014-12-01

The pores and throats of shales and mudrocks are predominantly found within a range of 1-100 nm, within this size range the flow of gas at reservoir conditions will fall within the slip-flow and low transition-flow regime (0.001 clays). Molecular dynamics (MD) simulations can be used to predict slip-flow in complex geometries, but due to prohibitive computational demand are generally limited to small volumes (one to several pores). Here we present a multi-relaxation-time lattice Boltzmann model (LBM) parameterized for slip-flow (Guo et al. 2008) and adapted here to complex geometries. LBMs are inherently parallelizable, such that flow in complex geometries of significant (near REV-scale) volumes can be readily simulated at a fraction of the computational cost of MD simulations. At the macroscopic-scale the LBM is parameterized with local effective viscosities at each node to capture the variance of the mean-free-path of gas molecules in a bounded system. The corrected mean-free-path for each lattice node is determined using the mean distance of the node to the pore-wall and Stop's correction for mean-free-paths in an infinite parallel-plate geometry. At the microscopic-scale, a combined bounce-back specular-reflection boundary condition is applied to the pore-wall nodes to capture Maxwellian-slip. The LBM simulation results are first validated in simple tube and channel geometries, where good agreement is found for Knudsen numbers below 0.1, and fair agreement is found for Knudsen numbers between 0.1 and 0.5. More complex geometries are then examined including triangular-ducts and ellipsoid-ducts, both with constant and tapering/expanding cross-sections, as well as a clay pore-network imaged from a hydrocarbon producing shale by sequential focused ion-beam scanning electron microscopy. These results are analyzed to determine grid-independent resolutions, and used to explore the relationship between effective permeability and Knudsen number in complex geometries.

Information flow analysis of interactome networks.

Directory of Open Access Journals (Sweden)

Patrycja Vasilyev Missiuro

2009-04-01

Full Text Available Recent studies of cellular networks have revealed modular organizations of genes and proteins. For example, in interactome networks, a module refers to a group of interacting proteins that form molecular complexes and/or biochemical pathways and together mediate a biological process. However, it is still poorly understood how biological information is transmitted between different modules. We have developed information flow analysis, a new computational approach that identifies proteins central to the transmission of biological information throughout the network. In the information flow analysis, we represent an interactome network as an electrical circuit, where interactions are modeled as resistors and proteins as interconnecting junctions. Construing the propagation of biological signals as flow of electrical current, our method calculates an information flow score for every protein. Unlike previous metrics of network centrality such as degree or betweenness that only consider topological features, our approach incorporates confidence scores of protein-protein interactions and automatically considers all possible paths in a network when evaluating the importance of each protein. We apply our method to the interactome networks of Saccharomyces cerevisiae and Caenorhabditis elegans. We find that the likelihood of observing lethality and pleiotropy when a protein is eliminated is positively correlated with the protein's information flow score. Even among proteins of low degree or low betweenness, high information scores serve as a strong predictor of loss-of-function lethality or pleiotropy. The correlation between information flow scores and phenotypes supports our hypothesis that the proteins of high information flow reside in central positions in interactome networks. We also show that the ranks of information flow scores are more consistent than that of betweenness when a large amount of noisy data is added to an interactome. Finally, we

Modelling and simulating in-stent restenosis with complex automata

NARCIS (Netherlands)

Hoekstra, A.G.; Lawford, P.; Hose, R.

2010-01-01

In-stent restenosis, the maladaptive response of a blood vessel to injury caused by the deployment of a stent, is a multiscale system involving a large number of biological and physical processes. We describe a Complex Automata Model for in-stent restenosis, coupling bulk flow, drug diffusion, and

Assessing the Possibility of Biological Complexity on Other Worlds, with an Estimate of the Occurrence of Complex Life in the Milky Way Galaxy

Directory of Open Access Journals (Sweden)

Louis N. Irwin

2014-05-01

Full Text Available Rational speculation about biological evolution on other worlds is one of the outstanding challenges in astrobiology. With the growing confirmation that multiplanetary systems abound in the universe, the prospect that life occurs redundantly throughout the cosmos is gaining widespread support. Given the enormous number of possible abodes for life likely to be discovered on an ongoing basis, the prospect that life could have evolved into complex, macro-organismic communities in at least some cases merits consideration. Toward that end, we here propose a Biological Complexity Index (BCI, designed to provide a quantitative estimate of the relative probability that complex, macro-organismic life forms could have emerged on other worlds. The BCI ranks planets and moons by basic, first-order characteristics detectable with available technology. By our calculation only 11 (~1.7% of the extrasolar planets known to date have a BCI above that of Europa; but by extrapolation, the total of such planets could exceed 100 million in our galaxy alone. This is the first quantitative assessment of the plausibility of complex life throughout the universe based on empirical data. It supports the view that the evolution of complex life on other worlds is rare in frequency but large in absolute number.

PeTTSy: a computational tool for perturbation analysis of complex systems biology models.

Science.gov (United States)

Domijan, Mirela; Brown, Paul E; Shulgin, Boris V; Rand, David A

2016-03-10

Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and

Ultraviolet-B radiation mobilizes uranium from uranium-dissolved organic carbon complexes in aquatic systems, demonstrated by asymmetrical flow field-flow fractionation.

Science.gov (United States)

Nehete, Sachin Vilas; Christensen, Terje; Salbu, Brit; Teien, Hans-Christian

2017-05-05

Humic substances have a tendency to form complexes with metal ions in aquatic medium, impacting the metal mobility, decreasing bioavailability and toxicity. Ultraviolet-B (UV-B) radiation exposure degrades the humic substance, changes their molecular weight distribution and their metal binding capacity in aquatic medium. In this study, we experimented the effect of UV-B radiation on the uranium complexed with fulvic acids and humic acids in a soft water system at different pH, uranium concentrations and radiant exposure. The concentration and distribution of uranium in a complexed form were investigated by asymmetrical flow field-flow fractionation coupled to multi detection technique (AsFlFFF-UV-ICP-MS). The major concentration of uranium present in complexes was primarily associated with average and higher molecular weight fulvic and humic acids components. The concentration of uranium in a complexed form increased with increasing fulvic and humic acid concentrations as well as pH of the solution. The higher molecular weight fraction of uranium was degraded due to the UV-B exposure, transforming about 50% of the uranium-dissolved organic carbon complexes into low molecular weight uranium species in complex form with organic ligands and/or free form. The result also suggests AsFlFFF-UV-ICP-MS to be an important separation and detection technique for understanding the interaction of radionuclides with dissolved organic matter, tracking size distribution changes during degradation of organic complexes for understanding mobility, bioavailability and ecosystem transfer of radionuclides as well as metals. Copyright © 2017 Elsevier B.V. All rights reserved.

Modeling of biological intelligence for SCM system optimization.

Science.gov (United States)

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

Directory of Open Access Journals (Sweden)

Shengyong Chen

2012-01-01

Full Text Available This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

Science.gov (United States)

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

Systems Biology and Health Systems Complexity in;

NARCIS (Netherlands)

Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

2016-01-01

Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language.

Science.gov (United States)

Elmarakeby, Haitham; Arefiyan, Mostafa; Myers, Elijah; Li, Song; Grene, Ruth; Heath, Lenwood S

2017-12-01

The Beacon Editor is a cross-platform desktop application for the creation and modification of signal transduction pathways using the Systems Biology Graphical Notation Activity Flow (SBGN-AF) language. Prompted by biologists' requests for enhancements, the Beacon Editor includes numerous powerful features for the benefit of creation and presentation.

Complex fluids modeling and algorithms

CERN Document Server

Saramito, Pierre

2016-01-01

This book presents a comprehensive overview of the modeling of complex fluids, including many common substances, such as toothpaste, hair gel, mayonnaise, liquid foam, cement and blood, which cannot be described by Navier-Stokes equations. It also offers an up-to-date mathematical and numerical analysis of the corresponding equations, as well as several practical numerical algorithms and software solutions for the approximation of the solutions. It discusses industrial (molten plastics, forming process), geophysical (mud flows, volcanic lava, glaciers and snow avalanches), and biological (blood flows, tissues) modeling applications. This book is a valuable resource for undergraduate students and researchers in applied mathematics, mechanical engineering and physics.

Weighted complex network analysis of the Beijing subway system: Train and passenger flows

Science.gov (United States)

Feng, Jia; Li, Xiamiao; Mao, Baohua; Xu, Qi; Bai, Yun

2017-05-01

In recent years, complex network theory has become an important approach to the study of the structure and dynamics of traffic networks. However, because traffic data is difficult to collect, previous studies have usually focused on the physical topology of subway systems, whereas few studies have considered the characteristics of traffic flows through the network. Therefore, in this paper, we present a multi-layer model to analyze traffic flow patterns in subway networks, based on trip data and an operation timetable obtained from the Beijing Subway System. We characterize the patterns in terms of the spatiotemporal flow size distributions of both the train flow network and the passenger flow network. In addition, we describe the essential interactions between these two networks based on statistical analyses. The results of this study suggest that layered models of transportation systems can elucidate fundamental differences between the coexisting traffic flows and can also clarify the mechanism that causes these differences.

Semantic Complex Event Processing over End-to-End Data Flows

Energy Technology Data Exchange (ETDEWEB)

Zhou, Qunzhi [University of Southern California; Simmhan, Yogesh; Prasanna, Viktor K.

2012-04-01

Emerging Complex Event Processing (CEP) applications in cyber physical systems like SmartPower Grids present novel challenges for end-to-end analysis over events, flowing from heterogeneous information sources to persistent knowledge repositories. CEP for these applications must support two distinctive features - easy specification patterns over diverse information streams, and integrated pattern detection over realtime and historical events. Existing work on CEP has been limited to relational query patterns, and engines that match events arriving after the query has been registered. We propose SCEPter, a semantic complex event processing framework which uniformly processes queries over continuous and archived events. SCEPteris built around an existing CEP engine with innovative support for semantic event pattern specification and allows their seamless detection over past, present and future events. Specifically, we describe a unified semantic query model that can operate over data flowing through event streams to event repositories. Compile-time and runtime semantic patterns are distinguished and addressed separately for efficiency. Query rewriting is examined and analyzed in the context of temporal boundaries that exist between event streams and their repository to avoid duplicate or missing results. The design and prototype implementation of SCEPterare analyzed using latency and throughput metrics for scenarios from the Smart Grid domain.

Wall modeled large eddy simulations of complex high Reynolds number flows with synthetic inlet turbulence

International Nuclear Information System (INIS)

Patil, Sunil; Tafti, Danesh

2012-01-01

Highlights: ► Large eddy simulation. ► Wall layer modeling. ► Synthetic inlet turbulence. ► Swirl flows. - Abstract: Large eddy simulations of complex high Reynolds number flows are carried out with the near wall region being modeled with a zonal two layer model. A novel formulation for solving the turbulent boundary layer equation for the effective tangential velocity in a generalized co-ordinate system is presented and applied in the near wall zonal treatment. This formulation reduces the computational time in the inner layer significantly compared to the conventional two layer formulations present in the literature and is most suitable for complex geometries involving body fitted structured and unstructured meshes. The cost effectiveness and accuracy of the proposed wall model, used with the synthetic eddy method (SEM) to generate inlet turbulence, is investigated in turbulent channel flow, flow over a backward facing step, and confined swirling flows at moderately high Reynolds numbers. Predictions are compared with available DNS, experimental LDV data, as well as wall resolved LES. In all cases, there is at least an order of magnitude reduction in computational cost with no significant loss in prediction accuracy.

Development trend of radiation biology research-systems radiation biology

International Nuclear Information System (INIS)

Min Rui

2010-01-01

Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

Biology and hemodynamics of aneurismal vasculopathies

International Nuclear Information System (INIS)

Pereira, Vitor Mendes; Brina, Olivier; Gonzalez, Ana Marcos; Narata, Ana Paula; Ouared, Rafik; Karl-Olof, Lovblad

2013-01-01

Aneurysm vasculopathies represents a group of vascular disorders that share a common morphological diagnosis: a vascular dilation, the aneurysm. They can have a same etiology and a different clinical presentation or morphology, or have different etiology and very similar anatomical geometry. The biology of the aneurysm formation is a complex process that will be a result of an endogenous predisposition and epigenetic factors later on including the intracranial hemodynamics. We describe the biology of saccular aneurysms, its growth and rupture, as well as, current concepts of hemodynamics derived from application of computational flow dynamics on patient specific vascular models. Furthermore, we describe different aneurysm phenotypes and its extremely variability on morphological and etiological presentation

Slope instability in complex 3D topography promoted by convergent 3D groundwater flow

Science.gov (United States)

Reid, M. E.; Brien, D. L.

2012-12-01

Slope instability in complex topography is generally controlled by the interaction between gravitationally induced stresses, 3D strengths, and 3D pore-fluid pressure fields produced by flowing groundwater. As an example of this complexity, coastal bluffs sculpted by landsliding commonly exhibit a progression of undulating headlands and re-entrants. In this landscape, stresses differ between headlands and re-entrants and 3D groundwater flow varies from vertical rainfall infiltration to lateral groundwater flow on lower permeability layers with subsequent discharge at the curved bluff faces. In plan view, groundwater flow converges in the re-entrant regions. To investigate relative slope instability induced by undulating topography, we couple the USGS 3D limit-equilibrium slope-stability model, SCOOPS, with the USGS 3D groundwater flow model, MODFLOW. By rapidly analyzing the stability of millions of potential failures, the SCOOPS model can determine relative slope stability throughout the 3D domain underlying a digital elevation model (DEM), and it can utilize both fully 3D distributions of pore-water pressure and material strength. The two models are linked by first computing a groundwater-flow field in MODFLOW, and then computing stability in SCOOPS using the pore-pressure field derived from groundwater flow. Using these two models, our analyses of 60m high coastal bluffs in Seattle, Washington showed augmented instability in topographic re-entrants given recharge from a rainy season. Here, increased recharge led to elevated perched water tables with enhanced effects in the re-entrants owing to convergence of groundwater flow. Stability in these areas was reduced about 80% compared to equivalent dry conditions. To further isolate these effects, we examined groundwater flow and stability in hypothetical landscapes composed of uniform and equally spaced, oscillating headlands and re-entrants with differing amplitudes. The landscapes had a constant slope for both

Of arrows and flows. Causality, determination, and specificity in the Central Dogma of molecular biology.

Science.gov (United States)

Fantini, Bernardino

2006-01-01

From its first proposal, the Central Dogma had a graphical form, complete with arrows of different types, and this form quickly became its standard presentation. In different scientific contexts, arrows have different meanings and in this particular case the arrows indicated the flow of information among different macromolecules. A deeper analysis illustrates that the arrows also imply a causal statement, directly connected to the causal role of genetic information. The author suggests a distinction between two different kinds of causal links, defined as 'physical causality' and 'biological determination', both implied in the production of biological specificity.

Modeling complex flow structures and drag around a submerged plant of varied posture

Science.gov (United States)

Boothroyd, Richard J.; Hardy, Richard J.; Warburton, Jeff; Marjoribanks, Timothy I.

2017-04-01

Although vegetation is present in many rivers, the bulk of past work concerned with modeling the influence of vegetation on flow has considered vegetation to be morphologically simple and has generally neglected the complexity of natural plants. Here we report on a combined flume and numerical model experiment which incorporates time-averaged plant posture, collected through terrestrial laser scanning, into a computational fluid dynamics model to predict flow around a submerged riparian plant. For three depth-limited flow conditions (Reynolds number = 65,000-110,000), plant dynamics were recorded through high-definition video imagery, and the numerical model was validated against flow velocities collected with an acoustic Doppler velocimeter. The plant morphology shows an 18% reduction in plant height and a 14% increase in plant length, compressing and reducing the volumetric canopy morphology as the Reynolds number increases. Plant shear layer turbulence is dominated by Kelvin-Helmholtz type vortices generated through shear instability, the frequency of which is estimated to be between 0.20 and 0.30 Hz, increasing with Reynolds number. These results demonstrate the significant effect that the complex morphology of natural plants has on in-stream drag, and allow a physically determined, species-dependent drag coefficient to be calculated. Given the importance of vegetation in river corridor management, the approach developed here demonstrates the necessity to account for plant motion when calculating vegetative resistance.

A numerical study on the flow upstream of a wind turbine on complex terran

DEFF Research Database (Denmark)

Meyer Forsting, Alexander Raul; Bechmann, Andreas; Troldborg, Niels

2016-01-01

The interaction of a wind turbine with the upstream flow-field in complex and flat terrain is studied using Reynolds-averaged Navier-Stokes (RANS) simulations with a two equation turbulence closure. The complex site modelled is Perdigao (Portugal), where a turbine is located on one of two parallel...... the wind turbine wake trajectory which in turn governs the orientation of the induction zone...

Spectroscopic, thermal, catalytic and biological studies of Cu(II) azo dye complexes

Science.gov (United States)

El-Sonbati, A. Z.; Diab, M. A.; El-Bindary, A. A.; Shoair, A. F.; Hussein, M. A.; El-Boz, R. A.

2017-08-01

New complexes of copper(II) with azo compounds of 5-amino-2-(aryl diazenyl)phenol (HLn) are prepared and investigated by elemental analyses, molar conductance, IR, 1H NMR, UV-Visible, mass, ESR spectra, magnetic susceptibility measurements and thermal analyses. The complexes have a square planar structure and general formula [Cu(Ln)(OAc)]H2O. Study the catalytic activities of Cu(II) complexes toward oxidation of benzyl alcohol derivatives to carbonyl compounds were tested using H2O2 as the oxidant. The intrinsic binding constants (Kb) of the ligands (HLn) and Cu(II) complexes (1-4) with CT-DNA are determined. The formed compounds have been tested for biological activity of antioxidants, antibacterial against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria and yeast Candida albicans. Antibiotic (Ampicillin) and antifungal against (Colitrimazole) and cytotoxic compounds HL1, HL2, HL3 and complex (1) showed moderate to good activity against S. aureus, E. coli and Candida albicans, and also to be moderate on antioxidants and toxic substances. Molecular docking is used to predict the binding between the ligands with the receptor of breast cancer (2a91).

Treatment of complex biological mixtures with pulsed electric fields An energy transfer characterization

International Nuclear Information System (INIS)

Schrive, Luc

2004-01-01

Sewage sludge from waste water treatment plants is a complex biological mixture and a problematic by-product because of valorisation restrictions. In order to limit its production, pulsed electric fields (PEF) were studied because of their biological effects and their potentially physico-chemical action. This work demonstrated a paradoxical phenomenon: cell lysis triggered a respirometric activation followed by a delayed lethality. This phenomenon was related to the leakage of internal compounds which were immediately bio-assimilated. At high energy expense, the plasmic membrane permeabilization led to cell death. Practically, with the technical configuration of the equipment, no hydrolysis was detected. This limitation decreases the interest for excess sludge reduction, but for the same reason, PEF cold sterilization technique can be assessed as a promising process. The representation of the electric energy transfer from electrodes to cell was exchanged by the study of mass transfer from the biological cell to the surrounding media under an electromotive force. Thus, the survival rate was modelled by a Sherwood number taking account of electrical, biological and hydraulic parameters. (author) [fr

Biological assessment of environmental flows for Oklahoma

Science.gov (United States)

Fisher, William L.; Seilheimer, Titus S.; Taylor, Jason M.

2012-01-01

Large-scale patterns in fish assemblage structure and functional groups are influenced by alterations in streamflow regime. In this study, we defined an objective threshold for alteration for Oklahoma streams using a combination of the expected range of 27 flow indices and a discriminant analysis to predict flow regime group. We found that fish functional groups in reference flow conditions had species that were more intolerant to flow alterations and preferences for stream habitat and faster flowing water. In contrast, altered sites had more tolerant species that preferred lentic habitat and slower water velocity. Ordination graphs of the presence and functional groups of species revealed an underlying geographical pattern roughly conforming to ecoregions, although there was separation between reference and altered sites within the larger geographical framework. Additionally, we found that reservoir construction and operation significantly altered fish assemblages in two different systems, Bird Creek in central Oklahoma and the Kiamichi River in southeastern Oklahoma. The Bird Creek flow regime shifted from a historically intermittent stream to one with stable perennial flows, and changes in fish assemblage structure covaried with changes in all five components of the flow regime. In contrast, the Kiamichi River flow regime did not change significantly for most flow components despite shifts in fish assemblage structure; however, most of the species associated with shifts in assemblage structure in the Kiamichi River system were characteristic of lentic environments and were likely related more to proximity of reservoirs in the drainage system than changes in flow. The spatial patterns in fish assemblage response to flow alteration, combined with different temporal responses of hydrology and fish assemblage structure at sites downstream of reservoirs, indicate that interactions between flow regime and aquatic biota vary depending on ecological setting. This

Program for Analyzing Flows in a Complex Network

Science.gov (United States)

Majumdar, Alok Kumar

2006-01-01

Generalized Fluid System Simulation Program (GFSSP) version 4 is a general-purpose computer program for analyzing steady-state and transient flows in a complex fluid network. The program is capable of modeling compressibility, fluid transients (e.g., water hammers), phase changes, mixtures of chemical species, and such externally applied body forces as gravitational and centrifugal ones. A graphical user interface enables the user to interactively develop a simulation of a fluid network consisting of nodes and branches. The user can also run the simulation and view the results in the interface. The system of equations for conservation of mass, energy, chemical species, and momentum is solved numerically by a combination of the Newton-Raphson and successive-substitution methods.

Complex variable boundary elements for fluid flow; Robni elementi kompleksne spremenljivke za pretok fluidov

Energy Technology Data Exchange (ETDEWEB)

Bizjak, D; Alujevic, A [Institut ' Jozef Stefan' , Ljubljana (Yugoslavia)

1988-07-01

The Complex Variable Boundary Element Method is a numerical method for solving two-dimensional problems of Laplace or Poisson type. It is based on the theory of analytic functions. This paper resumes the basic facts about the method. Application of the method to the stationary incompressible irrotational flow is carried out after that. At the end, a sample problem of flow through an abrupt area change channel is shown. (author)

Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions.

Science.gov (United States)

Vernon, Ian; Liu, Junli; Goldstein, Michael; Rowe, James; Topping, Jen; Lindsey, Keith

2018-01-02

Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to the needs of the analysis, and need to be compared to observed data of various forms. The correct analysis of such models usually requires a global parameter search, over a high dimensional parameter space, that incorporates and respects the most important sources of uncertainty. This can be an extremely difficult task, but it is essential for any meaningful inference or prediction to be made about any biological system. It hence represents a fundamental challenge for the whole of systems biology. Bayesian statistical methodology for the uncertainty analysis of complex models is introduced, which is designed to address the high dimensional global parameter search problem. Bayesian emulators that mimic the systems biology model but which are extremely fast to evaluate are embeded within an iterative history match: an efficient method to search high dimensional spaces within a more formal statistical setting, while incorporating major sources of uncertainty. The approach is demonstrated via application to a model of hormonal crosstalk in Arabidopsis root development, which has 32 rate parameters, for which we identify the sets of rate parameter values that lead to acceptable matches between model output and observed trend data. The multiple insights into the model's structure that this analysis provides are discussed. The methodology is applied to a second related model, and the biological consequences of the resulting comparison, including the evaluation of gene functions, are described. Bayesian uncertainty analysis for complex models using both emulators and history matching is shown to be a powerful technique that can greatly aid the study of a large class of systems biology models. It both provides insight into model behaviour

Biological regeneration of humic acid-loaded partially exhausted activated carbon (down flow system)

International Nuclear Information System (INIS)

Durrani, M.A.Q.J.; Martin, R.J.; Khaliq, F.

1995-01-01

This paper represents the report on the biological regeneration of partially exhausted (down flow) activated carbon following the experimental studies carried out at the university of Birmingham, UK. The Research investigated the extent of bio regeneration of humic acid of concentration 100 mg/l. Bio regeneration in the partial exhaustion system (down flow) was evaluated in terms of substrate removal. Bacterial counts in the effluents of regenerated GAC columns were significantly more than those of fresh carbon effluents. The regeneration performance of the bio regeneration, partially exhausted (with humic acid) carbon increased during initial cycles, later on, it deteriorated significantly with each successive regeneration cycle. Microbial fouling of the carbon, especially at the bottom of the carbon bed was found to produce a substantial deterioration of the bio regeneration performance. (author)

Flow characteristics of bounded self-organized dust vortex in a complex plasma

Science.gov (United States)

Laishram, Modhuchandra; Sharma, D.; Chattopdhyay, P. K.; Kaw, P. K.

2018-01-01

Dust clouds are often formed in many dusty plasma experiments, when micron size dust particles introduced in the plasma are confined by spatial non-uniformities of the potential. These formations show self-organized patterns like vortex or circulation flows. Steady-state equilibrium dynamics of such dust clouds is analyzed by 2D hydrodynamics for varying Reynolds number, Re, when the cloud is confined in an azimuthally symmetric cylindrical setup by an effective potential and is in a dynamic equilibrium with an unbounded sheared plasma flow. The nonconservative forcing due to ion flow shear generates finite vorticity in the confined dust clouds. In the linear limit (Re ≪ 1), the collective flow is characterized by a single symmetric and elongated vortex with scales correlating with the driving field and those generated by friction with the boundaries. However in the high Re limit, (Re ≥ 1), the nonlinear inertial transport (u . ∇u) is effective and the vortex structure is characterized by an asymmetric equilibrium and emergence of a circular core region with uniform vorticity, over which the viscous stress is negligible. The core domain is surrounded by a virtual boundary of highly convective flow followed by thin shear layers filled with low-velocity co- and counter-rotating vortices, enabling the smooth matching with external boundary conditions. In linear regime, the effective boundary layer thickness is recovered to scale with the dust kinematic viscosity as Δr ≈ μ1/3 and is modified as Δr ≈ (μL∥/u)1/2 in the nonlinear regime through a critical kinematic viscosity μ∗ that signifies a structural bifurcation of the flow field solutions. The flow characteristics recovered are relevant to many microscopic biological processes at lower Re, as well as gigantic vortex flows such as Jovian great red spot and white ovals at higher Re.

Experimental investigation of flow induced dust acoustic shock waves in a complex plasma

Energy Technology Data Exchange (ETDEWEB)

Jaiswal, S., E-mail: surabhijaiswal73@gmail.com; Bandyopadhyay, P.; Sen, A. [Institute for Plasma Research, Bhat, Gandhinagar, Gujarat 382428 (India)

2016-08-15

We report on experimental observations of flow induced large amplitude dust-acoustic shock waves in a complex plasma. The experiments have been carried out in a Π shaped direct current glow discharge experimental device using kaolin particles as the dust component in a background of Argon plasma. A strong supersonic flow of the dust fluid is induced by adjusting the pumping speed and neutral gas flow into the device. An isolated copper wire mounted on the cathode acts as a potential barrier to the flow of dust particles. A sudden change in the gas flow rate is used to trigger the onset of high velocity dust acoustic shocks whose dynamics are captured by fast video pictures of the evolving structures. The physical characteristics of these shocks are delineated through a parametric scan of their dynamical properties over a range of flow speeds and potential hill heights. The observed evolution of the shock waves and their propagation characteristics are found to compare well with model numerical results based on a modified Korteweg-de-Vries-Burgers type equation.

A model for complex flows of soft glassy materials with application to flows through fixed fiber beds

Energy Technology Data Exchange (ETDEWEB)

Sarkar, Arijit; Koch, Donald L., E-mail: dlk15@cornell.edu [School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853-5201 (United States)

2015-11-15

The soft glassy rheology (SGR) model has successfully described the time dependent simple shear rheology of a broad class of complex fluids including foams, concentrated emulsions, colloidal glasses, and solvent-free nanoparticle-organic hybrid materials (NOHMs). The model considers a distribution of mesoscopic fluid elements that hop from trap to trap at a rate which is enhanced by the work done to strain the fluid element. While an SGR fluid has a broad exponential distribution of trap energies, the rheology of NOHMs is better described by a narrower energy distribution and we consider both types of trap energy distributions in this study. We introduce a tensorial version of these models with a hopping rate that depends on the orientation of the element relative to the mean stress field, allowing a range of relative strengths of the extensional and simple shear responses of the fluid. As an application of these models we consider the flow of a soft glassy material through a dilute fixed bed of fibers. The dilute fixed bed exhibits a range of local linear flows which alternate in a chaotic manner with time in a Lagrangian reference frame. It is amenable to an analytical treatment and has been used to characterize the strong flow response of many complex fluids including fiber suspensions, dilute polymer solutions and emulsions. We show that the accumulated strain in the fluid elements has an abrupt nonlinear growth at a Deborah number of order one in a manner similar to that observed for polymer solutions. The exponential dependence of the hopping rate on strain leads to a fluid element deformation that grows logarithmically with Deborah number at high Deborah numbers. SGR fluids having a broad range of trap energies flowing through fixed beds can exhibit a range of rheological behaviors at small Deborah numbers ranging from a yield stress, to a power law response and finally to Newtonian behavior.

A model for complex flows of soft glassy materials with application to flows through fixed fiber beds

KAUST Repository

Sarkar, Arijit

2015-11-01

© 2015 The Society of Rheology. The soft glassy rheology (SGR) model has successfully described the time dependent simple shear rheology of a broad class of complex fluids including foams, concentrated emulsions, colloidal glasses, and solvent-free nanoparticle-organic hybrid materials (NOHMs). The model considers a distribution of mesoscopic fluid elements that hop from trap to trap at a rate which is enhanced by the work done to strain the fluid element. While an SGR fluid has a broad exponential distribution of trap energies, the rheology of NOHMs is better described by a narrower energy distribution and we consider both types of trap energy distributions in this study. We introduce a tensorial version of these models with a hopping rate that depends on the orientation of the element relative to the mean stress field, allowing a range of relative strengths of the extensional and simple shear responses of the fluid. As an application of these models we consider the flow of a soft glassy material through a dilute fixed bed of fibers. The dilute fixed bed exhibits a range of local linear flows which alternate in a chaotic manner with time in a Lagrangian reference frame. It is amenable to an analytical treatment and has been used to characterize the strong flow response of many complex fluids including fiber suspensions, dilute polymer solutions and emulsions. We show that the accumulated strain in the fluid elements has an abrupt nonlinear growth at a Deborah number of order one in a manner similar to that observed for polymer solutions. The exponential dependence of the hopping rate on strain leads to a fluid element deformation that grows logarithmically with Deborah number at high Deborah numbers. SGR fluids having a broad range of trap energies flowing through fixed beds can exhibit a range of rheological behaviors at small Deborah numbers ranging from a yield stress, to a power law response and finally to Newtonian behavior.

A model for complex flows of soft glassy materials with application to flows through fixed fiber beds

KAUST Repository

Sarkar, Arijit; Koch, Donald L.

2015-01-01

© 2015 The Society of Rheology. The soft glassy rheology (SGR) model has successfully described the time dependent simple shear rheology of a broad class of complex fluids including foams, concentrated emulsions, colloidal glasses, and solvent-free nanoparticle-organic hybrid materials (NOHMs). The model considers a distribution of mesoscopic fluid elements that hop from trap to trap at a rate which is enhanced by the work done to strain the fluid element. While an SGR fluid has a broad exponential distribution of trap energies, the rheology of NOHMs is better described by a narrower energy distribution and we consider both types of trap energy distributions in this study. We introduce a tensorial version of these models with a hopping rate that depends on the orientation of the element relative to the mean stress field, allowing a range of relative strengths of the extensional and simple shear responses of the fluid. As an application of these models we consider the flow of a soft glassy material through a dilute fixed bed of fibers. The dilute fixed bed exhibits a range of local linear flows which alternate in a chaotic manner with time in a Lagrangian reference frame. It is amenable to an analytical treatment and has been used to characterize the strong flow response of many complex fluids including fiber suspensions, dilute polymer solutions and emulsions. We show that the accumulated strain in the fluid elements has an abrupt nonlinear growth at a Deborah number of order one in a manner similar to that observed for polymer solutions. The exponential dependence of the hopping rate on strain leads to a fluid element deformation that grows logarithmically with Deborah number at high Deborah numbers. SGR fluids having a broad range of trap energies flowing through fixed beds can exhibit a range of rheological behaviors at small Deborah numbers ranging from a yield stress, to a power law response and finally to Newtonian behavior.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

KAUST Repository

Huang, Chao-Li; Ho, Chuan-Wen; Chiang, Yu-Chung; Shigemoto, Yasumasa; Hsu, Tsai-Wen; Hwang, Chi-Chuan; Ge, Xue-Jun; Chen, Charles; Wu, Tai-Han; Chou, Chang-Hung; Huang, Hao-Jen; Gojobori, Takashi; Osada, Naoki; Chiang, Tzen-Yuh

2014-01-01

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

KAUST Repository

Huang, Chao-Li

2014-11-11

Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.

Flow-controlled magnetic particle manipulation

Science.gov (United States)

Grate, Jay W [West Richland, WA; Bruckner-Lea, Cynthia J [Richland, WA; Holman, David A [Las Vegas, NV

2011-02-22

Inventive methods and apparatus are useful for collecting magnetic materials in one or more magnetic fields and resuspending the particles into a dispersion medium, and optionally repeating collection/resuspension one or more times in the same or a different medium, by controlling the direction and rate of fluid flow through a fluid flow path. The methods provide for contacting derivatized particles with test samples and reagents, removal of excess reagent, washing of magnetic material, and resuspension for analysis, among other uses. The methods are applicable to a wide variety of chemical and biological materials that are susceptible to magnetic labeling, including, for example, cells, viruses, oligonucleotides, proteins, hormones, receptor-ligand complexes, environmental contaminants and the like.

A microfluidic device for simultaneous measurement of viscosity and flow rate of blood in a complex fluidic network.

Science.gov (United States)

Jun Kang, Yang; Yeom, Eunseop; Lee, Sang-Joon

2013-01-01

Blood viscosity has been considered as one of important biophysical parameters for effectively monitoring variations in physiological and pathological conditions of circulatory disorders. Standard previous methods make it difficult to evaluate variations of blood viscosity under cardiopulmonary bypass procedures or hemodialysis. In this study, we proposed a unique microfluidic device for simultaneously measuring viscosity and flow rate of whole blood circulating in a complex fluidic network including a rat, a reservoir, a pinch valve, and a peristaltic pump. To demonstrate the proposed method, a twin-shaped microfluidic device, which is composed of two half-circular chambers, two side channels with multiple indicating channels, and one bridge channel, was carefully designed. Based on the microfluidic device, three sequential flow controls were applied to identify viscosity and flow rate of blood, with label-free and sensorless detection. The half-circular chamber was employed to achieve mechanical membrane compliance for flow stabilization in the microfluidic device. To quantify the effect of flow stabilization on flow fluctuations, a formula of pulsation index (PI) was analytically derived using a discrete fluidic circuit model. Using the PI formula, the time constant contributed by the half-circular chamber is estimated to be 8 s. Furthermore, flow fluctuations resulting from the peristaltic pumps are completely removed, especially under periodic flow conditions within short periods (T viscosity with respect to varying flow rate conditions [(a) known blood flow rate via a syringe pump, (b) unknown blood flow rate via a peristaltic pump]. As a result, the flow rate and viscosity of blood can be simultaneously measured with satisfactory accuracy. In addition, the proposed method was successfully applied to identify the viscosity of rat blood, which circulates in a complex fluidic network. These observations confirm that the proposed method can be used for

Speckle contrast diffuse correlation tomography of complex turbid medium flow

Energy Technology Data Exchange (ETDEWEB)

Huang, Chong; Irwin, Daniel; Lin, Yu; Shang, Yu; He, Lian; Kong, Weikai; Yu, Guoqiang [Department of Biomedical Engineering, University of Kentucky, Lexington, Kentucky 40506 (United States); Luo, Jia [Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40506 (United States)

2015-07-15

Purpose: Developed herein is a three-dimensional (3D) flow contrast imaging system leveraging advancements in the extension of laser speckle contrast imaging theories to deep tissues along with our recently developed finite-element diffuse correlation tomography (DCT) reconstruction scheme. This technique, termed speckle contrast diffuse correlation tomography (scDCT), enables incorporation of complex optical property heterogeneities and sample boundaries. When combined with a reflectance-based design, this system facilitates a rapid segue into flow contrast imaging of larger, in vivo applications such as humans. Methods: A highly sensitive CCD camera was integrated into a reflectance-based optical system. Four long-coherence laser source positions were coupled to an optical switch for sequencing of tomographic data acquisition providing multiple projections through the sample. This system was investigated through incorporation of liquid and solid tissue-like phantoms exhibiting optical properties and flow characteristics typical of human tissues. Computer simulations were also performed for comparisons. A uniquely encountered smear correction algorithm was employed to correct point-source illumination contributions during image capture with the frame-transfer CCD and reflectance setup. Results: Measurements with scDCT on a homogeneous liquid phantom showed that speckle contrast-based deep flow indices were within 12% of those from standard DCT. Inclusion of a solid phantom submerged below the liquid phantom surface allowed for heterogeneity detection and validation. The heterogeneity was identified successfully by reconstructed 3D flow contrast tomography with scDCT. The heterogeneity center and dimensions and averaged relative flow (within 3%) and localization were in agreement with actuality and computer simulations, respectively. Conclusions: A custom cost-effective CCD-based reflectance 3D flow imaging system demonstrated rapid acquisition of dense boundary

PANTHERE, simulation software of dose flow rates for complex nuclear installations

International Nuclear Information System (INIS)

Longeot, M.; Dupont, B.; Coatanea, C.; Schumm, S.; Zweers, M.; Malvagi, F.; Trama, J.C.

2010-01-01

The authors present the PANTHERE simulation software developed by EDF-SEPTEN to determine gamma dose flow rate in any point of complex industrial installations. They present the current industrial version (PANTHEREV1) and its different applications, and more particularly an investigation in the field of qualification of hardware under irradiation in case of severe accident. They present the currently under development version (PANTHEREV2) which will be exploited in 2011

Simulations of Turbulent Flow Over Complex Terrain Using an Immersed-Boundary Method

Science.gov (United States)

DeLeon, Rey; Sandusky, Micah; Senocak, Inanc

2018-02-01

We present an immersed-boundary method to simulate high-Reynolds-number turbulent flow over the complex terrain of Askervein and Bolund Hills under neutrally-stratified conditions. We reconstruct both the velocity and the eddy-viscosity fields in the terrain-normal direction to produce turbulent stresses as would be expected from the application of a surface-parametrization scheme based on Monin-Obukhov similarity theory. We find that it is essential to be consistent in the underlying assumptions for the velocity reconstruction and the eddy-viscosity relation to produce good results. To this end, we reconstruct the tangential component of the velocity field using a logarithmic velocity profile and adopt the mixing-length model in the near-surface turbulence model. We use a linear interpolation to reconstruct the normal component of the velocity to enforce the impermeability condition. Our approach works well for both the Askervein and Bolund Hills when the flow is attached to the surface, but shows slight disagreement in regions of flow recirculation, despite capturing the flow reversal.

Simulations of Turbulent Flow Over Complex Terrain Using an Immersed-Boundary Method

Science.gov (United States)

DeLeon, Rey; Sandusky, Micah; Senocak, Inanc

2018-06-01

We present an immersed-boundary method to simulate high-Reynolds-number turbulent flow over the complex terrain of Askervein and Bolund Hills under neutrally-stratified conditions. We reconstruct both the velocity and the eddy-viscosity fields in the terrain-normal direction to produce turbulent stresses as would be expected from the application of a surface-parametrization scheme based on Monin-Obukhov similarity theory. We find that it is essential to be consistent in the underlying assumptions for the velocity reconstruction and the eddy-viscosity relation to produce good results. To this end, we reconstruct the tangential component of the velocity field using a logarithmic velocity profile and adopt the mixing-length model in the near-surface turbulence model. We use a linear interpolation to reconstruct the normal component of the velocity to enforce the impermeability condition. Our approach works well for both the Askervein and Bolund Hills when the flow is attached to the surface, but shows slight disagreement in regions of flow recirculation, despite capturing the flow reversal.

Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems

Science.gov (United States)

Demongeot, Jacques; Goles, Eric; Morvan, Michel; Noual, Mathilde; Sené, Sylvain

2010-01-01

One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally. PMID:20700525

Attraction basins as gauges of robustness against boundary conditions in biological complex systems.

Directory of Open Access Journals (Sweden)

Jacques Demongeot

Full Text Available One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally.

Complex formation of blueberry (Vaccinium angustifolium) anthocyanins during freeze-drying and its influence on their biological activity.

Science.gov (United States)

Correa-Betanzo, Julieta; Padmanabhan, Priya; Corredig, Milena; Subramanian, Jayasankar; Paliyath, Gopinadhan

2015-03-25

Biological activity of polyphenols is influenced by their uptake and is highly influenced by their interactions with the food matrix. This study evaluated the complex formation of blueberry polyphenols with fruit matrixes such as pectin and cellulose and their effect on the biological and antiproliferative properties of human colon cell lines HT-29 and CRL 1790. Free or complexed polyphenols were isolated by dialyzing aqueous or methanolic blueberry homogenates. Seven phenolic compounds and thirteen anthocyanins were identified in blueberry extracts. Blueberry extracts showed varying degrees of antioxidant and antiproliferative activities, as well as α-glucosidase activity. Fruit matrix containing cellulose and pectin, or purified polygalacturonic acid and cellulose, did not retain polyphenols and showed very low antioxidant or antiproliferative activities. These findings suggest that interactions between polyphenols and the food matrix may be more complex than a simple association and may play an important role in the bioefficacy of blueberry polyphenols.

Application of Biologically Based Lumping To Investigate the Toxicokinetic Interactions of a Complex Gasoline Mixture.

Science.gov (United States)

Jasper, Micah N; Martin, Sheppard A; Oshiro, Wendy M; Ford, Jermaine; Bushnell, Philip J; El-Masri, Hisham

2016-03-15

People are often exposed to complex mixtures of environmental chemicals such as gasoline, tobacco smoke, water contaminants, or food additives. We developed an approach that applies chemical lumping methods to complex mixtures, in this case gasoline, based on biologically relevant parameters used in physiologically based pharmacokinetic (PBPK) modeling. Inhalation exposures were performed with rats to evaluate the performance of our PBPK model and chemical lumping method. There were 109 chemicals identified and quantified in the vapor in the chamber. The time-course toxicokinetic profiles of 10 target chemicals were also determined from blood samples collected during and following the in vivo experiments. A general PBPK model was used to compare the experimental data to the simulated values of blood concentration for 10 target chemicals with various numbers of lumps, iteratively increasing from 0 to 99. Large reductions in simulation error were gained by incorporating enzymatic chemical interactions, in comparison to simulating the individual chemicals separately. The error was further reduced by lumping the 99 nontarget chemicals. The same biologically based lumping approach can be used to simplify any complex mixture with tens, hundreds, or thousands of constituents.

PIV measurement of the complex and transient cross-flow over a circular cylinder

International Nuclear Information System (INIS)

Kuwabara, Joji; Someya, Satoshi; Okamoto, Koji

2007-01-01

This paper describe about measurement for the complex and transient cross-flow over a circular cylinder with the dynamic (time resolved) PIV (particle image velocimetry) techniques. The experiment was carried out water flow tunnel with a working section of 50x50 mm, at the Reynolds number 6.7 x 10 3 to 2.7 x 10 4 . This circular cylinder constructed with MEXFLON resin, the end of circular cylinder is rigidly supported and the other is free. The MEXFLON is fluorine resin; its refractive index is almost same as the water with high transparency. Very high speed water flow among the test section had been clearly visualized and captured by high speed camera. The fluctuations of the flow structure also are clearly obtained with high spatial and high temporal resolution, 512x512pixel with 10,000fps. It corresponds to set up number of thousands LDV array at the test section. Consequently, we found there are asynchronous vibration between parallel-ward and perpendicular-ward to main flow. (author)

Visualization of Flow Alternatives, Lower Missouri River

Science.gov (United States)

Jacobson, Robert B.; Heuser, Jeanne

2002-01-01

Background The U.S. Army Corps of Engineers (COE) 'Missouri River Master Water Control Manual' (Master Manual) review has resulted in consideration of many flow alternatives for managing the water in the river (COE, 2001; 1998a). The purpose of this report is to present flow-management alternative model results in a way that can be easily visualized and understood. This report was updated in October 2001 to focus on the specific flow-management alternatives presented by the COE in the 'Master Manual Revised Draft Environmental Impact Statement' (RDEIS; COE, 2001). The original version (February 2000) is available by clicking here. The COE, U.S. Fish and Wildlife Service (FWS), Missouri River states, and Missouri River basin tribes have been participating in discussions concerning water management of the Missouri River mainstem reservoir system (MRMRS), the Missouri River Bank Stabilization and Navigation Project, and the Kansas River reservoir system since 1986. These discussions include general input to the revision of the Master Manual as well as formal consultation under Section 7 of the Endangered Species Act. In 2000, the FWS issued a Biological Opinion that prescribed changes to reservoir management on the Missouri River that were believed to be necessary to preclude jeopardy to three endangered species, the pallid sturgeon, piping plover, and interior least tern (USFWS, 2000). The combined Missouri River system is large and complex, including many reservoirs, control structures, and free-flowing reaches extending over a broad region. The ability to assess future impacts of altered management scenarios necessarily involves complex, computational models that attempt to integrate physical, chemical, biological, and economic effects. Graphical visualization of the model output is intended to improve understanding of the differences among flow-management alternatives.

Numerical simulation of complex turbulent Flow over a backward-facing step

International Nuclear Information System (INIS)

Silveira Neto, A.

1991-06-01

A statistical and topological study of a complex turbulent flow over a backward-facing step is realized by means of Direct and Large-Eddy Simulations. Direct simulations are performed in an isothermal and in a stratified two-dimensional case. In the isothermal case coherent structures have been obtained by the numerical simulation in the mixing layer downstream of the step. In a second step a thermal stratification is imposed on this flow. The coherent structures are in this case produced in the immediate vicinity of the step and disappear dowstream for increasing stratification. Afterwards, large-eddy simulations are carried out in the three-dimensional case. The subgrid-scale model is a local adaptation to the physical space of the spectral eddy-viscosity concept. The statistics of turbulence are in good agreement with the experimental data, corresponding to a small step configuration. Furthermore, calculations at higher step configuration show that the eddy structure of the flow presents striking analogies with the plane shear layers, with large billows shed behind the step, and intense longitudinal vortices strained between these billows [fr

Dermal tumorigen PAH and complex mixtures for biological research

International Nuclear Information System (INIS)

Griest, W.H.; Guerin, M.R.; Ho, C.

1985-01-01

Thirteen commercially available, commonly reported four-five ring dermal tumorigen PAHs, were determined in a set of complex mixtures consisting of crude and upgraded coal liquids, and petroleum crude oils and their distillate fractions. Semi-preparative scale, normal phase high performance liquid chromatographic fractionation followed by capillary column gas chromatography or gas chromatography-mass spectroscopy were used for the measurements. Deuterated or carbon-14 labeled PAH served as internal standards or allowed recovery corrections. Approaches for the preparation and measurement of radiolabeled PAH were examined to provide chemical probes for biological study. Synthetic routes for production of 14 C labeled dihydrobenzo[a]pyrene and 14 C- or 3 H 10-azabenzo[a]pyrene are being studied to provide tracers for fundamental studies in tracheal transplant and skin penetration systems. (DT)

Beyond disease susceptibility-Leveraging genome-wide association studies for new insights into complex disease biology.

Science.gov (United States)

Lee, J C

2017-12-01

Genetic studies in complex diseases have been highly successful, but have also been largely one-dimensional: predominantly focusing on the genetic contribution to disease susceptibility. While this is undoubtedly important-indeed it is a pre-requisite for understanding the mechanisms underlying disease development-there are many other important aspects of disease biology that have received comparatively little attention. In this review, I will discuss how existing genetic data can be leveraged to provide new insights into other aspects of disease biology, why such insights could change the way we think about complex disease, and how this could provide opportunities for better therapies and/or facilitate personalised medicine. To do this, I will use the example of Crohn's disease-a chronic form of inflammatory bowel disease that has been one of the main success stories in complex disease genetics. Indeed, thanks to genetic studies, we now have a much more detailed understanding of the processes involved in Crohn's disease development, but still know relatively little about what determines the subsequent disease course (prognosis) and why this differs so considerably between individuals. I will discuss how we came to realise that genetic variation plays an important role in determining disease prognosis and how this has changed the way we think about Crohn's disease genetics. This will illustrate how phenotypic data can be used to leverage new insights from genetic data and will provide a broadly applicable framework that could yield new insights into the biology of multiple diseases. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Systematic metabolite annotation and identification in complex biological extracts : combining robust mass spectrometry fragmentation and nuclear magnetic resonance spectroscopy

NARCIS (Netherlands)

Hooft, van der J.J.J.

2012-01-01

Detailed knowledge of the chemical content of organisms, organs, tissues, and cells is needed to fully characterize complex biological systems. The high chemical variety of compounds present in biological systems is illustrated by the presence of a large variety of compounds, ranging from apolar

Flow cytometric life cycle analysis in cellular radiation biology

International Nuclear Information System (INIS)

Wood, J.C.S.

1982-01-01

Three approaches to flow cytometric histogram analysis were developed: (1) differential histogram analysis, (2) DNA histogram analysis, and (3) multiparameter data analysis. These techniques were applied to an important unresolved problem in radiation biology. The initial responses to irradiation of a mammalian cell which occur during the first two cell cycles following the irradiation are of considerable interest to the radiation biologist. During the first two post-irradiation cell cycles, cells which ultimately will survive repair radiation-induced damage, while some cells begin to express some of the radiation-induced nuclear and chomatin damage. Caffeine- and thymidine-treated, and untreated gamma-irradiated cell populations were studied with respect to the radiation-induced G2 delay, deficient DNA synthesis, and the appearance of cells with abnormal DNA contents. It is hypothesized that the measured deficiency in DNA synthesis observed in the first post-irradiation cell cycle may be a result of daughter cells from abnormal first post-irradiation mitoses

Modelling of groundwater flow and flow paths for a large regional domain in northeast Uppland. A three-dimensional, mathematical modelling of groundwater flows and flow paths on a super-regional scale, for different complexity levels of the flow domain

International Nuclear Information System (INIS)

Holmen, Johan G.; Stigsson, Martin; Marsic, Niko; Gylling, Bjoern

2003-12-01

paths from theoretical repository positions; Properties of the discharge areas for the flow paths from the repository; Magnitude and direction of groundwater flow at different depths. To be able to evaluate the importance of the entities above we have established a chain of models, in which the complexity of the flow domain is increased for each model. For all models a basic set of analyses have been carried out. By comparing the results of these analyses, it is possible to draw conclusions of the importance of different hydrogeological entities and level of hydrogeological complexity. In this study the flow pattern of the groundwater (the flow field) was analysed by the use of flow paths. The applied models create flow paths by use of simulated particles, particles that follow the flow of groundwater through the model (i.e. particle tracking). The flow paths were released at a depth that corresponds to a possible depth of a repository, i.e. depths between 490 and 540 m below ground surface. Paths were released in a regular pattern, one or several paths in each volume (cell or element) studied, regardless of the flow through the volume studied. Paths were released in a regular pattern considering (i) the whole model or (ii) areas inside of the shoreline (not below the Sea). The flow paths were analysed considering length and breakthrough time. Release positions that produced the longest path lengths and the longest breakthrough times were identified. Only advective flow paths were studied in the flow path analyses, diffusion, mechanical mixing and retardation were not included in the flow path analyses. The hydrogeological complexity of the models representing the domain studied was increased gradually; step by step different hydrogeological entities were added to the model: local topographic undulation, regional fracture zones, lakes, clay-areas, shore level progress, and density dependent flow. For all the studied cases, the conductivity and the porosity of the rock

Modelling of groundwater flow and flow paths for a large regional domain in northeast Uppland. A three-dimensional, mathematical modelling of groundwater flows and flow paths on a super-regional scale, for different complexity levels of the flow domain

Energy Technology Data Exchange (ETDEWEB)

Holmen, Johan G.; Stigsson, Martin [Golder Associates, Stockholm (Sweden); Marsic, Niko; Gylling, Bjoern [Kemakta Konsult AB, Stockholm (Sweden)

2003-12-01

flow paths from theoretical repository positions; Properties of the discharge areas for the flow paths from the repository; Magnitude and direction of groundwater flow at different depths. To be able to evaluate the importance of the entities above we have established a chain of models, in which the complexity of the flow domain is increased for each model. For all models a basic set of analyses have been carried out. By comparing the results of these analyses, it is possible to draw conclusions of the importance of different hydrogeological entities and level of hydrogeological complexity. In this study the flow pattern of the groundwater (the flow field) was analysed by the use of flow paths. The applied models create flow paths by use of simulated particles, particles that follow the flow of groundwater through the model (i.e. particle tracking). The flow paths were released at a depth that corresponds to a possible depth of a repository, i.e. depths between 490 and 540 m below ground surface. Paths were released in a regular pattern, one or several paths in each volume (cell or element) studied, regardless of the flow through the volume studied. Paths were released in a regular pattern considering (i) the whole model or (ii) areas inside of the shoreline (not below the Sea). The flow paths were analysed considering length and breakthrough time. Release positions that produced the longest path lengths and the longest breakthrough times were identified. Only advective flow paths were studied in the flow path analyses, diffusion, mechanical mixing and retardation were not included in the flow path analyses. The hydrogeological complexity of the models representing the domain studied was increased gradually; step by step different hydrogeological entities were added to the model: local topographic undulation, regional fracture zones, lakes, clay-areas, shore level progress, and density dependent flow. For all the studied cases, the conductivity and the porosity of the

Complex blood flow patterns in an idealized left ventricle: A numerical study

Science.gov (United States)

Tagliabue, Anna; Dedè, Luca; Quarteroni, Alfio

2017-09-01

In this paper, we study the blood flow dynamics in a three-dimensional (3D) idealized left ventricle of the human heart whose deformation is driven by muscle contraction and relaxation in coordination with the action of the mitral and aortic valves. We propose a simplified but realistic mathematical treatment of the valves function based on mixed time-varying boundary conditions (BCs) for the Navier-Stokes equations modeling the flow. These switchings in time BCs, from natural to essential and vice versa, model either the open or the closed configurations of the valves. At the numerical level, these BCs are enforced by means of the extended Nitsche's method (Tagliabue et al., Int. J. Numer. Methods Fluids, 2017). Numerical results for the 3D idealized left ventricle obtained by means of Isogeometric Analysis are presented, discussed in terms of both instantaneous and phase-averaged quantities of interest and validated against those available in the literature, both experimental and computational. The complex blood flow patterns are analysed to describe the characteristic fluid properties, to show the transitional nature of the flow, and to highlight its main features inside the left ventricle. The sensitivity of the intraventricular flow patterns to the mitral valve properties is also investigated.

Complex systems of biological interest stability under ionising radiations

International Nuclear Information System (INIS)

Maclot, Sylvain

2014-01-01

This PhD work presents the study of stability of molecular systems of biological interest in the gas phase after interaction with ionising radiations. The use of ionising radiation can probe the physical chemistry of complex systems at the molecular scale and thus consider their intrinsic properties. Beyond the fundamental aspect, this work is part of the overall understanding of radiation effects on living organisms and in particular the use of ionizing radiation in radiotherapy. Specifically, this study focused on the use of low-energy multiply charged ions (tens of keV) provided by the GANIL (Caen), which includes most of the experiments presented. In addition, experiments using VUV photons were also conducted at synchrotron ELETTRA (Trieste, Italy). The bio-molecular systems studied are amino acids and nucleic acid constituents. Using an experimental crossed beams device allows interaction between biomolecules and ionising radiation leads mainly to the ionization and fragmentation of the system. The study of its relaxation dynamics is by time-of-flight mass spectrometry coupled to a coincidences measurements method. It is shown that an approach combining experiment and theory allows a detailed study of the fragmentation dynamics of complex systems. The results indicate that fragmentation is generally governed by the Coulomb repulsion but the intramolecular rearrangements involve specific relaxation mechanisms. (author) [fr

Comprehension of complex biological processes by analytical methods: how far can we go using mass spectrometry?

International Nuclear Information System (INIS)

Gerner, C.

2013-01-01

Comprehensive understanding of complex biological processes is the basis for many biomedical issues of great relevance for modern society including risk assessment, drug development, quality control of industrial products and many more. Screening methods provide means for investigating biological samples without research hypothesis. However, the first boom of analytical screening efforts has passed and we again need to ask whether and how to apply screening methods. Mass spectrometry is a modern tool with unrivalled analytical capacities. This applies to all relevant characteristics of analytical methods such as specificity, sensitivity, accuracy, multiplicity and diversity of applications. Indeed, mass spectrometry qualifies to deal with complexity. Chronic inflammation is a common feature of almost all relevant diseases challenging our modern society; these diseases are apparently highly diverse and include arteriosclerosis, cancer, back pain, neurodegenerative diseases, depression and other. The complexity of mechanisms regulating chronic inflammation is the reason for the practical challenge to deal with it. The presentation shall give an overview of capabilities and limitations of the application of this analytical tool to solve critical questions with great relevance for our society. (author)

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

Science.gov (United States)

Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

7th Annual Systems Biology Symposium: Systems Biology and Engineering

Energy Technology Data Exchange (ETDEWEB)

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity.

Science.gov (United States)

Speijer, Dave

2011-05-01

Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes. Copyright © 2011 WILEY Periodicals, Inc.

Cu(II AND Zn(II COMPLEX COMPOUNDS WITH BIGUANIDES AROMATIC DERIVATIVES. SYNTHESIS, CHARACTERIZATION, BIOLOGICAL ACTIVITY

Directory of Open Access Journals (Sweden)

Ticuţa Negreanu-Pîrjol

2011-05-01

Full Text Available In this paper we report the synthesis, physical-chemical characterization and antimicrobial activity of some new complex compounds of hetero-aromatic biguanides ligands, chlorhexidine base (CHX and chlorhexidine diacetate (CHXac2 with metallic ions Cu(II and Zn(II, in different molar ratio. The synthesized complexes were characterized by elemental chemical analysis and differential thermal analysis. The stereochemistry of the metallic ions was determined by infrared spectra, UV-Vis, EPR spectroscopy and magnetic susceptibility in the aim to establish the complexes structures. The biological activity of the new complex compounds was identified in solid technique by measuring minimum inhibition diameter of bacterial and fungal culture, against three standard pathogen strains, Escherichia coli ATCC 25922, Staphilococcus aureus ATCC 25923 and Candida albicans ATCC 10231. The results show an increased specific antimicrobial activity for the complexes chlorhexidine:Cu(II 1:1 and 1:2 compared with the one of the Zn(II complexes.

Independent variable complexity for regional regression of the flow duration curve in ungauged basins

Science.gov (United States)

Fouad, Geoffrey; Skupin, André; Hope, Allen

2016-04-01

The flow duration curve (FDC) is one of the most widely used tools to quantify streamflow. Its percentile flows are often required for water resource applications, but these values must be predicted for ungauged basins with insufficient or no streamflow data. Regional regression is a commonly used approach for predicting percentile flows that involves identifying hydrologic regions and calibrating regression models to each region. The independent variables used to describe the physiographic and climatic setting of the basins are a critical component of regional regression, yet few studies have investigated their effect on resulting predictions. In this study, the complexity of the independent variables needed for regional regression is investigated. Different levels of variable complexity are applied for a regional regression consisting of 918 basins in the US. Both the hydrologic regions and regression models are determined according to the different sets of variables, and the accuracy of resulting predictions is assessed. The different sets of variables include (1) a simple set of three variables strongly tied to the FDC (mean annual precipitation, potential evapotranspiration, and baseflow index), (2) a traditional set of variables describing the average physiographic and climatic conditions of the basins, and (3) a more complex set of variables extending the traditional variables to include statistics describing the distribution of physiographic data and temporal components of climatic data. The latter set of variables is not typically used in regional regression, and is evaluated for its potential to predict percentile flows. The simplest set of only three variables performed similarly to the other more complex sets of variables. Traditional variables used to describe climate, topography, and soil offered little more to the predictions, and the experimental set of variables describing the distribution of basin data in more detail did not improve predictions

A general method for bead-enhanced quantitation by flow cytometry

Science.gov (United States)

Montes, Martin; Jaensson, Elin A.; Orozco, Aaron F.; Lewis, Dorothy E.; Corry, David B.

2009-01-01

Flow cytometry provides accurate relative cellular quantitation (percent abundance) of cells from diverse samples, but technical limitations of most flow cytometers preclude accurate absolute quantitation. Several quantitation standards are now commercially available which, when added to samples, permit absolute quantitation of CD4+ T cells. However, these reagents are limited by their cost, technical complexity, requirement for additional software and/or limited applicability. Moreover, few studies have validated the use of such reagents in complex biological samples, especially for quantitation of non-T cells. Here we show that addition to samples of known quantities of polystyrene fluorescence standardization beads permits accurate quantitation of CD4+ T cells from complex cell samples. This procedure, here termed single bead-enhanced cytofluorimetry (SBEC), was equally capable of enumerating eosinophils as well as subcellular fragments of apoptotic cells, moieties with very different optical and fluorescent characteristics. Relative to other proprietary products, SBEC is simple, inexpensive and requires no special software, suggesting that the method is suitable for the routine quantitation of most cells and other particles by flow cytometry. PMID:17067632

Reactive oxygen species are generated by the respiratory complex II - evidence for lack of contribution of the reverse electron flow in complex I

Czech Academy of Sciences Publication Activity Database

Moreno-Sanchez, R.; Hernandez-Esquivel, L.; Rivero-Segura, N.A.; Marin-Hernandez, A.; Neužil, Jiří; Ralph, S. J.; Rodriguez-Enriquez, S.

2013-01-01

Roč. 280, č. 3 (2013), s. 927-938 ISSN 1742-464X Institutional research plan: CEZ:AV0Z50520701 Keywords : anti-cancer drugs * mitochondria * respiratory complex II Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.986, year: 2013

Dose prescription complexity versus tumor control probability in biologically conformal radiotherapy

International Nuclear Information System (INIS)

South, C. P.; Evans, P. M.; Partridge, M.

2009-01-01

The technical feasibility and potential benefits of voxel-based nonuniform dose prescriptions for biologically heterogeneous tumors have been widely demonstrated. In some cases, an ''ideal'' dose prescription has been generated by individualizing the dose to every voxel within the target, but often this voxel-based prescription has been discretized into a small number of compartments. The number of dose levels utilized and the methods used for prescribing doses and assigning tumor voxels to different dose compartments have varied significantly. The authors present an investigation into the relationship between the complexity of the dose prescription and the tumor control probability (TCP) for a number of these methods. The linear quadratic model of cell killing was used in conjunction with a number of modeled tumors heterogeneous in clonogen density, oxygenation, or proliferation. Models based on simple mathematical functions, published biological data, and biological image data were investigated. Target voxels were assigned to dose compartments using (i) simple rules based on the initial biological distribution, (ii) iterative methods designed to maximize the achievable TCP, or (iii) methods based on an ideal dose prescription. The relative performance of the simple rules was found to depend on the form of heterogeneity of the tumor, while the iterative and ideal dose methods performed comparably for all models investigated. In all cases the maximum achievable TCP was approached within the first few (typically two to five) compartments. Results suggest that irrespective of the pattern of heterogeneity, the optimal dose prescription can be well approximated using only a few dose levels but only if both the compartment boundaries and prescribed dose levels are well chosen.

Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks.

Science.gov (United States)

Kastrup, Christian J; Runyon, Matthew K; Lucchetta, Elena M; Price, Jessica M; Ismagilov, Rustem F

2008-04-01

Understanding the spatial dynamics of biochemical networks is both fundamentally important for understanding life at the systems level and also has practical implications for medicine, engineering, biology, and chemistry. Studies at the level of individual reactions provide essential information about the function, interactions, and localization of individual molecular species and reactions in a network. However, analyzing the spatial dynamics of complex biochemical networks at this level is difficult. Biochemical networks are nonequilibrium systems containing dozens to hundreds of reactions with nonlinear and time-dependent interactions, and these interactions are influenced by diffusion, flow, and the relative values of state-dependent kinetic parameters. To achieve an overall understanding of the spatial dynamics of a network and the global mechanisms that drive its function, networks must be analyzed as a whole, where all of the components and influential parameters of a network are simultaneously considered. Here, we describe chemical concepts and microfluidic tools developed for network-level investigations of the spatial dynamics of these networks. Modular approaches can be used to simplify these networks by separating them into modules, and simple experimental or computational models can be created by replacing each module with a single reaction. Microfluidics can be used to implement these models as well as to analyze and perturb the complex network itself with spatial control on the micrometer scale. We also describe the application of these network-level approaches to elucidate the mechanisms governing the spatial dynamics of two networkshemostasis (blood clotting) and early patterning of the Drosophila embryo. To investigate the dynamics of the complex network of hemostasis, we simplified the network by using a modular mechanism and created a chemical model based on this mechanism by using microfluidics. Then, we used the mechanism and the model to

Coupling-induced complexity in nephron models of renal blood flow regulation

DEFF Research Database (Denmark)

Laugesen, Jakob Lund; Sosnovtseva, Olga; Mosekilde, Erik

2010-01-01

Marsh DJ. Coupling-induced complexity in nephron models of renal blood flow regulation. Am J Physiol Regul Integr Comp Physiol 298: R997-R1006, 2010. First published February 10, 2010; doi: 10.1152/ajpregu.00714.2009.-Tubular pressure and nephron blood flow time series display two interacting...... oscillations in rats with normal blood pressure. Tubulo-glomerular feedback (TGF) senses NaCl concentration in tubular fluid at the macula densa, adjusts vascular resistance of the nephron's afferent arteriole, and generates the slower, larger-amplitude oscillations (0.02-0.04 Hz). The faster smaller...... of glomerular pressure caused by fluctuations of blood pressure. The oscillations become irregular in animals with chronic high blood pressure. TGF feedback gain is increased in hypertensive rats, leading to a stronger interaction between the two mechanisms. With a mathematical model that simulates tubular...

Complex Flow: Workshop Report; January 17-18, 2012, University of Colorado, Boulder

Energy Technology Data Exchange (ETDEWEB)

2012-06-01

The Department of Energy's Wind Program organized a two-day workshop designed to examine complex wind flow into and out of the wind farm environment and the resulting impacts on the mechanical workings of individual wind turbines. An improved understanding of these processes will subsequently drive down the risk involved for wind energy developers, financiers, and owner/operators, thus driving down the cost of energy.

Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography

Energy Technology Data Exchange (ETDEWEB)

Nguyen, Son N.; Liyu, Andrey V.; Chu, Rosalie K.; Anderton, Christopher R.; Laskin, Julia

2017-01-17

A new approach for constant distance mode mass spectrometry imaging of biological samples using nanospray desorption electrospray ionization (nano-DESI MSI) was developed by integrating a shear-force probe with nano-DESI probe. The technical concept and basic instrumental setup as well as general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enables constant-distance imaging mode via a computer controlled closed feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus Subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites including non-ribosomal peptides (surfactin, plipastatin and iturin) and iron-bound heme on the surface of living bacterial colonies ranging in diameter from 10 mm to 13 mm with height variations of up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Constant-mode nano-DESI MSI is ideally suited for imaging biological samples of complex topography in their native state.

Portal vein blood flow is related to characteristics of the migrating motor complex of the gastrointestinal tract

DEFF Research Database (Denmark)

Qvist, Niels; Rafaelsen, Søren Rafael; Troensegaard, P.

1994-01-01

Objective: To measure variation in portal blood flow during the interdigestive state in relation to the migrating motor complex (MMC) in healthy volunteers. Design: Portal blood flow was measured by a duplex and colour Doppler technique with 5-min intervals during an entire MMC cycle. Total....... Conclusion: Blood flow in the portal vein varies with the characteristics of the MMC, a relationship which must be considered in future studies in health and disease....

Mixing and Processing of Complex Biological Fluids

National Research Council Canada - National Science Library

Liepmann, Dorian

2003-01-01

... of microfluidic control on the makeup and molecular structure of biological fluids. For this project, we focused on two critical fluids that are biologically significant and that are of critical importance to DoD...

BioInt: an integrative biological object-oriented application framework and interpreter.

Science.gov (United States)

Desai, Sanket; Burra, Prasad

2015-01-01

BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects.

Science.gov (United States)

Shi, Zhenyu; Vickers, Claudia E

2016-12-01

Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com.

Multiphase Flow Dynamics 2 Mechanical Interactions

CERN Document Server

Kolev, Nikolay Ivanov

2012-01-01

Multi-phase flows are part of our natural environment such as tornadoes, typhoons, air and water pollution and volcanic activities as well as part of industrial technology such as power plants, combustion engines, propulsion systems, or chemical and biological industry. The industrial use of multi-phase systems requires analytical and numerical strategies for predicting their behavior. .In its fourth extended edition the successful monograph package “Multiphase Flow Daynmics” contains theory, methods and practical experience for describing complex transient multi-phase processes in arbitrary geometrical configurations, providing a systematic presentation of the theory and practice of numerical multi-phase fluid dynamics. In the present second volume the methods for describing the mechanical interactions in multiphase dynamics are provided. This fourth edition includes various updates, extensions, improvements and corrections.   "The literature in the field of multiphase flows is numerous. Therefore, it i...

A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology.

Science.gov (United States)

Jafari, Mohieddin; Ansari-Pour, Naser; Azimzadeh, Sadegh; Mirzaie, Mehdi

It is nearly half a century past the age of the introduction of the Central Dogma (CD) of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.

A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology.

Directory of Open Access Journals (Sweden)

Mohieddin Jafari

Full Text Available It is nearly half a century past the age of the introduction of the Central Dogma (CD of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.

Y-12 National Security Complex Biological Monitoring and Abatement Program 2007 Calendar Yeare Report

Energy Technology Data Exchange (ETDEWEB)

Peterson, M.J.; Greeley, M. S. Jr.; Morris, G. W.; Roy, W. K.; Ryan, M. G.; Smith, J. G.; Southworth, G. R.

2008-07-01

The National Pollutant Discharge Elimination System (NPDES) permit issued for the Oak Ridge Y-12 National Security Complex (Y-12 Complex) which became effective May 1, 2006, continued a requirement for a Biological Monitoring and Abatement Program (BMAP). The BMAP was originally developed in 1985 to demonstrate that the effluent limitations established for the Y-12 Complex protected the classified uses of the receiving stream (East Fork Poplar Creek: EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). The objectives of the current BMAP are similar, specifically to assess stream ecological conditions relative to regulatory limits and criteria, to assess ecological impacts as well as recovery in response to Y-12 operations, and to investigate the causes of continuing impacts. The BMAP consists of three tasks that reflect complementary approaches to evaluating the effects of the Y-12 Complex discharges on the biotic integrity of EFPC. These tasks include: (1) bioaccumulation monitoring, (2) benthic macroinvertebrate community monitoring, and (3) fish community monitoring. As required by the NPDES permit, the BMAP benthic macroinvertebrate community monitoring task includes studies to annually evaluate the receiving stream's biological integrity in comparison to TN Water Quality Criteria. BMAP monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) appropriate habitat distribution, and (5) access. The primary sampling sites include upper EFPC at kilometers (EFKs) 24.4 and 23.4 [upstream and downstream of Lake Reality (LR) respectively]; EFK 18.7 (also EFK 18.2 and 19), located

Direct Numerical Simulation of Turbulent Flow Over Complex Bathymetry

Science.gov (United States)

Yue, L.; Hsu, T. J.

2017-12-01

Direct numerical simulation (DNS) is regarded as a powerful tool in the investigation of turbulent flow featured with a wide range of time and spatial scales. With the application of coordinate transformation in a pseudo-spectral scheme, a parallelized numerical modeling system was created aiming at simulating flow over complex bathymetry with high numerical accuracy and efficiency. The transformed governing equations were integrated in time using a third-order low-storage Runge-Kutta method. For spatial discretization, the discrete Fourier expansion was adopted in the streamwise and spanwise direction, enforcing the periodic boundary condition in both directions. The Chebyshev expansion on Chebyshev-Gauss-Lobatto points was used in the wall-normal direction, assuming there is no-slip on top and bottom walls. The diffusion terms were discretized with a Crank-Nicolson scheme, while the advection terms dealiased with the 2/3 rule were discretized with an Adams-Bashforth scheme. In the prediction step, the velocity was calculated in physical domain by solving the resulting linear equation directly. However, the extra terms introduced by coordinate transformation impose a strict limitation to time step and an iteration method was applied to overcome this restriction in the correction step for pressure by solving the Helmholtz equation. The numerical solver is written in object-oriented C++ programing language utilizing Armadillo linear algebra library for matrix computation. Several benchmarking cases in laminar and turbulent flow were carried out to verify/validate the numerical model and very good agreements are achieved. Ongoing work focuses on implementing sediment transport capability for multiple sediment classes and parameterizations for flocculation processes.

Design principles in biological networks

Science.gov (United States)

Goyal, Sidhartha

Much of biology emerges from networks of interactions. Even in a single bacterium such as Escherichia coli, there are hundreds of coexisting gene and protein networks. Although biological networks are the outcome of evolution, various physical and biological constraints limit their functional capacity. The focus of this thesis is to understand how functional constraints such as optimal growth in mircoorganisms and information flow in signaling pathways shape the metabolic network of bacterium E. coli and the quorum sensing network of marine bacterium Vibrio harveyi, respectively. Metabolic networks convert basic elemental sources into complex building-blocks eventually leading to cell's growth. Therefore, typically, metabolic pathways are often coupled both by the use of a common substrate and by stoichiometric utilization of their products for cell growth. We showed that such a coupled network with product-feedback inhibition may exhibit limit-cycle oscillations which arise via a Hopf bifurcation. Furthermore, we analyzed several representative metabolic modules and find that, in all cases, simple product-feedback inhibition allows nearly optimal growth, in agreement with the predicted growth-rate by the flux-balance analysis (FBA). Bacteria have fascinating and diverse social lives. They display coordinated group behaviors regulated by quorum sensing (QS) systems. The QS circuit of V. harveyi integrates and funnels different ecological information through a common phosphorelay cascade to a set of small regulatory RNAs (sRNAs) that enables collective behavior. We analyzed the signaling properties and information flow in the QS circuit, which provides a model for information flow in signaling networks more generally. A comparative study of post-transcriptional and conventional transcriptional regulation suggest a niche for sRNAs in allowing cells to transition quickly yet reliably between distinct states. Furthermore, we develop a new framework for analyzing signal

Photopolymerization of complex emulsions with irregular shapes fabricated by multiplex coaxial flow focusing

Science.gov (United States)

Wu, Qiang; Yang, Chaoyu; Yang, Jianxin; Huang, Fangsheng; Liu, Guangli; Zhu, Zhiqiang; Si, Ting; Xu, Ronald X.

2018-02-01

We fabricate complex emulsions with irregular shapes in the microscale by a simple but effective multiplex coaxial flow focusing process. A multiphase cone-jet structure is steadily formed, and the compound liquid jet eventually breaks up into Janus microdroplets due to the perturbations propagating along the jet interfaces. The microdroplet shapes can be exclusively controlled by interfacial tensions of adjacent phases. Crescent-moon-shaped microparticles and microcapsules with designated structural characteristics are further produced under ultraviolet light of photopolymerization after removing one hemisphere of the Janus microdroplets. These complex emulsions have potential applications in bioscience, food, functional materials, and controlled drug delivery.

Wind Tunnel Modeling Of Wind Flow Over Complex Terrain

Science.gov (United States)

Banks, D.; Cochran, B.

2010-12-01

This presentation will describe the finding of an atmospheric boundary layer (ABL) wind tunnel study conducted as part of the Bolund Experiment. This experiment was sponsored by Risø DTU (National Laboratory for Sustainable Energy, Technical University of Denmark) during the fall of 2009 to enable a blind comparison of various air flow models in an attempt to validate their performance in predicting airflow over complex terrain. Bohlund hill sits 12 m above the water level at the end of a narrow isthmus. The island features a steep escarpment on one side, over which the airflow can be expected to separate. The island was equipped with several anemometer towers, and the approach flow over the water was well characterized. This study was one of only two only physical model studies included in the blind model comparison, the other being a water plume study. The remainder were computational fluid dynamics (CFD) simulations, including both RANS and LES. Physical modeling of air flow over topographical features has been used since the middle of the 20th century, and the methods required are well understood and well documented. Several books have been written describing how to properly perform ABL wind tunnel studies, including ASCE manual of engineering practice 67. Boundary layer wind tunnel tests are the only modelling method deemed acceptable in ASCE 7-10, the most recent edition of the American Society of Civil Engineers standard that provides wind loads for buildings and other structures for buildings codes across the US. Since the 1970’s, most tall structures undergo testing in a boundary layer wind tunnel to accurately determine the wind induced loading. When compared to CFD, the US EPA considers a properly executed wind tunnel study to be equivalent to a CFD model with infinitesimal grid resolution and near infinite memory. One key reason for this widespread acceptance is that properly executed ABL wind tunnel studies will accurately simulate flow separation

Flow simulations about steady-complex and unsteady moving configurations using structured-overlapped and unstructured grids

Science.gov (United States)

Newman, James C., III

1995-01-01

The limiting factor in simulating flows past realistic configurations of interest has been the discretization of the physical domain on which the governing equations of fluid flow may be solved. In an attempt to circumvent this problem, many Computational Fluid Dynamic (CFD) methodologies that are based on different grid generation and domain decomposition techniques have been developed. However, due to the costs involved and expertise required, very few comparative studies between these methods have been performed. In the present work, the two CFD methodologies which show the most promise for treating complex three-dimensional configurations as well as unsteady moving boundary problems are evaluated. These are namely the structured-overlapped and the unstructured grid schemes. Both methods use a cell centered, finite volume, upwind approach. The structured-overlapped algorithm uses an approximately factored, alternating direction implicit scheme to perform the time integration, whereas, the unstructured algorithm uses an explicit Runge-Kutta method. To examine the accuracy, efficiency, and limitations of each scheme, they are applied to the same steady complex multicomponent configurations and unsteady moving boundary problems. The steady complex cases consist of computing the subsonic flow about a two-dimensional high-lift multielement airfoil and the transonic flow about a three-dimensional wing/pylon/finned store assembly. The unsteady moving boundary problems are a forced pitching oscillation of an airfoil in a transonic freestream and a two-dimensional, subsonic airfoil/store separation sequence. Accuracy was accessed through the comparison of computed and experimentally measured pressure coefficient data on several of the wing/pylon/finned store assembly's components and at numerous angles-of-attack for the pitching airfoil. From this study, it was found that both the structured-overlapped and the unstructured grid schemes yielded flow solutions of

The Benefits of Mouse Keeping--An Empirical Study on Students' Flow and Intrinsic Motivation in Biology Lessons

Science.gov (United States)

Meyer, Annika; Klingenberg, Konstantin; Wilde, Matthias

2016-01-01

Contact with living animals is an exceptional possibility within biology education to facilitate an intense immersion into the study topic and even allow for a flow experience (Csikszentmihalyi 2000). Further, it might affect the perceptions of the students' basic needs for autonomy and competence and thereby their quality of motivation (Deci and…

Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.

Science.gov (United States)

Transtrum, Mark K; Qiu, Peng

2016-05-01

The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior.

From Molecules to Life: Quantifying the Complexity of Chemical and Biological Systems in the Universe.

Science.gov (United States)

Böttcher, Thomas

2018-01-01

Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms. Entities with a certain level of information complexity directly require a functionally complex mechanism for their production or replication and are hence indicative for life-like systems. In order to describe entities combining molecular and information complexity, the term biogenic unit was introduced. Exemplified biogenic unit complexities were calculated for ribozymes, protein enzymes, multimeric protein complexes, and even an entire virus particle. Complexities of prokaryotic and eukaryotic cells, as well as multicellular organisms, were estimated. Thereby distinct evolutionary stages in complexity space were identified. The here developed approach to compare the complexity of biogenic units allows for the first time to address the gradual characteristics of prebiotic and life-like systems without the need for a definition of life. This operational concept may guide our search for life in the Universe, and it may direct the investigations of prebiotic trajectories that lead towards the evolution of complexity at the origins of life.

How nature works complexity in interdisciplinary research and applications

CERN Document Server

Sanayei, Ali; Zenil, Hector; Rössler, Otto

2014-01-01

This book is based on the outcome of the “2012 Interdisciplinary Symposium on Complex Systems” held at the island of Kos.  The book consists of 12 selected papers of the symposium starting with a comprehensive overview and classification of complexity problems, continuing by chapters about complexity, its observation, modeling and its applications to solving various problems including real-life applications. More exactly, readers will have an encounter with the structural complexity of vortex flows, the use of chaotic dynamics within evolutionary algorithms, complexity in synthetic biology, types of complexity hidden inside evolutionary dynamics and possible controlling methods, complexity of rugged landscapes, and more. All selected papers represent innovative ideas, philosophical overviews and state-of-the-art discussions on aspects of complexity.  The book will be useful as instructional material for senior undergraduate and entry-level graduate students in computer science, physics, applied mathemat...

Chemical and biological activity in open flows: A dynamical system approach

International Nuclear Information System (INIS)

Tel, Tamas; Moura, Alessandro de; Grebogi, Celso; Karolyi, Gyoergy

2005-01-01

Chemical and biological processes often take place in fluid flows. Many of them, like environmental or microfluidical ones, generate filamentary patterns which have a fractal structure, due to the presence of chaos in the underlying advection dynamics. In such cases, hydrodynamical stirring strongly couples to the reactivity of the advected species: the outcome of the reaction is then typically different from that of the same reaction taking place in a well-mixed environment. Here we review recent progress in this field, which became possible due to the application of methods taken from dynamical system theory. We place special emphasis on the derivation of effective rate equations which contain singular terms expressing the fact that the reaction takes place on a moving fractal catalyst, on the unstable foliation of the reaction free advection dynamics

A chemical-biological evaluation of rhodium(I) N-heterocyclic carbene complexes as prospective anticancer drugs.

Science.gov (United States)

Oehninger, Luciano; Küster, Laura Nadine; Schmidt, Claudia; Muñoz-Castro, Alvaro; Prokop, Aram; Ott, Ingo

2013-12-23

Rhodium(I) complexes bearing N-heterocyclic carbene (NHC) ligands have been widely used in catalytic chemistry, but there are very few reports of biological properties of these organometallics. A series of Rh(I)-NHC derivatives with 1,5-cyclooctadiene and CO as secondary ligands were synthesized, characterized, and biologically investigated as prospective antitumor drug candidates. Pronounced antiproliferative effects were noted for all complexes, along with moderate inhibitory activity of thioredoxin reductase (TrxR) and efficient binding to biomolecules (DNA, albumin). Biodistribution studies showed that the presence of albumin lowered the cellular uptake and confirmed the transport of rhodium into the nuclei. Changes in the mitochondrial membrane potential (MMP) were observed as well as DNA fragmentation in wild-type and daunorubicin- or vincristine-resistant Nalm-6 leukemia cells. Overall, these studies indicated that Rh(I)-NHC fragments could be used as partial structures of new antitumor agents, in particular in those drugs designed to address resistant malignant tissues. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulation of groundwater flow in the glacial aquifer system of northeastern Wisconsin with variable model complexity

Science.gov (United States)

Juckem, Paul F.; Clark, Brian R.; Feinstein, Daniel T.

2017-05-04

The U.S. Geological Survey, National Water-Quality Assessment seeks to map estimated intrinsic susceptibility of the glacial aquifer system of the conterminous United States. Improved understanding of the hydrogeologic characteristics that explain spatial patterns of intrinsic susceptibility, commonly inferred from estimates of groundwater age distributions, is sought so that methods used for the estimation process are properly equipped. An important step beyond identifying relevant hydrogeologic datasets, such as glacial geology maps, is to evaluate how incorporation of these resources into process-based models using differing levels of detail could affect resulting simulations of groundwater age distributions and, thus, estimates of intrinsic susceptibility.This report describes the construction and calibration of three groundwater-flow models of northeastern Wisconsin that were developed with differing levels of complexity to provide a framework for subsequent evaluations of the effects of process-based model complexity on estimations of groundwater age distributions for withdrawal wells and streams. Preliminary assessments, which focused on the effects of model complexity on simulated water levels and base flows in the glacial aquifer system, illustrate that simulation of vertical gradients using multiple model layers improves simulated heads more in low-permeability units than in high-permeability units. Moreover, simulation of heterogeneous hydraulic conductivity fields in coarse-grained and some fine-grained glacial materials produced a larger improvement in simulated water levels in the glacial aquifer system compared with simulation of uniform hydraulic conductivity within zones. The relation between base flows and model complexity was less clear; however, the relation generally seemed to follow a similar pattern as water levels. Although increased model complexity resulted in improved calibrations, future application of the models using simulated particle

Investigation of the complex electroviscous effects on electrolyte (single and multiphase) flow in porous medi.

Science.gov (United States)

Bolet, A. J. S.; Linga, G.; Mathiesen, J.

2017-12-01

Surface charge is an important control parameter for wall-bounded flow of electrolyte solution. The electroviscous effect has been studied theoretically in model geometries such as infinite capillaries. However, in more complex geometries a quantification of the electroviscous effect is a non-trival task due to strong non-linarites of the underlying equations. In general, one has to rely on numerical methods. Here we present numerical studies of the full three-dimensional steady state Stokes-Poisson-Nernst-Planck problem in order to model electrolyte transport in artificial porous samples. The simulations are performed using the finite element method. From the simulation, we quantity how the electroviscous effect changes the general flow permeability in complex three-dimensional porous media. The porous media we consider are mostly generated artificially by connecting randomly dispersed cylindrical pores. Furthermore, we present results of electric driven two-phase immiscible flow in two dimensions. The simulations are performed by augmenting the above equations with a phase field model to handle and track the interaction between the two fluids (using parameters corresponding to oil-water interfaces, where oil non-polar). In particular, we consider the electro-osmotic effect on imbibition due to charged walls and electrolyte-solution.

Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat

Czech Academy of Sciences Publication Activity Database

Šafář, Jan; Bartoš, Jan; Janda, Jaroslav; Bellec, A.; Kubaláková, Marie; Valárik, Miroslav; Pateyron, S.; Weiserová, Jitka; Tušková, Radka; Čihalíková, Jarmila; Vrána, Jan; Šimková, Hana; Faivre-Rampant, P.; Sourdille, P.; Caboche, M.; Bernard, M.; Doležel, Jaroslav; Chalhoub, B.

2004-01-01

Roč. 39, - (2004), s. 960-968 ISSN 0960-7412 R&D Projects: GA ČR GA522/03/0354; GA ČR GA521/04/0607; GA MZe QC1336 Institutional research plan: CEZ:AV0Z5038910 Keywords : wheat * flow sorting * DNA library Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.367, year: 2004

Rich complex behaviour of self-assembled nanoparticles far from equilibrium.

Science.gov (United States)

Ilday, Serim; Makey, Ghaith; Akguc, Gursoy B; Yavuz, Özgün; Tokel, Onur; Pavlov, Ihor; Gülseren, Oguz; Ilday, F Ömer

2017-04-26

A profoundly fundamental question at the interface between physics and biology remains open: what are the minimum requirements for emergence of complex behaviour from nonliving systems? Here, we address this question and report complex behaviour of tens to thousands of colloidal nanoparticles in a system designed to be as plain as possible: the system is driven far from equilibrium by ultrafast laser pulses that create spatiotemporal temperature gradients, inducing Marangoni flow that drags particles towards aggregation; strong Brownian motion, used as source of fluctuations, opposes aggregation. Nonlinear feedback mechanisms naturally arise between flow, aggregate and Brownian motion, allowing fast external control with minimal intervention. Consequently, complex behaviour, analogous to those seen in living organisms, emerges, whereby aggregates can self-sustain, self-regulate, self-replicate, self-heal and can be transferred from one location to another, all within seconds. Aggregates can comprise only one pattern or bifurcated patterns can coexist, compete, endure or perish.

Comparisons of complex network based models and real train flow model to analyze Chinese railway vulnerability

International Nuclear Information System (INIS)

Ouyang, Min; Zhao, Lijing; Hong, Liu; Pan, Zhezhe

2014-01-01

Recently numerous studies have applied complex network based models to study the performance and vulnerability of infrastructure systems under various types of attacks and hazards. But how effective are these models to capture their real performance response is still a question worthy of research. Taking the Chinese railway system as an example, this paper selects three typical complex network based models, including purely topological model (PTM), purely shortest path model (PSPM), and weight (link length) based shortest path model (WBSPM), to analyze railway accessibility and flow-based vulnerability and compare their results with those from the real train flow model (RTFM). The results show that the WBSPM can produce the train routines with 83% stations and 77% railway links identical to the real routines and can approach the RTFM the best for railway vulnerability under both single and multiple component failures. The correlation coefficient for accessibility vulnerability from WBSPM and RTFM under single station failures is 0.96 while it is 0.92 for flow-based vulnerability; under multiple station failures, where each station has the same failure probability fp, the WBSPM can produce almost identical vulnerability results with those from the RTFM under almost all failures scenarios when fp is larger than 0.62 for accessibility vulnerability and 0.86 for flow-based vulnerability

Development of Smoothed Particle Hydrodynamics for Flow in Complex Geometries and Application of Open Source Software for the Simulation of Turbulent Flow

DEFF Research Database (Denmark)

Obeidat, Anas Hassan MohD

devel-oping a computational method which can deal with complex fluid structure, simulate complex geometers that change topology is particular challenging as the connectivity of the computational domain may change dynamically, and still eÿcient is important. In this thesis we are presenting a remeshed...... engines removes combustion gases from the engine cylinder and fills up the cylinder with the fresh air charge for the next cycle. Understanding the scavenging flow is crucial for the development of such engines, since it a˙ects fuel consumption, engine cooling and production of pollutants. We consider...

Deciphering deterioration mechanisms of complex diseases based on the construction of dynamic networks and systems analysis

Science.gov (United States)

Li, Yuanyuan; Jin, Suoqin; Lei, Lei; Pan, Zishu; Zou, Xiufen

2015-03-01

The early diagnosis and investigation of the pathogenic mechanisms of complex diseases are the most challenging problems in the fields of biology and medicine. Network-based systems biology is an important technique for the study of complex diseases. The present study constructed dynamic protein-protein interaction (PPI) networks to identify dynamical network biomarkers (DNBs) and analyze the underlying mechanisms of complex diseases from a systems level. We developed a model-based framework for the construction of a series of time-sequenced networks by integrating high-throughput gene expression data into PPI data. By combining the dynamic networks and molecular modules, we identified significant DNBs for four complex diseases, including influenza caused by either H3N2 or H1N1, acute lung injury and type 2 diabetes mellitus, which can serve as warning signals for disease deterioration. Function and pathway analyses revealed that the identified DNBs were significantly enriched during key events in early disease development. Correlation and information flow analyses revealed that DNBs effectively discriminated between different disease processes and that dysfunctional regulation and disproportional information flow may contribute to the increased disease severity. This study provides a general paradigm for revealing the deterioration mechanisms of complex diseases and offers new insights into their early diagnoses.

Synthesis, spectroscopic characterization and in vitro cytotoxicities of new organometallic palladium complexes with biologically active β-diketones; Biological evaluation probing of the interaction mechanism with DNA/Protein and molecular docking

Science.gov (United States)

Karami, Kazem; Rafiee, Mina; Lighvan, Zohreh Mehri; Zakariazadeh, Mostafa; Faal, Ali Yeganeh; Esmaeili, Seyed-Alireza; Momtazi-Borojeni, Amir Abbas

2018-02-01

[Pd{(C,N)sbnd C6H4CH (CH3)NH}(CUR)] (3) and [Pd2{(C,N)sbnd C6H4CH(CH3)NH2}2(μ-N3CS2)] (4) [cur = 1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dion] novel organometallic complexes with biologically active ligands have been prepared and characterized via elemental analysis, multinuclear spectroscopic techniques (1H, and 13C NMR and IR) and their biological activities, including antitumoral activity and DNA-protein interactions have been investigated. Fluorescence spectroscopy used to study the interaction of the complexes with BSA have shown the affinity of the complexes for these proteins with relatively high binding constant values and the changed secondary structure of BSA in the presence of the complexes. In the meantime, spectroscopy and competitive titration have been applied to investigate the interaction of complexes with Warfarin and Ibuprofen site markers for sites I and II, respectively, with BSA. The results have suggested that the locations of complexes 3 and 4 are sites II and I, respectively. UV-Vis spectroscopy, emission titration and helix melting methods have been used to study the interaction of these complexes with CT-DNA, indicating that complexes are bound to CT-DNA by intercalation binding mode. In addition, good cytotoxic activity against MCF-7 (human breast cancer) and JURKAT (human leukemia) cell line has been shown by both complexes whereas low cytotoxicity was exerted on normal peripheral blood mononuclear cells.

Numerical simulation of swirling flow in complex hydroturbine draft tube using unsteady statistical turbulence models

Energy Technology Data Exchange (ETDEWEB)

Paik, Joongcheol [University of Minnesota; Sotiropoulos, Fotis [University of Minnesota; Sale, Michael J [ORNL

2005-06-01

A numerical method is developed for carrying out unsteady Reynolds-averaged Navier-Stokes (URANS) simulations and detached-eddy simulations (DESs) in complex 3D geometries. The method is applied to simulate incompressible swirling flow in a typical hydroturbine draft tube, which consists of a strongly curved 90 degree elbow and two piers. The governing equations are solved with a second-order-accurate, finite-volume, dual-time-stepping artificial compressibility approach for a Reynolds number of 1.1 million on a mesh with 1.8 million nodes. The geometrical complexities of the draft tube are handled using domain decomposition with overset (chimera) grids. Numerical simulations show that unsteady statistical turbulence models can capture very complex 3D flow phenomena dominated by geometry-induced, large-scale instabilities and unsteady coherent structures such as the onset of vortex breakdown and the formation of the unsteady rope vortex downstream of the turbine runner. Both URANS and DES appear to yield the general shape and magnitude of mean velocity profiles in reasonable agreement with measurements. Significant discrepancies among the DES and URANS predictions of the turbulence statistics are also observed in the straight downstream diffuser.

Lattice Boltzmann approach for complex nonequilibrium flows.

Science.gov (United States)

Montessori, A; Prestininzi, P; La Rocca, M; Succi, S

2015-10-01

We present a lattice Boltzmann realization of Grad's extended hydrodynamic approach to nonequilibrium flows. This is achieved by using higher-order isotropic lattices coupled with a higher-order regularization procedure. The method is assessed for flow across parallel plates and three-dimensional flows in porous media, showing excellent agreement of the mass flow with analytical and numerical solutions of the Boltzmann equation across the full range of Knudsen numbers, from the hydrodynamic regime to ballistic motion.

Complex Physical, Biophysical and Econophysical Systems

Science.gov (United States)

Dewar, Robert L.; Detering, Frank

1. Introduction to complex and econophysics systems: a navigation map / T. Aste and T. Di Matteo -- 2. An introduction to fractional diffusion / B. I. Henry, T.A.M. Langlands and P. Straka -- 3. Space plasmas and fusion plasmas as complex systems / R. O. Dendy -- 4. Bayesian data analysis / M. S. Wheatland -- 5. Inverse problems and complexity in earth system science / I. G. Enting -- 6. Applied fluid chaos: designing advection with periodically reoriented flows for micro to geophysical mixing and transport enhancement / G. Metcalfe -- 7. Approaches to modelling the dynamical activity of brain function based on the electroencephalogram / D. T. J. Liley and F. Frascoli -- 8. Jaynes' maximum entropy principle, Riemannian metrics and generalised least action bound / R. K. Niven and B. Andresen -- 9. Complexity, post-genomic biology and gene expression programs / R. B. H. Williams and O. J.-H. Luo -- 10. Tutorials on agent-based modelling with NetLogo and network analysis with Pajek / M. J. Berryman and S. D. Angus.

Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network

Directory of Open Access Journals (Sweden)

Pooja Sharma

2018-06-01

Full Text Available Protein complexes are known to play a major role in controlling cellular activity in a living being. Identifying complexes from raw protein protein interactions (PPIs is an important area of research. Earlier work has been limited mostly to yeast. Such protein complex identification methods, when applied to large human PPIs often give poor performance. We introduce a novel method called CSC to detect protein complexes. The method is evaluated in terms of positive predictive value, sensitivity and accuracy using the datasets of the model organism, yeast and humans. CSC outperforms several other competing algorithms for both organisms. Further, we present a framework to establish the usefulness of CSC in analyzing the influence of a given disease gene in a complex topologically as well as biologically considering eight major association factors. Keywords: Protein complex, Connectivity, Semantic similarity, Contribution

Interplay between Dephasing and Geometry and Directed Heat Flow in Exciton Transfer Complexes

OpenAIRE

Dubi, Yonatan

2015-01-01

The striking efficiency of energy transfer in natural photosynthetic systems and the recent evidence of long-lived quantum coherence in biological light harvesting complexes has triggered much excitement, due to the evocative possibility that these systems - essential to practically all life on earth -- use quantum mechanical effects to achieve optimal functionality. A large body of theoretical work has addressed the role of local environments in determining the transport properties of excito...

Absence of hydrocortisone from cytoplasmic hormone-protein complexes formed in vivo after administration of biologically active doses of [3H] hydrocortisone

International Nuclear Information System (INIS)

Voigt, J.; Grote, H.; Sekeris, C.E.

1981-01-01

After administration of [ 3 H] hydrocortisone to adrenalectomized rats, hormone-protein complexes were isolated from liver cytosol by DEAE-cellulose chromatography. After application of biologically active and inactive doses of hydrocortisone five binding components were detected eluting at the same salt concentrations as the hormone-protein complexes observed after incubation of cytosol with [ 3 H] hydrocortisone in vitro. The isolated hormone-protein fractions were acidified and extracted with ethylacetate and the steroids were analyzed by thin-layer chromatography. No significant amount of hydrocortisone could be detected in any of the complexes formed in vivo 5-60 min after administration of biologically active doses of hydrocortisone. 3xi,11β,17α,20xi, 21-Pentahydroxypregnane, steroidal carboxy acids, glucuronides and a very polar conjugate of hydrocortisone were found in the different fractions. After an in vivo dose of hydrocortisone of about 1/5000th of the minimal dose required for enzyme induction, hydrocortisone could be found in all the cytoplasmic hormone-protein complexes formed. In contrast to the cytoplasmic hormone-protein complexes, hydrocortisone could be readily demonstrated in nuclei isolated after the administration of biologically active doses of hormone, although acid metabolites were found to represent the main part of the radioactive compounds present in the nuclei. These acid metabolites were located in the nuclear envelope. (orig.)

High performance parallel computing of flows in complex geometries: I. Methods

International Nuclear Information System (INIS)

Gourdain, N; Gicquel, L; Montagnac, M; Vermorel, O; Staffelbach, G; Garcia, M; Boussuge, J-F; Gazaix, M; Poinsot, T

2009-01-01

Efficient numerical tools coupled with high-performance computers, have become a key element of the design process in the fields of energy supply and transportation. However flow phenomena that occur in complex systems such as gas turbines and aircrafts are still not understood mainly because of the models that are needed. In fact, most computational fluid dynamics (CFD) predictions as found today in industry focus on a reduced or simplified version of the real system (such as a periodic sector) and are usually solved with a steady-state assumption. This paper shows how to overcome such barriers and how such a new challenge can be addressed by developing flow solvers running on high-end computing platforms, using thousands of computing cores. Parallel strategies used by modern flow solvers are discussed with particular emphases on mesh-partitioning, load balancing and communication. Two examples are used to illustrate these concepts: a multi-block structured code and an unstructured code. Parallel computing strategies used with both flow solvers are detailed and compared. This comparison indicates that mesh-partitioning and load balancing are more straightforward with unstructured grids than with multi-block structured meshes. However, the mesh-partitioning stage can be challenging for unstructured grids, mainly due to memory limitations of the newly developed massively parallel architectures. Finally, detailed investigations show that the impact of mesh-partitioning on the numerical CFD solutions, due to rounding errors and block splitting, may be of importance and should be accurately addressed before qualifying massively parallel CFD tools for a routine industrial use.

Extraction of Multithread Channel Networks With a Reduced-Complexity Flow Model

Science.gov (United States)

Limaye, Ajay B.

2017-10-01

Quantitative measures of channel network geometry inform diverse applications in hydrology, sediment transport, ecology, hazard assessment, and stratigraphic prediction. These uses require a clear, objectively defined channel network. Automated techniques for extracting channels from topography are well developed for convergent channel networks and identify flow paths based on land-surface gradients. These techniques—even when they allow multiple flow paths—do not consistently capture channel networks with frequent bifurcations (e.g., in rivers, deltas, and alluvial fans). This paper uses multithread rivers as a template to develop a new approach for channel extraction suitable for channel networks with divergences. Multithread channels are commonly mapped using observed inundation extent, and I generalize this approach using a depth-resolving, reduced-complexity flow model to map inundation patterns for fixed topography across an arbitrary range of discharge. A case study for the Platte River, Nebraska, reveals that (1) the number of bars exposed above the water surface, bar area, and the number of wetted channel threads (i.e., braiding index) peak at intermediate discharge; (2) the anisotropic scaling of bar dimensions occurs for a range of discharge; and (3) the maximum braiding index occurs at a corresponding reference discharge that provides an objective basis for comparing the planform geometry of multithread rivers. Mapping by flow depth overestimates braiding index by a factor of 2. The new approach extends channel network extraction from topography to the full spectrum of channel patterns, with the potential for comparing diverse channel patterns at scales from laboratory experiments to natural landscapes.

Complex-Wide Waste Flow Analysis V1.0 verification and validation report

International Nuclear Information System (INIS)

Hsu, K.M.; Lundeen, A.S.; Oswald, K.B.; Shropshire, D.E.; Robinson, J.M.; West, W.H.

1997-01-01

The complex-wide waste flow analysis model (CWWFA) was developed to assist the Department of Energy (DOE) Environmental Management (EM) Office of Science and Technology (EM-50) to evaluate waste management scenarios with emphasis on identifying and prioritizing technology development opportunities to reduce waste flows and public risk. In addition, the model was intended to support the needs of the Complex-Wide Environmental Integration (EMI) team supporting the DOE's Accelerating Cleanup: 2006 Plan. CWWFA represents an integrated environmental modeling system that covers the life cycle of waste management activities including waste generation, interim process storage, retrieval, characterization and sorting, waste preparation and processing, packaging, final interim storage, transport, and disposal at a final repository. The CWWFA shows waste flows through actual site-specific and facility-specific conditions. The system requirements for CWWFA are documented in the Technical Requirements Document (TRD). The TRD is intended to be a living document that will be modified over the course of the execution of CWWFA development. Thus, it is anticipated that CWWFA will continue to evolve as new requirements are identified (i.e., transportation, small sites, new streams, etc.). This report provides a documented basis for system verification of CWWFA requirements. System verification is accomplished through formal testing and evaluation to ensure that all performance requirements as specified in the TRD have been satisfied. A Requirement Verification Matrix (RVM) was used to map the technical requirements to the test procedures. The RVM is attached as Appendix A. Since February of 1997, substantial progress has been made toward development of the CWWFA to meet the system requirements. This system verification activity provides a baseline on system compliance to requirements and also an opportunity to reevaluate what requirements need to be satisfied in FY-98

Experimental and Numerical Modelling of Flow over Complex Terrain: The Bolund Hill

Science.gov (United States)

Conan, Boris; Chaudhari, Ashvinkumar; Aubrun, Sandrine; van Beeck, Jeroen; Hämäläinen, Jari; Hellsten, Antti

2016-02-01

In the wind-energy sector, wind-power forecasting, turbine siting, and turbine-design selection are all highly dependent on a precise evaluation of atmospheric wind conditions. On-site measurements provide reliable data; however, in complex terrain and at the scale of a wind farm, local measurements may be insufficient for a detailed site description. On highly variable terrain, numerical models are commonly used but still constitute a challenge regarding simulation and interpretation. We propose a joint state-of-the-art study of two approaches to modelling atmospheric flow over the Bolund hill: a wind-tunnel test and a large-eddy simulation (LES). The approach has the particularity of describing both methods in parallel in order to highlight their similarities and differences. The work provides a first detailed comparison between field measurements, wind-tunnel experiments and numerical simulations. The systematic and quantitative approach used for the comparison contributes to a better understanding of the strengths and weaknesses of each model and, therefore, to their enhancement. Despite fundamental modelling differences, both techniques result in only a 5 % difference in the mean wind speed and 15 % in the turbulent kinetic energy (TKE). The joint comparison makes it possible to identify the most difficult features to model: the near-ground flow and the wake of the hill. When compared to field data, both models reach 11 % error for the mean wind speed, which is close to the best performance reported in the literature. For the TKE, a great improvement is found using the LES model compared to previous studies (20 % error). Wind-tunnel results are in the low range of error when compared to experiments reported previously (40 % error). This comparison highlights the potential of such approaches and gives directions for the improvement of complex flow modelling.

Redox-flow battery of actinide complexes

International Nuclear Information System (INIS)

Yamamura, Tomoo; Shiokawa, Yoshinobu

2006-01-01

Np battery and U battery were developed. We suggested that Np redox-flow battery should be (-)|Np 3+ ,Np 4+ ||NpO 2 + ,NpO 2 2+ |(+), and U battery (-)|[U III T 2 ] - ,[U IV T 2 ] 0 ||[U V O 2 T] - ,[U VI O 2 T] 0 |(+). The electromotive force at 50 % charge of Np and U battery is 1.10 V and 1.04 V, respectively. The energy efficiency of 70 mA/cm 2 of Np and U battery shows 99 % and 98 %, respectively. V redox-flow battery, electrode reactions of An battery, Np battery, U battery and future of U battery are described. The concept of V redox-flow battery, comparison of energy efficiency of Np, U and V battery, oxidation state and ionic species of 3d transition metals and main An, Purbe diagram of Np and U aqueous solution, shift of redox potential of β-diketones by pKa, and specifications of three redox-flow batteries are reported. (S.Y.)

Reynolds number and friction coefficient for axial-parallel flow through complex cross-sections

International Nuclear Information System (INIS)

Markfort, D.

1975-01-01

Thermal and hydraulic lay-out of reactor fuel elements and other heat transfer equipment makes use of established functional relationship between dimensionless characters, the former being transferred from circular tube to more complex geometries. The stringent requirement (from theory) for 'geometrical similarity' is bypassed by defining 'equivalent diameters'. But dimensionless numbers may be derived from 'flow-integral-conditions' while the geometrical components contained therein reduce if not completely abolish the requirement for geometrical similarity. The derivation is demonstrated by using the Reynolds number. A friction coefficient valid for any kind of flow regime can be defined using integral-conditions. Correlations of friction coefficient and Reynolds number using universal-velocity profiles confirm the analysis when compared to well known experimental data. (orig.) [de

PREFACE: Complex Networks: from Biology to Information Technology

Science.gov (United States)

Barrat, A.; Boccaletti, S.; Caldarelli, G.; Chessa, A.; Latora, V.; Motter, A. E.

2008-06-01

The field of complex networks is one of the most active areas in contemporary statistical physics. Ten years after seminal work initiated the modern study of networks, interest in the field is in fact still growing, as indicated by the ever increasing number of publications in network science. The reason for such a resounding success is most likely the simplicity and broad significance of the approach that, through graph theory, allows researchers to address a variety of different complex systems within a common framework. This special issue comprises a selection of contributions presented at the workshop 'Complex Networks: from Biology to Information Technology' held in July 2007 in Pula (Cagliari), Italy as a satellite of the general conference STATPHYS23. The contributions cover a wide range of problems that are currently among the most important questions in the area of complex networks and that are likely to stimulate future research. The issue is organised into four sections. The first two sections describe 'methods' to study the structure and the dynamics of complex networks, respectively. After this methodological part, the issue proceeds with a section on applications to biological systems. The issue closes with a section concentrating on applications to the study of social and technological networks. The first section, entitled Methods: The Structure, consists of six contributions focused on the characterisation and analysis of structural properties of complex networks: The paper Motif-based communities in complex networks by Arenas et al is a study of the occurrence of characteristic small subgraphs in complex networks. These subgraphs, known as motifs, are used to define general classes of nodes and their communities by extending the mathematical expression of the Newman-Girvan modularity. The same line of research, aimed at characterising network structure through the analysis of particular subgraphs, is explored by Bianconi and Gulbahce in Algorithm

Synthesis, Spectroscopic Characterization and Biological Activities of Transition Metal Complexes Derived from a Tridentate Schiff Base

Directory of Open Access Journals (Sweden)

J. Senthil Kumaran

2013-01-01

Full Text Available A new series of Cu (II, Ni (II, Co (II and Zn (II complexes have been synthesized from the Schiff base derived from 4-hydroxy-3-methoxybenzylidine-4-aminoantipyrine and 2-aminophenol. The structural features have been determined from their elemental analysis, magnetic susceptibility, molar conductance, Mass, IR, UV-Vis, 1H-NMR, 13C-NMR and ESR spectral studies. The redox behavior of the copper complex has been studied by cyclic voltammetry. The data confirm that the complexes have composition of ML2 type. The electronic absorption spectral data of the complexes propose an octahedral geometry around the central metal ion. All the metal complexes with DNA structure were guided by the presence of inter-molecular C–H⋯O and C–H⋯N hydrogen bonds. The biological activity of the synthesized compounds were tested against the bacterial species such as Bacillus subtilis, Staphylococcus aureus, Proteus vulgaris and fungal species such as Candida albicans by the well-diffusion method.

Choice of boundary condition for lattice-Boltzmann simulation of moderate-Reynolds-number flow in complex domains.

Science.gov (United States)

Nash, Rupert W; Carver, Hywel B; Bernabeu, Miguel O; Hetherington, James; Groen, Derek; Krüger, Timm; Coveney, Peter V

2014-02-01

Modeling blood flow in larger vessels using lattice-Boltzmann methods comes with a challenging set of constraints: a complex geometry with walls and inlets and outlets at arbitrary orientations with respect to the lattice, intermediate Reynolds (Re) number, and unsteady flow. Simple bounce-back is one of the most commonly used, simplest, and most computationally efficient boundary conditions, but many others have been proposed. We implement three other methods applicable to complex geometries [Guo, Zheng, and Shi, Phys. Fluids 14, 2007 (2002); Bouzidi, Firdaouss, and Lallemand, Phys. Fluids 13, 3452 (2001); Junk and Yang, Phys. Rev. E 72, 066701 (2005)] in our open-source application hemelb. We use these to simulate Poiseuille and Womersley flows in a cylindrical pipe with an arbitrary orientation at physiologically relevant Re number (1-300) and Womersley (4-12) numbers and steady flow in a curved pipe at relevant Dean number (100-200) and compare the accuracy to analytical solutions. We find that both the Bouzidi-Firdaouss-Lallemand (BFL) and Guo-Zheng-Shi (GZS) methods give second-order convergence in space while simple bounce-back degrades to first order. The BFL method appears to perform better than GZS in unsteady flows and is significantly less computationally expensive. The Junk-Yang method shows poor stability at larger Re number and so cannot be recommended here. The choice of collision operator (lattice Bhatnagar-Gross-Krook vs multiple relaxation time) and velocity set (D3Q15 vs D3Q19 vs D3Q27) does not significantly affect the accuracy in the problems studied.

Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

Energy Technology Data Exchange (ETDEWEB)

Manno, D; Filippo, E; Fiore, R; Serra, A [Dipartimento di Scienza dei Materiali, Universita del Salento, Lecce (Italy); Urso, E; Rizzello, A; Maffia, M [Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita del Salento, Lecce (Italy)

2010-04-23

Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP{sup C}. In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP{sup C} at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

Monitoring prion protein expression in complex biological samples by SERS for diagnostic applications

International Nuclear Information System (INIS)

Manno, D; Filippo, E; Fiore, R; Serra, A; Urso, E; Rizzello, A; Maffia, M

2010-01-01

Surface-enhanced Raman spectroscopy (SERS) allows a new insight into the analysis of cell physiology. In this work, the difficulty of producing suitable substrates that, besides permitting the amplification of the Raman signal, do not interact with the biological material causing alteration, has been overcome by a combined method of hydrothermal green synthesis and thermal annealing. The SERS analysis of the cell membrane has been performed with special attention to the cellular prion protein PrP C . In addition, SERS has also been used to reveal the prion protein-Cu(II) interaction in four different cell models (B104, SH-SY5Y, GN11, HeLa), expressing PrP C at different levels. A significant implication of the current work consists of the intriguing possibility of revealing and quantifying prion protein expression in complex biological samples by a cheap SERS-based method, replacing the expensive and time-consuming immuno-assay systems commonly employed.

Stopped Flow Kinetics of MnII Catalysed Periodate Oxidation of 2, 3- dimethylaniline - Evaluation of Stability Constant of the Ternary Intermediate Complex

Directory of Open Access Journals (Sweden)

Rajneesh Dutt Kaushik

2015-03-01

Full Text Available The formation of ternary intermediate unstable complex during the oxidation of aromatic amines by periodate ion catalysed by MnII has been proposed in case of some anilines. This paper is the first report on stopped-flow kinetic study and evaluation of stability constant of ternary complex forming in the MnII - catalysed periodate oxidation of 2, 3-dimethylaniline (D in acetone-water medium. Stop-flow spectrophotometric method was used to study the ternary complex formation and to determine its stability constant. The stop-flow trace shows the reaction to occur in two steps. The first step, which is presumably the formation of ternary complex, is relatively fast while the second stage is relatively quite slow. The stability constant evaluated for D - MnII - IO4- ternary complex by determining  equilibrium absorbance is (2.2 ± 1.0 × 105. Kinetics of ternary complex formation was defined by the rate law(A  under pseudo first order conditions. ln{[C2]eq / ( [C2]eq -[C2]} = kobs . t (A where, kobs is the pseudo first order rate constant, [C2] is concentration of ternary complex at given time t, and [C2]eq is the equilibrium concentration of ternary complex. © 2015 BCREC UNDIP. All rights reservedReceived: 3rd October 2014; Revised: 4th December 2014; Accepted: 15th December 2014How to Cite: Kaushik, R.D., Agarwal, R., Tyagi, P., Singh, O., Singh, J. (2015. Stopped Flow Kinetics of MnII Catalysed Periodate Oxidation of 2,3-dimethylaniline - Evaluation of Stability Constant of the Ternary Intermediate Complex. Bulletin of Chemical Reaction Engineering & Catalysis, 10 (1: 78-87. (doi:10.9767/bcrec.10.1.7621.78-87Permalink/DOI: http://dx.doi.org/10.9767/bcrec.10.1.7621.78-87

Modeling Groundwater Flow System of a Drainage Basin in the Basement Complex Environment of Southwestern Nigera

Science.gov (United States)

Akinwumiju, Akinola S.; Olorunfemi, Martins O.

2018-05-01

This study attempted to model the groundwater flow system of a drainage basin within the Basement Complex environment of Southwestern Nigeria. Four groundwater models were derived from Vertical Electrical Sounding (VES) Data, remotely sensed data, geological information (hydrolineaments and lithology) and borehole data. Subsequently, two sub-surface (local and regional) flow systems were delineated in the study area. While the local flow system is controlled by surface topography, the regional flow system is controlled by the networks of intermediate and deep seated faults/fractures. The local flow system is characterized by convergence, divergence, inflow and outflow in places, while the regional flow system is dominated by NNE-SSW and W-E flow directions. Minor flow directions include NNW-SSE and E-W with possible linkages to the main flow-paths. The NNE-SSW regional flow system is a double open ended flow system with possible linkage to the Niger Trough. The W-E regional flow system is a single open ended system that originates within the study area (with possible linkage to the NNE-SSW regional flow system) and extends to Ikogosi in the adjoining drainage basin. Thus, the groundwater drainage basin of the study area is much larger and extensive than its surface drainage basin. The all year round flowing (perennial) rivers are linked to groundwater outcrops from faults/fractures and contact zones. Consequently, larger percentage of annual rainwater usually leaves the basin in form of runoff and base flow. Therefore, the basin is categorized as a donor basin but with suspected subsurface water input at its northeastern axis.

Quantify the complexity of turbulence

Science.gov (United States)

Tao, Xingtian; Wu, Huixuan

2017-11-01

Many researchers have used Reynolds stress, power spectrum and Shannon entropy to characterize a turbulent flow, but few of them have measured the complexity of turbulence. Yet as this study shows, conventional turbulence statistics and Shannon entropy have limits when quantifying the flow complexity. Thus, it is necessary to introduce new complexity measures- such as topology complexity and excess information-to describe turbulence. Our test flow is a classic turbulent cylinder wake at Reynolds number 8100. Along the stream-wise direction, the flow becomes more isotropic and the magnitudes of normal Reynolds stresses decrease monotonically. These seem to indicate the flow dynamics becomes simpler downstream. However, the Shannon entropy keeps increasing along the flow direction and the dynamics seems to be more complex, because the large-scale vortices cascade to small eddies, the flow is less correlated and more unpredictable. In fact, these two contradictory observations partially describe the complexity of a turbulent wake. Our measurements (up to 40 diameters downstream the cylinder) show that the flow's degree-of-complexity actually increases firstly and then becomes a constant (or drops slightly) along the stream-wise direction. University of Kansas General Research Fund.

Decoding complex flow-field patterns in visual working memory.

Science.gov (United States)

Christophel, Thomas B; Haynes, John-Dylan

2014-05-01

There has been a long history of research on visual working memory. Whereas early studies have focused on the role of lateral prefrontal cortex in the storage of sensory information, this has been challenged by research in humans that has directly assessed the encoding of perceptual contents, pointing towards a role of visual and parietal regions during storage. In a previous study we used pattern classification to investigate the storage of complex visual color patterns across delay periods. This revealed coding of such contents in early visual and parietal brain regions. Here we aim to investigate whether the involvement of visual and parietal cortex is also observable for other types of complex, visuo-spatial pattern stimuli. Specifically, we used a combination of fMRI and multivariate classification to investigate the retention of complex flow-field stimuli defined by the spatial patterning of motion trajectories of random dots. Subjects were trained to memorize the precise spatial layout of these stimuli and to retain this information during an extended delay. We used a multivariate decoding approach to identify brain regions where spatial patterns of activity encoded the memorized stimuli. Content-specific memory signals were observable in motion sensitive visual area MT+ and in posterior parietal cortex that might encode spatial information in a modality independent manner. Interestingly, we also found information about the memorized visual stimulus in somatosensory cortex, suggesting a potential crossmodal contribution to memory. Our findings thus indicate that working memory storage of visual percepts might be distributed across unimodal, multimodal and even crossmodal brain regions. Copyright © 2014 Elsevier Inc. All rights reserved.

Three-dimensional models of cancer for pharmacology and cancer cell biology: capturing tumor complexity in vitro/ex vivo.

Science.gov (United States)

Hickman, John A; Graeser, Ralph; de Hoogt, Ronald; Vidic, Suzana; Brito, Catarina; Gutekunst, Matthias; van der Kuip, Heiko

2014-09-01

Cancers are complex and heterogeneous pathological "organs" in a dynamic interplay with their host. Models of human cancer in vitro, used in cancer biology and drug discovery, are generally highly reductionist. These cancer models do not incorporate complexity or heterogeneity. This raises the question as to whether the cancer models' biochemical circuitry (not their genome) represents, with sufficient fidelity, a tumor in situ. Around 95% of new anticancer drugs eventually fail in clinical trial, despite robust indications of activity in existing in vitro pre-clinical models. Innovative models are required that better capture tumor biology. An important feature of all tissues, and tumors, is that cells grow in three dimensions. Advances in generating and characterizing simple and complex (with added stromal components) three-dimensional in vitro models (3D models) are reviewed in this article. The application of stirred bioreactors to permit both scale-up/scale-down of these cancer models and, importantly, methods to permit controlled changes in environment (pH, nutrients, and oxygen) are also described. The challenges of generating thin tumor slices, their utility, and potential advantages and disadvantages are discussed. These in vitro/ex vivo models represent a distinct move to capture the realities of tumor biology in situ, but significant characterization work still remains to be done in order to show that their biochemical circuitry accurately reflects that of a tumor. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detection of circulating immune complexes by Raji cell assay: comparison of flow cytometric and radiometric methods

International Nuclear Information System (INIS)

Kingsmore, S.F.; Crockard, A.D.; Fay, A.C.; McNeill, T.A.; Roberts, S.D.; Thompson, J.M.

1988-01-01

Several flow cytometric methods for the measurement of circulating immune complexes (CIC) have recently become available. We report a Raji cell flow cytometric assay (FCMA) that uses aggregated human globulin (AHG) as primary calibrator. Technical advantages of the Raji cell flow cytometric assay are discussed, and its clinical usefulness is evaluated in a method comparison study with the widely used Raji cell immunoradiometric assay. FCMA is more precise and has greater analytic sensitivity for AHG. Diagnostic sensitivity by the flow cytometric method is superior in systemic lupus erythematosus (SLE), rheumatoid arthritis, and vasculitis patients: however, diagnostic specificity is similar for both assays, but the reference interval of FCMA is narrower. Significant correlations were found between CIC levels obtained with both methods in SLE, rheumatoid arthritis, and vasculitis patients and in longitudinal studies of two patients with cerebral SLE. The Raji cell FCMA is recommended for measurement of CIC levels to clinical laboratories with access to a flow cytometer

Intermittency in Complex Flows

Science.gov (United States)

Ben Mahjoub, Otman; Redondo, Jose M.

2017-04-01

Experimental results of the complex turbulent wake of a cilinder in 2D [1] and 3D flows [2] were used to investigate the scaling of structure functions, similar research was also performed on wave propagation and breaking in the Ocean [3], in the the stratified Atmosphere (ABL) [4] and in a 100large flume (UPC) for both regular and irregular waves, where long time series of waves propagating and generating breaking turbulence velocity rms and higher order measurements were taken in depth. [3,5] by means of a velocimeter SONTEK3-D. The probability distribution functions of the velocity differences and their non Gaussian distribution related to the energy spectrum indicate that irregularity is an important source of turbulence. From Kolmogorov's K41 and K61 intermittency correction: the p th-order longitudinal velocity structure function δul at scale l in the inertial range of three-dimensional fully developed turbulence is related by ⟨δup⟩ = ⟨(u(x+ l)- u(x))p⟩ ˜ ɛp0/3lp/3 l where ⟨...⟩ represents the spatial average over flow domain, with ɛ0 the mean energy dissipation per unit mass and l is the separation distance. The importance of the random nature of the energy dissipation led to the K62 theory of intermittency, but locality and non-homogeneity are key issues. p p/3 p/3 ξd ⟨δul⟩ ˜ ⟨ɛl ⟩l ˜ l and ξp = p 3 + τp/3 , where now ɛl is a fractal energy dissipation at scale l, τp/3 is the scaling of and ξp is the scaling exponent of the velocity structure function of order p. Both in K41 and K62, the structure functions of third order related to skewness is ξ3 = 1. But this is not true either. We show that scaling exponents ξp do deviate from early studies that only investigated homogeneous turbulence, where a large inertial range dominates. The use of multi-fractal analysis and improvements on Structure function calculations on standard Enhanced mixing is an essential property of turbulence and efforts to alter and to control

Informing biological design by integration of systems and synthetic biology.

Science.gov (United States)

Smolke, Christina D; Silver, Pamela A

2011-03-18

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

From the track to the ocean: Using flow control to improve marine bio-logging tags for cetaceans.

Directory of Open Access Journals (Sweden)

Giovani Fiore

Full Text Available Bio-logging tags are an important tool for the study of cetaceans, but superficial tags inevitably increase hydrodynamic loading. Substantial forces can be generated by tags on fast-swimming animals, potentially affecting behavior and energetics or promoting early tag removal. Streamlined forms have been used to reduce loading, but these designs can accelerate flow over the top of the tag. This non-axisymmetric flow results in large lift forces (normal to the animal that become the dominant force component at high speeds. In order to reduce lift and minimize total hydrodynamic loading this work presents a new tag design (Model A that incorporates a hydrodynamic body, a channel to reduce fluid speed differences above and below the housing and wing to redirect flow to counter lift. Additionally, three derivatives of the Model A design were used to examine the contribution of individual flow control features to overall performance. Hydrodynamic loadings of four models were compared using computational fluid dynamics (CFD. The Model A design eliminated all lift force and generated up to ~30 N of downward force in simulated 6 m/s aligned flow. The simulations were validated using particle image velocimetry (PIV to experimentally characterize the flow around the tag design. The results of these experiments confirm the trends predicted by the simulations and demonstrate the potential benefit of flow control elements for the reduction of tag induced forces on the animal.

Modelling and simulation of regenerators with complex flow arrangements for active magnetocaloric refrigeration

DEFF Research Database (Denmark)

Lei, Tian; Nielsen, Kaspar Kirstein; Engelbrecht, Kurt

2014-01-01

Compared to a conventional vapor compression refrigera-tion system, a magnetocaloric refrigerator has many advantages, such as potentially high efficiency, low vibration and avoidance of refrigerants that deplete the ozone layer and cause the green-house effect. As a main component of the active...... magnetic re-generative refrigerator, the regenerator plays an important role in the cooling performance and efficiency of the whole system. However, the regenerator design is constrained by several exter-nal factors, such as the geometry of the magnetic field source and flow resistance. In this work, novel...... regenerators with complex flow arrange-ments, providing high performance at lower pressure drop, are investigated. Correspondingly a one dimensional model is pre-sented and comparative studies between novel and conventional regenerators are carried out by simulation. The effect of regen-erator geometries...

Biology and Mechanics of Blood Flows Part II: Mechanics and Medical Aspects

CERN Document Server

Thiriet, Marc

2008-01-01

Biology and Mechanics of Blood Flows presents the basic knowledge and state-of-the-art techniques necessary to carry out investigations of the cardiovascular system using modeling and simulation. Part II of this two-volume sequence, Mechanics and Medical Aspects, refers to the extraction of input data at the macroscopic scale for modeling the cardiovascular system, and complements Part I, which focuses on nanoscopic and microscopic components and processes. This volume contains chapters on anatomy, physiology, continuum mechanics, as well as pathological changes in the vasculature walls including the heart and their treatments. Methods of numerical simulations are given and illustrated in particular by application to wall diseases. This authoritative book will appeal to any biologist, chemist, physicist, or applied mathematician interested in the functioning of the cardiovascular system.

Synthesis, spectroscopic and biological studies of transition metal complexes of novel schiff bases derived from cephradine and sugars

International Nuclear Information System (INIS)

Naz, N.; Iqbal, M.Z.

2011-01-01

Fe(II), Co(II) and Ni(II) metal complexes of novel schiff bases derived from Cephradine and sugars (D-Glucose, L. Arabinose and D-Galactose) were synthesized and characterized by elemental analysis, magnetic susceptibility, thermal analysis, electronic absorption and FT-IR spectral studies. It has been found that schiff bases behave as bi-dentate-ligands forming complexes with 1:2 (metal:ligand) stoichiometry. the neutral nature of the complexes was confirmed by their low conductance values. The biological activities of complexes have been evaluated against two gram negative (Escherichia coli and Pseudomonas aeruginosa) and two gram positive (Bacillus subtilis and staphylococcus aureus) bacteria by Agar diffusion disc method. It has been found that the complexes have higher activity as compared to the pure Cephradine against the same bacteria. (author)

Quantification of biopharmaceuticals and biomarkers in complex biological matrices: a comparison of liquid chromatography coupled to tandem mass spectrometry and ligand binding assays

NARCIS (Netherlands)

Bults, Peter; van de Merbel, Nico C; Bischoff, Rainer

2015-01-01

The quantification of proteins (biopharmaceuticals or biomarkers) in complex biological samples such as blood plasma requires exquisite sensitivity and selectivity, as all biological matrices contain myriads of proteins that are all made of the same 20 proteinogenic amino acids, notwithstanding

Towards physical principles of biological evolution

Science.gov (United States)

Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

2018-03-01

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice

The influence of venous blood flow on the retinal ganglion cell complex in patients with primary open angle glaucoma

Directory of Open Access Journals (Sweden)

N. I. Kurysheva

2014-07-01

Full Text Available Purpose: To study the influence of venous blood flow on the ganglion cell complex (GCC in patients with preperimetric and perimetric open angle glaucoma.Methods: 74 patients were included in the research. 59 eyes and 62 eyes were diagnosed with preperimetric and perimetric open angle glaucoma respectively. The mean age was 56.5±10.5 years. 22 (12 female and 10 male healthy individuals constituted the control group. The ganglion cell complex and retinal nerve fibre layer were evaluated with the help of optical coherence tomography (RTVue-100 OCT, Optovue, Inc., Fremont, CA. Ocular blood flow was measured by Color Doppler Imaging (multifunctional VOLUSON 730 ProSystem. The statistical analysis included correlation between GCC and RNFL thickness in both glaucoma groups.Results: The results showed a statistically significant reduction of venous blood flow velocity in both glaucoma groups compared to the control group. No difference in venous blood flow parameters between two glaucoma groups was found, except resistance index, which was higher in perimetric group in comparison to preperimetric group. A correlation was also obtained between venous blood flow parameters and GCC and RNFL thickness in both glaucoma groups.Conclusion: Early GCC damage in glaucoma might occur due to venous blood flow reduction. This fact may be of great value in understanding glaucoma pathogenesis and search for novel treatment options.

Multiphase Flow Dynamics 1 Fundamentals

CERN Document Server

Kolev, Nikolay Ivanov

2012-01-01

Multi-phase flows are part of our natural environment such as tornadoes, typhoons, air and water pollution and volcanic activities as well as part of industrial technology such as power plants, combustion engines, propulsion systems, or chemical and biological industry. The industrial use of multi-phase systems requires analytical and numerical strategies for predicting their behavior. In its fourth extended edition the successful monograph package “Multiphase Flow Dynmics” contains theory, methods and practical experience for describing complex transient multi-phase processes in arbitrary geometrical configurations, providing a systematic presentation of the theory and practice of numerical multi-phase fluid dynamics. In the present first volume the local volume and time averaging is used to derive a complete set of conservation equations for three fluids each of them having multi components as constituents. Large parts of the book are devoted on the design of successful numerical methods for solving the...

Large Eddy Simulations of Complex Flows in IC-Engine's Exhaust Manifold and Turbine

OpenAIRE

Fjällman, Johan

2014-01-01

The thesis deals with the flow in pipe bends and radial turbines geometries that are commonly found in an Internal Combustion Engine (ICE). The development phase of internal combustion engines relies more and more on simulations as an important complement to experiments. This is partly because of the reduction in development cost and the shortening of the development time. This is one of the reasons for the need of more accurate and predictive simulations. By using more complex computational ...

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

Science.gov (United States)

Moodie, Stuart; Le Novère, Nicolas; Demir, Emek; Mi, Huaiyu; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Integration of FULLSWOF2D and PeanoClaw: Adaptivity and Local Time-Stepping for Complex Overland Flows

KAUST Repository

Unterweger, K.; Wittmann, R.; Neumann, P.; Weinzierl, T.; Bungartz, H.-J.

2015-01-01

© Springer International Publishing Switzerland 2015. We propose to couple our adaptive mesh refinement software PeanoClaw with existing solvers for complex overland flows that are tailored to regular Cartesian meshes. This allows us to augment them

Drosophila melanogaster--the model organism of choice for the complex biology of multi-cellular organisms

Science.gov (United States)

Beckingham, Kathleen M.; Armstrong, J. Douglas; Texada, Michael J.; Munjaal, Ravi; Baker, Dean A.

2005-01-01

Drosophila melanogaster has been intensely studied for almost 100 years. The sophisticated array of genetic and molecular tools that have evolved for analysis of gene function in this organism are unique. Further, Drosophila is a complex multi-cellular organism in which many aspects of development and behavior parallel those in human beings. These combined advantages have permitted research in Drosophila to make seminal contributions to the understanding of fundamental biological processes and ensure that Drosophila will continue to provide unique insights in the genomic era. An overview of the genetic methodologies available in Drosophila is given here, together with examples of outstanding recent contributions of Drosophila to our understanding of cell and organismal biology. The growing contribution of Drosophila to our knowledge of gravity-related responses is addressed.

Morphodynamics of Travertine Dam/Waterfall Growth due to the Interaction of Biological Activity, Water Flow and Limestone Emplacement

Science.gov (United States)

Izumi, N.; Parker, G.

2012-12-01

Plitvice Lakes in Croatia are characterized by a step-like train of lakes and waterfalls. The waterfalls are located at the crests of naturally-emplaced dams. The top of each dam grows upward at the rate of a few millimeters per year. It is thought that the upward growth of these dams is caused by the interaction of water flow and biological activity, resulting in the precipitation of dissolved limestone. Dam evolution is initiated by the growth of mosses that favor swift, shallow water. Bacteria that inhabit the roots of the moss excrete solid limestone (travertine) from the water. The limestone fossilizes the moss, and then more moss grows on top of the travertine deposit. In this way, the natural dam can grow over to 10 m high, impounding the water behind it to form a lake. We propose a simple model to explain the formation of natural limestone dams by the interaction between water flow and biologically-mediated travertine deposition. We assume for simplicity that light is the only factor determining the growth of moss, which is then colonized by travertine-emplacing bacteria. We also assume that the water is saturated with dissolved limestone, so that the process is not limited by limestone availability. Photosynthesis, and thus the growth rate of moss are crudely approximated as decreasing linearly with depth. We employ the shallow water equations to describe water flow over the dam. In order to obtain a profile of permanent form for a dam migrating upward and downstream at constant speed, we solve the problem in a moving coordinate system. When water flows over the dam, it is accelerated in the streamwise direction, and the water surface forms a backwater curve. The flow regime changes from Froude-subcritical to Froude-supercritical at a point slightly downstream of the crest of the dam. Farther downstream, the flow attains a threshold velocity beyond which moss is detached. This threshold point defines the downstream end of the active part of the dam. The

Cognition and biology: perspectives from information theory.

Science.gov (United States)

Wallace, Rodrick

2014-02-01

The intimate relation between biology and cognition can be formally examined through statistical models constrained by the asymptotic limit theorems of communication theory, augmented by methods from statistical mechanics and nonequilibrium thermodynamics. Cognition, often involving submodules that act as information sources, is ubiquitous across the living state. Less metabolic free energy is consumed by permitting crosstalk between biological information sources than by isolating them, leading to evolutionary exaptations that assemble shifting, tunable cognitive arrays at multiple scales, and levels of organization to meet dynamic patterns of threat and opportunity. Cognition is thus necessary for life, but it is not sufficient: An organism represents a highly patterned outcome of path-dependent, blind, variation, selection, interaction, and chance extinction in the context of an adequate flow of free energy and an environment fit for development. Complex, interacting cognitive processes within an organism both record and instantiate those evolutionary and developmental trajectories.

Robustness analysis of complex networks with power decentralization strategy via flow-sensitive centrality against cascading failures

Science.gov (United States)

Guo, Wenzhang; Wang, Hao; Wu, Zhengping

2018-03-01

Most existing cascading failure mitigation strategy of power grids based on complex network ignores the impact of electrical characteristics on dynamic performance. In this paper, the robustness of the power grid under a power decentralization strategy is analysed through cascading failure simulation based on AC flow theory. The flow-sensitive (FS) centrality is introduced by integrating topological features and electrical properties to help determine the siting of the generation nodes. The simulation results of the IEEE-bus systems show that the flow-sensitive centrality method is a more stable and accurate approach and can enhance the robustness of the network remarkably. Through the study of the optimal flow-sensitive centrality selection for different networks, we find that the robustness of the network with obvious small-world effect depends more on contribution of the generation nodes detected by community structure, otherwise, contribution of the generation nodes with important influence on power flow is more critical. In addition, community structure plays a significant role in balancing the power flow distribution and further slowing the propagation of failures. These results are useful in power grid planning and cascading failure prevention.

The complex jujube genome provides insights into fruit tree biology.

Science.gov (United States)

Liu, Meng-Jun; Zhao, Jin; Cai, Qing-Le; Liu, Guo-Cheng; Wang, Jiu-Rui; Zhao, Zhi-Hui; Liu, Ping; Dai, Li; Yan, Guijun; Wang, Wen-Jiang; Li, Xian-Song; Chen, Yan; Sun, Yu-Dong; Liu, Zhi-Guo; Lin, Min-Juan; Xiao, Jing; Chen, Ying-Ying; Li, Xiao-Feng; Wu, Bin; Ma, Yong; Jian, Jian-Bo; Yang, Wei; Yuan, Zan; Sun, Xue-Chao; Wei, Yan-Li; Yu, Li-Li; Zhang, Chi; Liao, Sheng-Guang; He, Rong-Jun; Guang, Xuan-Min; Wang, Zhuo; Zhang, Yue-Yang; Luo, Long-Hai

2014-10-28

The jujube (Ziziphus jujuba Mill.), a member of family Rhamnaceae, is a major dry fruit and a traditional herbal medicine for more than one billion people. Here we present a high-quality sequence for the complex jujube genome, the first genome sequence of Rhamnaceae, using an integrated strategy. The final assembly spans 437.65 Mb (98.6% of the estimated) with 321.45 Mb anchored to the 12 pseudo-chromosomes and contains 32,808 genes. The jujube genome has undergone frequent inter-chromosome fusions and segmental duplications, but no recent whole-genome duplication. Further analyses of the jujube-specific genes and transcriptome data from 15 tissues reveal the molecular mechanisms underlying some specific properties of the jujube. Its high vitamin C content can be attributed to a unique high level expression of genes involved in both biosynthesis and regeneration. Our study provides insights into jujube-specific biology and valuable genomic resources for the improvement of Rhamnaceae plants and other fruit trees.

Radiosynthesis and biological evaluation of the 99mTc-tricarbonyl moxifloxacin dithiocarbamate complex as a potential Staphylococcus aureus infection radiotracer

International Nuclear Information System (INIS)

Shah, Syed Qaiser; Khan, Muhammad Rafiullah

2011-01-01

In the present investigation, radiosynthesis of the 99m Tc-tricarbonyl moxifloxacin dithiocarbamate complex ( 99m Tc(CO) 3 -MXND) and its biological evaluation in male Wister rats (MWR) artificially infected with Staphylococcus aureus (S. aureus) was assessed. The 99m Tc(CO) 3 -MXND complex was radiochemically examined in terms of stability in saline and in serum and biologically its in-vitro binding with S. aureus and percent absorption in MWR models. Radiochemically the 99m Tc(CO) 3 -MXND complex showed more than 90% stability in saline up to 240 min and in serum 14.95% undesirable species was appeared within 16 h. In-vitro the 99m Tc(CO) 3 -MXND complex showed saturated binding with S. aureus. In MWR artificially infected with live S. aureus the complex showed about six fold higher uptakes in the infected muscle as compared to the normal muscle. However, insignificant change in the uptake of 99m Tc(CO) 3 -MXND complex in the infected and inflamed or normal muscle was observed in the MWR infected with heat killed S. aureus. The 99m Tc(CO) 3 -MXND complex disappeared from the circulatory system and appeared in the urinary system within 60-90 min followed by excretion through normal route of urinary system. Based on the elevated and stable radiochemical succumb in saline, serum, saturated in-vitro binding with S. aureus and higher accumulation in the target organ of the MWR, we recommend the 99m Tc(CO) 3 -MXND complex for radio-localization of the infection induced by S. aureus in human.

Industrial systems biology and its impact on synthetic biology of yeast cell factories

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

Synthesis, Characterization and Biological Evaluation of Transition Metal Complexes Derived from N, S Bidentate Ligands

Directory of Open Access Journals (Sweden)

Enis Nadia Md Yusof

2015-05-01

Full Text Available Two bidentate NS ligands were synthesized by the condensation reaction of S-2-methylbenzyldithiocarbazate (S2MBDTC with 2-methoxybenzaldehyde (2MB and 3-methoxybenzaldehyde (3MB. The ligands were reacted separately with acetates of Cu(II, Ni(II and Zn(II yielding 1:2 (metal:ligand complexes. The metal complexes formed were expected to have a general formula of [M(NS2] where M = Cu2+, Ni2+, and Zn2+. These compounds were characterized by elemental analysis, molar conductivity, magnetic susceptibility and various spectroscopic techniques. The magnetic susceptibility measurements and spectral results supported the predicted coordination geometry in which the Schiff bases behaved as bidentate NS donor ligands coordinating via the azomethine nitrogen and thiolate sulfur. The molecular structures of the isomeric S2M2MBH (1 and S2M3MBH (2 were established by X-ray crystallography to have very similar l-shaped structures. The Schiff bases and their metal complexes were evaluated for their biological activities against estrogen receptor-positive (MCF-7 and estrogen receptor-negative (MDA-MB-231 breast cancer cell lines. Only the Cu(II complexes showed marked cytotoxicity against the cancer cell lines. Both Schiff bases and other metal complexes were found to be inactive. In concordance with the cytotoxicity studies, the DNA binding studies indicated that Cu(II complexes have a strong DNA binding affinity.

Remote Sensing of Complex Flows by Doppler Wind Lidar: Issues and Preliminary Recommendations

Energy Technology Data Exchange (ETDEWEB)

Clifton, Andrew [National Renewable Energy Lab. (NREL), Golden, CO (United States); Boquet, Matthieu [Leosphere, Orsay (France); Burin Des Roziers, Edward [UL International Gmbh, Freemont, CA (United States); Westerhellweg, Annette [UL International Gmbh, Freemont, CA (United States); Hofsass, Martin [Univ. of Stuttgart (Germany). Stuttgart Wind Energy; Klaas, Tobias [Fraunhofer Inst. for Wind Energy and Energy System Technology, Freiburg (Germany); Vogstad, Klaus [Meventus, Hamburg (Germany); Clive, Peter [Sgurr Energy, Glasgow (United Kingdom); Harris, Mike [ZephIR Limited, Kirkcudbrightshire (United Kingdom); Wylie, Scott [ZephIR Limited, Kirkcudbrightshire (United Kingdom); Osler, Evan [Renewable NRG Systems, Hinesburg, VT (United States); Banta, Bob [National Oceanic and Atmospheric Administration (NOAA), Boulder, CO (United States); Choukulkar, Aditya [National Oceanic and Atmospheric Administration (NOAA), Boulder, CO (United States); Lundquist, Julie [Univ. of Colorado, Boulder, CO (United States); Aitken, Matthew [Univ. of Colorado, Boulder, CO (United States)

2015-12-01

Remote sensing of winds using lidar has become popular and useful in the wind energy industry. Extensive experience has been gained with using lidar for applications including land-based and offshore resource assessment, plant operations, and turbine control. Prepared by members of International Energy Agency Task 32, this report describes the state of the art in the use of Doppler wind lidar for resource assessment in complex flows. The report will be used as input for future recommended practices on this topic.

Social insect colony as a biological regulatory system: modelling information flow in dominance networks.

Science.gov (United States)

Nandi, Anjan K; Sumana, Annagiri; Bhattacharya, Kunal

2014-12-06

Social insects provide an excellent platform to investigate flow of information in regulatory systems since their successful social organization is essentially achieved by effective information transfer through complex connectivity patterns among the colony members. Network representation of such behavioural interactions offers a powerful tool for structural as well as dynamical analysis of the underlying regulatory systems. In this paper, we focus on the dominance interaction networks in the tropical social wasp Ropalidia marginata-a species where behavioural observations indicate that such interactions are principally responsible for the transfer of information between individuals about their colony needs, resulting in a regulation of their own activities. Our research reveals that the dominance networks of R. marginata are structurally similar to a class of naturally evolved information processing networks, a fact confirmed also by the predominance of a specific substructure-the 'feed-forward loop'-a key functional component in many other information transfer networks. The dynamical analysis through Boolean modelling confirms that the networks are sufficiently stable under small fluctuations and yet capable of more efficient information transfer compared to their randomized counterparts. Our results suggest the involvement of a common structural design principle in different biological regulatory systems and a possible similarity with respect to the effect of selection on the organization levels of such systems. The findings are also consistent with the hypothesis that dominance behaviour has been shaped by natural selection to co-opt the information transfer process in such social insect species, in addition to its primal function of mediation of reproductive competition in the colony. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Analysis of Metal Flow Behavior and Residual Stress Formation of Complex Functional Profiles under High-Speed Cold Roll-Beating

Directory of Open Access Journals (Sweden)

Fengkui Cui

2018-01-01

Full Text Available To obtain a good surface layer performance of the complex functional profile during the high-speed cold roll-beating forming process, this paper analyzed the metal plastic flow and residual stress-formed mechanism by using a theoretical model of the metal flow and residual stress generation. By using simulation software, the cold roll-beating forming process of a spline shaft was simulated and analyzed. The metal flow and residual stress formation law in the motion were researched. In a practical experiment, the changes in the grains in the spline tooth profile section and the residual stress distribution on the tooth profile were studied. A microcorrespondence relationship was established between the metal plastic flow and the residual stress generation. The conclusions indicate that the rate at which the metal flow decreases changes gradually at different metal layers. The residual stress value is directly related to the plastic flow difference. As the roll-beating speed increases, the uneven degree of plastic deformation at the workpiece surface increases, and the residual stress in the tooth profile is generally greater. At the same roll-beating speed, the rate change trend of the metal flow decreases gradually from the surface to the inner layer and from the dedendum to the addendum. The residual stress distribution on the surface of the tooth profile decreases from the dedendum to the addendum. These findings provide a basis and guidance for the controlled use of residual stress, obtaining better surface layer quality in the high-speed cold roll-beating process of the complex functional profile.

Artificial vesicles as an animal cell model for the study of biological application of non-thermal plasma

International Nuclear Information System (INIS)

Ki, S H; Park, J K; Sung, C; Lee, C B; Uhm, H; Choi, E H; Baik, K Y

2016-01-01

Artificial cell-like model systems can provide information which is hard to obtain with real biological cells. Giant unilamellar vesicles (GUV) containing intra-membrane DNA or OH radical-binding molecules are used to visualize the cytolytic activity of OH radicals. Changes in the GUV membrane are observed by microscopy or flow cytometry as performed for animal cells after non-thermal plasma treatment. The experimental data shows that OH radicals can be detected inside the membrane, although the biological effects are not as significant as for H 2 O 2 . This artificial model system can provide a systemic means to elucidate the complex interactions between biological materials and non-thermal plasma. (paper)

Influence of the nucleobase on the physicochemical characteristics and biological activities of Sb{sup V}-ribonucleoside complexes

Energy Technology Data Exchange (ETDEWEB)

Ferreira, Claudio S.; Demicheli, Cynthia, E-mail: demichel@netuno.lcc.ufmg.b [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Quimica; Rocha, Iara C.M. da; Melo, Maria N. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Parasitologia; Monte Neto, Rubens L.; Frezard, Frederic [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Fisiologia e Biofisica

2010-07-01

The influence of the nucleobase (uracyl, U; cytosine, C; adenine, A; guanine, G) on the physicochemical characteristics and in vitro biological activities of Sb{sup V}-ribonucleoside complexes has been investigated. The 1:1 Sb-U and Sb-C complexes were characterized by NMR and ESI-MS spectroscopies and elemental analysis. The stability constant and the apparent association and dissociation rate constants of 1:1 Sb{sup V}-U, Sb{sup V}-C and Sb{sup V}-A complexes were determined. Although Sb{sup V} most probably binds via oxygen atoms to the same 2' and 3' positions in the different nucleosides, the ribose conformational changes and the physicochemical characteristics of the complex depend on the nucleobase. The nucleobase had a strong influence on the cytotoxicity against macrophages and the antileishmanial activity of the Sb{sup V}-ribonucleoside complexes. The Sb{sup V}-purine complexes were more cytotoxic and more effective against Leishmania chagasi than the Sb{sup V}-pyrimidine complexes, supporting the model that the interaction of Sb{sup V} with purine nucleosides may mediate the antileishmanial activity of pentavalent antimonial drugs. (author)

The complexity of finding arc-disjoint branching flows

DEFF Research Database (Denmark)

Bang-Jensen, J.; Havet, Frédéric; Yeo, Anders

2016-01-01

The concept of arc-disjoint flows in networks was recently introduced in Bang-Jensen and Bessy (2014). This is a very general framework within which many well-known and important problems can be formulated. In particular, the existence of arc-disjoint branching flows, that is, flows which send on...

Synthesis, characterization and biological assay of Salicylaldehyde Schiff base Cu(II) complexes and their precursors

Science.gov (United States)

Iftikhar, Bushra; Javed, Kanwal; Khan, Muhammad Saif Ullah; Akhter, Zareen; Mirza, Bushra; Mckee, Vickie

2018-03-01

Three new Schiff base ligands were synthesized by the reaction of Salicylaldehyde with semi-aromatic diamines, prepared by the reduction of corresponding dinitro-compounds, and were further used for the formation of complexes with Cu(II) metal ion. The structural features of the synthesized compounds were confirmed by their physical properties and infrared, electronic and NMR spectroscopic techniques. The studies revealed that the synthesized Schiff bases existed as tetradentate ligands and bonded to the metal ion through the phenolic oxygen and azomethine nitrogen. One of the dinitro precursors was also analyzed by single crystal X-ray crystallography, which showed that it crystallizes in monoclinic system with space group P2/n. The thermal behavior of the Cu(II) complexes was determined by thermogravimetric analysis (TGA) and kinetic parameters were evaluated from the data. Schiff base ligands, their precursors and metal complexes were also screened for antibacterial, antifungal, antitumor, Brine shrimp lethality, DPPH free radical scavenging and DNA damage assays. The results of these analyses indicated the substantial potential of the synthesized Schiff bases, their precursors and Cu(II) complexes in biological field as future drugs.

Analysis and computer simulation for transient flow in complex system of liquid piping

International Nuclear Information System (INIS)

Mitry, A.M.

1985-01-01

This paper is concerned with unsteady state analysis and development of a digital computer program, FLUTRAN, that performs a simulation of transient flow behavior in a complex system of liquid piping. The program calculates pressure and flow transients in the liquid filled piping system. The analytical model is based on the method of characteristics solution to the fluid hammer continuity and momentum equations. The equations are subject to wide variety of boundary conditions to take into account the effect of hydraulic devices. Water column separation is treated as a boundary condition with known head. Experimental tests are presented that exhibit transients induced by pump failure and valve closure in the McGuire Nuclear Station Low Level Intake Cooling Water System. Numerical simulation is conducted to compare theory with test data. Analytical and test data are shown to be in good agreement and provide validation of the model

Numerical Simulation of Complex Multi-Fluid Flows using a Combined Immersed Boundary and Volume of Fluid Approach

NARCIS (Netherlands)

Deen, N.G.; van Sint Annaland, M.; Kuipers, J.A.M.

2007-01-01

In this paper a simulation model is presented for the Direct Numerical Simulation (DNS) of complex multi-fluid flows in which simultaneously (moving) deformable (drops or bubbles) and non-deformable (moving) elements (particles) are present, possibly with the additional presence of free surfaces.

Direct numerical simulation of complex multi-fluid flows using a combined front tracking and immersed boundary method

NARCIS (Netherlands)

Deen, N.G.; van Sint Annaland, M.; Kuipers, J.A.M.

2009-01-01

In this paper a simulation model is presented for the Direct Numerical Simulation (DNS) of complex multi-fluid flows in which simultaneously (moving) deformable (drops or bubbles) and non-deformable (moving) elements (particles) are present, possibly with the additional presence of free surfaces.

Startup and long term operation of enhanced biological phosphorus removal in continuous-flow reactor with granules.

Science.gov (United States)

Li, Dong; Lv, Yufeng; Zeng, Huiping; Zhang, Jie

2016-07-01

The startup and long term operation of enhanced biological phosphorus removal (EBPR) in a continuous-flow reactor (CFR) with granules were investigated in this study. Through reducing the settling time from 9min to 3min gradually, the startup of EBPR in a CFR with granules was successfully realized in 16days. Under continuous-flow operation, the granules with good phosphorus and COD removal performance were stably operated for more than 6months. And the granules were characterized with particle size of around 960μm, loose structure and good settling ability. During the startup phase, polysaccharides (PS) was secreted excessively by microorganisms to resist the influence from the variation of operational mode. Results of relative quantitative PCR indicated that granules dominated by polyphosphate-accumulating organisms (PAOs) were easier accumulated in the CFR because more excellent settling ability was needed in the system. Copyright © 2016 Elsevier Ltd. All rights reserved.

SWIM: a computational tool to unveiling crucial nodes in complex biological networks.

Science.gov (United States)

Paci, Paola; Colombo, Teresa; Fiscon, Giulia; Gurtner, Aymone; Pavesi, Giulio; Farina, Lorenzo

2017-03-20

SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called "fight-club hubs", characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called "switch genes", appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance. Here, we applied SWIM to a large panel of cancer datasets from The Cancer Genome Atlas, in order to highlight switch genes that could be critically associated with the drastic changes in the physiological state of cells or tissues induced by the cancer development. We discovered that switch genes are found in all cancers we studied and they encompass protein coding genes and non-coding RNAs, recovering many known key cancer players but also many new potential biomarkers not yet characterized in cancer context. Furthermore, SWIM is amenable to detect switch genes in different organisms and cell conditions, with the potential to uncover important players in biologically relevant scenarios, including but not limited to human cancer.

Y-12 National Security Complex Biological Monitoring And Abatement Program 2008 Calendar Year Report

Energy Technology Data Exchange (ETDEWEB)

Peterson, M. J.; Greeley Jr., M. S.; Mathews, T. J.; Morris, G. W.; Roy, W. K.; Ryon, M. G.; Smith, J. G.; Southworth, G. R.

2009-07-01

The National Pollutant Discharge Elimination System (NPDES) permit issued for the Oak Ridge Y-12 National Security Complex (Y-12 Complex) which became effective May 1, 2006, continued a requirement for a Biological Monitoring and Abatement Program (BMAP). The BMAP was originally developed in 1985 to demonstrate that the effluent limitations established for the Y-12 Complex protected the classified uses of the receiving stream (East Fork Poplar Creek: EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). The objectives of the current BMAP are similar, specifically to assess stream ecological conditions relative to regulatory limits and criteria, to assess ecological impacts as well as recovery in response to Y-12 operations, and to investigate the causes of continuing impacts. The BMAP consists of three tasks that reflect complementary approaches to evaluating the effects of the Y-12 Complex discharges on the biotic integrity of EFPC. These tasks include: (1) bioaccumulation monitoring, (2) benthic macroinvertebrate community monitoring, and (3) fish community monitoring. As required by the NPDES permit, the BMAP benthic macroinvertebrate community monitoring task includes studies to annually evaluate the receiving stream's biological integrity in comparison to TN Water Quality Criteria. BMAP monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) appropriate habitat distribution, and (5) access. The primary sampling sites include upper EFPC at kilometers (EFKs) 24.4 and 23.4 [upstream and downstream of Lake Reality (LR) respectively]; EFK 18.7 (also EFK 18.2 and 19), located off

Complexity attack resistant flow lookup achemes for IPv6: a measurement based comparison

OpenAIRE

Malone, David; Tobin, R. Joshua

2008-01-01

In this paper we look at the problem of choosing a good flow state lookup scheme for IPv6 firewalls. We want to choose a scheme which is fast when dealing with typical traffic, but whose performance will not degrade unnecessarily when subject to a complexity attack. We demonstrate the existing problem and, using captured traffic, assess a number of replacement schemes that are hash and tree based. Our aim is to improve FreeBSD’s ipfw firewall, and so finally we implement the most pro...

[Effects of therapeutic complexes including balneoradonokinesitherapy, electromyostimulation and low-frequency magnetotherapy on regional blood flow in patients with postrraumatic gonarthritis].

Science.gov (United States)

Raspopova, E A; Udartsev, E Iu

2006-01-01

Balneoradonokinesitherapy alone and its combination with electrostimulation and low-frequency magnetotherapy were used for the treatment of regional blood flow disorders in 76 patients with posttraumatic gonarthritis. Balneoradonokinesitherapy in combination with electromyostimulation improved blood circulation. When low-frequency magnetotherapy was added to the latter complex, the regress of regional blood flow disorders of a damaged extremity was most significant.

The Benefits of Mouse Keeping—an Empirical Study on Students' Flow and Intrinsic Motivation in Biology Lessons

Science.gov (United States)

Meyer, Annika; Klingenberg, Konstantin; Wilde, Matthias

2016-02-01

Contact with living animals is an exceptional possibility within biology education to facilitate an intense immersion into the study topic and even allow for a flow experience (Csikszentmihalyi 2000). Further, it might affect the perceptions of the students' basic needs for autonomy and competence and thereby their quality of motivation (Deci and Ryan 1985, 2002). Still, there is little empirical evidence about the duration of the exposure with living animals that is required. We investigated the students' flow experience, and the students' motivation, reported retrospectively in three different treatments: lessons involving short-term or long-term contact with living harvest mice and a control group without living animals. Our sample consisted of 156 fifth graders (10.76 years, SD = 0.513). The test instruments were adapted versions of the Flow Short Scale (FSS, Rheinberg et al. 2003) and of the Intrinsic Motivation Inventory (IMI, Ryan 1982). As expected, the control group produced significantly lower scores for both FSS and IMI. In addition, we found a significant difference between students with short-term versus long-term contact. Whereas the flow experience was indistinguishable for all pupils who had contact with living animals, those with long-term experience reported significantly higher intrinsic motivation.

A timeless biology.

Science.gov (United States)

Tozzi, Arturo; Peters, James F; Chafin, Clifford; De Falco, Domenico; Torday, John S

2018-05-01

Contrary to claims that physics is timeless while biology is time-dependent, we take the opposite standpoint: physical systems' dynamics are constrained by the arrow of time, while living assemblies are time-independent. Indeed, the concepts of "constraints" and "displacements" shed new light on the role of continuous time flow in life evolution, allowing us to sketch a physical gauge theory for biological systems in long timescales. In the very short timescales of biological systems' individual lives, time looks like "frozen" and "fixed", so that the second law of thermodynamics is momentarily wrecked. The global symmetries (standing for biological constrained trajectories, i.e. the energetic gradient flows dictated by the second law of thermodynamics in long timescales) are broken by local "displacements" where time is held constant, i.e., modifications occurring in living systems. Such displacements stand for brief local forces, able to temporarily "break" the cosmic increase in entropy. The force able to restore the symmetries (called "gauge field") stands for the very long timescales of biological evolution. Therefore, at the very low speeds of life evolution, time is no longer one of the four phase space coordinates of a spacetime Universe: it becomes just a gauge field superimposed to three-dimensional biological systems. We discuss the implications in biology: when assessing living beings, the underrated role of isolated "spatial" modifications needs to be emphasized, living apart the evolutionary role of time. Copyright © 2017 Elsevier Ltd. All rights reserved.

Use of complementary PIV and LDV techniques to study industrial complex flows

International Nuclear Information System (INIS)

Cahen, C.; Benard, J.; Barcoula, M.; Hofmann, F.

1996-06-01

Cracks detected in some nuclear vessels led to design a scale mockup in order to understand the origin of this problem and where experimental results and computation could be compared. Two methods, LDV (Laser Doppler Velocimetry) and PIV (Particle Image Velocimetry), were used to measure the velocity field. It appeared that the two methods were complementary: LDV was dedicated to measure precisely the velocity and the turbulent energy fields, PIV was used to capture flow patterns as the location of stagnation point. If LDV is a local pointwise measurement, classical PIV is intrinsically A 2D image measurement. Consequently, a detailed analysis is done of the 3D effects upon the 2D measurements. The methodology of this analysis is presented. The results have demonstrated the capability of the code to predict such a complex flow even though some discrepancies were found. PIV needs some improvements especially in terms of an higher capacity of processing large set of data a methodology to compute the actual measurement accuracy. (authors). 4 refs., 12 figs

From structure of the complex to understanding of the biology

Energy Technology Data Exchange (ETDEWEB)

Rossmann, Michael G., E-mail: mr@purdue.edu [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Arisaka, Fumio [Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Kanamaru, Shuji [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Graduate School and School of Bioscience and Biotechnology, Tokyo Institute of Technology, 5249 Nagatsuta-cho, Yokohama 226-8501-B39 (Japan); Kostyuchenko, Victor A. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Mesyanzhinov, Vadim V.; Shneider, Mikhail M. [Laboratory of Molecular Bioengineering, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya Street, Moscow, 117997 (Russian Federation); Morais, Marc C.; Leiman, Petr G. [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States); Palermo, Laura M.; Parrish, Colin R. [James A. Baker Institute, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 (United States); Xiao, Chuan [Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 (United States)

2007-01-01

The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.

From structure of the complex to understanding of the biology

International Nuclear Information System (INIS)

Rossmann, Michael G.; Arisaka, Fumio; Battisti, Anthony J.; Bowman, Valorie D.; Chipman, Paul R.; Fokine, Andrei; Hafenstein, Susan; Kanamaru, Shuji; Kostyuchenko, Victor A.; Mesyanzhinov, Vadim V.; Shneider, Mikhail M.; Morais, Marc C.; Leiman, Petr G.; Palermo, Laura M.; Parrish, Colin R.; Xiao, Chuan

2007-01-01

The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques. The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle

Multiphase Flow Dynamics 3 Thermal Interactions

CERN Document Server

Kolev, Nikolay Ivanov

2012-01-01

Multi-phase flows are part of our natural environment such as tornadoes, typhoons, air and water pollution and volcanic activities as well as part of industrial technology such as power plants, combustion engines, propulsion systems, or chemical and biological industry. The industrial use of multi-phase systems requires analytical and numerical strategies for predicting their behavior. .In its fourth extended edition the successful monograph package “Multiphase Flow Daynmics” contains theory, methods and practical experience for describing complex transient multi-phase processes in arbitrary geometrical configurations, providing a systematic presentation of the theory and practice of numerical multi-phase fluid dynamics. In the present third volume methods for describing of the thermal interactions in multiphase dynamics are provided. In addition a large number of valuable experiments is collected and predicted using the methods introduced in this monograph. In this way the accuracy of the methods is reve...

An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes.

Science.gov (United States)

Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

2009-11-01

We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a approximately 21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes.

Complex traffic flow that allows as well as hampers lane-changing intrinsically contains social-dilemma structures

Science.gov (United States)

Iwamura, Yoshiro; Tanimoto, Jun

2018-02-01

To investigate an interesting question as to whether or not social dilemma structures can be found in a realistic traffic flow reproduced by a model, we built a new microscopic model in which an intentional driver may try lane-changing to go in front of other vehicles and may hamper others’ lane-changes. Our model consists of twofold parts; cellular automaton emulating a real traffic flow and evolutionary game theory to implement a driver’s decision making-process. Numerical results reveal that a social dilemma like the multi-player chicken game or prisoner’s dilemma game emerges depending on the traffic phase. This finding implies that a social dilemma, which has been investigated by applied mathematics so far, hides behind a traffic flow, which has been explored by fluid dynamics. Highlight - Complex system of traffic flow with consideration of driver’s decision making process is concerned. - A new model dovetailing cellular automaton with game theory is established. - Statistical result from numerical simulations reveals a social dilemma structure underlying traffic flow. - The social dilemma is triggered by a driver’s egocentric actions of lane-changing and hampering other’s lane-change.

Synthesis, Characterization and Spectral Studies of Noble Heterobinuclear Complexes of Transition Metal Ions and their Biological Activity

Directory of Open Access Journals (Sweden)

Netra Pal Singh

2011-01-01

Full Text Available Some noble heterobinuclear complexes of transition metal ions with bis(salicylaldehydemalonyl-dihydrazone in the presence of 5-nitroindazole Cu(II / Ni(II- chloride of the type [ML1M‘L2Cl2] or [ML1FeL2Cl2]Cl, where M = Ni(II, Cu(II and M' = Mn(II, Co(II, have been prepared. All the complexes have been characterized by IR, UV vis and EPR spectroscopy, elemental analysis, magnetic moment and molar conductance measurement. Spectral studies and magnetic moment measurement in DMF suggest the covalent nature of the complexes, except the [ML1FeL2Cl2]Cl complex which is 1:1 electrolyte. An octahedral geometry is proposed for M‘ and square planer for M for the heterobinuclear complexes. The low value of magnetic moment and overlapping EPR signals are due to spin crossover since both of the metals have unpaired electrons with same molecular symmetry. The lowering of the magnetic moment has been discussed. The biological activity (antifungal and antibacterial of the represented compounds has been studied.

Co(II) and Cd(II) Complexes Derived from Heterocyclic Schiff-Bases: Synthesis, Structural Characterisation, and Biological Activity

Science.gov (United States)

Ahmed, Riyadh M.; Yousif, Enaam I.; Al-Jeboori, Mohamad J.

2013-01-01

New monomeric cobalt and cadmium complexes with Schiff-bases, namely, N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]furan-2-carbohydrazide (L1) and N′-[(E)-(3-hydroxy-4-methoxyphenyl)methylidene]thiophene-2-carbohydrazide (L2) are reported. Schiff-base ligands L1 and L2 were derived from condensation of 3-hydroxy-4-methoxybenzaldehyde (iso-vanillin) with furan-2-carboxylic acid hydrazide and thiophene-2-carboxylic acid hydrazide, respectively. Complexes of the general formula [M(L)2]Cl2 (where M = Co(II) or Cd(II), L = L1 or L2) have been obtained from the reaction of the corresponding metal chloride with the ligands. The ligands and their metal complexes were characterised by spectroscopic methods (FTIR, UV-Vis, 1H, and 13C NMR spectra), elemental analysis, metal content, magnetic measurement, and conductance. These studies revealed the formation of four-coordinate complexes in which the geometry about metal ion is tetrahedral. Biological activity of the ligands and their metal complexes against gram positive bacterial strain Bacillus (G+) and gram negative bacteria Pseudomonas (G−) revealed that the metal complexes become less resistive to the microbial activities as compared to the free ligands. PMID:24027449

Biomedical tracers: technetium-99 m complexing sulfur polydentate ligands

International Nuclear Information System (INIS)

Bendennoune, A.

1994-01-01

Cyclic and acyclic tetra sulfur ligands have been synthesized and some of them have been labelled with technetium-99m. These works have two different aims: 1- Development of methods permitting to obtain easily potential technetium complexing sulfur polydentate chelates. 2- Research of positive and neutral complexes of this metal likely to replace thalium-201 in the coronary flow estimation and [TcO-HMPAO] sup 0 complex in the cerebral scintigraphy, respectively. In this work, first, different ways for obtaining dithioetherdithiols and cyclic tetrathioethers containing functional groups have been carried out, then complexation of the core of nitrutechnetium (TcN) sup 2+ at tracers scale, by dithioetherdithiols, using exchange reaction with [sup 9 sup 9 sup m TcNCl sub 4 ] sup - ion complex or sup 99 sup m TcN Cl sub 2 [P(CH sub 2 CH sub 2 CN) sub 3 ] sub 2 has been studied. Finally, biological distribution in swiss mouse of these technetiated complexes has been studied. 135 refs., 30 figs., 13 tabs. (F.M.)

A Tryptoline Ring-Distortion Strategy Leads to Complex and Diverse Biologically Active Molecules from the Indole Alkaloid Yohimbine.

Science.gov (United States)

Paciaroni, Nicholas G; Ratnayake, Ranjala; Matthews, James H; Norwood, Verrill M; Arnold, Austin C; Dang, Long H; Luesch, Hendrik; Huigens, Robert W

2017-03-28

High-throughput screening (HTS) is the primary driver to current drug-discovery efforts. New therapeutic agents that enter the market are a direct reflection of the structurally simple compounds that make up screening libraries. Unlike medically relevant natural products (e.g., morphine), small molecules currently being screened have a low fraction of sp 3 character and few, if any, stereogenic centers. Although simple compounds have been useful in drugging certain biological targets (e.g., protein kinases), more sophisticated targets (e.g., transcription factors) have largely evaded the discovery of new clinical agents from screening collections. Herein, a tryptoline ring-distortion strategy is described that enables the rapid synthesis of 70 complex and diverse compounds from yohimbine (1); an indole alkaloid. The compounds that were synthesized had architecturally complex and unique scaffolds, unlike 1 and other scaffolds. These compounds were subjected to phenotypic screens and reporter gene assays, leading to the identification of new compounds that possessed various biological activities, including antiproliferative activities against cancer cells with functional hypoxia-inducible factors, nitric oxide inhibition, and inhibition and activation of the antioxidant response element. This tryptoline ring-distortion strategy can begin to address diversity problems in screening libraries, while occupying biologically relevant chemical space in areas critical to human health. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Novel flow quantification of the carotid bulb and the common carotid artery with vector flow ultrasound

DEFF Research Database (Denmark)

Pedersen, Mads Møller; Pihl, Michael Johannes; Haugaard, Per

2014-01-01

technique transverse oscillation the blood velocities of both the axial and the transverse directions are obtained and the complexity of blood flow can be visualized. The aim of the study was to determine the technical performance and interpretation of vector concentration as a tool for estimation of flow...... (US) using a commercial vector flow ultrasound scanner (ProFocus, BK Medical, Denmark) with a linear 5 MHz transducer transverse oscillation vector flow software. CCA and CB areas were marked in one cardiac cycle from each volunteer. The complex flow was assessed by medical expert evaluation...... and by vector concentration calculation. A vortex with complex flow was found in all carotid bulbs, whereas the CCA had mainly laminar flow. The medical experts evaluated the flow to be mainly laminar in the CCA (0.82 +/- 0.14) and mainly complex (0.23 +/- 0.22) in the CB. Likewise, the estimated vector...

The interaction of two spheres in a simple-shear flow of complex fluids

Science.gov (United States)

Firouznia, Mohammadhossein; Metzger, Bloen; Ovarlez, Guillaume; Hormozi, Sarah

2017-11-01

We study the interaction of two small freely-moving spheres in a linear flow field of Newtonian, shear thinning and yield stress fluids. We perform a series of experiments over a range of shear rates as well as different shear histories using an original apparatus and with the aid of conventional rheometry, Particle Image Velocimetry and Particle Tracking Velocimetry. Showing that the non-Newtonian nature of the suspending fluid strongly affects the shape of particle trajectories and the irreversibility. An important point is that non-Newtonian effects can be varied and unusual. Depending on the shear rate, nonideal shear thinning and yield stress suspending fluids might show elasticity that needs to be taken into account. The flow field around one particle is studied in different fluids when subjected to shear. Then using these results to explain the two particle interactions in a simple-shear flow we show how particle-particle contact and non-Newtonian behaviors result in relative trajectories with fore-aft asymmetry. Well-resolved velocity and stress fields around the particles are presented here. Finally, we discuss how the relative particle trajectories may affect the microstructure of complex suspensions and consequently the bulk rheology. NSF (Grant No. CBET-1554044-CAREER).

Immersed boundary methods for high-resolution simulation of atmospheric boundary-layer flow over complex terrain

Science.gov (United States)

Lundquist, Katherine Ann

Mesoscale models, such as the Weather Research and Forecasting (WRF) model, are increasingly used for high resolution simulations, particularly in complex terrain, but errors associated with terrain-following coordinates degrade the accuracy of the solution. Use of an alternative Cartesian gridding technique, known as an immersed boundary method (IBM), alleviates coordinate transformation errors and eliminates restrictions on terrain slope which currently limit mesoscale models to slowly varying terrain. In this dissertation, an immersed boundary method is developed for use in numerical weather prediction. Use of the method facilitates explicit resolution of complex terrain, even urban terrain, in the WRF mesoscale model. First, the errors that arise in the WRF model when complex terrain is present are presented. This is accomplished using a scalar advection test case, and comparing the numerical solution to the analytical solution. Results are presented for different orders of advection schemes, grid resolutions and aspect ratios, as well as various degrees of terrain slope. For comparison, results from the same simulation are presented using the IBM. Both two-dimensional and three-dimensional immersed boundary methods are then described, along with details that are specific to the implementation of IBM in the WRF code. Our IBM is capable of imposing both Dirichlet and Neumann boundary conditions. Additionally, a method for coupling atmospheric physics parameterizations at the immersed boundary is presented, making IB methods much more functional in the context of numerical weather prediction models. The two-dimensional IB method is verified through comparisons of solutions for gentle terrain slopes when using IBM and terrain-following grids. The canonical case of flow over a Witch of Agnesi hill provides validation of the basic no-slip and zero gradient boundary conditions. Specified diurnal heating in a valley, producing anabatic winds, is used to validate the

Immersed Boundary Methods for High-Resolution Simulation of Atmospheric Boundary-Layer Flow Over Complex Terrain

Energy Technology Data Exchange (ETDEWEB)

Lundquist, K A [Univ. of California, Berkeley, CA (United States)

2010-05-12

Mesoscale models, such as the Weather Research and Forecasting (WRF) model, are increasingly used for high resolution simulations, particularly in complex terrain, but errors associated with terrain-following coordinates degrade the accuracy of the solution. Use of an alternative Cartesian gridding technique, known as an immersed boundary method (IBM), alleviates coordinate transformation errors and eliminates restrictions on terrain slope which currently limit mesoscale models to slowly varying terrain. In this dissertation, an immersed boundary method is developed for use in numerical weather prediction. Use of the method facilitates explicit resolution of complex terrain, even urban terrain, in the WRF mesoscale model. First, the errors that arise in the WRF model when complex terrain is present are presented. This is accomplished using a scalar advection test case, and comparing the numerical solution to the analytical solution. Results are presented for different orders of advection schemes, grid resolutions and aspect ratios, as well as various degrees of terrain slope. For comparison, results from the same simulation are presented using the IBM. Both two-dimensional and three-dimensional immersed boundary methods are then described, along with details that are specific to the implementation of IBM in the WRF code. Our IBM is capable of imposing both Dirichlet and Neumann boundary conditions. Additionally, a method for coupling atmospheric physics parameterizations at the immersed boundary is presented, making IB methods much more functional in the context of numerical weather prediction models. The two-dimensional IB method is verified through comparisons of solutions for gentle terrain slopes when using IBM and terrain-following grids. The canonical case of flow over a Witch of Agnesi hill provides validation of the basic no-slip and zero gradient boundary conditions. Specified diurnal heating in a valley, producing anabatic winds, is used to validate the

Intra-operative Vector Flow Imaging Using Ultrasound of the Ascending Aorta among 40 Patients with Normal, Stenotic and Replaced Aortic Valves

DEFF Research Database (Denmark)

Hansen, Kristoffer Lindskov; Møller-Sørensen, Hasse; Kjaergaard, Jesper

2016-01-01

Stenosis of the aortic valve gives rise to more complex blood flows with increased velocities. The angleindependent vector flow ultrasound technique transverse oscillation was employed intra-operatively on the ascending aorta of (I) 20 patients with a healthy aortic valve and 20 patients with aor...... replacement corrects some of these changes. Transverse oscillation may be useful for assessment of aortic stenosis and optimization of valve surgery. (E-mail: lindskov@gmail.com) 2016 World Federation for Ultrasound in Medicine & Biology...... with aortic stenosis before (IIa) and after (IIb) valve replacement. The results indicate that aortic stenosis increased flow complexity (p , 0.0001), induced systolic backflow (p , 0.003) and reduced systolic jet width (p , 0.0001). After valve replacement, the systolic backflow and jet width were normalized...

Peak expiratory flow rate (PEFR) among Nuclear Fuel Complex (NFC) employees

International Nuclear Information System (INIS)

Vijay Rao, J.; Venkaiah, K.; Mohan Rao, N.

2010-01-01

At Nuclear Fuel Complex (NFC), employees are exposed to ammonia, hydrofluoric acid, acetone, etc., which are respiratory toxicants and inhalation of these pollutants may produce irritation and obstruction in airways. Due to nature of their occupation, tradesman working in plants are having longer duration of exposure (LDE) and others, such as supervisors, scientific officers, helpers, etc., that occasionally visit plants are having shorter duration of exposure (SDE) to these pollutants. The peak expiratory flow rate (PEFR) is an index to diagnose obstruction in larger airways and this is metered with mini peak flow meter among 835 NFC employees. Using ANOVA test, PEFR value was compared according to age and smoking. The value was compared between LDE and SDE employees according to smoking and duration of employment. The multiple regression equation for prediction of PEFR was developed. Age, smokers and higher duration of LDE employees demonstrated significantly lower PEFR value. In comparison to 10 year duration, 30 and above year duration of employment, LDE employees showed a higher decline in PEFR, that is 95 L (17.6%) and in SDE employees, that is 41L (7.8%). This may be due to longer duration of employment of LD employees smoking prevention and follow up study is suggested. (author)

Discrete Adjoint-Based Design for Unsteady Turbulent Flows On Dynamic Overset Unstructured Grids

Science.gov (United States)

Nielsen, Eric J.; Diskin, Boris

2012-01-01

A discrete adjoint-based design methodology for unsteady turbulent flows on three-dimensional dynamic overset unstructured grids is formulated, implemented, and verified. The methodology supports both compressible and incompressible flows and is amenable to massively parallel computing environments. The approach provides a general framework for performing highly efficient and discretely consistent sensitivity analysis for problems involving arbitrary combinations of overset unstructured grids which may be static, undergoing rigid or deforming motions, or any combination thereof. General parent-child motions are also accommodated, and the accuracy of the implementation is established using an independent verification based on a complex-variable approach. The methodology is used to demonstrate aerodynamic optimizations of a wind turbine geometry, a biologically-inspired flapping wing, and a complex helicopter configuration subject to trimming constraints. The objective function for each problem is successfully reduced and all specified constraints are satisfied.

Approaching complexity by stochastic methods: From biological systems to turbulence

Energy Technology Data Exchange (ETDEWEB)

Friedrich, Rudolf [Institute for Theoretical Physics, University of Muenster, D-48149 Muenster (Germany); Peinke, Joachim [Institute of Physics, Carl von Ossietzky University, D-26111 Oldenburg (Germany); Sahimi, Muhammad [Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089-1211 (United States); Reza Rahimi Tabar, M., E-mail: mohammed.r.rahimi.tabar@uni-oldenburg.de [Department of Physics, Sharif University of Technology, Tehran 11155-9161 (Iran, Islamic Republic of); Institute of Physics, Carl von Ossietzky University, D-26111 Oldenburg (Germany); Fachbereich Physik, Universitaet Osnabrueck, Barbarastrasse 7, 49076 Osnabrueck (Germany)

2011-09-15

This review addresses a central question in the field of complex systems: given a fluctuating (in time or space), sequentially measured set of experimental data, how should one analyze the data, assess their underlying trends, and discover the characteristics of the fluctuations that generate the experimental traces? In recent years, significant progress has been made in addressing this question for a class of stochastic processes that can be modeled by Langevin equations, including additive as well as multiplicative fluctuations or noise. Important results have emerged from the analysis of temporal data for such diverse fields as neuroscience, cardiology, finance, economy, surface science, turbulence, seismic time series and epileptic brain dynamics, to name but a few. Furthermore, it has been recognized that a similar approach can be applied to the data that depend on a length scale, such as velocity increments in fully developed turbulent flow, or height increments that characterize rough surfaces. A basic ingredient of the approach to the analysis of fluctuating data is the presence of a Markovian property, which can be detected in real systems above a certain time or length scale. This scale is referred to as the Markov-Einstein (ME) scale, and has turned out to be a useful characteristic of complex systems. We provide a review of the operational methods that have been developed for analyzing stochastic data in time and scale. We address in detail the following issues: (i) reconstruction of stochastic evolution equations from data in terms of the Langevin equations or the corresponding Fokker-Planck equations and (ii) intermittency, cascades, and multiscale correlation functions.

Approaching complexity by stochastic methods: From biological systems to turbulence

International Nuclear Information System (INIS)

Friedrich, Rudolf; Peinke, Joachim; Sahimi, Muhammad; Reza Rahimi Tabar, M.

2011-01-01

This review addresses a central question in the field of complex systems: given a fluctuating (in time or space), sequentially measured set of experimental data, how should one analyze the data, assess their underlying trends, and discover the characteristics of the fluctuations that generate the experimental traces? In recent years, significant progress has been made in addressing this question for a class of stochastic processes that can be modeled by Langevin equations, including additive as well as multiplicative fluctuations or noise. Important results have emerged from the analysis of temporal data for such diverse fields as neuroscience, cardiology, finance, economy, surface science, turbulence, seismic time series and epileptic brain dynamics, to name but a few. Furthermore, it has been recognized that a similar approach can be applied to the data that depend on a length scale, such as velocity increments in fully developed turbulent flow, or height increments that characterize rough surfaces. A basic ingredient of the approach to the analysis of fluctuating data is the presence of a Markovian property, which can be detected in real systems above a certain time or length scale. This scale is referred to as the Markov-Einstein (ME) scale, and has turned out to be a useful characteristic of complex systems. We provide a review of the operational methods that have been developed for analyzing stochastic data in time and scale. We address in detail the following issues: (i) reconstruction of stochastic evolution equations from data in terms of the Langevin equations or the corresponding Fokker-Planck equations and (ii) intermittency, cascades, and multiscale correlation functions.

Curvilinear immersed-boundary method for simulating unsteady flows in shallow natural streams with arbitrarily complex obstacles

Science.gov (United States)

Kang, Seokkoo; Borazjani, Iman; Sotiropoulos, Fotis

2008-11-01

Unsteady 3D simulations of flows in natural streams is a challenging task due to the complexity of the bathymetry, the shallowness of the flow, and the presence of multiple nature- and man-made obstacles. This work is motivated by the need to develop a powerful numerical method for simulating such flows using coherent-structure-resolving turbulence models. We employ the curvilinear immersed boundary method of Ge and Sotiropoulos (Journal of Computational Physics, 2007) and address the critical issue of numerical efficiency in large aspect ratio computational domains and grids such as those encountered in long and shallow open channels. We show that the matrix-free Newton-Krylov method for solving the momentum equations coupled with an algebraic multigrid method with incomplete LU preconditioner for solving the Poisson equation yield a robust and efficient procedure for obtaining time-accurate solutions in such problems. We demonstrate the potential of the numerical approach by carrying out a direct numerical simulation of flow in a long and shallow meandering stream with multiple hydraulic structures.

Cobalt(II) complexes with azole-pyridine type ligands for non-aqueous redox-flow batteries: Tunable electrochemistry via structural modification

Science.gov (United States)

Armstrong, Craig G.; Toghill, Kathryn E.

2017-05-01

A single species redox flow battery employing a new class of cobalt(II) complexes with 'tunable' tridentate azole-pyridine type ligands is reported. Four structures were synthesised and their electrochemical, physical and battery characteristics were investigated as a function of successive substitution of the ligand terminal pyridyl donors. The Co(II/I) and Co(III/II) couples are stable and quasi-reversible on gold and glassy carbon electrodes, however redox potentials are tunable allowing the cobalt potential difference to be preferentially increased from 1.07 to 1.91 V via pyridine substitution with weaker σ-donating/π-accepting 3,5-dimethylpyrazole groups. The charge-discharge properties of the system were evaluated using an H-type glass cell and graphite rod electrodes. The complexes delivered high Coulombic efficiencies of 89.7-99.8% and very good voltaic efficiencies of 70.3-81.0%. Consequently, energy efficiencies are high at 63.1-80.8%, marking an improvement on other similar non-aqueous systems. Modification of the ligands also improved solubility from 0.18 M to 0.50 M via pyridyl substitution with 3,5-dimethylpyrazole, though the low solubility of the complexes limits the overall energy capacity to between 2.58 and 12.80 W h L-1. Preliminary flow cell studies in a prototype flow cell are also demonstrated.

Repair Responses of Dental Pulp to Tooth Injury and Biological Properties of Dentin-pulp Complex

OpenAIRE

大島, 勇人; Ohshima, Hayato

2004-01-01

Regeneration-the creation of a new tissue after the original one has been lost-is the fundamental biological capability in an organism. Numerous organs are considered to contain stem cells referred to as adult stem cells, even in the adult. Adult stem cells can give rise to a limited set of adult tissue types. In the field of clinical dentistry, it is well-known that the dentin-pulp complex is capable of repair after tooth injuries such as tooth replantation/transplantation or restorative pro...

Temperature-dependent phase transitions in zeptoliter volumes of a complex biological membrane

International Nuclear Information System (INIS)

Nikiforov, Maxim P; Jesse, Stephen; Kalinin, Sergei V; Hohlbauch, Sophia; Proksch, Roger; King, William P; Voitchovsky, Kislon; Contera, Sonia Antoranz

2011-01-01

Phase transitions in purple membrane have been a topic of debate for the past two decades. In this work we present studies of a reversible transition of purple membrane in the 50-60 deg. C range in zeptoliter volumes under different heating regimes (global heating and local heating). The temperature of the reversible phase transition is 52 ± 5 deg. C for both local and global heating, supporting the hypothesis that this transition is mainly due to a structural rearrangement of bR molecules and trimers. To achieve high resolution measurements of temperature-dependent phase transitions, a new scanning probe microscopy-based method was developed. We believe that our new technique can be extended to other biological systems and can contribute to the understanding of inhomogeneous phase transitions in complex systems.

Bions: a family of biomimetic mineralo-organic complexes derived from biological fluids.

Directory of Open Access Journals (Sweden)

Cheng-Yeu Wu

Full Text Available Mineralo-organic nanoparticles form spontaneously in human body fluids when the concentrations of calcium and phosphate ions exceed saturation. We have shown previously that these mineralo-organic nanoparticles possess biomimetic properties and can reproduce the whole phenomenology of the so-called nanobacteria-mineralized entities initially described as the smallest microorganisms on earth. Here, we examine the possibility that various charged elements and ions may form mineral nanoparticles with similar properties in biological fluids. Remarkably, all the elements tested, including sodium, magnesium, aluminum, calcium, manganese, iron, cobalt, nickel, copper, zinc, strontium, and barium form mineralo-organic particles with bacteria-like morphologies and other complex shapes following precipitation with phosphate in body fluids. Upon formation, these mineralo-organic particles, which we term bions, invariably accumulate carbonate apatite during incubation in biological fluids; yet, the particles also incorporate additional elements and thus reflect the ionic milieu in which they form. Bions initially harbor an amorphous mineral phase that gradually converts to crystals in culture. Our results show that serum produces a dual inhibition-seeding effect on bion formation. Using a comprehensive proteomic analysis, we identify a wide range of proteins that bind to these mineral particles during incubation in medium containing serum. The two main binding proteins identified, albumin and fetuin-A, act as both inhibitors and seeders of bions in culture. Notably, bions possess several biomimetic properties, including the possibility to increase in size and number and to be sub-cultured in fresh culture medium. Based on these results, we propose that bions represent biological, mineralo-organic particles that may form in the body under both physiological and pathological homeostasis conditions. These mineralo-organic particles may be part of a

Industrial systems biology and its impact on synthetic biology of yeast cell factories.

Science.gov (United States)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-06-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae).

Science.gov (United States)

Birnbaum, Kenneth; Desalle, Rob; Peters, Charles M; Benfey, Philip N

2003-11-01

Maintaining crop diversity on farms where cultivars can evolve is a conservation goal, but few tools are available to assess the long-term maintenance of genetic diversity on farms. One important issue for on-farm conservation is gene flow from crops with a narrow genetic base into related populations that are genetically diverse. In a case study of avocado (Persea americana var. americana) in one of its centers of diversity (San Jerónimo, Costa Rica), we used 10 DNA microsatellite markers in a parentage analysis to estimate gene flow from commercialized varieties into a traditional crop population. Five commercialized genotypes comprised nearly 40% of orchard trees, but they contributed only about 14.5% of the gametes to the youngest cohort of trees. Although commercialized varieties and the diverse population were often planted on the same farm, planting patterns appeared to keep the two types of trees separated on small scales, possibly explaining the limited gene flow. In a simulation that combined gene flow estimates, crop biology, and graft tree management, loss of allelic diversity was less than 10% over 150 yr, and selection was effective in retaining desirable alleles in the diverse subpopulation. Simulations also showed that, in addition to gene flow, managing the genetic makeup and life history traits of the invasive commercialized varieties could have a significant impact on genetic diversity in the target population. The results support the feasibility of on-farm crop conservation, but simulations also showed that higher levels of gene flow could lead to severe losses of genetic diversity even if farmers continue to plant diverse varieties.

The relationship between dynamic and average flow rates of the coolant in the channels of complex shape

Science.gov (United States)

Fedoseev, V. N.; Pisarevsky, M. I.; Balberkina, Y. N.

2018-01-01

This paper presents interconnection of dynamic and average flow rates of the coolant in a channel of complex geometry that is a basis for a generalization model of experimental data on heat transfer in various porous structures. Formulas for calculation of heat transfer of fuel rods in transversal fluid flow are acquired with the use of the abovementioned model. It is shown that the model describes a marginal case of separated flows in twisting channels where coolant constantly changes its flow direction and mixes in the communicating channels with large intensity. Dynamic speed is suggested to be identified by power for pumping. The coefficient of proportionality in general case depends on the geometry of the channel and the Reynolds number (Re). A calculation formula of the coefficient of proportionality for the narrow line rod packages is provided. The paper presents a comparison of experimental data and calculated values, which shows usability of the suggested models and calculation formulas.

Biological activities of some Fluoroquinolones-metal complexes

African Journals Online (AJOL)

McRoy

DNA cleavage studies of some synthesized metal complexes of fluoroquinolone ... Although the FQs are generally characterized by a broad antimicrobial spectrum ..... six Coordinate 3rd metal complexes with N- (5 –Phenyl-3,4- thiadiazol-2-yl).

Redox non-innocent bis(2,6-diimine-pyridine) ligand-iron complexes as anolytes for flow battery applications.

Science.gov (United States)

Duarte, Gabriel M; Braun, Jason D; Giesbrecht, Patrick K; Herbert, David E

2017-12-21

Diiminepyridines are a well-known class of "non-innocent" ligands that confer additional redox activity to coordination complexes beyond metal-centred oxidation/reduction. Here, we demonstrate that metal coordination complexes (MCCs) of diiminepyridine (DIP) ligands with iron are suitable anolytes for redox-flow battery applications, with enhanced capacitance and stability compared with bipyridine analogs, and access to storage of up to 1.6 electron equivalents. Substitution of the ligand is shown to be a key factor in the cycling stability and performance of MCCs based on DIP ligands, opening the door to further optimization.

Industrial energy-flow management

International Nuclear Information System (INIS)

Lampret, Marko; Bukovec, Venceslav; Paternost, Andrej; Krizman, Srecko; Lojk, Vito; Golobic, Iztok

2007-01-01

Deregulation of the energy market has created new opportunities for the development of new energy-management methods based on energy assets, risk management, energy efficiency and sustainable development. Industrial energy-flow management in pharmaceutical systems, with a responsible approach to sustainable development, is a complex task. For this reason, an energy-information centre, with over 14,000 online measured data/nodes, was implemented. This paper presents the energy-flow rate, exergy-flow rate and cost-flow rate diagrams, with emphasis on cost-flow rate per energy unit or exergy unit of complex pharmaceutical systems

Excitation of nonlinear wave patterns in flowing complex plasmas

Science.gov (United States)

Jaiswal, S.; Bandyopadhyay, P.; Sen, A.

2018-01-01

We describe experimental observations of nonlinear wave structures excited by a supersonic mass flow of dust particles over an electrostatic potential hill in a dusty plasma medium. The experiments have been carried out in a Π- shaped experimental (DPEx) device in which micron sized Kaolin particles are embedded in a DC glow discharge Argon plasma. An equilibrium dust cloud is formed by maintaining the pumping speed and gas flow rate and the dust flow is induced either by suddenly reducing the height of a potential hill or by suddenly reducing the gas flow rate. For a supersonic flow of the dust fluid precursor solitons are seen to propagate in the upstream direction while wake structures propagate in the downstream direction. For flow speeds with a Mach number greater than 2 the dust particles flowing over the potential hill give rise to dispersive dust acoustic shock waves. The experimental results compare favorably with model theories based on forced K-dV and K-dV Burger's equations.

Traffic and Granular Flow ’07

CERN Document Server

Chevoir, François; Gondret, Philippe; Lassarre, Sylvain; Lebacque, Jean-Patrick; Schreckenberg, Michael

2009-01-01

This book covers several research fields, all of which deal with transport. Three main topics are treated: road traffic, granular matter, and biological transport. Different points of view, i.e. modelling, simulations, experiments, and phenomenological observations, are considered. Sub-topics include: highway or urban vehicular traffic (dynamics of traffic, macro/micro modelling, measurements, data analysis, security issues, psychological issues), pedestrian traffic, animal traffic (e.g. social insects), collective motion in biological systems (molecular motors...), granular flow (dense flows, intermittent flows, solid/liquid transition, jamming, force networks, fluid and solid friction), networks (biological networks, urban traffic, the internet, vulnerability of networks, optimal transport networks) and cellular automata applied to the various aforementioned fields.

The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

Science.gov (United States)

Pollard, Thomas D

2014-12-02

This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Biological design in science classrooms

Science.gov (United States)

Scott, Eugenie C.; Matzke, Nicholas J.

2007-01-01

Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront “intelligent design” (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older “creation science” movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education. PMID:17494747

Biomimetic Flow Sensors

NARCIS (Netherlands)

Casas, J.; Liu, Chang; Krijnen, Gijsbertus J.M.

2012-01-01

Biomimetic flow sensors are biologically inspired devices that measure the speed and direction of fluids. This survey starts by describing the role and functioning of airflow-sensing hairs in arthropods and in fishes, carries on with the biomimetic MEMS implementations, both for air and water flow

Cage-Like Porous Carbon with Superhigh Activity and Br2 -Complex-Entrapping Capability for Bromine-Based Flow Batteries.

Science.gov (United States)

Wang, Chenhui; Lai, Qinzhi; Xu, Pengcheng; Zheng, Daoyuan; Li, Xianfeng; Zhang, Huamin

2017-06-01

Bromine-based flow batteries receive wide attention in large-scale energy storage because of their attractive features, such as high energy density and low cost. However, the Br 2 diffusion and relatively low activity of Br 2 /Br - hinder their further application. Herein, a cage-like porous carbon (CPC) with specific pore structure combining superhigh activity and Br 2 -complex-entrapping capability is designed and fabricated. According to the results of density functional theory (DFT) calculation, the pore size of the CPC (1.1 nm) is well designed between the size of Br - (4.83 Å), MEP + (9.25 Å), and Br 2 complex (MEPBr 3 12.40 Å), wherein Br - is oxidized to Br 2 , which forms a Br 2 complex with the complexing agent immediately and is then entrapped in the cage via pore size exclusion. In addition, the active sites produced during the carbon dioxide activation process dramatically accelerate the reaction rate of Br 2 /Br - . In this way, combining a high Br 2 -entrapping-capability and high specific surface areas, the CPC shows very impressive performance. The zinc bromine flow battery assembled with the prepared CPC shows a Coulombic efficiency of 98% and an energy efficiency of 81% at the current density of 80 mA cm -2 , which are among the highest values ever reported. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biological Screening of Newly Synthesized BIAN N-Heterocyclic Gold Carbene Complexes in Zebrafish Embryos

Science.gov (United States)

Farooq, Muhammad; Abu Taha, Nael; Butorac, Rachel R.; Evans, Daniel Anthony; Elzatahry, Ahmed A.; Elsayed, Elsayed Ahmed; Wadaan, Mohammad A. M.; Al-Deyab, Salem S.; Cowley, Alan H.

2015-01-01

N-Heterocyclic carbene (NHC) metal complexes possess diverse biological activities but have yet to be extensively explored as potential chemotherapeutic agents. We have previously reported the synthesis of a new class of NHC metal complexes N-heterocyclic with acetate [IPr(BIAN)AuOAc] and chloride [IPr(BIAN)AuCl] ligands. In the experiments reported herein, the zebrafish embryos were exposed to serial dilutions of each of these complexes for 10–12 h. One hundred percent mortality was observed at concentrations ≥50 µM. At sub-lethal concentrations (10–30 µM), both compounds influenced zebrafish embryonic development. However, quite diverse categories of abnormalities were found in exposed embryos with each compound. Severe brain deformation and notochord degeneration were evident in the case of [IPr(BIAN)AuOAc]. The zebrafish embryos treated with [IPr(BIAN)AuCl] exhibited stunted growth and consequently had smaller body sizes. A depletion of 30%–40% glutathione was detected in the treated embryos, which could account for one of the possible mechanism of neurotoxicity. The fact that these compounds are capable of both affecting the growth and also compromising antioxidant systems by elevating intracellular ROS production implies that they could play an important role as a new breed of therapeutic molecules. PMID:26501273

Improving off-line accelerated tryptic digestion. Towards fast-lane proteolysis of complex biological samples.

Science.gov (United States)

Vukovic, Jadranka; Loftheim, Håvard; Winther, Bjørn; Reubsaet, J Léon E

2008-06-27

Off-line digestion of proteins using immobilized trypsin beads is studied with respect to the format of the digestion reactor, the digestion conditions, the comparison with in-solution digestion and its use in complex biological samples. The use of the filter vial as the most appropriate digestion reactor enables simple, efficient and easy-to-handle off-line digestion of the proteins on trypsin beads. It was shown that complex proteins like bovine serum albumin (BSA) need much longer time (89 min) and elevated temperature (37 degrees C) to be digested to an acceptable level compared to smaller proteins like cytochrome c (5 min, room temperature). Comparing the BSA digestion using immobilized trypsin beads with conventional in-solution digestion (overnight at 37 degrees C), it was shown that comparable results were obtained with respect to sequence coverage (>90%) and amount of missed cleavages (in both cases around 20 peptides with 1 or 2 missed cleavages were detected). However, the digestion using immobilized trypsin beads was considerable less time consuming. Good reproducibility and signal intensities were obtained for the digestion products of BSA in a complex urine sample. In addition to this, peptide products of proteins typically present in urine were identified.

Complex chemistry

International Nuclear Information System (INIS)

Kim, Bong Gon; Kim, Jae Sang; Kim, Jin Eun; Lee, Boo Yeon

2006-06-01

This book introduces complex chemistry with ten chapters, which include development of complex chemistry on history coordination theory and Warner's coordination theory and new development of complex chemistry, nomenclature on complex with conception and define, chemical formula on coordination compound, symbol of stereochemistry, stereo structure and isomerism, electron structure and bond theory on complex, structure of complex like NMR and XAFS, balance and reaction on solution, an organo-metallic chemistry, biology inorganic chemistry, material chemistry of complex, design of complex and calculation chemistry.

Alkali Metal Ion Complexes with Phosphates, Nucleotides, Amino Acids, and Related Ligands of Biological Relevance. Their Properties in Solution.

Science.gov (United States)

Crea, Francesco; De Stefano, Concetta; Foti, Claudia; Lando, Gabriele; Milea, Demetrio; Sammartano, Silvio

2016-01-01

Alkali metal ions play very important roles in all biological systems, some of them are essential for life. Their concentration depends on several physiological factors and is very variable. For example, sodium concentrations in human fluids vary from quite low (e.g., 8.2 mmol dm(-3) in mature maternal milk) to high values (0.14 mol dm(-3) in blood plasma). While many data on the concentration of Na(+) and K(+) in various fluids are available, the information on other alkali metal cations is scarce. Since many vital functions depend on the network of interactions occurring in various biofluids, this chapter reviews their complex formation with phosphates, nucleotides, amino acids, and related ligands of biological relevance. Literature data on this topic are quite rare if compared to other cations. Generally, the stability of alkali metal ion complexes of organic and inorganic ligands is rather low (usually log K  Na(+) > K(+) > Rb(+) > Cs(+). For example, for citrate it is: log K ML = 0.88, 0.80, 0.48, 0.38, and 0.13 at 25 °C and infinite dilution. Some considerations are made on the main aspects related to the difficulties in the determination of weak complexes. The importance of the alkali metal ion complexes was also studied in the light of modelling natural fluids and in the use of these cations as probes for different processes. Some empirical relationships are proposed for the dependence of the stability constants of Na(+) complexes on the ligand charge, as well as for correlations among log K values of NaL, KL or LiL species (L = generic ligand).

Radiocharacterization of the 99mTc-rufloxacin complex and biological evaluation in Staphylococcus aureus infected rat model

International Nuclear Information System (INIS)

Syed Qaiser Shah; Muhammad Rafiullah Khan

2011-01-01

99m Tc-rufloxacin ( 99m Tc-RUN) complex was prepared by reaction of different amounts of reduced sodium pertechnetate with different amount of Rufloxacin (RUN) antibiotic for the in vivo scintigraphic localization of the Staphylococcus aureus (S. aureus) infectious foci in Male Wister Rats (MWR) model. The 99m Tc-RUN complex was radiochemically and biologically characterized in terms of radiochemical stability in saline, serum, in vitro binding with S. aureus and biodistribution in artificially infected with S. aureus MWR. The 99m Tc-RUN complex showed stability more than 90% up to 240 min in normal saline with a maximum stability value of 98.10 ± 0.18% at 30 min after reconstitution. At 37 deg C the complex showed in vitro permanence in serum up to 16 h with 13.90% side products during incubation. The 99m Tc-RUN complex showed saturated in vitro binding with S. aureus at different intervals with a maximum uptake value of 71.50%. Infected to normal muscle, infected to inflamed and inflamed to normal muscles ratios were approximately 6.04, 4.31 and 1.40. Based on the stability of the complex in saline, serum, in vitro binding with S. aureus and biodistribution results, the 99m Tc-RUN complex is recommended for in vivo scintigraphic localization of the S. aureus in vivo infectious foci in human. (author)

Syntheses, structural elucidation, thermal properties, theoretical quantum chemical studies (DFT and biological studies of barbituric–hydrazone complexes

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Amina A. Soayed

2015-03-01

Full Text Available Condensation of barbituric acid with hydrazine hydrate yielded barbiturichydrazone (L which was characterized using IR, 1H NMR and mass spectra. The Co(II, Ni(II and Cu(II complexes derived from this ligand have been synthesized and structurally characterized by elemental analyses, spectroscopic methods (IR, UV–Vis and ESR and thermal analyses (TGA, DTG and DTA and the structures were further elucidated using quantum chemical density functional theory. Complexes of L were found to have the ML.nH2O stoichiometry with either tetrahedral or octahedral geometry. The ESR data showed the Cu(II complex to be in a tetragonal geometry. Theoretical investigation of the electronic structure of metal complexes at the TD-DFT/B3LYP level of theory has been carried out and discussed. The fundamental vibrational wavenumbers were calculated and a good agreement between observed and scaled calculated wavenumbers was achieved. Thermal studies were performed to deduce the stabilities of the ligand and complexes. Thermodynamic parameters, such as the order of reactions (n, activation energy ΔE∗, enthalpy of reaction ΔH∗ and entropy ΔS∗ were calculated from DTA curves using Horowitz–Metzger method. The ligand L and its complexes have been screened for their antifungal and antibacterial activities and were found to possess better biological activities compared to those of unsubstituted barbituric acid complexes.

Shatter Complex Formation in the Twin Craters Lava Flow, Zuni-Bandera Field, New Mexico

Science.gov (United States)

von Meerscheidt, H. C.; Bleacher, J. E.; Brand, B. D.; deWet, A.; Samuels, R.; Hamilton, C.; Garry, W. B.; Bandfield, J. L.

2013-12-01

. Prominent ';a';a channels travel around the bluff, leaving a 'wake' of uncovered ground on the downstream side. We interpret this shatter area to have been a branching tube network within an active sheet. The limestone bluff acted as an obstacle that caused a backup of lava within the tubes, driving episodes of shattering. The mounds likely represent earlier solidified sections between active, possibly braided, tube branches, which remained as mounds within the shatter area after the adjacent crust subsided. When lava broke out from the pressurized sheet-like lobe, it formed the ';a';a channels. This section of the flow field is interpreted using inferences from shatter ring formation, but is perhaps better termed a shatter sheet or shatter complex. This study has implications for understanding lava flow dynamics at constriction points, as well as the evolution and morphology of shatter rings.

Hyperspectral imaging flow cytometer

Science.gov (United States)

Sinclair, Michael B.; Jones, Howland D. T.

2017-10-25

A hyperspectral imaging flow cytometer can acquire high-resolution hyperspectral images of particles, such as biological cells, flowing through a microfluidic system. The hyperspectral imaging flow cytometer can provide detailed spatial maps of multiple emitting species, cell morphology information, and state of health. An optimized system can image about 20 cells per second. The hyperspectral imaging flow cytometer enables many thousands of cells to be characterized in a single session.

A versatile embedded boundary adaptive mesh method for compressible flow in complex geometry

KAUST Repository

Almarouf, Mohamad Abdulilah Alhusain Alali

2017-02-25

We present an embedded ghost-fluid method for numerical solutions of the compressible Navier Stokes (CNS) equations in arbitrary complex domains. A PDE multidimensional extrapolation approach is used to reconstruct the solution in the ghost-fluid regions and imposing boundary conditions on the fluid-solid interface, coupled with a multi-dimensional algebraic interpolation for freshly cleared cells. The CNS equations are numerically solved by the second order multidimensional upwind method. Block-structured adaptive mesh refinement, implemented with the Chombo framework, is utilized to reduce the computational cost while keeping high resolution mesh around the embedded boundary and regions of high gradient solutions. The versatility of the method is demonstrated via several numerical examples, in both static and moving geometry, ranging from low Mach number nearly incompressible flows to supersonic flows. Our simulation results are extensively verified against other numerical results and validated against available experimental results where applicable. The significance and advantages of our implementation, which revolve around balancing between the solution accuracy and implementation difficulties, are briefly discussed as well.

A versatile embedded boundary adaptive mesh method for compressible flow in complex geometry

KAUST Repository

Almarouf, Mohamad Abdulilah Alhusain Alali; Samtaney, Ravi

2017-01-01

We present an embedded ghost-fluid method for numerical solutions of the compressible Navier Stokes (CNS) equations in arbitrary complex domains. A PDE multidimensional extrapolation approach is used to reconstruct the solution in the ghost-fluid regions and imposing boundary conditions on the fluid-solid interface, coupled with a multi-dimensional algebraic interpolation for freshly cleared cells. The CNS equations are numerically solved by the second order multidimensional upwind method. Block-structured adaptive mesh refinement, implemented with the Chombo framework, is utilized to reduce the computational cost while keeping high resolution mesh around the embedded boundary and regions of high gradient solutions. The versatility of the method is demonstrated via several numerical examples, in both static and moving geometry, ranging from low Mach number nearly incompressible flows to supersonic flows. Our simulation results are extensively verified against other numerical results and validated against available experimental results where applicable. The significance and advantages of our implementation, which revolve around balancing between the solution accuracy and implementation difficulties, are briefly discussed as well.

Multiphase flow dynamics 1 fundamentals

CERN Document Server

Kolev, Nikolay Ivanov

2004-01-01

Multi-phase flows are part of our natural environment such as tornadoes, typhoons, air and water pollution and volcanic activities as well as part of industrial technology such as power plants, combustion engines, propulsion systems, or chemical and biological industry. The industrial use of multi-phase systems requires analytical and numerical strategies for predicting their behavior. In its third extended edition this monograph contains theory, methods and practical experience for describing complex transient multi-phase processes in arbitrary geometrical configurations, providing a systematic presentation of the theory and practice of numerical multi-phase fluid dynamics. In the present first volume the fundamentals of multiphase dynamics are provided. This third edition includes various updates, extensions and improvements in all book chapters.

Convective thermal fluxes in unsteady non-homogeneous flows generating complex three dimensional vorticity patterns

Science.gov (United States)

Tellez Alvarez, Jackson David; Redondo, Jose Manuel; Sanchez, Jesu Mary

2016-04-01

fresh water in order to form density interfaces. The Reynolds number can be reduced adding Glicerine the set of dimensionless parameters define different conditions of both numeric and small scale laboratory applied often in modeling environmental flows. Fields of velocity, density and their gradients are computed using advanced visualization [8 9]. Visualizations are performed by PIV, Particle tracking and shadowgraph. When convective heating and cooling takes place the patterns depend on the parameter space region of the initial conditions We also map the different transitions between two and three dimensional convection in an enclosure with several complex driven flows. The size of the water tank is of 0.2 x 0.2 x 0.1 m and the heat sources or sinks can be regulated both in power and sign [2-4]. The thermal convective driven flows are generated by Seebeck and Peltier effects in 4 wall extended positions of 0.05 x 0.05 cm each. The parameter range of convective cell array varies strongly with the Topology of the boundary conditions. At present side heat fluxes are considered and estimated as a function of Rayleigh, Peclet and Nusselt numbers, [4-6] The evolution of the mixing fronts are compared and the topological characteristics of the merging of plumes and jets in different configurations presenting detailed comparison of the evolution of RM and RT, Jets and Plumes in overall mixing. The relation between structure functions, fractal analysis and spectral analysis can be very useful to determine the evolution of scales. Experimental and numerical results on the advance of a mixing or non-mixing front occurring at a density interface due to body forces [12] can be compared with the convective fronts. The evolution of the turbulent mixing layer and its complex configuration is studied taking into account the dependence on the initial modes at the early stages, Self-similar information [13]. Spectral and Fractal analysis on the images seems very useful in order to

Bathyphotometer bioluminescence potential measurements: A framework for characterizing flow agitators and predicting flow-stimulated bioluminescence intensity

Science.gov (United States)

Latz, Michael I.; Rohr, Jim

2013-07-01

Bathyphotometer measurements of bioluminescence are used as a proxy for the abundance of luminescent organisms for studying population dynamics; the interaction of luminescent organisms with physical, chemical, and biological oceanographic processes; and spatial complexity especially in coastal areas. However, the usefulness of bioluminescence measurements has been limited by the inability to compare results from different bathyphotometer designs, or even the same bathyphotometer operating at different volume flow rates. The primary objective of this study was to compare measurements of stimulated bioluminescence of four species of cultured dinoflagellates, the most common source of bioluminescence in coastal waters, using two different bathyphotometer flow agitators as a function of bathyphotometer volume flow rate and dinoflagellate concentration. For both the NOSC and BIOLITE flow agitators and each species of dinoflagellate tested, there was a critical volume flow rate, above which average bioluminescence intensity, designated as bathyphotometer bioluminescence potential (BBP), remained relatively constant and scaled directly with dinoflagellate cell concentration. At supra-critical volume flow rates, the ratio of BIOLITE to NOSC BBP was nearly constant for the same species studied, but varied between species. The spatial pattern and residence time of flash trajectories within the NOSC flow agitator indicated the presence of dominant secondary recirculating flows, where most of the bioluminescence was detected. A secondary objective (appearing in the Appendix) was to study the feasibility of using NOSC BBP to scale flow-stimulated bioluminescence intensity across similar flow fields, where the contributing composition of luminescent species remained the same. Fully developed turbulent pipe flow was chosen because it is hydrodynamically well characterized. Average bioluminescence intensity in a 2.54-cm i.d. pipe was highly correlated with wall shear stress and

Fluorescence-intensity multiplexing: simultaneous seven-marker, two-color immunophenotyping using flow cytometry.

Science.gov (United States)

Bradford, Jolene A; Buller, Gayle; Suter, Michael; Ignatius, Michael; Beechem, Joseph M

2004-10-01

Conventional immuno-based multiparameter flow cytometric analysis has been limited by the requirement of a dedicated detection channel for each antibody-fluorophore set. To address the need to resolve multiple biological targets simultaneously, flow cytometers with as many as 10-15 detection channels have been developed. In this study, a new Zenon immunolabeling technology is developed that allows for multiple antigen detection per detection channel using a single fluorophore, through a unique method of fluorescence-intensity multiplexing. By varying the Zenon labeling reagent-to-antibody molar ratio, the fluorescence intensity of the antibody-labeled cellular targets can be used as a unique identifier. Although demonstrated in the present study with lymphocyte immunophenotyping, this approach is broadly applicable for any immuno-based multiplexed flow cytomety assay. Lymphocyte immunophenotyping of 38 clinical blood specimens using CD3, CD4, CD8, CD16, CD56, CD19, and CD20 antibodies was performed using conventional flow cytometric analysis and fluorescence-intensity multiplexing analysis. Conventional analysis measures a single antibody-fluorophore per photomultiplier tube (PMT). Fluorescence-intensity multiplex analysis simultaneously measures seven markers with two PMTs, using Zenon labeling reagent-antibody complexes in a single tube: CD19, CD4, CD8, and CD16 antibodies labeled with Zenon Alexa Fluor 488 Mouse IgG(1) labeling reagent and CD56, CD3, and CD20 antibodies labeled with Zenon R-Phycoerythrin (R-PE) Mouse IgG(1) or IgG(2b) labeling reagents. The lymphocyte immunophenotyping results from fluorescence-intensity multiplexing using Zenon labeling reagents in a single tube were comparable to results from conventional flow cytometric analysis. Simultaneous evaluation of multiple antigens using a single fluorophore can be performed using antibodies labeled with varying ratios of a Zenon labeling reagent. Labeling two sets of antibodies with different Zenon

Partial Purification of a Megadalton DNA Replication Complex by Free Flow Electrophoresis.

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Caroline M Li

Full Text Available We describe a gentle and rapid method to purify the intact multiprotein DNA replication complex using free flow electrophoresis (FFE. In particular, we applied FFE to purify the human cell DNA synthesome, which is a multiprotein complex that is fully competent to carry-out all phases of the DNA replication process in vitro using a plasmid containing the simian virus 40 (SV40 origin of DNA replication and the viral large tumor antigen (T-antigen protein. The isolated native DNA synthesome can be of use in studying the mechanism by which mammalian DNA replication is carried-out and how anti-cancer drugs disrupt the DNA replication or repair process. Partially purified extracts from HeLa cells were fractionated in a native, liquid based separation by FFE. Dot blot analysis showed co-elution of many proteins identified as part of the DNA synthesome, including proliferating cell nuclear antigen (PCNA, DNA topoisomerase I (topo I, DNA polymerase δ (Pol δ, DNA polymerase ɛ (Pol ɛ, replication protein A (RPA and replication factor C (RFC. Previously identified DNA synthesome proteins co-eluted with T-antigen dependent and SV40 origin-specific DNA polymerase activity at the same FFE fractions. Native gels show a multiprotein PCNA containing complex migrating with an apparent relative mobility in the megadalton range. When PCNA containing bands were excised from the native gel, mass spectrometric sequencing analysis identified 23 known DNA synthesome associated proteins or protein subunits.

Partial Purification of a Megadalton DNA Replication Complex by Free Flow Electrophoresis.

Science.gov (United States)

Li, Caroline M; Miao, Yunan; Lingeman, Robert G; Hickey, Robert J; Malkas, Linda H

2016-01-01

We describe a gentle and rapid method to purify the intact multiprotein DNA replication complex using free flow electrophoresis (FFE). In particular, we applied FFE to purify the human cell DNA synthesome, which is a multiprotein complex that is fully competent to carry-out all phases of the DNA replication process in vitro using a plasmid containing the simian virus 40 (SV40) origin of DNA replication and the viral large tumor antigen (T-antigen) protein. The isolated native DNA synthesome can be of use in studying the mechanism by which mammalian DNA replication is carried-out and how anti-cancer drugs disrupt the DNA replication or repair process. Partially purified extracts from HeLa cells were fractionated in a native, liquid based separation by FFE. Dot blot analysis showed co-elution of many proteins identified as part of the DNA synthesome, including proliferating cell nuclear antigen (PCNA), DNA topoisomerase I (topo I), DNA polymerase δ (Pol δ), DNA polymerase ɛ (Pol ɛ), replication protein A (RPA) and replication factor C (RFC). Previously identified DNA synthesome proteins co-eluted with T-antigen dependent and SV40 origin-specific DNA polymerase activity at the same FFE fractions. Native gels show a multiprotein PCNA containing complex migrating with an apparent relative mobility in the megadalton range. When PCNA containing bands were excised from the native gel, mass spectrometric sequencing analysis identified 23 known DNA synthesome associated proteins or protein subunits.

Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds.

Science.gov (United States)

Fang, Lingzhao; Sahana, Goutam; Ma, Peipei; Su, Guosheng; Yu, Ying; Zhang, Shengli; Lund, Mogens Sandø; Sørensen, Peter

2017-08-10

A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the genomic variants of complex traits might be enriched in a subset of genomic regions defined by genes grouped on the basis of "Gene Ontology" (GO), and that incorporating this independent biological information into genomic prediction models might improve their predictive ability. Four complex traits (i.e., milk, fat and protein yields, and mastitis) together with imputed sequence variants in Holstein (HOL) and Jersey (JER) cattle were analysed. We first carried out a post-GWAS analysis in a HOL training population to assess the degree of enrichment of the association signals in the gene regions defined by each GO term. We then extended the genomic best linear unbiased prediction model (GBLUP) to a genomic feature BLUP (GFBLUP) model, including an additional genomic effect quantifying the joint effect of a group of variants located in a genomic feature. The GBLUP model using a single random effect assumes that all genomic variants contribute to the genomic relationship equally, whereas GFBLUP attributes different weights to the individual genomic relationships in the prediction equation based on the estimated genomic parameters. Our results demonstrate that the immune-relevant GO terms were more associated with mastitis than milk production, and several biologically meaningful GO terms improved the prediction accuracy with GFBLUP for the four traits, as compared with GBLUP. The improvement of the genomic prediction between breeds (the average increase across the four traits was 0.161) was more apparent than that it was within the HOL (the average increase across the four traits was 0.020). Our genomic feature modelling approaches provide a framework to simultaneously explore the genetic architecture and genomic prediction of complex traits by taking advantage of

Particle image velocimetry measurement of complex flow structures in the diffuser and spherical casing of a reactor coolant pump

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Yongchao Zhang

2018-04-01

Full Text Available Understanding of turbulent flow in the reactor coolant pump (RCP is a premise of the optimal design of the RCP. Flow structures in the RCP, in view of the specially devised spherical casing, are more complicated than those associated with conventional pumps. Hitherto, knowledge of the flow characteristics of the RCP has been far from sufficient. Research into the nonintrusive measurement of the internal flow of the RCP has rarely been reported. In the present study, flow measurement using particle image velocimetry is implemented to reveal flow features of the RCP model. Velocity and vorticity distributions in the diffuser and spherical casing are obtained. The results illuminate the complexity of the flows in the RCP. Near the lower end of the discharge nozzle, three-dimensional swirling flows and flow separation are evident. In the diffuser, the imparity of the velocity profile with respect to different axial cross sections is verified, and the velocity increases gradually from the shroud to the hub. In the casing, velocity distribution is nonuniform over the circumferential direction. Vortices shed consistently from the diffuser blade trailing edge. The experimental results lend sound support for the optimal design of the RCP and provide validation of relevant numerical algorithms. Keywords: Diffuser, Flow Structures, Particle Image Velocimetry, Reactor Coolant Pump, Spherical Casing, Velocity Distribution

First steps towards a generic sample preparation scheme for inorganic engineered nanoparticles in a complex matrix for detection, characterization, and quantification by asymmetric flow-field flow fractionation coupled to multi-angle light scattering and ICP-MS

DEFF Research Database (Denmark)

Wagner, Stephan; Legros, Samuel; Löschner, Katrin

2015-01-01

content by asymmetric flow-field flow fractionation coupled to a multi-angle light scattering detector and an inductively coupled plasma mass spectrometer. Following the proposed generic procedure SiO2-ENPs were separated from a tomato soup. Two potential sample preparation methods were tested these being...... quality criteria for method development is urgently needed for standardized and systematic development of procedures for separation of ENPs from a complex matrix. The chosen analytical technique was shown to be suitable for detecting SiO2-ENPs in a complex food matrix like tomato soup and may therefore...

Phylogenetics and genetic diversity of the Cotesia flavipes complex of parasitoid wasps (Hymenoptera: Braconidae), biological control agents of lepidopteran stemborers.

Science.gov (United States)

Muirhead, Kate A; Murphy, Nicholas P; Sallam, Nader; Donnellan, Stephen C; Austin, Andrew D

2012-06-01

The Cotesia flavipes complex of parasitoid wasps (Hymenoptera: Braconidae) are economically important for the biological control of lepidopteran stemboring pests associated with gramineous crops. Some members of the complex successfully parasitize numerous stemborer pest species, however certain geographic populations have demonstrated variation in the range of hosts that they parasitize. In addition, the morphology of the complex is highly conserved and considerable confusion surrounds the identity of species and host-associated biotypes. We generated nucleotide sequence data for two mtDNA genes (COI, 16S) and three anonymous nuclear loci (CfBN, CfCN, CfEN) for the C. flavipes complex. To analyze genetic variation and relationships among populations we used (1) concatenated mtDNA and nDNA data, (2) a nDNA multilocus network approach, and (3) two species tree inference methods, i.e. Bayesian estimation of species trees (BEST) and Bayesian inference of species trees from multilocus data with (*)BEAST. All phylogenetic analyses provide strong support for monophyly of the complex and the presence of at least four species, C. chilonis (from China and Japan), C. sesamiae (from Africa), C. flavipes (originating from the Indo-Asia region but introduced into Africa and the New World), and C. nonagriae (from Australia and Papua New Guinea). Haplotype diversity of geographic populations relates to historical biogeographic barriers and biological control introductions, and reflects previous reports of ecological variation in these species. Strong discordance was found between the mitochondrial and nuclear markers in the Papua New Guinea haplotypes, which may be an outcome of hybridization and introgression of C. flavipes and C. nonagriae. The position of Cotesia flavipes from Japan was not well supported in any analysis and was the sister taxon to C. nonagriae (mtDNA, (*)BEAST), C. flavipes (nDNA) or C. flavipes+C. nonagriae (BEST) and, may represent a cryptic species. The

Linking Biological Responses of Terrestrial N Eutrophication to the Final Ecosystem Goods and Services Classification System

Science.gov (United States)

Bell, M. D.; Clark, C.; Blett, T.

2015-12-01

The response of a biological indicator to N deposition can indicate that an ecosystem has surpassed a critical load and is at risk of significant change. The importance of this exceedance is often difficult to digest by policy makers and public audiences if the change is not linked to a familiar ecosystem endpoint. A workshop was held to bring together scientists, resource managers, and policy makers with expertise in ecosystem functioning, critical loads, and economics in an effort to identify the ecosystem services impacted by air pollution. This was completed within the framework of the Final Ecosystem Goods and Services (FEGS) Classification System to produce a product that identified distinct interactions between society and the effects of nitrogen pollution. From each change in a biological indicator, we created multiple ecological production functions to identify the cascading effects of the change to a measureable ecosystem service that a user interacts with either by enjoying, consuming, or appreciating the good or service, or using it as an input in the human economy. This FEGS metric was then linked to a beneficiary group that interacts with the service. Chains detailing the links from the biological indicator to the beneficiary group were created for aquatic and terrestrial acidification and eutrophication at the workshop, and here we present a subset of the workshop results by highlighting for 9 different ecosystems affected by terrestrial eutrophication. A total of 213 chains that linked to 37 unique FEGS metrics and impacted 15 beneficiary groups were identified based on nitrogen deposition mediated changes to biological indicators. The chains within each ecosystem were combined in flow charts to show the complex, overlapping relationships among biological indicators, ecosystem services, and beneficiary groups. Strength of relationship values were calculated for each chain based on support for the link in the scientific literature. We produced the

Polyploidy in the Olive Complex (Olea europaea): Evidence from Flow Cytometry and Nuclear Microsatellite Analyses

Science.gov (United States)

Besnard, G.; Garcia-Verdugo, C.; Rubio De Casas, R.; Treier, U. A.; Galland, N.; Vargas, P.

2008-01-01

Background Phylogenetic and phylogeographic investigations have been previously performed to study the evolution of the olive tree complex (Olea europaea). A particularly high genomic diversity has been found in north-west Africa. However, to date no exhaustive study has been addressed to infer putative polyploidization events and their evolutionary significance in the diversification of the olive tree and its relatives. Methods Representatives of the six olive subspecies were investigated using (a) flow cytometry to estimate genome content, and (b) six highly variable nuclear microsatellites to assess the presence of multiple alleles at co-dominant loci. In addition, nine individuals from a controlled cross between two individuals of O. europaea subsp. maroccana were characterized with microsatellites to check for chromosome inheritance. Key Results Based on flow cytometry and genetic analyses, strong evidence for polyploidy was obtained in subspp. cerasiformis (tetraploid) and maroccana (hexaploid), whereas the other subspecies appeared to be diploids. Agreement between flow cytometry and genetic analyses gives an alternative approach to chromosome counting to determine ploidy level of trees. Lastly, abnormalities in chromosomes inheritance leading to aneuploid formation were revealed using microsatellite analyses in the offspring from the controlled cross in subsp. maroccana. Conclusions This study constitutes the first report for multiple polyploidy in olive tree relatives. Formation of tetraploids and hexaploids may have played a major role in the diversification of the olive complex in north-west Africa. The fact that polyploidy is found in narrow endemic subspecies from Madeira (subsp. cerasiformis) and the Agadir Mountains (subsp. maroccana) suggests that polyploidization has been favoured to overcome inbreeding depression. Lastly, based on previous phylogenetic analyses, we hypothesize that subsp. cerasiformis resulted from hybridization between ancestors

Numerical Leak Detection in a Pipeline Network of Complex Structure with Unsteady Flow

Science.gov (United States)

Aida-zade, K. R.; Ashrafova, E. R.

2017-12-01

An inverse problem for a pipeline network of complex loopback structure is solved numerically. The problem is to determine the locations and amounts of leaks from unsteady flow characteristics measured at some pipeline points. The features of the problem include impulse functions involved in a system of hyperbolic differential equations, the absence of classical initial conditions, and boundary conditions specified as nonseparated relations between the states at the endpoints of adjacent pipeline segments. The problem is reduced to a parametric optimal control problem without initial conditions, but with nonseparated boundary conditions. The latter problem is solved by applying first-order optimization methods. Results of numerical experiments are presented.

High stability and biological activity of the copper(II) complexes of alloferon 1 analogues containing tryptophan.

Science.gov (United States)

Kadej, Agnieszka; Kuczer, Mariola; Czarniewska, Elżbieta; Urbański, Arkadiusz; Rosiński, Grzegorz; Kowalik-Jankowska, Teresa

2016-10-01

Copper(II) complex formation processes between the alloferon 1 (Allo1) (HGVSGHGQHGVHG) analogues where the tryptophan residue is introducing in the place His residue H1W, H6W, H9W and H12W have been studied by potentiometric, UV-visible, CD and EPR spectroscopic, and MS methods. For all analogues of alloferon 1 complex speciation have been obtained for a 1:1 metal-to-ligand molar ratio and 2:1 of H1W because of precipitation at higher (2:1, 3:1 and 4:1) ratios. At physiological pH7.4 and a 1:1 metal-to-ligand molar ratio the tryptophan analogues of alloferon 1 form the CuH -1 L and/or CuH -2 L complexes with the 4N binding mode. The introduction of tryptophan in place of histidine residues changes the distribution diagram of the complexes formed with the change of pH and their stability constants compared to the respective substituted alanine analogues of alloferon 1. The CuH -1 L, CuH -2 L and CuH -3 L complexes of the tryptophan analogues are more stable from 1 to 5 log units in comparison to those of the alanine analogues. This stabilization of the complexes may result from cation(Cu(II))-π and indole/imidazole ring interactions. The induction of apoptosis in vivo, in Tenebrio molitor cells by the ligands and their copper(II) complexes at pH7.4 was studied. The biological results show that copper(II) ions in vivo did not cause any apparent apoptotic features. The most active were the H12W peptide and Cu(II)-H12W complex formed at pH7.4. Copyright © 2016 Elsevier Inc. All rights reserved.

Analytical Tools to Improve Optimization Procedures for Lateral Flow Assays

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Helen V. Hsieh

2017-05-01

Full Text Available Immunochromatographic or lateral flow assays (LFAs are inexpensive, easy to use, point-of-care medical diagnostic tests that are found in arenas ranging from a doctor’s office in Manhattan to a rural medical clinic in low resource settings. The simplicity in the LFA itself belies the complex task of optimization required to make the test sensitive, rapid and easy to use. Currently, the manufacturers develop LFAs by empirical optimization of material components (e.g., analytical membranes, conjugate pads and sample pads, biological reagents (e.g., antibodies, blocking reagents and buffers and the design of delivery geometry. In this paper, we will review conventional optimization and then focus on the latter and outline analytical tools, such as dynamic light scattering and optical biosensors, as well as methods, such as microfluidic flow design and mechanistic models. We are applying these tools to find non-obvious optima of lateral flow assays for improved sensitivity, specificity and manufacturing robustness.

Detection and isolation of cell-derived microparticles are compromised by protein complexes resulting from shared biophysical parameters.

Science.gov (United States)

György, Bence; Módos, Károly; Pállinger, Eva; Pálóczi, Krisztina; Pásztói, Mária; Misják, Petra; Deli, Mária A; Sipos, Aron; Szalai, Anikó; Voszka, István; Polgár, Anna; Tóth, Kálmán; Csete, Mária; Nagy, György; Gay, Steffen; Falus, András; Kittel, Agnes; Buzás, Edit I

2011-01-27

Numerous diseases, recently reported to associate with elevated microvesicle/microparticle (MP) counts, have also long been known to be characterized by accelerated immune complex (IC) formation. The goal of this study was to investigate the potential overlap between parameters of protein complexes (eg, ICs or avidin-biotin complexes) and MPs, which might perturb detection and/or isolation of MPs. In this work, after comprehensive characterization of MPs by electron microscopy, atomic force microscopy, dynamic light-scattering analysis, and flow cytometry, for the first time, we drive attention to the fact that protein complexes, especially insoluble ICs, overlap in biophysical properties (size, light scattering, and sedimentation) with MPs. This, in turn, affects MP quantification by flow cytometry and purification by differential centrifugation, especially in diseases in which IC formation is common, including not only autoimmune diseases, but also hematologic disorders, infections, and cancer. These data may necessitate reevaluation of certain published data on patient-derived MPs and contribute to correct the clinical laboratory assessment of the presence and biologic functions of MPs in health and disease.

Coupling Analysis of Low-Speed Multiphase Flow and High-Frequency Electromagnetic Field in a Complex Pipeline Structure

Directory of Open Access Journals (Sweden)

Xiaokai Huo

2014-01-01

Full Text Available Accurate estimation of water content in an oil-water mixture is a key technology in oil exploration and production. Based on the principles of the microwave transmission line (MTL, the logging probe is an important water content measuring apparatus. However, the effects of mixed fluid flow on the measurement of electromagnetic field parameters are rarely considered. This study presents the coupling model for low-speed multiphase flow and high-frequency electromagnetic field in a complex pipeline structure. We derived the S-parameter equations for the stratified oil/water flow model. The corresponding relationship between the S-parameters and water holdup is established. Evident coupling effects of the fluid flow and the electromagnetic field are confirmed by comparing the calculated S-parameters for both stratified and homogeneous flow patterns. In addition, a multiple-solution problem is analyzed for the inversion of dielectric constant from the S-parameters. The most sensitive phase angle range is determined to improve the detection of variation in the dielectric constant. Suggestions are proposed based on the influence of the oil/water layer on measurement sensitivity to optimize the geometric parameters of a device structure. The method proposed elucidates how accuracy and sensitivity can be improved in water holdup measurements under high water content conditions.

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

Top-down models in biology: explanation and control of complex living systems above the molecular level.

Science.gov (United States)

Pezzulo, Giovanni; Levin, Michael

2016-11-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).

Modification of the protein corona–nanoparticle complex by physiological factors

Energy Technology Data Exchange (ETDEWEB)

Braun, Nicholas J.; DeBrosse, Madeleine C.; Hussain, Saber M. [Molecular Bioeffects Branch, Bioeffects Division, Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright Patterson AFB, 2729 R. St, Bldg 837, Dayton, OH, 45433 (United States); Comfort, Kristen K., E-mail: kcomfort1@udayton.edu [Department of Chemical and Materials Engineering, University of Dayton, 524 Kettering Laboratories, 300 College Park, Dayton, OH 45469 (United States)

2016-07-01

Nanoparticle (NP) effects in a biological system are driven through the formation and structure of the protein corona–NP complex, which is dynamic by nature and dependent upon factors from both the local environment and NP physicochemical parameters. To date, considerable data has been gathered regarding the structure and behavior of the protein corona in blood, plasma, and traditional cell culture medium. However, there exists a knowledge gap pertaining to the protein corona in additional biological fluids and following incubation in a dynamic environment. Using 13 nm gold NPs (AuNPs), functionalized with either polyethylene glycol or tannic acid, we demonstrated that both particle characteristics and the associated protein corona were altered when exposed to artificial physiological fluids and under dynamic flow. Furthermore, the magnitude of observed behavioral shifts were dependent upon AuNP surface chemistry. Lastly, we revealed that exposure to interstitial fluid produced protein corona modifications, reshaping of the nano-cellular interface, modified AuNP dosimetry, and induction of previously unseen cytotoxicity. This study highlights the need to elucidate both NP and protein corona behavior in biologically representative environments in an effort to increase accurate interpretation of data and transfer of this knowledge to efficacy, behavior, and safety of nano-based applications. - Highlights: • Dynamic flow increased the size of the gold nanoparticle protein corona. • Exposure to biological fluids altered protein corona size and composition. • Interstitial fluid modified the nano-cellular interface and deposition efficiency. • Tannic acid coated nanoparticles induced toxicity in an interstitial environment.

Modification of the protein corona–nanoparticle complex by physiological factors

International Nuclear Information System (INIS)

Braun, Nicholas J.; DeBrosse, Madeleine C.; Hussain, Saber M.; Comfort, Kristen K.

2016-01-01

Nanoparticle (NP) effects in a biological system are driven through the formation and structure of the protein corona–NP complex, which is dynamic by nature and dependent upon factors from both the local environment and NP physicochemical parameters. To date, considerable data has been gathered regarding the structure and behavior of the protein corona in blood, plasma, and traditional cell culture medium. However, there exists a knowledge gap pertaining to the protein corona in additional biological fluids and following incubation in a dynamic environment. Using 13 nm gold NPs (AuNPs), functionalized with either polyethylene glycol or tannic acid, we demonstrated that both particle characteristics and the associated protein corona were altered when exposed to artificial physiological fluids and under dynamic flow. Furthermore, the magnitude of observed behavioral shifts were dependent upon AuNP surface chemistry. Lastly, we revealed that exposure to interstitial fluid produced protein corona modifications, reshaping of the nano-cellular interface, modified AuNP dosimetry, and induction of previously unseen cytotoxicity. This study highlights the need to elucidate both NP and protein corona behavior in biologically representative environments in an effort to increase accurate interpretation of data and transfer of this knowledge to efficacy, behavior, and safety of nano-based applications. - Highlights: • Dynamic flow increased the size of the gold nanoparticle protein corona. • Exposure to biological fluids altered protein corona size and composition. • Interstitial fluid modified the nano-cellular interface and deposition efficiency. • Tannic acid coated nanoparticles induced toxicity in an interstitial environment.

EPR Characterization of Dinitrosyl Iron Complexes with Thiol-Containing Ligands as an Approach to Their Identification in Biological Objects: An Overview.

Science.gov (United States)

Vanin, Anatoly F

2018-06-01

The overview demonstrates how the use of only one physico-chemical approach, viz., the electron paramagnetic resonance method, allowed detection and identification of dinitrosyl iron complexes with thiol-containing ligands in various animal and bacterial cells. These complexes are formed in biological objects in the paramagnetic (electron paramagnetic resonance-active) mononuclear and diamagnetic (electron paramagnetic resonance-silent) binuclear forms and control the activity of nitrogen monoxide, one of the most universal regulators of metabolic processes in the organism. The analysis of electronic and spatial structures of dinitrosyl iron complex sheds additional light on the mechanism whereby dinitrosyl iron complex with thiol-containing ligands function in human and animal cells as donors of nitrogen monoxide and its ionized form, viz., nitrosonium ions (NO + ).

Complex flow morphologies in shock-accelerated gaseous flows

Science.gov (United States)

Kumar, S.; Vorobieff, P.; Orlicz, G.; Palekar, A.; Tomkins, C.; Goodenough, C.; Marr-Lyon, M.; Prestridge, K. P.; Benjamin, R. F.

2007-11-01

A Mach 1.2 planar shock wave impulsively and simultaneously accelerates a row of three heavy gas (SF 6) cylinders surrounded by a lighter gas (air), producing pairs of vortex columns. The heavy gas cylinders (nozzle diameter D) are initially equidistant in the spanwise direction (center to center spacing S), with S/D=1.5. The interaction of the vortex columns is investigated with planar laser-induced fluorescence (PLIF) in the plane normal to the axes of the cylinders. Several distinct post-shock morphologies are observed, apparently due to rather small variations of the initial conditions. We report the variation of the streamwise and spanwise growth rates of the integral scales for these flow morphologies.

Evidence from lava flows for complex polarity transitions: The new composite Steens Mountain reversal record

Science.gov (United States)

Jarboe, Nicholas A.; Coe, Robert S.; Glen, Jonathan M. G.

2011-01-01

Geomagnetic polarity transitions may be significantly more complex than are currently depicted in many sedimentary and lava-flow records. By splicing together paleomagnetic results from earlier studies at Steens Mountain with those from three newly studied sections of Oregon Plateau flood basalts at Catlow Peak and Poker Jim Ridge 70–90 km to the southeast and west, respectively, we provide support for this interpretation with the most detailed account of a magnetic field reversal yet observed in volcanic rocks. Forty-five new distinguishable transitional (T) directions together with 30 earlier ones reveal a much more complex and detailed record of the 16.7 Ma reversed (R)-to-normal (N) polarity transition that marks the end of Chron C5Cr. Compared to the earlier R-T-N-T-N reversal record, the new record can be described as R-T-N-T-N-T-R-T-N. The composite record confirms earlier features, adds new west and up directions and an entire large N-T-R-T segment to the path, and fills in directions on the path between earlier directional jumps. Persistent virtual geomagnetic pole (VGP) clusters and separate VGPs have a preference for previously described longitudinal bands from transition study compilations, which suggests the presence of features at the core–mantle boundary that influence the flow of core fluid and distribution of magnetic flux. Overall the record is consistent with the generalization that VGP paths vary greatly from reversal to reversal and depend on the location of the observer. Rates of secular variation confirm that the flows comprising these sections were erupted rapidly, with maximum rates estimated to be 85–120 m ka−1 at Catlow and 130–195 m ka−1 at Poker Jim South. Paleomagnetic poles from other studies are combined with 32 non-transitional poles found here to give a clockwise rotation of the Oregon Plateau of 11.4°± 5.6° with respect to the younger Columbia River Basalt Group flows to the north and 14.5°± 4.6° with respect

Development and operation of an integrated sampling probe and gas analyzer for turbulent mixing studies in complex supersonic flows

Science.gov (United States)

Wiswall, John D.

For many aerospace applications, mixing enhancement between co-flowing streams has been identified as a critical and enabling technology. Due to short fuel residence times in scramjet combustors, combustion is limited by the molecular mixing of hydrogen (fuel) and air. Determining the mixedness of fuel and air in these complex supersonic flowfields is critical to the advancement of novel injection schemes currently being developed at UTA in collaboration with NASA Langley and intended to be used on a future two-stage to orbit (~Mach 16) hypersonic air-breathing vehicle for space access. Expanding on previous work, an instrument has been designed, fabricated, and tested in order to measure mean concentrations of injected helium (a passive scalar used instead of hazardous hydrogen) and to quantitatively characterize the nature of the high-frequency concentration fluctuations encountered in the compressible, turbulent, and high-speed (up to Mach 3.5) complex flows associated with the new supersonic injection schemes. This important high-frequency data is not yet attainable when employing other techniques such as Laser Induced Fluorescence, Filtered Rayleigh Scattering or mass spectroscopy in the same complex supersonic flows. The probe operates by exploiting the difference between the thermodynamic properties of two species through independent massflow measurements and calibration. The probe samples isokinetically from the flowfield's area of interest and the helium concentration may be uniquely determined by hot-film anemometry and internally measured stagnation conditions. The final design has a diameter of 0.25" and is only 2.22" long. The overall accuracy of the probe is 3% in molar fraction of helium. The frequency response of mean concentration measurements is estimated at 103 Hz, while high-frequency hot-film measurements were conducted at 60 kHz. Additionally, the work presents an analysis of the probe's internal mixing effects and the effects of the spatial

Octamer-binding protein 4 affects the cell biology and phenotypic transition of lung cancer cells involving β-catenin/E-cadherin complex degradation.

Science.gov (United States)

Chen, Zhong-Shu; Ling, Dong-Jin; Zhang, Yang-De; Feng, Jian-Xiong; Zhang, Xue-Yu; Shi, Tian-Sheng

2015-03-01

Clinical studies have reported evidence for the involvement of octamer‑binding protein 4 (Oct4) in the tumorigenicity and progression of lung cancer; however, the role of Oct4 in lung cancer cell biology in vitro and its mechanism of action remain to be elucidated. Mortality among lung cancer patients is more frequently due to metastasis rather than their primary tumors. Epithelial‑mesenchymal transition (EMT) is a prominent biological event for the induction of epithelial cancer metastasis. The aim of the present study was to investigate whether Oct4 had the capacity to induce lung cancer cell metastasis via the promoting the EMT in vitro. Moreover, the effect of Oct4 on the β‑catenin/E‑cadherin complex, associated with EMT, was examined using immunofluorescence and immunoprecipitation assays as well as western blot analysis. The results demonstrated that Oct4 enhanced cell invasion and adhesion accompanied by the downregulation of epithelial marker cytokeratin, and upregulation of the mesenchymal markers vimentin and N‑cadherin. Furthermore, Oct4 induced EMT of lung cancer cells by promoting β‑catenin/E‑cadherin complex degradation and regulating nuclear localization of β‑catenin. In conclusion, the present study indicated that Oct4 affected the cell biology of lung cancer cells in vitro through promoting lung cancer cell metastasis via EMT; in addition, the results suggested that the association and degradation of the β‑catenin/E‑cadherin complex was regulated by Oct4 during the process of EMT.

Biological activities of some Fluoroquinolones-metal complexes

African Journals Online (AJOL)

McRoy

Background: Metal ions play a vital role in the design of more biologically active drugs. Aim: The paper reviewed the .... 2H2O by direct reaction of copper(II) sulphate pentahydrate with ciprofloxacin in distilled water. ... membered ring and the chloride ion completes the seven coordination around the Ca2+ion.[37-39].

Omics/systems biology and cancer cachexia.

Science.gov (United States)

Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

2016-06-01

Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

Biologically removing sulfur from dilute gas flows

Science.gov (United States)

Ruitenberg, R.; Dijkman, H.; Buisman, C. J. N.

1999-05-01

A biological process has been developed to clean off-gases containing sulfur dioxide from industrial installations. The sulfur dioxide is converted into hydrogen sulfide, which can then be oxidized to elemental sulfur if not used on-site. The process produces no waste products that require disposal and has a low reagent consumption.

The biology of personalized cancer medicine: facing individual complexities underlying hallmark capabilities.

Science.gov (United States)

De Palma, Michele; Hanahan, Douglas

2012-04-01

It is a time of great promise and expectation for the applications of knowledge about mechanisms of cancer toward more effective and enduring therapies for human disease. Conceptualizations such as the hallmarks of cancer are providing an organizing principle with which to distill and rationalize the abject complexities of cancer phenotypes and genotypes across the spectrum of the human disease. A countervailing reality, however, involves the variable and often transitory responses to most mechanism-based targeted therapies, returning full circle to the complexity, arguing that the unique biology and genetics of a patient's tumor will in the future necessarily need to be incorporated into the decisions about optimal treatment strategies, the frontier of personalized cancer medicine. This perspective highlights considerations, metrics, and methods that may prove instrumental in charting the landscape of evaluating individual tumors so to better inform diagnosis, prognosis, and therapy. Integral to the consideration is remarkable heterogeneity and variability, evidently embedded in cancer cells, but likely also in the cell types composing the supportive and interactive stroma of the tumor microenvironment (e.g., leukocytes and fibroblasts), whose diversity in form, regulation, function, and abundance may prove to rival that of the cancer cells themselves. By comprehensively interrogating both parenchyma and stroma of patients' cancers with a suite of parametric tools, the promise of mechanism-based therapy may truly be realized. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Efficient sample preparation from complex biological samples using a sliding lid for immobilized droplet extractions.

Science.gov (United States)

Casavant, Benjamin P; Guckenberger, David J; Beebe, David J; Berry, Scott M

2014-07-01

Sample preparation is a major bottleneck in many biological processes. Paramagnetic particles (PMPs) are a ubiquitous method for isolating analytes of interest from biological samples and are used for their ability to thoroughly sample a solution and be easily collected with a magnet. There are three main methods by which PMPs are used for sample preparation: (1) removal of fluid from the analyte-bound PMPs, (2) removal of analyte-bound PMPs from the solution, and (3) removal of the substrate (with immobilized analyte-bound PMPs). In this paper, we explore the third and least studied method for PMP-based sample preparation using a platform termed Sliding Lid for Immobilized Droplet Extractions (SLIDE). SLIDE leverages principles of surface tension and patterned hydrophobicity to create a simple-to-operate platform for sample isolation (cells, DNA, RNA, protein) and preparation (cell staining) without the need for time-intensive wash steps, use of immiscible fluids, or precise pinning geometries. Compared to other standard isolation protocols using PMPs, SLIDE is able to perform rapid sample preparation with low (0.6%) carryover of contaminants from the original sample. The natural recirculation occurring within the pinned droplets of SLIDE make possible the performance of multistep cell staining protocols within the SLIDE by simply resting the lid over the various sample droplets. SLIDE demonstrates a simple easy to use platform for sample preparation on a range of complex biological samples.

Systematics and biology of Cotesia typhae sp. n. (Hymenoptera, Braconidae, Microgastrinae, a potential biological control agent against the noctuid Mediterranean corn borer, Sesamia nonagrioides

Directory of Open Access Journals (Sweden)

Laure Kaiser

2017-07-01

Full Text Available Many parasitoid species are subjected to strong selective pressures from their host, and their adaptive response may result in the formation of genetically differentiated populations, called host races. When environmental factors and reproduction traits prevent gene flow, host races become distinct species. Such a process has recently been documented within the Cotesia flavipes species complex, all of which are larval parasitoids of moth species whose larvae are stem borers of Poales. A previous study on the African species C. sesamiae, incorporating molecular, ecological and biological data on various samples, showed that a particular population could be considered as a distinct species, because it was specialized at both host (Sesamia nonagrioides and plant (Typha domingensis levels, and reproductively isolated from other C. sesamiae. Due to its potential for the biological control of S. nonagrioides, a serious corn pest in Mediterranean countries and even in Iran, we describe here Cotesia typhae Fernandez-Triana sp. n. The new species is characterized on the basis of morphological, molecular, ecological and geographical data, which proved to be useful for future collection and rapid identification of the species within the species complex. Fecundity traits and parasitism success on African and European S. nonagrioides populations, estimated by laboratory studies, are also included.

Experimental observations of flow instabilities and rapid mixing of two dissimilar viscoelastic liquids

Directory of Open Access Journals (Sweden)

Hiong Yap Gan

2012-12-01

Full Text Available Viscoelastically induced flow instabilities, via a simple planar microchannel, were previously used to produce rapid mixing of two dissimilar polymeric liquids (i.e. at least a hundredfold different in shear viscosity even at a small Reynolds number. The unique advantage of this mixing technology is that viscoelastic liquids are readily found in chemical and biological samples like organic and polymeric liquids, blood and crowded proteins samples; their viscoelastic properties could be exploited. As such, an understanding of the underlying interactions will be important especially in rapid microfluidic mixing involving multiple-stream flow of complex (viscoelastic fluids in biological assays. Here, we use the same planar device to experimentally show that the elasticity ratio (i.e. the ratio of stored elastic energy to be relaxed between two liquids indeed plays a crucial role in the entire flow kinematics and the enhanced mixing. We demonstrate here that the polymer stretching dynamics generated in the upstream converging flow and the polymer relaxation events occurring in the downstream channel are not exclusively responsible for the transverse flow mixing, but the elasticity ratio is also equally important. The role of elasticity ratio for transverse flow instability and the associated enhanced mixing were illustrated based on experimental observations. A new parameter Deratio = Deside / Demain (i.e. the ratio of the Deborah number (De of the sidestream to the mainstream liquids is introduced to correlate the magnitude of energy discontinuity between the two liquids. A new Deratio-Demain operating space diagram was constructed to present the observation of the effects of both elasticity and energy discontinuity in a compact manner, and for a general classification of the states of flow development.

Synthetic biology: engineering molecular computers

CERN Multimedia

CERN. Geneva

2018-01-01

Complicated systems cannot survive the rigors of a chaotic environment, without balancing mechanisms that sense, decide upon and counteract the exerted disturbances. Especially so with living organisms, forced by competition to incredible complexities, escalating also their self-controlling plight. Therefore, they compute. Can we harness biological mechanisms to create artificial computing systems? Biology offers several levels of design abstraction: molecular machines, cells, organisms... ranging from the more easily-defined to the more inherently complex. At the bottom of this stack we find the nucleic acids, RNA and DNA, with their digital structure and relatively precise interactions. They are central enablers of designing artificial biological systems, in the confluence of engineering and biology, that we call Synthetic biology. In the first part, let us follow their trail towards an overview of building computing machines with molecules -- and in the second part, take the case study of iGEM Greece 201...

Flow Characteristics of Ground Vehicle Wake and Its Response to Flow Control

Science.gov (United States)

Sellappan, Prabu; McNally, Jonathan; Alvi, Farrukh

2017-11-01

Air pollution, fuel shortages, and cost savings are some of the many incentives for improving the aerodynamics of vehicles. Reducing wake-induced aerodynamic drag, which is dependent on flow topology, on modern passenger vehicles is important for improving fuel consumption rates which directly affect the environment. In this research, an active flow control technique is applied on a generic ground vehicle, a 25°Ahmed model, to investigate its effect on the flow topology in the near-wake. The flow field of this canonical bluff body is extremely rich, with complex and unsteady flow features such as trailing wake vortices and c-pillar vortices. The spatio-temporal response of these flow features to the application of steady microjet actuators is investigated. The responses are characterized independently through time-resolved and volumetric velocity field measurements. The accuracy and cost of volumetric measurements in this complex flow field through Stereoscopic- and Tomographic- Particle Image Velocimetry (PIV) will also be commented upon. National Science Foundation PIRE Program.

A Method for Selective Depletion of Zn(II) Ions from Complex Biological Media and Evaluation of Cellular Consequences of Zn(II) Deficiency

Science.gov (United States)

Richardson, Christopher E. R.; Cunden, Lisa S.; Butty, Vincent L.; Nolan, Elizabeth M.; Lippard, Stephen J.; Shoulders, Matthew D.

2018-01-01

We describe the preparation, evaluation, and application of an S100A12 protein-conjugated solid support, hereafter the “A12-resin,” that can remove 99% of Zn(II) from complex biological solutions without significantly perturbing the concentrations of other metal ions. The A12-resin can be applied to selectively deplete Zn(II) from diverse tissue culture media and from other biological fluids, including human serum. To further demonstrate the utility of this approach, we investigated metabolic, transcriptomic, and metallomic responses of HEK293 cells cultured in medium depleted of Zn(II) using S100A12. The resulting data provide insight into how cells respond to acute Zn(II) deficiency. We expect that the A12-resin will facilitate interrogation of disrupted Zn(II) homeostasis in biological settings, uncovering novel roles for Zn(II) in biology. PMID:29334734

Tracer tests and image analysis of biological clogging in a two-dimentsional sandbox experiment

DEFF Research Database (Denmark)

Kildsgaard, J.; Engesgaard, Peter Knudegaard

2002-01-01

A two-dimensional flow experiment on biological clogging was carried out by biostimulating a sandbox packed with sand inoculated with bacteria. Biostimulation. consisted of continuously injecting nutrients (acetate and nitrate). Clogging was visualized by frequently carrying out colored tracer...... experiments using Brilliant Blue. The tracer experiments were recorded with a digital camera and converted to concentration maps using an image-analysis method that revealed in detail the complex spreading pattern surrounding clogged areas. Clogging resulted in a finger-like spreading of the tracer around...

Mechanical Biological Treatment

DEFF Research Database (Denmark)

Bilitewski, B-; Oros, Christiane; Christensen, Thomas Højlund

2011-01-01

The basic processes and technologies of composting and anaerobic digestion, as described in the previous chapters, are usually used for specific or source-separated organic waste flows. However, in the 1990s mechanical biological waste treatment technologies (MBT) were developed for unsorted...... or residual waste (after some recyclables removed at the source). The concept was originally to reduce the amount of waste going to landfill, but MBT technologies are today also seen as plants recovering fuel as well as material fractions. As the name suggests the technology combines mechanical treatment...... technologies (screens, sieves, magnets, etc.) with biological technologies (composting, anaerobic digestion). Two main technologies are available: Mechanical biological pretreatment (MBP), which first removes an RDF fraction and then biologically treats the remaining waste before most of it is landfilled...

Determination of drugs in biological fluids by direct injection of samples for liquid-chromatographic analysis.

Science.gov (United States)

Mullett, Wayne M

2007-03-10

The analysis of drugs in various biological fluids is an important criterion for the determination of the physiological performance of a drug. After sampling of the biological fluid, the next step in the analytical process is sample preparation. The complexity of biological fluids adds to the challenge of direct determination of the drug by chromatographic analysis, therefore demanding a sample preparation step that is often time-consuming, tedious, and frequently overlooked. However, direct on-line injection methods offer the advantage of reducing sample preparation steps and enabling effective pre-concentration and clean-up of biological fluids. These procedures can be automated and therefore reduce the requirements for handling potentially infectious biomaterial, improve reproducibility, and minimize sample manipulations and potential contamination. The objective of this review is to present an overview of the existing literature with emphasis on advances in automated sample preparation methods for liquid-chromatographic methods. More specifically, this review concentrates on the use of direct injection techniques, such as restricted-access materials, turbulent-flow chromatography and other automated on-line solid-phase extraction (SPE) procedures. It also includes short overviews of emerging automated extraction-phase technologies, such as molecularly imprinted polymers, in-tube solid-phase micro-extraction, and micro-extraction in a packed syringe for a more selective extraction of analytes from complex samples, providing further improvements in the analysis of biological materials. Lastly, the outlook for these methods and potential new applications for these technologies are briefly discussed.

Research Collaboration Workshop for Women in Mathematical Biology

CERN Document Server

Miller, Laura

2017-01-01

Inspired by the Research Collaboration Workshop for Women in Mathematical Biology, this volume contains research and review articles that cover topics ranging from models of animal movement to the flow of blood cells in the embryonic heart. Hosted by the National Institute for Mathematics and Biological Synthesis (NIMBioS), the workshop brought together women working in biology and mathematics to form four research groups that encouraged multidisciplinary collaboration and lifetime connections in the STEM field. This volume introduces many of the topics from the workshop, including the aerodynamics of spider ballooning; sleep, circadian rhythms, and pain; blood flow regulation in the kidney; and the effects of antimicrobial therapy on gut microbiota and microbiota and Clostridium difficile. Perfect for students and researchers in mathematics and biology, the papers included in this volume offer an introductory glimpse at recent research in mathematical biology. .

Rhodium complexes as therapeutic agents.

Science.gov (United States)

Ma, Dik-Lung; Wang, Modi; Mao, Zhifeng; Yang, Chao; Ng, Chan-Tat; Leung, Chung-Hang

2016-02-21

The landscape of inorganic medicinal chemistry has been dominated by the investigation of platinum, and to a lesser extent ruthenium, complexes over the past few decades. Recently, complexes based on other metal centers such as rhodium have attracted attention due to their tunable chemical and biological properties as well as distinct mechanisms of action. This perspective highlights recent examples of rhodium complexes that show diverse biological activities against various targets, including enzymes and protein-protein interactions.

Site-specific distribution of claudin-based paracellular channels with roles in biological fluid flow and metabolism.

Science.gov (United States)

Tanaka, Hiroo; Tamura, Atsushi; Suzuki, Koya; Tsukita, Sachiko

2017-10-01

The claudins are a family of membrane proteins with at least 27 members in humans and mice. The extracellular regions of claudin proteins play essential roles in cell-cell adhesion and the paracellular barrier functions of tight junctions (TJs) in epithelial cell sheets. Furthermore, the extracellular regions of some claudins function as paracellular channels in the paracellular barrier that allow the selective passage of water, ions, and/or small organic solutes across the TJ in the extracellular space. Structural analyses have revealed a common framework of transmembrane, cytoplasmic, and extracellular regions among the claudin-based paracellular barriers and paracellular channels; however, differences in the claudins' extracellular regions, such as their charges and conformations, determine their properties. Among the biological systems that involve fluid flow and metabolism, it is noted that hepatic bile flow, renal Na + reabsorption, and intestinal nutrient absorption are dynamically regulated via site-specific distributions of paracellular channel-forming claudins in tissue. Here, we focus on how site-specific distributions of claudin-2- and claudin-15-based paracellular channels drive their organ-specific functions in the liver, kidney, and intestine. © 2017 New York Academy of Sciences.

On the Edge of Mathematics and Biology Integration: Improving Quantitative Skills in Undergraduate Biology Education

Science.gov (United States)

Feser, Jason; Vasaly, Helen; Herrera, Jose

2013-01-01

In this paper, the authors describe how two institutions are helping their undergraduate biology students build quantitative competencies. Incorporation of quantitative skills and reasoning in biology are framed through a discussion of two cases that both concern introductory biology courses, but differ in the complexity of the mathematics and the…

Effect of long-term smoking on salivary flow rate and salivary pH

OpenAIRE

Mala Singh; Navin Anand Ingle; Navpreet Kaur; Pramod Yadav; Ekta Ingle

2015-01-01

Introduction: Saliva is a complex and important body fluid which is very essential for oral health and it is the first biological fluid that is exposed to cigarette smoke, which contains numerous toxic compositions responsible for structural and functional changes in saliva. Aim: To evaluate the long-term effect of smoking on salivary flow rate (SFR) and salivary pH. Materials and Methods: The subjects of the study were divided into smokers and nonsmokers. Each group comprised of 35 male adul...

Flow Cytometry Technician | Center for Cancer Research

Science.gov (United States)

PROGRAM DESCRIPTION The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). KEY ROLES/RESPONSIBILITIES The Flow Cytometry Core (Flow Core) of the Cancer and Inflammation Program (CIP) is a service core which supports the research efforts of the CCR by providing expertise in the field of flow cytometry (using analyzers and sorters) with the goal of gaining a more thorough understanding of the biology of cancer and cancer cells. The Flow Core provides service to 12-15 CIP laboratories and more than 22 non-CIP laboratories. Flow core staff provide technical advice on the experimental design of applications, which include immunological phenotyping, cell function assays, and cell cycle analysis. Work is performed per customer requirements, and no independent research is involved. The Flow Cytometry Technician will be responsible for: Monitor performance of and maintain high dimensional flow cytometer analyzers and cell sorters Operate high dimensional flow cytometer analyzers and cell sorters Monitoring lab supply levels and order lab supplies, perform various record keeping responsibilities Assist in the training of scientific end users on the use of flow cytometry in their research, as well as how to operate and troubleshoot the bench-top analyzer instruments Experience with sterile technique and tissue culture

Ionic interactions in biological and physical systems: a variational treatment.

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Eisenberg, Bob

2013-01-01

Chemistry is about chemical reactions. Chemistry is about electrons changing their configurations as atoms and molecules react. Chemistry has for more than a century studied reactions as if they occurred in ideal conditions of infinitely dilute solutions. But most reactions occur in salt solutions that are not ideal. In those solutions everything (charged) interacts with everything else (charged) through the electric field, which is short and long range extending to the boundaries of the system. Mathematics has recently been developed to deal with interacting systems of this sort. The variational theory of complex fluids has spawned the theory of liquid crystals (or vice versa). In my view, ionic solutions should be viewed as complex fluids, particularly in the biological and engineering context. In both biology and electrochemistry ionic solutions are mixtures highly concentrated (to approximately 10 M) where they are most important, near electrodes, nucleic ids, proteins, active sites of enzymes, and ionic channels. Ca2+ is always involved in biological solutions because the concentration (really free energy per mole) of Ca2+ in a particular location is the signal that controls many biological functions. Such interacting systems are not simple fluids, and it is no wonder that analysis of interactions, such as the Hofmeister series, rooted in that tradition has not succeeded as one would hope. Here, we present a variational treatment of ard spheres in a frictional dielectric with the hope that such a treatment of an lectrolyte as a complex fluid will be productive. The theory automatically extends to spatially nonuniform boundary conditions and the nonequilibrium systems and flows they produce. The theory is unavoidably self-consistent since differential equations are derived (not assumed) from models of (Helmholtz free) nergy and dissipation of the electrolyte. The origin of the Hofmeister series is (in my view) an inverse problem that becomes well posed when

Assessing complexity of skin blood flow oscillations in response to locally applied heating and pressure in rats: Implications for pressure ulcer risk

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Liao, Fuyuan; O'Brien, William D.; Jan, Yih-Kuen

2013-10-01

The objective of this study was to investigate the effects of local heating on the complexity of skin blood flow oscillations (BFO) under prolonged surface pressure in rats. Eleven Sprague-Dawley rats were studied: 7 rats underwent surface pressure with local heating (△t=10 °C) and 4 rats underwent pressure without heating. A pressure of 700 mmHg was applied to the right trochanter area of rats for 3 h. Skin blood flow was measured using laser Doppler flowmetry. The loading period was divided into nonoverlapping 30 min epochs. For each epoch, multifractal detrended fluctuation analysis (MDFA) was utilized to compute DFA coefficients and complexity of endothelial related metabolic, neurogenic, and myogenic frequencies of BFO. The results showed that under surface pressure, local heating led to a significant decrease in DFA coefficients of myogenic frequency during the initial epoch of loading period, a sustained decrease in complexity of myogenic frequency, and a significantly higher degree of complexity of metabolic frequency during the later phase of loading period. Surrogate tests showed that the reduction in complexity of myogenic frequency was associated with a loss of nonlinearity whereas increased complexity of metabolic frequency was associated with enhanced nonlinearity. Our results indicate that increased metabolic activity and decreased myogenic response due to local heating manifest themselves not only in magnitudes of metabolic and myogenic frequencies but also in their structural complexity. This study demonstrates the feasibility of using complexity analysis of BFO to monitor the ischemic status of weight-bearing skin and risk of pressure ulcers.

Microfluidics to Mimic Blood Flow in Health and Disease

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Sebastian, Bernhard; Dittrich, Petra S.

2018-01-01

Throughout history, capillary systems have aided the establishment of the fundamental laws of blood flow and its non-Newtonian properties. The advent of microfluidics technology in the 1990s propelled the development of highly integrated lab-on-a-chip platforms that allow highly accurate replication of vascular systems' dimensions, mechanical properties, and biological complexity. Applications include the detection of pathological changes to red blood cells, white blood cells, and platelets at unparalleled sensitivity and the efficacy assessment of drug treatment. Recent efforts have aimed at the development of microfluidics-based tests usable in a clinial environment or the replication of more complex diseases such as thrombosis. These microfluidic disease models enable the study of onset and progression of disease as well as the identification of key players and risk factors, which have led to a spectrum of clinically relevant findings.

Reduction theories elucidate the origins of complex biological rhythms generated by interacting delay-induced oscillations.

Directory of Open Access Journals (Sweden)

Ikuhiro Yamaguchi

Full Text Available Time delay is known to induce sustained oscillations in many biological systems such as electroencephalogram (EEG activities and gene regulations. Furthermore, interactions among delay-induced oscillations can generate complex collective rhythms, which play important functional roles. However, due to their intrinsic infinite dimensionality, theoretical analysis of interacting delay-induced oscillations has been limited. Here, we show that the two primary methods for finite-dimensional limit cycles, namely, the center manifold reduction in the vicinity of the Hopf bifurcation and the phase reduction for weak interactions, can successfully be applied to interacting infinite-dimensional delay-induced oscillations. We systematically derive the complex Ginzburg-Landau equation and the phase equation without delay for general interaction networks. Based on the reduced low-dimensional equations, we demonstrate that diffusive (linearly attractive coupling between a pair of delay-induced oscillations can exhibit nontrivial amplitude death and multimodal phase locking. Our analysis provides unique insights into experimentally observed EEG activities such as sudden transitions among different phase-locked states and occurrence of epileptic seizures.

A flood-based information flow analysis and network minimization method for gene regulatory networks.

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Pavlogiannis, Andreas; Mozhayskiy, Vadim; Tagkopoulos, Ilias

2013-04-24

Biological networks tend to have high interconnectivity, complex topologies and multiple types of interactions. This renders difficult the identification of sub-networks that are involved in condition- specific responses. In addition, we generally lack scalable methods that can reveal the information flow in gene regulatory and biochemical pathways. Doing so will help us to identify key participants and paths under specific environmental and cellular context. This paper introduces the theory of network flooding, which aims to address the problem of network minimization and regulatory information flow in gene regulatory networks. Given a regulatory biological network, a set of source (input) nodes and optionally a set of sink (output) nodes, our task is to find (a) the minimal sub-network that encodes the regulatory program involving all input and output nodes and (b) the information flow from the source to the sink nodes of the network. Here, we describe a novel, scalable, network traversal algorithm and we assess its potential to achieve significant network size reduction in both synthetic and E. coli networks. Scalability and sensitivity analysis show that the proposed method scales well with the size of the network, and is robust to noise and missing data. The method of network flooding proves to be a useful, practical approach towards information flow analysis in gene regulatory networks. Further extension of the proposed theory has the potential to lead in a unifying framework for the simultaneous network minimization and information flow analysis across various "omics" levels.

Integration of FULLSWOF2D and PeanoClaw: Adaptivity and Local Time-Stepping for Complex Overland Flows

KAUST Repository

Unterweger, K.

2015-01-01

© Springer International Publishing Switzerland 2015. We propose to couple our adaptive mesh refinement software PeanoClaw with existing solvers for complex overland flows that are tailored to regular Cartesian meshes. This allows us to augment them with spatial adaptivity and local time-stepping without altering the computational kernels. FullSWOF2D—Full Shallow Water Overland Flows—here is our software of choice though all paradigms hold for other solvers as well.We validate our hybrid simulation software in an artificial test scenario before we provide results for a large-scale flooding scenario of the Mecca region. The latter demonstrates that our coupling approach enables the simulation of complex “real-world” scenarios.

Framework based on communicability and flow to analyze complex network dynamics

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Gilson, M.; Kouvaris, N. E.; Deco, G.; Zamora-López, G.

2018-05-01

Graph theory constitutes a widely used and established field providing powerful tools for the characterization of complex networks. The intricate topology of networks can also be investigated by means of the collective dynamics observed in the interactions of self-sustained oscillations (synchronization patterns) or propagationlike processes such as random walks. However, networks are often inferred from real-data-forming dynamic systems, which are different from those employed to reveal their topological characteristics. This stresses the necessity for a theoretical framework dedicated to the mutual relationship between the structure and dynamics in complex networks, as the two sides of the same coin. Here we propose a rigorous framework based on the network response over time (i.e., Green function) to study interactions between nodes across time. For this purpose we define the flow that describes the interplay between the network connectivity and external inputs. This multivariate measure relates to the concepts of graph communicability and the map equation. We illustrate our theory using the multivariate Ornstein-Uhlenbeck process, which describes stable and non-conservative dynamics, but the formalism can be adapted to other local dynamics for which the Green function is known. We provide applications to classical network examples, such as small-world ring and hierarchical networks. Our theory defines a comprehensive framework that is canonically related to directed and weighted networks, thus paving a way to revise the standards for network analysis, from the pairwise interactions between nodes to the global properties of networks including community detection.

The route from problem to solution in multistep continuous flow synthesis of pharmaceutical compounds.

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Bana, Péter; Örkényi, Róbert; Lövei, Klára; Lakó, Ágnes; Túrós, György István; Éles, János; Faigl, Ferenc; Greiner, István

2017-12-01

Recent advances in the field of continuous flow chemistry allow the multistep preparation of complex molecules such as APIs (Active Pharmaceutical Ingredients) in a telescoped manner. Numerous examples of laboratory-scale applications are described, which are pointing towards novel manufacturing processes of pharmaceutical compounds, in accordance with recent regulatory, economical and quality guidances. The chemical and technical knowledge gained during these studies is considerable; nevertheless, connecting several individual chemical transformations and the attached analytics and purification holds hidden traps. In this review, we summarize innovative solutions for these challenges, in order to benefit chemists aiming to exploit flow chemistry systems for the synthesis of biologically active molecules. Copyright © 2016 Elsevier Ltd. All rights reserved.

An Embedded Ghost-Fluid Method for Compressible Flow in Complex Geometry

KAUST Repository