Molecular Dynamics Simulations Suggest Ligand’s Binding to Nicotinamidase/Pyrazinamidase

Science.gov (United States)

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

2012-01-01

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA’s activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM’s unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand’s binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs. PMID:22761821

Dynamic binding of visual features by neuronal/stimulus synchrony.

Science.gov (United States)

Iwabuchi, A

1998-05-01

When people see a visual scene, certain parts of the visual scene are treated as belonging together and we regard them as a perceptual unit, which is called a "figure". People focus on figures, and the remaining parts of the scene are disregarded as "ground". In Gestalt psychology this process is called "figure-ground segregation". According to current perceptual psychology, a figure is formed by binding various visual features in a scene, and developments in neuroscience have revealed that there are many feature-encoding neurons, which respond to such features specifically. It is not known, however, how the brain binds different features of an object into a coherent visual object representation. Recently, the theory of binding by neuronal synchrony, which argues that feature binding is dynamically mediated by neuronal synchrony of feature-encoding neurons, has been proposed. This review article portrays the problem of figure-ground segregation and features binding, summarizes neurophysiological and psychophysical experiments and theory relevant to feature binding by neuronal/stimulus synchrony, and suggests possible directions for future research on this topic.

Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics.

Directory of Open Access Journals (Sweden)

Suryani Lukman

Full Text Available The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD. In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs. Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3. Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart. Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1 a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2 possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.

Discrete event dynamic system (DES)-based modeling for dynamic material flow in the pyroprocess

International Nuclear Information System (INIS)

Lee, Hyo Jik; Kim, Kiho; Kim, Ho Dong; Lee, Han Soo

2011-01-01

A modeling and simulation methodology was proposed in order to implement the dynamic material flow of the pyroprocess. Since the static mass balance provides the limited information on the material flow, it is hard to predict dynamic behavior according to event. Therefore, a discrete event system (DES)-based model named, PyroFlow, was developed at the Korea Atomic Energy Research Institute (KAERI). PyroFlow is able to calculate dynamic mass balance and also show various dynamic operational results in real time. By using PyroFlow, it is easy to rapidly predict unforeseeable results, such as throughput in unit process, accumulated product in buffer and operation status. As preliminary simulations, bottleneck analyses in the pyroprocess were carried out and consequently it was presented that operation strategy had influence on the productivity of the pyroprocess.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

International Nuclear Information System (INIS)

Aradi, Balint; Frauenheim, Thomas

2015-01-01

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materials science, chemistry, and biology

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

Science.gov (United States)

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Nonlinear dynamics of two-phase flow

International Nuclear Information System (INIS)

Rizwan-uddin

1986-01-01

Unstable flow conditions can occur in a wide variety of laboratory and industry equipment that involve two-phase flow. Instabilities in industrial equipment, which include boiling water reactor (BWR) cores, steam generators, heated channels, cryogenic fluid heaters, heat exchangers, etc., are related to their nonlinear dynamics. These instabilities can be of static (Ledinegg instability) or dynamic (density wave oscillations) type. Determination of regions in parameters space where these instabilities can occur and knowledge of system dynamics in or near these regions is essential for the safe operation of such equipment. Many two-phase flow engineering components can be modeled as heated channels. The set of partial differential equations that describes the dynamics of single- and two-phase flow, for the special case of uniform heat flux along the length of the channel, can be reduced to a set of two coupled ordinary differential equations [in inlet velocity v/sub i/(t) and two-phase residence time tau(t)] involving history integrals: a nonlinear ordinary functional differential equation and an integral equation. Hence, to solve these equations, the dependent variables must be specified for -(nu + tau) ≤ t ≤ 0, where nu is the single-phase residence time. This system of nonlinear equations has been solved analytically using asymptotic expansion series for finite but small perturbations and numerically using finite difference techniques

Hydrophobic interaction chromatography in dual salt system increases protein binding capacity.

Science.gov (United States)

Senczuk, Anna M; Klinke, Ralph; Arakawa, Tsutomu; Vedantham, Ganesh; Yigzaw, Yinges

2009-08-01

Hydrophobic interaction chromatography (HIC) uses weakly hydrophobic resins and requires a salting-out salt to promote protein-resin interaction. The salting-out effects increase with protein and salt concentration. Dynamic binding capacity (DBC) is dependent on the binding constant, as well as on the flow characteristics during sample loading. DBC increases with the salt concentration but decreases with increasing flow rate. Dynamic and operational binding capacity have a major raw material cost/processing time impact on commercial scale production of monoclonal antibodies. In order to maximize DBC the highest salt concentration without causing precipitation is used. We report here a novel method to maintain protein solubility while increasing the DBC by using a combination of two salting-out salts (referred to as dual salt). In a series of experiments, we explored the dynamic capacity of a HIC resin (TosoBioscience Butyl 650M) with combinations of salts. Using a model antibody, we developed a system allowing us to increase the dynamic capacity up to twofold using the dual salt system over traditional, single salt system. We also investigated the application of this novel approach to several other proteins and salt combinations, and noted a similar protein solubility and DBC increase. The observed increase in DBC in the dual salt system was maintained at different linear flow rates and did not impact selectivity.

Dynamics of TBP binding to the TATA box

Science.gov (United States)

Schluesche, Peter; Heiss, Gregor; Meisterernst, Michael; Lamb, Don C.

2008-02-01

Gene expression is highly controlled and regulated in living cells. One of the first steps in gene transcription is recognition of the promoter site by the TATA box Binding Protein (TBP). TBP recruits other transcriptions factors and eventually the RNA polymerase II to transcribe the DNA in mRNA. We developed a single pair Förster Resonance Energy Transfer (spFRET) assay to investigate the mechanism of gene regulation. Here, we apply this assay to investigate the initial binding process of TBP to the adenovirus major late (AdML) promoter site. From the spFRET measurements, we were able to identify two conformations of the TBP-DNA complex that correspond to TBP bound in the correct and the opposite orientation. Increased incubation times or the presence of the transcription factor TFIIA improved the alignment of TBP on the promoter site. Binding of TBP to the TATA box shows a rich dynamics with abrupt transitions between multiple FRET states. A frame-wise histogram analysis revealed the presence of at least six discrete states, showing that TBP binding is more complicated than previously thought. Hence, the spFRET assay is very sensitive to the conformation of the TBP-DNA complex and is very promising tool for investigating the pathway of TBP binding in detail.

Binding stability of peptides on major histocompatibility complex class I proteins: role of entropy and dynamics

Science.gov (United States)

Gul, Ahmet; Erman, Burak

2018-03-01

Prediction of peptide binding on specific human leukocyte antigens (HLA) has long been studied with successful results. We herein describe the effects of entropy and dynamics by investigating the binding stabilities of 10 nanopeptides on various HLA Class I alleles using a theoretical model based on molecular dynamics simulations. The fluctuational entropies of the peptides are estimated over a temperature range of 310-460 K. The estimated entropies correlate well with experimental binding affinities of the peptides: peptides that have higher binding affinities have lower entropies compared to non-binders, which have significantly larger entropies. The computation of the entropies is based on a simple model that requires short molecular dynamics trajectories and allows for approximate but rapid determination. The paper draws attention to the long neglected dynamic aspects of peptide binding, and provides a fast computation scheme that allows for rapid scanning of large numbers of peptides on selected HLA antigens, which may be useful in defining the right peptides for personal immunotherapy.

Modeling axisymmetric flows dynamics of films, jets, and drops

CERN Document Server

Middleman, Stanley

1995-01-01

This concise book is intended to fulfill two purposes: to provide an important supplement to classic texts by carrying fluid dynamics students on into the realm of free boundary flows; and to demonstrate the art of mathematical modeling based on knowledge, intuition, and observation. In the authors words, the overall goal is make the complex simple, without losing the essence--the virtue--of the complexity.Modeling Axisymmetric Flows: Dynamics of Films, Jets, and Drops is the first book to cover the topics of axisymmetric laminar flows; free-boundary flows; and dynamics of drops, jets, and films. The text also features comparisons of models to experiments, and it includes a large selection of problems at the end of each chapter.Key Features* Contains problems at the end of each chapter* Compares real-world experimental data to theory* Provides one of the first comprehensive examinations of axisymmetric laminar flows, free-boundary flows, and dynamics of drops, jets, and films* Includes development of basic eq...

Vesicle dynamics in shear and capillary flows

International Nuclear Information System (INIS)

Noguchi, Hiroshi; Gompper, Gerhard

2005-01-01

The deformation of vesicles in flow is studied by a mesoscopic simulation technique, which combines multi-particle collision dynamics for the solvent with a dynamically triangulated surface model for the membrane. Shape transitions are investigated both in simple shear flows and in cylindrical capillary flows. We focus on reduced volumes, where the discocyte shape of fluid vesicles is stable, and the prolate shape is metastable. In simple shear flow at low membrane viscosity, the shear induces a transformation from discocyte to prolate with increasing shear rate, while at high membrane viscosity, the shear induces a transformation from prolate to discocyte, or tumbling motion accompanied by oscillations between these two morphologies. In capillary flow, at small flow velocities the symmetry axis of the discocyte is found not to be oriented perpendicular to the cylinder axis. With increasing flow velocity, a transition to a prolate shape occurs for fluid vesicles, while vesicles with shear-elastic membranes (like red blood cells) transform into a coaxial parachute-like shape

Rarefield gas dynamics fundamentals, simulations and micro flows

CERN Document Server

Shen, Ching

2006-01-01

This book elucidates the methods of molecular gas dynamics or rarefied gas dynamics which treat the problems of gas flows when the discrete molecular effects of the gas prevail under the circumstances of low density, the emphasis being on the basis of the methods, the direct simulation Monte Carlo method applied to the simulation of non-equilibrium effects and the frontier subjects related to low speed microscale rarefied gas flows. It provides a solid basis for the study of molecular gas dynamics for senior students and graduates in the aerospace and mechanical engineering departments of universities and colleges. It gives a general acquaintance of modern developments of rarefied gas dynamics in various regimes and leads to the frontier topics of non-equilibrium rarefied gas dynamics and low speed microscale gas dynamics. It will be also of benefit to the scientific and technical researchers engaged in aerospace high altitude aerodynamic force and heating design and in the research on gas flow in MEMS.

Energy flow theory of nonlinear dynamical systems with applications

CERN Document Server

Xing, Jing Tang

2015-01-01

This monograph develops a generalised energy flow theory to investigate non-linear dynamical systems governed by ordinary differential equations in phase space and often met in various science and engineering fields. Important nonlinear phenomena such as, stabilities, periodical orbits, bifurcations and chaos are tack-led and the corresponding energy flow behaviors are revealed using the proposed energy flow approach. As examples, the common interested nonlinear dynamical systems, such as, Duffing’s oscillator, Van der Pol’s equation, Lorenz attractor, Rössler one and SD oscillator, etc, are discussed. This monograph lights a new energy flow research direction for nonlinear dynamics. A generalised Matlab code with User Manuel is provided for readers to conduct the energy flow analysis of their nonlinear dynamical systems. Throughout the monograph the author continuously returns to some examples in each chapter to illustrate the applications of the discussed theory and approaches. The book can be used as ...

A dynamic model of renal blood flow autoregulation

DEFF Research Database (Denmark)

Holstein-Rathlou, N H; Marsh, D J

1994-01-01

To test whether a mathematical model combining dynamic models of the tubuloglomerular feedback (TGF) mechanism and the myogenic mechanism was sufficient to explain dynamic autoregulation of renal blood flow, we compared model simulations with experimental data. To assess the dynamic characteristics...... of renal autoregulation, a broad band perturbation of the arterial pressure was employed in both the simulations and the experiments. Renal blood flow and tubular pressure were used as response variables in the comparison. To better approximate the situation in vivo where a large number of individual...... data, which shows a unimodal curve for the admittance phase. The ability of the model to reproduce the experimental data supports the hypothesis that dynamic autoregulation of renal blood flow is due to the combined action of TGF and the myogenic response....

Modelling flow dynamics in water distribution networks using ...

African Journals Online (AJOL)

One such approach is the Artificial Neural Networks (ANNs) technique. The advantage of ANNs is that they are robust and can be used to model complex linear and non-linear systems without making implicit assumptions. ANNs can be trained to forecast flow dynamics in a water distribution network. Such flow dynamics ...

Photocatalytic oxidation dynamics of acetone on TiO2: tight-binding quantum chemical molecular dynamics study

International Nuclear Information System (INIS)

Lv Chen; Wang Xiaojing; Agalya, Govindasamy; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira

2005-01-01

The clarification of the excited states dynamics on TiO 2 surface is important subject for the design of the highly active photocatalysts. In the present study, we applied our novel tight-binding quantum chemical molecular dynamics method to the investigation on the photocatalytic oxidation dynamics of acetone by photogenerated OH radicals on the hydrated anatase TiO 2 surface. The elucidated photocatalytic reaction mechanism strongly supports the previous experimental proposal and finally the effectiveness of our new approach for the clarification of the photocatalytic reaction dynamics employing the large simulation model was confirmed

Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways.

Science.gov (United States)

Chu, Wen-Ting; Chu, Xiakun; Wang, Jin

2017-09-19

The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding.

Flow dynamics of volume-heated boiling pools

International Nuclear Information System (INIS)

Ginsberg, T.; Jones, O.C.; Chen, J.C.

1979-01-01

Safety analyses of fast breeder reactors require understanding of the two-phase fluid dynamic and heat transfer characteristics of volume-heated boiling pool systems. Design of direct contact three-phase boilers, of practical interest in the chemical industries also requires understanding of the fundamental two-phase flow and heat transfer behavior of volume boiling systems. Several experiments have been recently reported relevant to the boundary heat-loss mechanisms of boiling pool systems. Considerably less is known about the two-phase fluid dynamic behavior of such systems. This paper describes an experimental investigation of the steady-state flow dynamics of volume-heated boiling pool systems

AN OVERVIEW ON PULSATILE FLOW DYNAMICS

OpenAIRE

Çarpinlioğlu, Melda Özdinç

2015-01-01

Pulsatile flow dynamics in reference to the relevant experimental research on the manner between the time periods of 1997- 2015 is presented in this paper. The flow field under discussion is generated through a rigid circular cross-sectional pipe as an axial slightly- compressible and sinusoidal one in a controlled range of the oscillation parameters. Laminar and turbulent flow regimes are considered with a particular emphasis devoted to the transitional characteristics of laminar pulsatile f...

Improved Low Power FPGA Binding of Datapaths from Data Flow Graphs with NSGA II -based Schedule Selection

Directory of Open Access Journals (Sweden)

BHUVANESWARI, M. C.

2013-11-01

Full Text Available FPGAs are increasingly being used to implement data path intensive algorithms for signal processing and image processing applications. In High Level Synthesis of Data Flow Graphs targeted at FPGAs, the effect of interconnect resources such as multiplexers must be considered since they contribute significantly to the area and switching power. We propose a binding framework for behavioral synthesis of Data Flow Graphs (DFGs onto FPGA targets with power reduction as the main criterion. The technique uses a multi-objective GA, NSGA II for design space exploration to identify schedules that have the potential to yield low-power bindings from a population of non-dominated solutions. A greedy constructive binding technique reported in the literature is adapted for interconnect minimization. The binding is further subjected to a perturbation process by altering the register and multiplexer assignments. Results obtained on standard DFG benchmarks indicate that our technique yields better power aware bindings than the constructive binding approach with little or no area overhead.

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...

Evaluation of flow accelerated corrosion by coupled analysis of corrosion and flow dynamics (2), flow dynamics calculations for determining mixing factors and mass transfer coefficients

International Nuclear Information System (INIS)

Uehara, Yasushi; Uchida, Shunsuke; Naitoh, Masanori; Okada, Hidetoshi; Koshizuka, Seiichi

2009-01-01

In order to predict and mitigate flow accelerated corrosion (FAC) of carbon steel piping in PWR and BWR secondary systems, computer program packages for evaluating FAC have been developed by coupling one through three dimensional (1-3D) computational flow dynamics (CFD) models and corrosion models. To evaluate corrosive conditions, e.g., oxygen concentration and electrochemical corrosion potential (ECP) along the flow path, flow pattern and temperature in each elemental volume were obtained with 1D computational flow dynamics (CFD) codes. Precise flow turbulence and mass transfer coefficients at the structure surface were calculated with 3D CFD codes to determine wall thinning rates. One of the engineering options is application of k-ε calculation as a 3D CFD code, which has limitation of detail evaluation of flow distribution at very surface of large scale piping. A combination of k-ε calculation and wall function was proposed to evaluate precise distribution of mass transfer coefficients with reasonable CPU volume and computing time and, at the same time, reasonable accuracy. (author)

Dynamic exercise enhances regional cerebral artery mean flow velocity

DEFF Research Database (Denmark)

Linkis, P; Jørgensen, L G; Olesen, H L

1995-01-01

Dynamic exercise enhances regional cerebral artery mean flow velocity. J. Appl. Physiol. 78(1): 12-16, 1995.--Anterior (ACA) and middle (MCA) cerebral artery mean flow velocities (Vmean) and pulsatility indexes were determined using transcranial Doppler in 14 subjects during dynamic exercise afte...

Flow cytometric analysis of lectin binding to in vitro-cultured Perkinsus marinus surface carbohydrates

Science.gov (United States)

Gauthier, J.D.; Jenkins, J.A.; La Peyre, Jerome F.

2004-01-01

Parasite surface glycoconjugates are frequently involved in cellular recognition and colonization of the host. This study reports on the identification of Perkinsus marinus surface carbohydrates by flow cytometric analyses of fluorescein isothiocyanate-conjugated lectin binding. Lectin-binding specificity was confirmed by sugar inhibition and Kolmogorov-Smirnov statistics. Clear, measurable fluorescence peaks were discriminated, and no parasite autofluorescence was observed. Parasites (GTLA-5 and Perkinsus-1 strains) harvested during log and stationary phases of growth in a protein-free medium reacted strongly with concanavalin A and wheat germ agglutinin, which bind to glucose-mannose and N-acetyl-D-glucosamine (GlcNAc) moieties, respectively. Both P. marinus strains bound with lower intensity to Maclura pomifera agglutinin, Bauhinia purpurea agglutinin, soybean agglutinin (N-acetyl-D-galactosamine-specific lectins), peanut agglutinin (PNA) (terminal galactose specific), and Griffonia simplicifolia II (GlcNAc specific). Only background fluorescence levels were detected with Ulex europaeus agglutinin I (L-fucose specific) and Limulus polyphemus agglutinin (sialic acid specific). The lectin-binding profiles were similar for the 2 strains except for a greater relative binding intensity of PNA for Perkinsus-1 and an overall greater lectin-binding capacity of Perkinsus-1 compared with GTLA-5. Growth stage comparisons revealed increased lectin-binding intensities during stationary phase compared with log phase of growth. This is the first report of the identification of surface glycoconjugates on a Perkinsus spp. by flow cytometry and the first to demonstrate that differential surface sugar expression is growth phase and strain dependent. ?? American Society of Parasitologists 2004.

Dynamic Characteristics of The DSI-Type Constant-Flow Valves

Science.gov (United States)

Kang, Yuan; Hu, Sheng-Yan; Chou, Hsien-Chin; Lee, Hsing-Han

Constant flow valves have been presented in industrial applications or academic studies, which compensate recess pressures of a hydrostatic bearing to resist load fluctuating. The flow rate of constant-flow valves can be constant in spite of the pressure changes in recesses, however the design parameters must be specified. This paper analyzes the dynamic responses of DSI-type constant-flow valves that is designed as double pistons on both ends of a spool with single feedback of working pressure and regulating restriction at inlet. In this study the static analysis presents the specific relationships among design parameters for constant flow rate and the dynamic analyses give the variations around the constant flow rate as the working pressure fluctuates.

Flow-pattern identification and nonlinear dynamics of gas-liquid two-phase flow in complex networks.

Science.gov (United States)

Gao, Zhongke; Jin, Ningde

2009-06-01

The identification of flow pattern is a basic and important issue in multiphase systems. Because of the complexity of phase interaction in gas-liquid two-phase flow, it is difficult to discern its flow pattern objectively. In this paper, we make a systematic study on the vertical upward gas-liquid two-phase flow using complex network. Three unique network construction methods are proposed to build three types of networks, 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 by the community-detection algorithm based on K -mean clustering, useful and interesting results are found which can be used for identifying five vertical upward gas-liquid two-phase flow patterns. To investigate the dynamic characteristics of gas-liquid two-phase flow, we construct 50 FDCNs under different flow conditions, and find that the power-law exponent and the network information entropy, which are sensitive to the flow pattern transition, can both characterize the nonlinear dynamics of gas-liquid two-phase flow. Furthermore, we construct FSCN and demonstrate how network statistic can be used to reveal the fluid structure of gas-liquid two-phase flow. In this paper, from a different perspective, we not only introduce complex network theory to the study of gas-liquid two-phase flow but also indicate that complex network may be a powerful tool for exploring nonlinear time series in practice.

Dynamic self-organization in particle-laden channel flow

NARCIS (Netherlands)

Geurts, Bernardus J.; Vreman, A.W.

2006-01-01

We study dynamic flow-structuring and mean-flow properties of turbulent particle-laden riser-flow at significant particle volume fractions of about 1.5%. We include particle–particle as well as particle–fluid interactions through inelastic collisions and drag forces, in a so-called four-way coupled

Candida glabrata binds to glycosylated and lectinic receptors on the coronary endothelial luminal membrane and inhibits flow sense and cardiac responses to agonists.

Science.gov (United States)

Torres-Tirado, David; Knabb, Maureen; Castaño, Irene; Patrón-Soberano, Araceli; De Las Peñas, Alejandro; Rubio, Rafael

2016-01-01

Candida glabrata (CG) is an opportunistic fungal pathogen that initiates infection by binding to host cells via specific lectin-like adhesin proteins. We have previously shown the importance of lectin-oligosaccharide binding in cardiac responses to flow and agonists. Because of the lectinic-oligosaccharide nature of CG binding, we tested the ability of CG to alter the agonist- and flow-induced changes in cardiac function in isolated perfused guinea pig hearts. Both transmission and scanning electron microscopy showed strong attachment of CG to the coronary endothelium, even after extensive washing. CG shifted the coronary flow vs. auricular-ventricular (AV) delay relationship upward, indicating that greater flow was required to achieve the same AV delay. This effect was completely reversed with mannose, partially reversed with galactose and N-acetylgalactosamine, but hyaluronan had no effect. Western blot analysis was used to determine binding of CG to isolated coronary endothelial luminal membrane (CELM) receptors, and the results indicate that flow-sensitive CELM receptors, ANG II type I, α-adrenergic 1A receptor, endothelin-2, and VCAM-1 bind to CG. In addition, CG inhibited agonist-induced effects of bradykinin, angiotensin, and phenylephrine on AV delay, coronary perfusion pressure, and left ventricular pressure. Mannose reversed the inhibitory effects of CG on the agonist responses. These results suggest that CG directly binds to flow-sensitive CELM receptors via lectinic-oligosaccharide interactions with mannose and disrupts the lectin-oligosaccharide binding necessary for flow-induced cardiac responses. Copyright © 2016 the American Physiological Society.

Development of Methods for Obtaining Position Image and Chemical Binding Information from Flow Experiments of Porous Media

Energy Technology Data Exchange (ETDEWEB)

Haugan, Are

1998-12-01

Existing oil reservoirs might be more fully exploited if the properties of the flow of oil and water in porous media were better known. In laboratory experiments it is important to collect as much information as possible to make a descriptive model of the system, including position imaging and chemical binding information. This thesis develops nuclear methods for obtaining position image and chemical binding information from flow experiments of porous media. A combined positron emission tomography and single photon emission computed tomography system to obtain position images, and a time-differential perturbed angular correlation system to obtain chemical binding information, have been built and thoroughly tested. 68 refs., 123 figs., 14 tabs.

Particle hopping vs. fluid-dynamical models for traffic flow

Energy Technology Data Exchange (ETDEWEB)

Nagel, K.

1995-12-31

Although particle hopping models have been introduced into traffic science in the 19509, their systematic use has only started recently. Two reasons for this are, that they are advantageous on modem computers, and that recent theoretical developments allow analytical understanding of their properties and therefore more confidence for their use. In principle, particle hopping models fit between microscopic models for driving and fluiddynamical models for traffic flow. In this sense, they also help closing the conceptual gap between these two. This paper shows connections between particle hopping models and traffic flow theory. It shows that the hydrodynamical limits of certain particle hopping models correspond to the Lighthill-Whitham theory for traffic flow, and that only slightly more complex particle hopping models produce already the correct traffic jam dynamics, consistent with recent fluid-dynamical models for traffic flow. By doing so, this paper establishes that, on the macroscopic level, particle hopping models are at least as good as fluid-dynamical models. Yet, particle hopping models have at least two advantages over fluid-dynamical models: they straightforwardly allow microscopic simulations, and they include stochasticity.

Flow-cytometric determination of high-density-lipoprotein binding sites on human leukocytes

International Nuclear Information System (INIS)

Schmitz, G.; Wulf, G.; Bruening, T.A.; Assmann, G.

1987-01-01

In this method, leukocytes were isolated from 6 mL of EDTA-blood by density-gradient centrifugation and subsequently incubated with rhodamine isothiocyanate (RITC)-conjugated high-density lipoproteins (HDL). The receptor-bound conjugate particles were determined by fluorescent flow cytometry and compared with 125 I-labeled HDL binding data for the same cells. Human granulocytes express the highest number of HDL binding sites (9.4 x 10(4)/cell), followed by monocytes (7.3 x 10(4)/cell) and lymphocytes (4.0 x 10(4)/cell). Compared with conventional analysis of binding of 125 I-labeled HDL in tissue-culture dishes, the present determination revealed significantly lower values for nonspecific binding. In competition studies, the conjugate competes for the same binding sites as 125 I-labeled HDL. With the use of tetranitromethane-treated HDL3, which fails to compete for the HDL receptor sites while nonspecific binding is not affected, we could clearly distinguish between 37 degrees C surface binding and specific 37 degrees C uptake of RITC-HDL3, confirming that the HDL receptor leads bound HDL particles into an intracellular pathway rather than acting as a docking type of receptor. Patients with familial dysbetalipoproteinemia showed a significantly higher number of HDL binding sites in the granulocyte population but normal in lymphocytes and monocytes, indicating increased uptake of cholesterol-containing lipoproteins. In patients with familial hypercholesterolemia, HDL binding was increased in all three cell types, indicating increased cholesterol uptake and increased cholesterol synthesis. The present method allows rapid determination of HDL binding sites in leukocytes from patients with various forms of hyper- and dyslipoproteinemias

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations

Science.gov (United States)

Ge, Yushu; van der Kamp, Marc; Malaisree, Maturos; Liu, Dan; Liu, Yi; Mulholland, Adrian J.

2017-11-01

Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations.

Science.gov (United States)

Ge, Yushu; van der Kamp, Marc; Malaisree, Maturos; Liu, Dan; Liu, Yi; Mulholland, Adrian J

2017-11-01

Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.

Unique structure and dynamics of the EphA5 ligand binding domain mediate its binding specificity as revealed by X-ray crystallography, NMR and MD simulations.

Directory of Open Access Journals (Sweden)

Xuelu Huan

Full Text Available The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions with 9 ephrin-A and ephrin-B ligands initiate bidirectional signals controlling many physiological and pathological processes. Most interactions occur between receptor and ephrins of the same class, and only EphA4 can bind all A and B ephrins. To understand the structural and dynamic principles that enable Eph receptors to utilize the same jellyroll β-sandwich fold to bind ephrins, the VAPB-MSP domain, peptides and small molecules, we have used crystallography, NMR and molecular dynamics (MD simulations to determine the first structure and dynamics of the EphA5 ligand-binding domain (LBD, which only binds ephrin-A ligands. Unexpectedly, despite being unbound, the high affinity ephrin-binding pocket of EphA5 resembles that of other Eph receptors bound to ephrins, with a helical conformation over the J-K loop and an open pocket. The openness of the pocket is further supported by NMR hydrogen/deuterium exchange data and MD simulations. Additionally, the EphA5 LBD undergoes significant picosecond-nanosecond conformational exchanges over the loops, as revealed by NMR and MD simulations, but lacks global conformational exchanges on the microsecond-millisecond time scale. This is markedly different from the EphA4 LBD, which shares 74% sequence identity and 87% homology. Consequently, the unbound EphA5 LBD appears to comprise an ensemble of open conformations that have only small variations over the loops and appear ready to bind ephrin-A ligands. These findings show how two proteins with high sequence homology and structural similarity are still able to achieve distinctive binding specificities through different dynamics, which may represent a general mechanism whereby the same protein fold can serve for different functions. Our findings also suggest that a promising strategy to design agonists/antagonists with high affinity and selectivity

An evaluation of Dynamic TOPMODEL for low flow simulation

Science.gov (United States)

Coxon, G.; Freer, J. E.; Quinn, N.; Woods, R. A.; Wagener, T.; Howden, N. J. K.

2015-12-01

Hydrological models are essential tools for drought risk management, often providing input to water resource system models, aiding our understanding of low flow processes within catchments and providing low flow predictions. However, simulating low flows and droughts is challenging as hydrological systems often demonstrate threshold effects in connectivity, non-linear groundwater contributions and a greater influence of water resource system elements during low flow periods. These dynamic processes are typically not well represented in commonly used hydrological models due to data and model limitations. Furthermore, calibrated or behavioural models may not be effectively evaluated during more extreme drought periods. A better understanding of the processes that occur during low flows and how these are represented within models is thus required if we want to be able to provide robust and reliable predictions of future drought events. In this study, we assess the performance of dynamic TOPMODEL for low flow simulation. Dynamic TOPMODEL was applied to a number of UK catchments in the Thames region using time series of observed rainfall and potential evapotranspiration data that captured multiple historic droughts over a period of several years. The model performance was assessed against the observed discharge time series using a limits of acceptability framework, which included uncertainty in the discharge time series. We evaluate the models against multiple signatures of catchment low-flow behaviour and investigate differences in model performance between catchments, model diagnostics and for different low flow periods. We also considered the impact of surface water and groundwater abstractions and discharges on the observed discharge time series and how this affected the model evaluation. From analysing the model performance, we suggest future improvements to Dynamic TOPMODEL to improve the representation of low flow processes within the model structure.

Characterization of Flow Dynamics and Reduced-Order Description of Experimental Two-Phase Pipe Flow

Science.gov (United States)

Viggiano, Bianca; SkjæRaasen, Olaf; Tutkun, Murat; Cal, Raul Bayoan

2017-11-01

Multiphase pipe flow is investigated using proper orthogonal decomposition for tomographic X-ray data, where holdup, cross sectional phase distributions and phase interface characteristics are obtained. Instantaneous phase fractions of dispersed flow and slug flow are analyzed and a reduced order dynamical description is generated. The dispersed flow displays coherent structures in the first few modes near the horizontal center of the pipe, representing the liquid-liquid interface location while the slug flow case shows coherent structures that correspond to the cyclical formation and breakup of the slug in the first 10 modes. The reconstruction of the fields indicate that main features are observed in the low order dynamical descriptions utilizing less than 1 % of the full order model. POD temporal coefficients a1, a2 and a3 show interdependence for the slug flow case. The coefficients also describe the phase fraction holdup as a function of time for both dispersed and slug flow. These flows are highly applicable to petroleum transport pipelines, hydroelectric power and heat exchanger tubes to name a few. The mathematical representations obtained via proper orthogonal decomposition will deepen the understanding of fundamental multiphase flow characteristics.

Dynamic subgrid scale model of large eddy simulation of cross bundle flows

International Nuclear Information System (INIS)

Hassan, Y.A.; Barsamian, H.R.

1996-01-01

The dynamic subgrid scale closure model of Germano et. al (1991) is used in the large eddy simulation code GUST for incompressible isothermal flows. Tube bundle geometries of staggered and non-staggered arrays are considered in deep bundle simulations. The advantage of the dynamic subgrid scale model is the exclusion of an input model coefficient. The model coefficient is evaluated dynamically for each nodal location in the flow domain. Dynamic subgrid scale results are obtained in the form of power spectral densities and flow visualization of turbulent characteristics. Comparisons are performed among the dynamic subgrid scale model, the Smagorinsky eddy viscosity model (that is used as the base model for the dynamic subgrid scale model) and available experimental data. Spectral results of the dynamic subgrid scale model correlate better with experimental data. Satisfactory turbulence characteristics are observed through flow visualization

A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow

NARCIS (Netherlands)

Hunt, T.A.; Hunt, Thomas A.; Bernardi, Stefano; Todd, B.D.

2010-01-01

In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose

Nonlinear dynamics in flow through unsaturated fractured porous media: Status and perspectives

International Nuclear Information System (INIS)

Faybishenko, Boris

2002-01-01

The need has long been recognized to improve predictions of flow and transport in partially saturated heterogeneous soils and fractured rock of the vadose zone for many practical applications, such as remediation of contaminated sites, nuclear waste disposal in geological formations, and climate predictions. Until recently, flow and transport processes in heterogeneous subsurface media with oscillating irregularities were assumed to be random and were not analyzed using methods of nonlinear dynamics. The goals of this paper are to review the theoretical concepts, present the results, and provide perspectives on investigations of flow and transport in unsaturated heterogeneous soils and fractured rock, using the methods of nonlinear dynamics and deterministic chaos. The results of laboratory and field investigations indicate that the nonlinear dynamics of flow and transport processes in unsaturated soils and fractured rocks arise from the dynamic feedback and competition between various nonlinear physical processes along with complex geometry of flow paths. Although direct measurements of variables characterizing the individual flow processes are not technically feasible, their cumulative effect can be characterized by analyzing time series data using the models and methods of nonlinear dynamics and chaos. Identifying flow through soil or rock as a nonlinear dynamical system is important for developing appropriate short- and long-time predictive models, evaluating prediction uncertainty, assessing the spatial distribution of flow characteristics from time series data, and improving chemical transport simulations. Inferring the nature of flow processes through the methods of nonlinear dynamics could become widely used in different areas of the earth sciences

Nonlinear dynamics in flow through unsaturated fractured-porous media: Status and perspectives

Energy Technology Data Exchange (ETDEWEB)

Faybishenko, Boris

2002-11-27

The need has long been recognized to improve predictions of flow and transport in partially saturated heterogeneous soils and fractured rock of the vadose zone for many practical applications, such as remediation of contaminated sites, nuclear waste disposal in geological formations, and climate predictions. Until recently, flow and transport processes in heterogeneous subsurface media with oscillating irregularities were assumed to be random and were not analyzed using methods of nonlinear dynamics. The goals of this paper are to review the theoretical concepts, present the results, and provide perspectives on investigations of flow and transport in unsaturated heterogeneous soils and fractured rock, using the methods of nonlinear dynamics and deterministic chaos. The results of laboratory and field investigations indicate that the nonlinear dynamics of flow and transport processes in unsaturated soils and fractured rocks arise from the dynamic feedback and competition between various nonlinear physical processes along with complex geometry of flow paths. Although direct measurements of variables characterizing the individual flow processes are not technically feasible, their cumulative effect can be characterized by analyzing time series data using the models and methods of nonlinear dynamics and chaos. Identifying flow through soil or rock as a nonlinear dynamical system is important for developing appropriate short- and long-time predictive models, evaluating prediction uncertainty, assessing the spatial distribution of flow characteristics from time series data, and improving chemical transport simulations. Inferring the nature of flow processes through the methods of nonlinear dynamics could become widely used in different areas of the earth sciences.

Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations.

Science.gov (United States)

König, Carolin; Skånberg, Robin; Hotz, Ingrid; Ynnerman, Anders; Norman, Patrick; Linares, Mathieu

2018-03-25

A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-β(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol -1 due to the interactions between the anionic carboxyl groups of the probe and the cationic ε-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

Dynamics of zonal flows and self-regulating drift-wave turbulence

International Nuclear Information System (INIS)

Diamond, P.H.; Fleischer, J.; Rosenbluth, M.N.; Hinton, F.L.; Malkov, M.; Smolyakov, A.

1999-01-01

We present a theory of zonal flow - drift wave dynamics. Zonal flows are generated by modulational instability of a drift wave spectrum, and are damped by collisions. Drift waves undergo random shearing-induced refraction, resulting in increased mean square radial wavenumber. Drift waves and zonal flows together form a simple dynamical system, which has a single stable fixed point. In this state, the fluctuation intensity and turbulent diffusivity are ultimately proportional to the collisional zonal flow damping. The implications of these results for transport models is discussed. (author)

Dynamics of zonal flows and self-regulating drift-wave turbulence

International Nuclear Information System (INIS)

Diamond, P.H.; Fleischer, J.; Rosenbluth, M.; Hinton, F.L.; Malkov, M.; Smolyakov, A.

2001-01-01

We present a theory of zonal flow - drift wave dynamics. Zonal flows are generated by modulational instability of a drift wave spectrum, and are damped by collisions. Drift waves undergo random shearing-induced refraction, resulting in increased mean square radial wavenumber. Drift waves and zonal flows together form a simple dynamical system, which has a single stable fixed point. In this state, the fluctuation intensity and turbulent diffusivity are ultimately proportional to the collisional zonal flow damping. The implications of these results for transport models is discussed. (author)

Multiphase Flow Dynamics 5 Nuclear Thermal Hydraulics

CERN Document Server

Kolev, Nikolay Ivanov

2012-01-01

The present Volume 5 of the successful book package "Multiphase Flow Dynamics" is devoted to nuclear thermal hydraulics which is a substantial part of nuclear reactor safety. It provides knowledge and mathematical tools for adequate description of the process of transferring the fission heat released in materials due to nuclear reactions into its environment. It step by step introduces into the heat release inside the fuel, temperature fields in the fuels, the "simple" boiling flow in a pipe described using ideas of different complexity like equilibrium, non equilibrium, homogeneity, non homogeneity. Then the "simple" three-fluid boiling flow in a pipe is described by gradually involving the mechanisms like entrainment and deposition, dynamic fragmentation, collisions, coalescence, turbulence. All heat transfer mechanisms are introduced gradually discussing their uncertainty. Different techniques are introduced like boundary layer treatments or integral methods. Comparisons with experimental data at each step...

Multiphase flow dynamics 5 nuclear thermal hydraulics

CERN Document Server

Kolev, Nikolay Ivanov

2015-01-01

This Volume 5 of the successful book package "Multiphase Flow Dynamics" is devoted to nuclear thermal hydraulics which is a substantial part of nuclear reactor safety. It provides knowledge and mathematical tools for adequate description of the process of transferring the fission heat released in materials due to nuclear reactions into its environment. It step by step introduces into the heat release inside the fuel, temperature fields in the fuels, the "simple" boiling flow in a pipe described using ideas of different complexity like equilibrium, non equilibrium, homogeneity, non homogeneity. Then the "simple" three-fluid boiling flow in a pipe is described by gradually involving the mechanisms like entrainment and deposition, dynamic fragmentation, collisions, coalescence, turbulence. All heat transfer mechanisms are introduced gradually discussing their uncertainty. Different techniques are introduced like boundary layer treatments or integral methods. Comparisons with experimental data at each step demons...

Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

Directory of Open Access Journals (Sweden)

Jeffrey M Sanders

Full Text Available The epidermal growth factor receptor (EGFR is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of

Global workspace dynamics: Cortical "binding and propagation enables conscious contents.

Directory of Open Access Journals (Sweden)

Bernard J Baars

2013-05-01

Full Text Available A global workspace is a hub of binding and propagation in a population of loosely coupled signaling elements. Global workspace (GW architectures recruit many distributed, specialized agents to help resolve focal ambiguities. In the brain, conscious experiences may reflect a global workspace function. For animals the natural world is full of fitness-related ambiguities, suggesting a general adaptive pressure for brains to resolve focal ambiguities quickly and accurately. In humans and related species the cortico-thalamic (C-T core is believed to underlie conscious aspects of perception, thinking, learning, feelings of knowing, emotions, imagery, working memory and executive control. The C-T core has many anatomical hubs, but conscious percepts are unitary and internally consistent at any given moment. The repertoire of conscious contents is a large, open set. These points suggest that a brain-based GW capacity cannot be localized in a single anatomical hub. Rather, it should be sought in a dynamic capacity for adaptive binding and propagation of neural signals over multi-hub networks. We refer to this as dynamic global workspace theory (dGW. In this view, conscious contents can arise in any region of the C-T core when multiple signal streams settle on a winner-take-all equilibrium. The resulting bound gestalt may ignite an any-to-many broadcast, lasting ~100-200 ms, and trigger widespread adaptation in established networks. Binding and broadcasting may involve theta/gamma or alpha/gamma phase coupling. Conscious contents (qualia may reflect their sources in cortex. Sensory percepts may bind and broadcast from posterior regions, while non-sensory feelings of knowing (FOKs may be frontotemporal. The small focal capacity of conscious contents may be the biological price to pay for global access. We propose that in the intact brain the hippocampal/rhinal complex may support conscious event organization as well as episodic memory coding.

Flow injection on-line oxidizing fluorometry coupled to dialysis sampling for the study of carbamazepine-protein binding

Energy Technology Data Exchange (ETDEWEB)

Zhang Zhiqi [School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China)]. E-mail: zqzhang@snnu.edu.cn; Liang Guoxi [School of Chemistry and Materials Science, Shaanxi Normal University, Xi' an 710062 (China)

2005-04-22

The mechanism of binding of carbamazepine (CBZ) with bovine serum albumin (BSA) has been investigated in vitro based on a new flow injection fluorometry coupled to the technique of dialysis sampling. The CBZ and BSA were mixed in different molar ratios in 0.050 mol L{sup -1} phosphate buffer (containing 0.9% NaCl), pH 7.4, and incubated at 37 {+-} 0.5 deg. C in a water bath. The dialysis sampler was utilized to sample free CBZ from mixed solution with a relative dialytic efficiency of 7.6%. Then the CBZ in dialysis solution was injected into carrier and on-line oxidized by lead dioxide solid-phase reactor into fluorescent product with a maximum excitation wavelength of 355 nm and a maximum emission wavelength of 478 nm. The fluorescence intensity measured was linear proportional with the concentration of free CBZ in mixed solution over the range of 1 x 10{sup -5} to 2 x 10{sup -4} mol L{sup -1} with the detection limit of 6 x 10{sup -6} mol L{sup -1}. According to the fluorescence measurement results from mixed solution, the association constant (K) estimated for CBZ-BSA binding and the number of the binding site (n) with Scatchard analysis were 1.08 x 10{sup 4} L mol{sup -1} and 0.94, respectively. Stern-Volmer plots indicated the presence of dynamic component in the quenching mechanism. The acting force was suggested to be mainly hydrophobic and the distance between the acceptor and donor was 3.12 nm. The estimated binding parameters agreed well with literature values.

Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Denis Bucher

2011-04-01

Full Text Available Periplasmic binding proteins (PBPs are a large family of molecular transporters that play a key role in nutrient uptake and chemotaxis in Gram-negative bacteria. All PBPs have characteristic two-domain architecture with a central interdomain ligand-binding cleft. Upon binding to their respective ligands, PBPs undergo a large conformational change that effectively closes the binding cleft. This conformational change is traditionally viewed as a ligand induced-fit process; however, the intrinsic dynamics of the protein may also be crucial for ligand recognition. Recent NMR paramagnetic relaxation enhancement (PRE experiments have shown that the maltose binding protein (MBP - a prototypical member of the PBP superfamily - exists in a rapidly exchanging (ns to µs regime mixture comprising an open state (approx 95%, and a minor partially closed state (approx 5%. Here we describe accelerated MD simulations that provide a detailed picture of the transition between the open and partially closed states, and confirm the existence of a dynamical equilibrium between these two states in apo MBP. We find that a flexible part of the protein called the balancing interface motif (residues 175-184 is displaced during the transformation. Continuum electrostatic calculations indicate that the repacking of non-polar residues near the hinge region plays an important role in driving the conformational change. Oscillations between open and partially closed states create variations in the shape and size of the binding site. The study provides a detailed description of the conformational space available to ligand-free MBP, and has implications for understanding ligand recognition and allostery in related proteins.

Development of a dynamic flow imaging phantom for dynamic contrast-enhanced CT

International Nuclear Information System (INIS)

Driscoll, B.; Keller, H.; Coolens, C.

2011-01-01

Purpose: Dynamic contrast enhanced CT (DCE-CT) studies with modeling of blood flow and tissue perfusion are becoming more prevalent in the clinic, with advances in wide volume CT scanners allowing the imaging of an entire organ with sub-second image frequency and sub-millimeter accuracy. Wide-spread implementation of perfusion DCE-CT, however, is pending fundamental validation of the quantitative parameters that result from dynamic contrast imaging and perfusion modeling. Therefore, the goal of this work was to design and construct a novel dynamic flow imaging phantom capable of producing typical clinical time-attenuation curves (TACs) with the purpose of developing a framework for the quantification and validation of DCE-CT measurements and kinetic modeling under realistic flow conditions. Methods: The phantom is based on a simple two-compartment model and was printed using a 3D printer. Initial analysis of the phantom involved simple flow measurements and progressed to DCE-CT experiments in order to test the phantoms range and reproducibility. The phantom was then utilized to generate realistic input TACs. A phantom prediction model was developed to compute the input and output TACs based on a given set of five experimental (control) parameters: pump flow rate, injection pump flow rate, injection contrast concentration, and both control valve positions. The prediction model is then inversely applied to determine the control parameters necessary to generate a set of desired input and output TACs. A protocol was developed and performed using the phantom to investigate image noise, partial volume effects and CT number accuracy under realistic flow conditionsResults: This phantom and its surrounding flow system are capable of creating a wide range of physiologically relevant TACs, which are reproducible with minimal error between experiments (σ/μ 2 ) for the input function between 0.95 and 0.98, while the maximum enhancement differed by no more than 3.3%. The

Crystal Structures and Binding Dynamics of Odorant-Binding Protein 3 from two aphid species Megoura viciae and Nasonovia ribisnigri.

Science.gov (United States)

Northey, Tom; Venthur, Herbert; De Biasio, Filomena; Chauviac, Francois-Xavier; Cole, Ambrose; Ribeiro, Karlos Antonio Lisboa; Grossi, Gerarda; Falabella, Patrizia; Field, Linda M; Keep, Nicholas H; Zhou, Jing-Jiang

2016-04-22

Aphids use chemical cues to locate hosts and find mates. The vetch aphid Megoura viciae feeds exclusively on the Fabaceae, whereas the currant-lettuce aphid Nasonovia ribisnigri alternates hosts between the Grossulariaceae and Asteraceae. Both species use alarm pheromones to warn of dangers. For N. ribisnigri this pheromone is a single component (E)-β-farnesene but M. viciae uses a mixture of (E)-β-farnesene, (-)-α-pinene, β-pinene, and limonene. Odorant-binding proteins (OBP) are believed to capture and transport such semiochemicals to their receptors. Here, we report the first aphid OBP crystal structures and examine their molecular interactions with the alarm pheromone components. Our study reveals some unique structural features: 1) the lack of an internal ligand binding site; 2) a striking groove in the surface of the proteins as a putative binding site; 3) the N-terminus rather than the C-terminus occupies the site closing off the conventional OBP pocket. The results from fluorescent binding assays, molecular docking and dynamics demonstrate that OBP3 from M. viciae can bind to all four alarm pheromone components and the differential ligand binding between these very similar OBP3s from the two aphid species is determined mainly by the direct π-π interactions between ligands and the aromatic residues of OBP3s in the binding pocket.

Molecular Dynamics Simulations of Insulin: Elucidating the Conformational Changes that Enable Its Binding.

Directory of Open Access Journals (Sweden)

Anastasios Papaioannou

Full Text Available A sequence of complex conformational changes is required for insulin to bind to the insulin receptor. Recent experimental evidence points to the B chain C-terminal (BC-CT as the location of these changes in insulin. Here, we present molecular dynamics simulations of insulin that reveal new insights into the structural changes occurring in the BC-CT. We find three key results: 1 The opening of the BC-CT is inherently stochastic and progresses through an open and then a "wide-open" conformation--the wide-open conformation is essential for receptor binding, but occurs only rarely. 2 The BC-CT opens with a zipper-like mechanism, with a hinge at the Phe24 residue, and is maintained in the dominant closed/inactive state by hydrophobic interactions of the neighboring Tyr26, the critical residue where opening of the BC-CT (activation of insulin is initiated. 3 The mutation Y26N is a potential candidate as a therapeutic insulin analogue. Overall, our results suggest that the binding of insulin to its receptor is a highly dynamic and stochastic process, where initial docking occurs in an open conformation and full binding is facilitated through interactions of insulin receptor residues with insulin in its wide-open conformation.

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...

Particle algorithms for population dynamics in flows

International Nuclear Information System (INIS)

Perlekar, Prasad; Toschi, Federico; Benzi, Roberto; Pigolotti, Simone

2011-01-01

We present and discuss particle based algorithms to numerically study the dynamics of population subjected to an advecting flow condition. We discuss few possible variants of the algorithms and compare them in a model compressible flow. A comparison against appropriate versions of the continuum stochastic Fisher equation (sFKPP) is also presented and discussed. The algorithms can be used to study populations genetics in fluid environments.

ON THE ANALYSIS OF IMPEDANCE-DRIVEN REVERSE FLOW DYNAMICS

Directory of Open Access Journals (Sweden)

LEE V. C.-C.

2017-02-01

Full Text Available Impedance pump is a simple valve-less pumping mechanism, where an elastic tube is joined to a more rigid tube, at both ends. By inducing a periodic asymmetrical compression on the elastic tube will produce a unidirectional flow within the system. This pumping concept offers a low energy, low noise alternative, which makes it an effective driving mechanism, especially for micro-fluidic systems. In addition, the wave-based mechanism through which pumping occurs infers many benefits in terms of simplicity of design and manufacturing. Adjustment of simple parameters such as the excitation frequencies or compression locations will reverse the direction of flow, providing a very versatile range of flow outputs. This paper describes the experimental analysis of such impedance-driven flow with emphasis on the dynamical study of the reverse flow in open-loop environment. In this study, tapered section with converging steps is introduced at both ends of the elastic tube to amplify the magnitude of reverse flow. Study conducted shows that the reverse peak flow is rather significant with estimate of 23% lower than the forward peak flow. The flow dynamics on the other hand has shown to exhibit different characteristics as per the forward peak flow. The flow characteristics is then studied and showed that the tapered sections altered the impedance within the system and hence induce a higher flow in the reverse direction.

Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.

Directory of Open Access Journals (Sweden)

M Olivia Kim

2015-10-01

Full Text Available BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer's disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate, as well as structural flexibility in the flap region. Thus, the coupling of protonation and conformational equilibria is essential to a full in silico characterization of BACE-1. In this work, we perform constant pH replica exchange molecular dynamics simulations on both apo BACE-1 and five BACE-1-inhibitor complexes to examine the effect of pH on dynamics and inhibitor binding properties of BACE-1. In our simulations, we find that solution pH controls the conformational flexibility of apo BACE-1, whereas bound inhibitors largely limit the motions of the holo enzyme at all levels of pH. The microscopic pKa values of titratable residues in BACE-1 including its aspartyl dyad are computed and compared between apo and inhibitor-bound states. Changes in protonation between the apo and holo forms suggest a thermodynamic linkage between binding of inhibitors and protons localized at the dyad. Utilizing our recently developed computational protocol applying the binding polynomial formalism to the constant pH molecular dynamics (CpHMD framework, we are able to obtain the pH-dependent binding free energy profiles for various BACE-1-inhibitor complexes. Our results highlight the importance of correctly addressing the binding-induced protonation changes in protein-ligand systems where binding accompanies a net proton transfer. This work comprises the first application of our CpHMD-based free energy computational method to protein-ligand complexes and illustrates the value of CpHMD as an all-purpose tool for obtaining pH-dependent dynamics and binding free energies of biological systems.

Development of dynamic PIV for droplet jet flow

International Nuclear Information System (INIS)

Okamoto, K.; Hong, S. D.; Bi, W. T.; Sugii, Y.; Madarame, H.; Hayami, H.

2003-01-01

The Particle Image Velocimetry (PIV) can capture velocity vector fields with high spatial resolution. In this study, the Dynamic PIV system up to 10kHz temporal resolution was developed with combining the High-speed camera and high speed Laser with Double pulse option. The 1024 x 1024 pixel images with frame straddling were captured in 2kHz. Also, PIV data were measured in 512 x 256 pixel in 10kHz. The system had been applied to capture the water droplet flow. The transient characteristics of the droplet flow can be clearly captured using the developed Dynamic PIV System

Topological fluid dynamics of interfacial flows

DEFF Research Database (Denmark)

Brøns, Morten

1994-01-01

The topological description of flows in the vicinity of a solid boundary, that is familiar from the aerodynamics literature, has recently been extended to the case of flow at a liquid–gas interface or a free surface by Lugt [Phys. Fluids 30, 3647 (1987)]. Lugt's work is revisited in a more general...... setting, including nonconstant curvature of the interface and gradients of surface tension, using tools of modern nonlinear dynamics. Bifurcations of the flow pattern occur at degenerate configurations. Using the theory of unfolding, this paper gives a complete description of the bifurcations that depend...... on terms up to the second order. The general theory of this paper is applied to the topology of streamlines during the breaking of a wave and to the flow below a stagnant surface film. Physics of Fluids is copyrighted by The American Institute of Physics....

Flow Mode Dependent Partitioning Processes of Preferential Flow Dynamics in Unsaturated Fractures - Findings From Analogue Percolation Experiments

Science.gov (United States)

Kordilla, J.; Noffz, T.; Dentz, M.; Sauter, M.

2017-12-01

To assess the vulnerability of an aquifer system it is of utmost importance to recognize the high potential for a rapid mass transport offered by ow through unsaturated fracture networks. Numerical models have to reproduce complex effects of gravity-driven flow dynamics to generate accurate predictions of flow and transport. However, the non-linear characteristics of free surface flow dynamics and partitioning behaviour at unsaturated fracture intersections often exceed the capacity of classical volume-effective modelling approaches. Laboratory experiments that manage to isolate single aspects of the mass partitioning process can enhance the understanding of underlying dynamics, which ultimately influence travel time distributions on multiple scales. Our analogue fracture network consists of synthetic cubes with dimensions of 20 x 20 x 20 cm creating simple geometries of a single or a cascade of consecutive horizontal fractures. Gravity-driven free surface flow (droplets; rivulets) is established via a high precision multichannel dispenser at flow rates ranging from 1.5 to 4.5 ml/min. Single-inlet experiments show the influence of variable flow rate, atmospheric pressure and temperature on the stability of flow modes and allow to delineate a droplet and rivulet regime. The transition between these regimes exhibits mixed flow characteristics. In addition, multi-inlet setups with constant total infow rates decrease the variance induced by erratic free-surface flow dynamics. We investigate the impacts of variable aperture widths, horizontal offsets of vertical fracture surfaces, and alternating injection methods for both flow regimes. Normalized fracture inflow rates allow to demonstrate and compare the effects of variable geometric features. Firstly, the fracture filling can be described by plug flow. At later stages it transitions into a Washburn-type flow, which we compare to an analytical solution for the case of rivulet flow. Observations show a considerably

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

International Nuclear Information System (INIS)

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Fernandez-Alberti, Sebastian; Roitberg, Adrian E.

2015-01-01

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

Energy Technology Data Exchange (ETDEWEB)

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Fernandez-Alberti, Sebastian, E-mail: sfalberti@gmail.com [Universidad Nacional de Quilmes, Roque Saenz Peña 352, B1876BXD Bernal (Argentina); Roitberg, Adrian E. [Departments of Physics and Chemistry, University of Florida, Gainesville, Florida 32611 (United States)

2015-06-28

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

Calculation of the dynamic air flow resistivity of fibre materials

DEFF Research Database (Denmark)

Tarnow, Viggo

1997-01-01

The acoustic attenuation of acoustic fiber materials is mainly determined by the dynamic resistivity to an oscillating air flow. The dynamic resistance is calculated for a model with geometry close to the geometry of real fibre material. The model constists of parallel cylinders placed randomly.......The second procedure is an extension to oscillating air flow of the Brinkman self-consistent procedure for dc flow. The procedures are valid for volume concentrations of cylinders less than 0.1. The calculations show that for the density of fibers of interest for acoustic fibre materials the simple self...

Hydro-dynamic damping theory in flowing water

Science.gov (United States)

Monette, C.; Nennemann, B.; Seeley, C.; Coutu, A.; Marmont, H.

2014-03-01

Fluid-structure interaction (FSI) has a major impact on the dynamic response of the structural components of hydroelectric turbines. On mid-head to high-head Francis runners, the rotor-stator interaction (RSI) phenomenon always has to be considered carefully during the design phase to avoid operational issues later on. The RSI dynamic response amplitudes are driven by three main factors: (1) pressure forcing amplitudes, (2) excitation frequencies in relation to natural frequencies and (3) damping. The prediction of the two first factors has been largely documented in the literature. However, the prediction of fluid damping has received less attention in spite of being critical when the runner is close to resonance. Experimental damping measurements in flowing water on hydrofoils were presented previously. Those results showed that the hydro-dynamic damping increased linearly with the flow. This paper presents development and validation of a mathematical model, based on momentum exchange, to predict damping due to fluid structure interaction in flowing water. The model is implemented as an analytical procedure for simple structures, such as cantilever beams, but is also implemented in more general ways using three different approaches for more complex structures such as runner blades: a finite element procedure, a CFD modal work based approach and a CFD 1DOF approach. The mathematical model and all three implementation approaches are shown to agree well with experimental results.

Regulation of Cellular Dynamics and Chromosomal Binding Site Preference of Linker Histones H1.0 and H1.X.

Science.gov (United States)

Okuwaki, Mitsuru; Abe, Mayumi; Hisaoka, Miharu; Nagata, Kyosuke

2016-11-01

Linker histones play important roles in the genomic organization of mammalian cells. Of the linker histone variants, H1.X shows the most dynamic behavior in the nucleus. Recent research has suggested that the linker histone variants H1.X and H1.0 have different chromosomal binding site preferences. However, it remains unclear how the dynamics and binding site preferences of linker histones are determined. Here, we biochemically demonstrated that the DNA/nucleosome and histone chaperone binding activities of H1.X are significantly lower than those of other linker histones. This explains why H1.X moves more rapidly than other linker histones in vivo Domain swapping between H1.0 and H1.X suggests that the globular domain (GD) and C-terminal domain (CTD) of H1.X independently contribute to the dynamic behavior of H1.X. Our results also suggest that the N-terminal domain (NTD), GD, and CTD cooperatively determine the preferential binding sites, and the contribution of each domain for this determination is different depending on the target genes. We also found that linker histones accumulate in the nucleoli when the nucleosome binding activities of the GDs are weak. Our results contribute to understanding the molecular mechanisms of dynamic behaviors, binding site selection, and localization of linker histones. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Comparative study of incompressible and isothermal compressible flow solvers for cavitating flow dynamics

Energy Technology Data Exchange (ETDEWEB)

Park, Sun Ho [Korea Maritime and Ocean University, Busan (Korea, Republic of); Rhee, Shin Hyung [Seoul National University, Seoul (Korea, Republic of)

2015-08-15

Incompressible flow solvers are generally used for numerical analysis of cavitating flows, but with limitations in handling compressibility effects on vapor phase. To study compressibility effects on vapor phase and cavity interface, pressure-based incompressible and isothermal compressible flow solvers based on a cell-centered finite volume method were developed using the OpenFOAM libraries. To validate the solvers, cavitating flow around a hemispherical head-form body was simulated and validated against the experimental data. The cavity shedding behavior, length of a re-entrant jet, drag history, and the Strouhal number were compared between the two solvers. The results confirmed that computations of the cavitating flow including compressibility effects improved the reproduction of cavitation dynamics.

Molecular Dynamics Insights into Polyamine-DNA Binding Modes: Implications for Cross-Link Selectivity.

Science.gov (United States)

Bignon, Emmanuelle; Chan, Chen-Hui; Morell, Christophe; Monari, Antonio; Ravanat, Jean-Luc; Dumont, Elise

2017-09-18

Biogenic polyamines, which play a role in DNA condensation and stabilization, are ubiquitous and are found at millimolar concentration in the nucleus of eukaryotic cells. The interaction modes of three polyamines-putrescine (Put), spermine (Spm), and spermidine (Spd)-with a self-complementary 16 base pair (bp) duplex, are investigated by all-atom explicit-solvent molecular dynamics. The length of the amine aliphatic chain leads to a change of the interaction mode from minor groove binding to major groove binding. Through all-atom dynamics, noncovalent interactions that stabilize the polyamine-DNA complex and prefigure the reactivity, leading to the low-barrier formation of deleterious DNA-polyamine cross-links, after one-electron oxidation of a guanine nucleobase, are unraveled. The binding strength is quantified from the obtained trajectories by molecular mechanics generalized Born surface area post-processing (MM-GBSA). The values of binding free energies provide the same affinity order, Putbinding modes and carbon-nitrogen distances along the series of polyamines illustrate the selectivity towards deleterious DNA-polyamine cross-link formation through the extraction of average approaching distances between the C8 atom of guanines and the ammonium group. These results imply that the formation of DNA-polyamine cross-links involves deprotonation of the guanine radical cation to attack the polyamines, which must be positively charged to lie in the vicinity of the B-helix. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatio-temporal organization of dynamics in a two-dimensional periodically driven vortex flow: A Lagrangian flow network perspective.

Science.gov (United States)

Lindner, Michael; Donner, Reik V

2017-03-01

We study the Lagrangian dynamics of passive tracers in a simple model of a driven two-dimensional vortex resembling real-world geophysical flow patterns. Using a discrete approximation of the system's transfer operator, we construct a directed network that describes the exchange of mass between distinct regions of the flow domain. By studying different measures characterizing flow network connectivity at different time-scales, we are able to identify the location of dynamically invariant structures and regions of maximum dispersion. Specifically, our approach allows us to delimit co-existing flow regimes with different dynamics. To validate our findings, we compare several network characteristics to the well-established finite-time Lyapunov exponents and apply a receiver operating characteristic analysis to identify network measures that are particularly useful for unveiling the skeleton of Lagrangian chaos.

Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases.

Directory of Open Access Journals (Sweden)

Ly Le

2010-09-01

Full Text Available Oseltamivir (Tamiflu is currently the frontline antiviral drug employed to fight the flu virus in infected individuals by inhibiting neuraminidase, a flu protein responsible for the release of newly synthesized virions. However, oseltamivir resistance has become a critical problem due to rapid mutation of the flu virus. Unfortunately, how mutations actually confer drug resistance is not well understood. In this study, we employ molecular dynamics (MD and steered molecular dynamics (SMD simulations, as well as graphics processing unit (GPU-accelerated electrostatic mapping, to uncover the mechanism behind point mutation induced oseltamivir-resistance in both H5N1 "avian" and H1N1pdm "swine" flu N1-subtype neuraminidases. The simulations reveal an electrostatic binding funnel that plays a key role in directing oseltamivir into and out of its binding site on N1 neuraminidase. The binding pathway for oseltamivir suggests how mutations disrupt drug binding and how new drugs may circumvent the resistance mechanisms.

Dynamic membrane filtration in tangential flow

International Nuclear Information System (INIS)

Anon.

1993-01-01

Oil-containing waste water is produced in many cleaning processes and also on production of compressed air. Dynamic membrane filtration in the tangential flow mode has proved effective in the treatment of these stable emulsions. The possible applications of ceramic membrane filters are illustrated for a variety of examples. (orig.) [de

Dynamics of flow behind backward-facing step in a narrow channel

Directory of Open Access Journals (Sweden)

Uruba V.

2013-04-01

Full Text Available The results and their analysis from experiments obtained by TR-PIV are presented on the model of backward-facing step in a narrow channel. The recirculation zone is studied in details. Mean structures are evaluated from fluctuating velocity fields. Then dynamics of the flow is characterized with help of POD (BOD technique. Substantial differences in high energy dynamical structures behaviour within the back-flow region and further downstream behind the flow reattachment have been found.

Instantaneous aerosol dynamics in a turbulent flow

KAUST Repository

Zhou, Kun

2012-01-01

Dibutyl phthalate aerosol particles evolution dynamics in a turbulent mixing layer is simulated by means of direct numerical simulation for the flow field and the direct quadrature method of moments for the aerosol evolution. Most par

Separation Dynamics of Controlled Internal Flow in an Adverse Pressure Gradient

Science.gov (United States)

Peterson, C. J.; Vukasinovic, B.; Glezer, A.

2017-11-01

The effects of fluidic actuation on the dynamic evolution of aggressive internal flow separation is investigated at speeds up to M = 0.4 within a constant-width diffuser branching off of a primary flow duct. It is shown that a spanwise array of fluidic actuators upstream of the separation actively controls the flow constriction (and losses) within the diffuser and consequently the local pressure gradient at its entrance. The effectiveness of the actuation, as may be measured by the increased flow rate that is diverted through the diffuser, scales with its flow rate coefficient. In the presence of actuation (0.7% mass fraction), the mass flow rate in the primary duct increases by 10% while the fraction of the diverted mass flow rate in the diffuser increases by more than 45%. The flow dynamics near separation in the absence and presence of actuation are characterized using high speed particle image velocimetry and analyzed using proper orthogonal and spectral decompositions. In particular, the spectral contents of the incipient boundary layer separation are compared in the absence and presence of actuation with emphasis on the changes in local dynamics near separation as the characteristic cross stream scale of the boundary layer increases with separation delay.

Lattice fluid dynamics from perfect discretizations of continuum flows

International Nuclear Information System (INIS)

Katz, E.; Wiese, U.

1998-01-01

We use renormalization group methods to derive equations of motion for large scale variables in fluid dynamics. The large scale variables are averages of the underlying continuum variables over cubic volumes and naturally exist on a lattice. The resulting lattice dynamics represents a perfect discretization of continuum physics, i.e., grid artifacts are completely eliminated. Perfect equations of motion are derived for static, slow flows of incompressible, viscous fluids. For Hagen-Poiseuille flow in a channel with a square cross section the equations reduce to a perfect discretization of the Poisson equation for the velocity field with Dirichlet boundary conditions. The perfect large scale Poisson equation is used in a numerical simulation and is shown to represent the continuum flow exactly. For nonsquare cross sections one can use a numerical iterative procedure to derive flow equations that are approximately perfect. copyright 1998 The American Physical Society

Visual Analysis of Inclusion Dynamics in Two-Phase Flow.

Science.gov (United States)

Karch, Grzegorz Karol; Beck, Fabian; Ertl, Moritz; Meister, Christian; Schulte, Kathrin; Weigand, Bernhard; Ertl, Thomas; Sadlo, Filip

2018-05-01

In single-phase flow visualization, research focuses on the analysis of vector field properties. In two-phase flow, in contrast, analysis of the phase components is typically of major interest. So far, visualization research of two-phase flow concentrated on proper interface reconstruction and the analysis thereof. In this paper, we present a novel visualization technique that enables the investigation of complex two-phase flow phenomena with respect to the physics of breakup and coalescence of inclusions. On the one hand, we adapt dimensionless quantities for a localized analysis of phase instability and breakup, and provide detailed inspection of breakup dynamics with emphasis on oscillation and its interplay with rotational motion. On the other hand, we present a parametric tightly linked space-time visualization approach for an effective interactive representation of the overall dynamics. We demonstrate the utility of our approach using several two-phase CFD datasets.

A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery

Science.gov (United States)

Cholko, Timothy; Chen, Wei; Tang, Zhiye; Chang, Chia-en A.

2018-05-01

Abnormal activity of cyclin-dependent kinase 8 (CDK8) along with its partner protein cyclin C (CycC) is a common feature of many diseases including colorectal cancer. Using molecular dynamics (MD) simulations, this study determined the dynamics of the CDK8-CycC system and we obtained detailed breakdowns of binding energy contributions for four type-I and five type-II CDK8 inhibitors. We revealed system motions and conformational changes that will affect ligand binding, confirmed the essentialness of CycC for inclusion in future computational studies, and provide guidance in development of CDK8 binders. We employed unbiased all-atom MD simulations for 500 ns on twelve CDK8-CycC systems, including apoproteins and protein-ligand complexes, then performed principal component analysis (PCA) and measured the RMSF of key regions to identify protein dynamics. Binding pocket volume analysis identified conformational changes that accompany ligand binding. Next, H-bond analysis, residue-wise interaction calculations, and MM/PBSA were performed to characterize protein-ligand interactions and find the binding energy. We discovered that CycC is vital for maintaining a proper conformation of CDK8 to facilitate ligand binding and that the system exhibits motion that should be carefully considered in future computational work. Surprisingly, we found that motion of the activation loop did not affect ligand binding. Type-I and type-II ligand binding is driven by van der Waals interactions, but electrostatic energy and entropic penalties affect type-II binding as well. Binding of both ligand types affects protein flexibility. Based on this we provide suggestions for development of tighter-binding CDK8 inhibitors and offer insight that can aid future computational studies.

Supercritical droplet dynamics and emission in low speed cross-flows

International Nuclear Information System (INIS)

Chae, J. W.; Yang, H. S.; Yoon, W. S.

2008-01-01

Droplet dynamics and emission of a supercritical droplet in crossing gas stream are numerically investigated. Effects of ambient pressure and velocity of nitrogen gas on the dynamics of the supercritical oxygen droplet are parametrically examined. Unsteady conservative axisymmetric Navier-Stokes equations in curvilinear coordinates are preconditioned and solved by dual-time stepping method. A unified property evaluation scheme based on a fundamental equation of state and extended corresponding-state principle is established to deal with thermodynamic non-idealities and transport anomalies. At lower pressures and velocities of nitrogen cross flows, both the diffusion and the convection are important in determining the droplet dynamics. Relative flow motion causes a secondary breakup and cascading vortices, and the droplet lifetime is reduced with increasing in ambient pressure. At higher ambient pressures and velocities, however, the droplet dynamics become convection-controlled while the secondary breakup is hindered by reduced diffusivity of the oxygen. Gas-phase mixing depends on the convection and diffusion velocities in conjunction with corresponding droplet deformation and flow interaction. Supercritical droplet dynamics and emission is not similar with respect to the pressure and velocity of the ambient gas and thus provides no scale

A dynamically coupled allosteric network underlies binding cooperativity in Src kinase.

Science.gov (United States)

Foda, Zachariah H; Shan, Yibing; Kim, Eric T; Shaw, David E; Seeliger, Markus A

2015-01-20

Protein tyrosine kinases are attractive drug targets because many human diseases are associated with the deregulation of kinase activity. However, how the catalytic kinase domain integrates different signals and switches from an active to an inactive conformation remains incompletely understood. Here we identify an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. Surprisingly, reactants (ATP and peptide substrates) bind with negative cooperativity to Src kinase while products (ADP and phosphopeptide) bind with positive cooperativity. We confirm the molecular details of the signal relay through the allosteric network by biochemical studies. Experiments on two additional protein tyrosine kinases indicate that the allosteric network may be largely conserved among these enzymes. Our work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity.

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.

Dynamic behaviors of cavitation bubble for the steady cavitating flow

Science.gov (United States)

Cai, Jun; Huai, Xiulan; Li, Xunfeng

2009-12-01

In this paper, by introducing the flow velocity item into the classical Rayleigh-Plesset dynamic equation, a new equation, which does not involve the time term and can describe the motion of cavitation bubble in the steady cavitating flow, has been obtained. By solving the new motion equation using Runge-Kutta fourth order method with adaptive step size control, the dynamic behaviors of cavitation bubble driven by the varying pressure field downstream of a venturi cavitation reactor are numerically simulated. The effects of liquid temperature (corresponding to the saturated vapor pressure of liquid), cavitation number and inlet pressure of venturi on radial motion of bubble and pressure pulse due to the radial motion are analyzed and discussed in detail. Some dynamic behaviors of bubble different from those in previous papers are displayed. In addition, the internal relationship between bubble dynamics and process intensification is also discussed. The simulation results reported in this work reveal the variation laws of cavitation intensity with the flow conditions of liquid, and will lay a foundation for the practical application of hydrodynamic cavitation technology.

Dynamics and statistics of heavy particles in turbulent flows

NARCIS (Netherlands)

Cencini, M.; Bec, J.; Biferale, L.; Boffetta, G.; Celani, A.; Lanotte, A.; Musacchio, S.; Toschi, F.

2006-01-01

We present the results of direct numerical simulations (DNS) of turbulent flows seeded with millions of passive inertial particles. The maximum Reynolds number is Re¿~ 200. We consider particles much heavier than the carrier flow in the limit when the Stokes drag force dominates their dynamical

Combined modeling of cell aggregation and adhesion mediated by receptor–ligand interactions under shear flow

Directory of Open Access Journals (Sweden)

Yu Du

2015-11-01

Full Text Available Blood cell aggregation and adhesion to endothelial cells under shear flow are crucial to many biological processes such as thrombi formation, inflammatory cascade, and tumor metastasis, in which these cellular interactions are mainly mediated by the underlying receptor–ligand bindings. While theoretical modeling of aggregation dynamics and adhesion kinetics of interacting cells have been well studied separately, how to couple these two processes remains unclear. Here we develop a combined model that couples cellular aggregation dynamics and adhesion kinetics under shear flow. The impacts of shear rate (or shear stress and molecular binding affinity were elucidated. This study provides a unified model where the action of a fluid flow drives cell aggregation and adhesion under the modulations of the mechanical shear flow and receptor–ligand interaction kinetics. It offers an insight into understanding the relevant biological processes and functions.

Coupling-constant flows and dynamical symmetry breaking

International Nuclear Information System (INIS)

Yamagishi, H.

1981-01-01

The Coleman-Weinberg theory is reformulated in terms of flows in coupling-constant space. It is shown that the existence of dynamical symmetry breaking is governed essentially by the b functions. An application is made to the massless Weinberg-Salam model

Differences in dynamic autoregulation of renal blood flow between SHR and WKY rats

DEFF Research Database (Denmark)

Chen, Y M; Holstein-Rathlou, N H

1993-01-01

by chaotic fluctuations. We sought to determine whether this change was associated with a change in the dynamic autoregulation of renal blood flow. In halothane-anesthetized 250- to 320-g SHR and WKY rats, renal blood flow was measured during "white noise" forcing of arterial blood pressure. The frequency...... conclude that the change in the dynamics of TGF leads to a change in the dynamic autoregulation of renal blood flow between SHR and WKY rats. This change results in a more efficient dynamic autoregulation of renal blood flow in the SHR compared with the WKY rats. The functional consequences of this......In halothane-anesthetized Wistar-Kyoto (WKY) rats the single-nephron blood flow and the proximal tubule pressure oscillate at a frequency of 35-50 mHz because of the operation of the tubuloglomerular feedback (TGF) mechanism. In spontaneously hypertensive rats (SHR) the oscillations are replaced...

Integrin activation dynamics between the RGD-binding site and the headpiece hinge.

Science.gov (United States)

Puklin-Faucher, Eileen; Vogel, Viola

2009-12-25

Integrins form mechanical links between the extracellular matrix and the cytoskeleton. Although integrin activation is known to be regulated by an allosteric conformational change, which can be induced from the extracellular or intracellular end of the molecule, little is known regarding the sequence of structural events by which signals propagate between distant sites. Here, we reveal with molecular dynamics simulations of the FnIII(10)-bound alpha(V)beta(3) integrin headpiece how the binding pocket and interdomain betaA/hybrid domain hinge on the distal end of the betaA domain are allosterically linked via a hydrophobic T-junction between the middle of the alpha1 helix and top of the alpha7 helix. The key results of this study are: 1) that this T-junction is induced by ligand binding and hinge opening, and thus displays bidirectionality; 2) that formation of this junction can be accelerated by ligand-mediated force; and 3) how formation of this junction is inhibited by Ca(2+) in place of Mg(2+) at the site adjacent to the metal ion-dependent adhesion site ("ADMIDAS"). Together with recent experimental evidence that integrin complexes can form catch bonds (i.e. become strengthened under force), as well as earlier evidence that Ca(2+) at the ADMIDAS results in lower binding affinity, these simulations provide a common structural model for the dynamic process by which integrins become activated.

Instabilities and vortex dynamics in shear flow of magnetized plasmas

International Nuclear Information System (INIS)

Tajima, T.; Horton, W.; Morrison, P.J.; Schutkeker, J.; Kamimura, T.; Mima, K.; Abe, Y.

1990-03-01

Gradient-driven instabilities and the subsequent nonlinear evolution of generated vortices in sheared E x B flows are investigated for magnetized plasmas with and without gravity (magnetic curvature) and magnetic shear by using theory and implicit particle simulations. In the linear eigenmode analysis, the instabilities considered are the Kelvin-Helmholtz (K-H) instability and the resistive interchange instability. The presence of the shear flow can stabilize these instabilities. The dynamics of the K-H instability and the vortex dynamics can be uniformly described by the initial flow pattern with a vorticity localization parameter ε. The observed growth of the K-H modes is exponential in time for linearly unstable modes, secular for marginal mode, and absent until driven nonlinearly for linearly stable modes. The distance between two vortex centers experiences rapid merging while the angle θ between the axis of vortices and the external shear flow increases. These vortices proceed toward their overall coalescence, while shedding small-scale vortices and waves. The main features of vortex dynamics of the nonlinear coalescence and the tilt or the rotational instabilities of vortices are shown to be given by using a low dimension Hamiltonian representation for interacting vortex cores in the shear flow. 24 refs., 19 figs., 1 tab

Are international fund flows related to exchange rate dynamics?

NARCIS (Netherlands)

Li, Suxiao; de Haan, Jakob; Scholtens, Bert

2018-01-01

Employing monthly data for 53 countries between 1996 and 2015, we investigate the relationship between international fund flows and exchange rate dynamics. We find strong co-movement between funds flows (as measured with the EPFR Global data base) and bilateral real exchange rates vis-à-vis the USD.

Universal dynamics in the onset of a Hagen-Poiseuille flow

DEFF Research Database (Denmark)

Mortensen, Asger; Bruus, Henrik

2006-01-01

The dynamics in the onset of a Hagen-Poiseuille flow of an incompressible liquid in a channel of circular cross section is well-studied theoretically. We use an eigenfunction expansion in a Hilbert space formalism to generalize the results to channels of an arbitrary cross section. We find that t...... that the steady state is reached after a characteristic time scale tau=(A/P)(2)(1/nu), where A and P are the cross-sectional area and perimeter, respectively, and nu is the kinematic viscosity of the liquid. For the initial dynamics of the flow rate Q for t......The dynamics in the onset of a Hagen-Poiseuille flow of an incompressible liquid in a channel of circular cross section is well-studied theoretically. We use an eigenfunction expansion in a Hilbert space formalism to generalize the results to channels of an arbitrary cross section. We find...

Field flow fractionation for assessing neonatal Fc receptor and Fcγ receptor binding to monoclonal antibodies in solution.

Science.gov (United States)

Pollastrini, Joey; Dillon, Thomas M; Bondarenko, Pavel; Chou, Robert Y-T

2011-07-01

Analysis of the strength and stoichiometry of immunoglobulin G (IgG) binding to neonatal Fc receptor (FcRn) and Fcγ receptor (FcγR) is important for evaluating the pharmacokinetics and effector functions of therapeutic monoclonal antibody (mAb) products, respectively. The current standard for assessing FcγR and FcRn binding is composed of cell-based and surface plasmon resonance (SPR) assays. In this work, asymmetrical flow field flow fractionation (AF4) was evaluated to establish the true stoichiometry of IgG binding in solution. AF4 and liquid chromatography-mass spectrometry (LC-MS) were applied to directly observe IgG/FcγR and IgG/FcRn complexes, which were not observed using nonequilibrium size exclusion chromatography (SEC) analysis. Human serum albumin (HSA), an abundant component of human blood and capable of binding FcRn, was studied in combination with FcRn and IgG. AF4 demonstrated that the majority of large complexes of IgG/FcRn/HSA were at an approximate 1:2:1 molar ratio. In addition, affinity measurements of the complex were performed in the sub-micromolar affinity range. A significant decrease in binding was detected for IgG molecules with increased oxidation in the Fc region. AF4 was useful in detecting weak binding between full-length IgG/Fc fragments and Fc receptors and the effect of chemical modifications on binding. AF4 is a useful technique in the assessment of mAb product quality attributes. Copyright © 2011 Elsevier Inc. All rights reserved.

Traffic flow dynamics data, models and simulation

CERN Document Server

Treiber, Martin

2013-01-01

This textbook provides a comprehensive and instructive coverage of vehicular traffic flow dynamics and modeling. It makes this fascinating interdisciplinary topic, which to date was only documented in parts by specialized monographs, accessible to a broad readership. Numerous figures and problems with solutions help the reader to quickly understand and practice the presented concepts. This book is targeted at students of physics and traffic engineering and, more generally, also at students and professionals in computer science, mathematics, and interdisciplinary topics. It also offers material for project work in programming and simulation at college and university level. The main part, after presenting different categories of traffic data, is devoted to a mathematical description of the dynamics of traffic flow, covering macroscopic models which describe traffic in terms of density, as well as microscopic many-particle models in which each particle corresponds to a vehicle and its driver. Focus chapters on ...

Dynamic Transitions and Baroclinic Instability for 3D Continuously Stratified Boussinesq Flows

Science.gov (United States)

Şengül, Taylan; Wang, Shouhong

2018-02-01

The main objective of this article is to study the nonlinear stability and dynamic transitions of the basic (zonal) shear flows for the three-dimensional continuously stratified rotating Boussinesq model. The model equations are fundamental equations in geophysical fluid dynamics, and dynamics associated with their basic zonal shear flows play a crucial role in understanding many important geophysical fluid dynamical processes, such as the meridional overturning oceanic circulation and the geophysical baroclinic instability. In this paper, first we derive a threshold for the energy stability of the basic shear flow, and obtain a criterion for local nonlinear stability in terms of the critical horizontal wavenumbers and the system parameters such as the Froude number, the Rossby number, the Prandtl number and the strength of the shear flow. Next, we demonstrate that the system always undergoes a dynamic transition from the basic shear flow to either a spatiotemporal oscillatory pattern or circle of steady states, as the shear strength of the basic flow crosses a critical threshold. Also, we show that the dynamic transition can be either continuous or catastrophic, and is dictated by the sign of a transition number, fully characterizing the nonlinear interactions of different modes. Both the critical shear strength and the transition number are functions of the system parameters. A systematic numerical method is carried out to explore transition in different flow parameter regimes. In particular, our numerical investigations show the existence of a hypersurface which separates the parameter space into regions where the basic shear flow is stable and unstable. Numerical investigations also yield that the selection of horizontal wave indices is determined only by the aspect ratio of the box. We find that the system admits only critical eigenmodes with roll patterns aligned with the x-axis. Furthermore, numerically we encountered continuous transitions to multiple

A Dynamic Growth Model for Flows of Foreign Direct Investment

OpenAIRE

Yi-Hui Chiang; Yiming Li; Chih-Young Hung

2007-01-01

In this work, we for the first time study the dynamic flows of the foreign direct investment (FDI) with a dynamic growth theory. We define the FDI flow as a process which transmits throughout a given social system by way of diverse communication channels. In model formulation, seven assumptions are thus proposed and the foreign capital policy of the host country is considered as an external influence; in addition, the investment policy of the investing country is modeled as an internal influe...

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

International Nuclear Information System (INIS)

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

2004-01-01

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

Development of an advanced fluid-dynamic analysis code: α-flow

International Nuclear Information System (INIS)

Akiyama, Mamoru

1990-01-01

A Project for development of large scale three-dimensional fluid-dynamic analysis code, α-FLOW, coping with the recent advancement of supercomputers and workstations, has been in progress. This project is called the α-Project, which has been promoted by the Association for Large Scale Fluid Dynamics Analysis Code comprising private companies and research institutions such as universities. The developmental period for the α-FLOW is four years, March 1989 to March 1992. To date, the major portions of basic design and program preparation have been completed and the project is in the stage of testing each module. In this paper, the present status of the α-Project, design policy and outline of α-FLOW are described. (author)

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

African Journals Online (AJOL)

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

RECOGNITION DYNAMICS OF ESCHERICHIA COLI THIOREDOXIN PROBED USING MOLECULAR DYNAMICS AND BINDING FREE ENERGY CALCULATIONS

Directory of Open Access Journals (Sweden)

M. S. Shahul Hameed

2016-03-01

Full Text Available E. coli thioredoxin has been regarded as a hub protein as it interacts with, and regulates, numerous target proteins involved in a wide variety of cellular processes. Thioredoxin can form complexes with a variety of target proteins with a wide range of affinity, using a consensus binding surface. In this study an attempt to deduce the molecular basis for the observed multispecificity of E. coli thioredoxin has been made. In this manuscript it has been shown that structural plasticity, adaptable and exposed hydrophobic binding surface, surface electrostatics, closely clustered multiple hot spot residues and conformational changes brought about by the redox status of the protein have been shown to account for the observed multispecificity and molecular recognition of thioredoxin. Dynamical differences between the two redox forms of the enzyme have also been studied to account for their differing interactions with some target proteins.

Analysis of the flow dynamics characteristics of an axial piston pump based on the computational fluid dynamics method

Directory of Open Access Journals (Sweden)

Bin Zhang

2017-01-01

Full Text Available To improve its working performance, the flow ripple characteristics of an axial piston pump were investigated with software which uses computational fluid dynamics (CFD technology. The simulation accuracy was significantly optimized through the use of the improved compressible fluid model. Flow conditions of the pump were tested using a pump flow ripple test rig, and the simulation results of the CFD model showed good agreement with the experimental data. Additionally, the composition of the flow ripple was analyzed using the improved CFD model, and the results showed that the compression ripple makes up 88% of the flow ripple. The flow dynamics of the piston pump is mainly caused by the pressure difference between the intake and discharge ports of the valve plates and the fluid oil compressibility.

Edge Sheared Flows and Blob Dynamics

Energy Technology Data Exchange (ETDEWEB)

Myra, J.; D' Ippolito, D.; Russell, D., E-mail: jrmyra@lodestar.com [Lodestar Research Corporation, Boulder (United States); Davis, W. M.; Zweben, S. [Princeton Plasma Physics Laboratory, Princeton (United States); Terry, J.; LaBombard, B. [Massachusetts Institute of Technology, Cambridge (United States)

2012-09-15

Full text: A study of sheared flows in the edge and scrape-off layer (SOL) and their interaction with blob-filaments is presented. Edge sheared flows are believed to be important for the L-H, and H-L transitions. Blob generation and dynamics impacts both the (near-separatrix) scrape-off-layer (SOL) width critical for power handling in the divertor, and the interaction of plasma in the far SOL with plasma-facing components. These topics are critical for ITER and future devices. A fluid-based 2D curvature-interchange model embedded in the SOLT code is employed to study these issues. Sheared binormal flows both regulate the power flux crossing the separatrix and control the character of emitted turbulence structures such as blob-filaments. At a critical power level (depending on parameters) the laminar flows containing intermittent, but bound, structures give way to full-blown blob emissions signifying a transition from quasi-diffusive to convective transport. In order to diagnose sheared flows in experiments and assess their interaction with blobs, a blob-tracking algorithm has been developed and applied to both NSTX and Alcator C-Mod data. Blob motion and ellipticity can be affected by sheared flows, and are diagnosed and compared with seeded blob simulations. A picture of the interaction of blobs and sheared flows is emerging from advances in the theory and simulation of edge turbulence, combined with ever-improving capabilities for edge diagnostics and their analysis. (author)

Nonlinear Dynamics of Non-uniform Current-Vortex Sheets in Magnetohydrodynamic Flows

Science.gov (United States)

Matsuoka, C.; Nishihara, K.; Sano, T.

2017-04-01

A theoretical model is proposed to describe fully nonlinear dynamics of interfaces in two-dimensional MHD flows based on an idea of non-uniform current-vortex sheet. Application of vortex sheet model to MHD flows has a crucial difficulty because of non-conservative nature of magnetic tension. However, it is shown that when a magnetic field is initially parallel to an interface, the concept of vortex sheet can be extended to MHD flows (current-vortex sheet). Two-dimensional MHD flows are then described only by a one-dimensional Lagrange parameter on the sheet. It is also shown that bulk magnetic field and velocity can be calculated from their values on the sheet. The model is tested by MHD Richtmyer-Meshkov instability with sinusoidal vortex sheet strength. Two-dimensional ideal MHD simulations show that the nonlinear dynamics of a shocked interface with density stratification agrees fairly well with that for its corresponding potential flow. Numerical solutions of the model reproduce properly the results of the ideal MHD simulations, such as the roll-up of spike, exponential growth of magnetic field, and its saturation and oscillation. Nonlinear evolution of the interface is found to be determined by the Alfvén and Atwood numbers. Some of their dependence on the sheet dynamics and magnetic field amplification are discussed. It is shown by the model that the magnetic field amplification occurs locally associated with the nonlinear dynamics of the current-vortex sheet. We expect that our model can be applicable to a wide variety of MHD shear flows.

Flow dynamics and energy efficiency of flow in the left ventricle during myocardial infarction.

Science.gov (United States)

Vasudevan, Vivek; Low, Adriel Jia Jun; Annamalai, Sarayu Parimal; Sampath, Smita; Poh, Kian Keong; Totman, Teresa; Mazlan, Muhammad; Croft, Grace; Richards, A Mark; de Kleijn, Dominique P V; Chin, Chih-Liang; Yap, Choon Hwai

2017-10-01

Cardiovascular disease is a leading cause of death worldwide, where myocardial infarction (MI) is a major category. After infarction, the heart has difficulty providing sufficient energy for circulation, and thus, understanding the heart's energy efficiency is important. We induced MI in a porcine animal model via circumflex ligation and acquired multiple-slice cine magnetic resonance (MR) images in a longitudinal manner-before infarction, and 1 week (acute) and 4 weeks (chronic) after infarction. Computational fluid dynamic simulations were performed based on MR images to obtain detailed fluid dynamics and energy dynamics of the left ventricles. Results showed that energy efficiency flow through the heart decreased at the acute time point. Since the heart was observed to experience changes in heart rate, stroke volume and chamber size over the two post-infarction time points, simulations were performed to test the effect of each of the three parameters. Increasing heart rate and stroke volume were found to significantly decrease flow energy efficiency, but the effect of chamber size was inconsistent. Strong complex interplay was observed between the three parameters, necessitating the use of non-dimensional parameterization to characterize flow energy efficiency. The ratio of Reynolds to Strouhal number, which is a form of Womersley number, was found to be the most effective non-dimensional parameter to represent energy efficiency of flow in the heart. We believe that this non-dimensional number can be computed for clinical cases via ultrasound and hypothesize that it can serve as a biomarker for clinical evaluations.

Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells

DEFF Research Database (Denmark)

Pedersen, Natasja Wulff; Chandran, P. Anoop; Qian, Yu

2017-01-01

Manual analysis of flow cytometry data and subjective gate-border decisions taken by individuals continue to be a source of variation in the assessment of antigen-specific T cells when comparing data across laboratories, and also over time in individual labs. Therefore, strategies to provide...... automated analysis of major histocompatibility complex (MHC) multimer-binding T cells represent an attractive solution to decrease subjectivity and technical variation. The challenge of using an automated analysis approach is that MHC multimer-binding T cell populations are often rare and therefore...... laboratories. We used three different methods, FLOw Clustering without K (FLOCK), Scalable Weighted Iterative Flow-clustering Technique (SWIFT), and ReFlow to analyze flow cytometry data files from 28 laboratories. Each laboratory screened for antigen-responsive T cell populations with frequency ranging from 0...

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.

Integrin Activation Dynamics between the RGD-binding Site and the Headpiece Hinge*

Science.gov (United States)

Puklin-Faucher, Eileen; Vogel, Viola

2009-01-01

Integrins form mechanical links between the extracellular matrix and the cytoskeleton. Although integrin activation is known to be regulated by an allosteric conformational change, which can be induced from the extracellular or intracellular end of the molecule, little is known regarding the sequence of structural events by which signals propagate between distant sites. Here, we reveal with molecular dynamics simulations of the FnIII10-bound αVβ3 integrin headpiece how the binding pocket and interdomain βA/hybrid domain hinge on the distal end of the βA domain are allosterically linked via a hydrophobic T-junction between the middle of the α1 helix and top of the α7 helix. The key results of this study are: 1) that this T-junction is induced by ligand binding and hinge opening, and thus displays bidirectionality; 2) that formation of this junction can be accelerated by ligand-mediated force; and 3) how formation of this junction is inhibited by Ca2+ in place of Mg2+ at the site adjacent to the metal ion-dependent adhesion site (“ADMIDAS”). Together with recent experimental evidence that integrin complexes can form catch bonds (i.e. become strengthened under force), as well as earlier evidence that Ca2+ at the ADMIDAS results in lower binding affinity, these simulations provide a common structural model for the dynamic process by which integrins become activated. PMID:19762919

Non-linear dynamics and alternating 'flip' solutions in ferrofluidic Taylor-Couette flow

Science.gov (United States)

Altmeyer, Sebastian

2018-04-01

This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow - flow confined between two concentric independently rotating cylinders. We detected alternating 'flip' solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion.

Dynamic ADMM for Real-time Optimal Power Flow: Preprint

Energy Technology Data Exchange (ETDEWEB)

Dall-Anese, Emiliano [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

2018-02-23

This paper considers distribution networks featuring distributed energy resources (DERs), and develops a dynamic optimization method to maximize given operational objectives in real time while adhering to relevant network constraints. The design of the dynamic algorithm is based on suitable linearizations of the AC power flow equations, and it leverages the so-called alternating direction method of multipliers (ADMM). The steps of the ADMM, however, are suitably modified to accommodate appropriate measurements from the distribution network and the DERs. With the aid of these measurements, the resultant algorithm can enforce given operational constraints in spite of inaccuracies in the representation of the AC power flows, and it avoids ubiquitous metering to gather the state of non-controllable resources. Optimality and convergence of the propose algorithm are established in terms of tracking of the solution of a convex surrogate of the AC optimal power flow problem.

Dynamics of flexible fibers transported in confined viscous flows

Science.gov (United States)

Cappello, Jean; Duprat, Camille; Du Roure, Olivia; Nagel, Mathias; Gallaire, François; Lindner, Anke

2017-11-01

The dynamics of elongated objects has been extensively studied in unbounded media as for example the sedimentation of fibers at low Reynolds numbers. It has recently been shown that these transport dynamics are strongly modified by bounding walls. Here we focus on the dynamics of flexible fibers confined by the top and bottom walls of a microchannel and transported in pressure-driven flows. We combine well-controlled microfluidic experiments and simulations using modified Brinkmann equations. We control shape, orientation, and mechanical properties of our fibers using micro-fabrication techniques and in-situ characterization methods. These elastic fibers can be deformed by viscous and pressure forces leading to very rich transport dynamics coupling lateral drift with shape evolution. We show that the bending of a perpendicular fiber is proportional to an elasto-viscous number and we fully characterize the influence of the confinement on the deformation of the fiber. Experiments on parallel flexible fibers reveal the existence of a buckling threshold. The European Research Council is acknowledged for funding the work through a consolidator Grant (ERC PaDyFlow 682367).

CrossFlow: Cross-Organizational Workflow Management in Dynamic Virtual Enterprises

NARCIS (Netherlands)

Grefen, P.W.P.J.; Aberer, Karl; Hoffner, Yigal; Ludwig, Heiko

In this report, we present the approach to cross-organizational workflow management of the CrossFlow project. CrossFlow is a European research project aiming at the support of cross-organizational workflows in dynamic virtual enterprises. The cooperation in these virtual enterprises is based on

CrossFlow : cross-organizational workflow management in dynamic virtual enterprises

NARCIS (Netherlands)

Grefen, P.W.P.J.; Aberer, K.; Hoffner, Y.

2000-01-01

This paper gives a detailed overview of the approach to cross-organizational workflow management developed in the CrossFlow project. CrossFlow is a European research project aiming at the support of cross-organizational workflows in dynamic virtual enterprises. The cooperation in these virtual

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...

Multiphase flow dynamics 1 fundamentals

CERN Document Server

Kolev, Nikolay Ivanov

2015-01-01

In its fifth extended edition the successful monograph package “Multiphase Flow Dynamics” 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 obtained system of partial differential equations. Finally the analysis is repeated for boundary fitted curvilinear coordinate systems designing methods applicable for interconnected multi-blocks. This fifth edition includes various updates, extensions, improvements and corrections, as well as  a completely new chapter containing the basic physics describing the multi-phase flow in tu...

The Dynamics of the Impact of Past Performance on Mutual Fund Flows

NARCIS (Netherlands)

Goriaev, A.P.; Nijman, T.E.; Werker, B.J.M.

2002-01-01

This study reconsiders the determinants of flows into US growth funds, focusing in particular on the dynamics of the impact of past performance on flows.We model the flow-performance relationship at the monthly frequency, allowing for dependence of the sensitivity of flows to past performance on

Highly Specific Binding on Antifouling Zwitterionic Polymer-Coated Microbeads as Measured by Flow Cytometry.

Science.gov (United States)

van Andel, Esther; de Bus, Ian; Tijhaar, Edwin J; Smulders, Maarten M J; Savelkoul, Huub F J; Zuilhof, Han

2017-11-08

Micron- and nano-sized particles are extensively used in various biomedical applications. However, their performance is often drastically hampered by the nonspecific adsorption of biomolecules, a process called biofouling, which can cause false-positive and false-negative outcomes in diagnostic tests. Although antifouling coatings have been extensively studied on flat surfaces, their use on micro- and nanoparticles remains largely unexplored, despite the widespread experimental (specifically, clinical) uncertainties that arise because of biofouling. Here, we describe the preparation of magnetic micron-sized beads coated with zwitterionic sulfobetaine polymer brushes that display strong antifouling characteristics. These coated beads can then be equipped with recognition elements of choice, to enable the specific binding of target molecules. First, we present a proof of principle with biotin-functionalized beads that are able to specifically bind fluorescently labeled streptavidin from a complex mixture of serum proteins. Moreover, we show the versatility of the method by demonstrating that it is also possible to functionalize the beads with mannose moieties to specifically bind the carbohydrate-binding protein concanavalin A. Flow cytometry was used to show that thus-modified beads only bind specifically targeted proteins, with minimal/near-zero nonspecific protein adsorption from other proteins that are present. These antifouling zwitterionic polymer-coated beads, therefore, provide a significant advancement for the many bead-based diagnostic and other biosensing applications that require stringent antifouling conditions.

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

Flow dynamics around downwelling submarine canyons

Directory of Open Access Journals (Sweden)

J. M. Spurgin

2014-10-01

Full Text Available Flow dynamics around a downwelling submarine canyon were analysed with the Massachusetts Institute of Technology general circulation model. Blanes Canyon (northwestern Mediterranean was used for topographic and initial forcing conditions. Fourteen scenarios were modelled with varying forcing conditions. Rossby and Burger numbers were used to determine the significance of Coriolis acceleration and stratification (respectively and their impacts on flow dynamics. A new non-dimensional parameter (χ was introduced to determine the significance of vertical variations in stratification. Some simulations do see brief periods of upwards displacement of water during the 10-day model period; however, the presence of the submarine canyon is found to enhance downwards advection of density in all model scenarios. High Burger numbers lead to negative vorticity and a trapped anticyclonic eddy within the canyon, as well as an increased density anomaly. Low Burger numbers lead to positive vorticity, cyclonic circulation, and weaker density anomalies. Vertical variations in stratification affect zonal jet placement. Under the same forcing conditions, the zonal jet is pushed offshore in more uniformly stratified domains. The offshore jet location generates upwards density advection away from the canyon, while onshore jets generate downwards density advection everywhere within the model domain. Increasing Rossby values across the canyon axis, as well as decreasing Burger values, increase negative vertical flux at shelf break depth (150 m. Increasing Rossby numbers lead to stronger downwards advection of a passive tracer (nitrate, as well as stronger vorticity within the canyon. Results from previous studies are explained within this new dynamic framework.

Deterministic chaotic dynamics of Raba River flow (Polish Carpathian Mountains)

Science.gov (United States)

Kędra, Mariola

2014-02-01

Is the underlying dynamics of river flow random or deterministic? If it is deterministic, is it deterministic chaotic? This issue is still controversial. The application of several independent methods, techniques and tools for studying daily river flow data gives consistent, reliable and clear-cut results to the question. The outcomes point out that the investigated discharge dynamics is not random but deterministic. Moreover, the results completely confirm the nonlinear deterministic chaotic nature of the studied process. The research was conducted on daily discharge from two selected gauging stations of the mountain river in southern Poland, the Raba River.

Collective flow as a probe of heavy-ion reaction dynamics

International Nuclear Information System (INIS)

Awes, T.C.

1997-01-01

Collective flow of nuclear matter probes the dynamics of heavy-ion reactions and can provide information about the nuclear-matter equation of state. In particular, the incident energy dependences of collective flow may be a sensitive means to deduce the existence of a Quark Gluon Plasma phase in the equation of state. Collective flow measurements from 30 A MeV to 200 A GeV incident energies are briefly reviewed. Preliminary results on collective flow from the WA98 experiment at the CERN SPS are presented

Estimation of flow stress of radiation induced F/M steels using molecular dynamics and discrete dislocation dynamics approach

International Nuclear Information System (INIS)

More, Ameya; Dutta, B.K.; Durgaprasad, P.V.; Arya, A.K.

2012-01-01

Fe-Cr based Ferritic/Martensitic (F/M) steels are the candidate structural materials for future fusion reactors. In this work, a multi-scale approach comprising atomistic Molecular Dynamics (MD) simulations and Discrete Dislocation Dynamics (DDD) simulations are used to model the effect of irradiation dose on the flow stress of F/M steels. At the atomic scale, molecular dynamics simulations are used to study the dislocation interaction with irradiation induced defects, i.e. voids and He bubbles. Whereas, the DDD simulations are used to estimate the change in flow stress of the material as a result of irradiation hardening. (author)

Dynamics and Instabilities of Free Surface and Vortex Flows

DEFF Research Database (Denmark)

Tophøj, Laust Emil Hjerrild

2012-01-01

This PhD thesis consists of two main parts. The first part describes the dynamics of an ideal fluid on a stationary free surface of a given shape. It turns out that one can formulate a set of self-contained equations of momentum conservation for the tangential flow, with no reference to the flow ......)]. Finally, an experimental work on elastic collisions of wet spheres is briefly discussed....

Characterizing dynamic hysteresis and fractal statistics of chaotic two-phase flow and application to fuel cells

International Nuclear Information System (INIS)

Burkholder, Michael B.; Litster, Shawn

2016-01-01

In this study, we analyze the stability of two-phase flow regimes and their transitions using chaotic and fractal statistics, and we report new measurements of dynamic two-phase pressure drop hysteresis that is related to flow regime stability and channel water content. Two-phase flow dynamics are relevant to a variety of real-world systems, and quantifying transient two-phase flow phenomena is important for efficient design. We recorded two-phase (air and water) pressure drops and flow images in a microchannel under both steady and transient conditions. Using Lyapunov exponents and Hurst exponents to characterize the steady-state pressure fluctuations, we develop a new, measurable regime identification criteria based on the dynamic stability of the two-phase pressure signal. We also applied a new experimental technique by continuously cycling the air flow rate to study dynamic hysteresis in two-phase pressure drops, which is separate from steady-state hysteresis and can be used to understand two-phase flow development time scales. Using recorded images of the two-phase flow, we show that the capacitive dynamic hysteresis is related to channel water content and flow regime stability. The mixed-wettability microchannel and in-channel water introduction used in this study simulate a polymer electrolyte fuel cell cathode air flow channel.

Characterizing dynamic hysteresis and fractal statistics of chaotic two-phase flow and application to fuel cells

Energy Technology Data Exchange (ETDEWEB)

Burkholder, Michael B.; Litster, Shawn, E-mail: litster@andrew.cmu.edu [Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States)

2016-05-15

In this study, we analyze the stability of two-phase flow regimes and their transitions using chaotic and fractal statistics, and we report new measurements of dynamic two-phase pressure drop hysteresis that is related to flow regime stability and channel water content. Two-phase flow dynamics are relevant to a variety of real-world systems, and quantifying transient two-phase flow phenomena is important for efficient design. We recorded two-phase (air and water) pressure drops and flow images in a microchannel under both steady and transient conditions. Using Lyapunov exponents and Hurst exponents to characterize the steady-state pressure fluctuations, we develop a new, measurable regime identification criteria based on the dynamic stability of the two-phase pressure signal. We also applied a new experimental technique by continuously cycling the air flow rate to study dynamic hysteresis in two-phase pressure drops, which is separate from steady-state hysteresis and can be used to understand two-phase flow development time scales. Using recorded images of the two-phase flow, we show that the capacitive dynamic hysteresis is related to channel water content and flow regime stability. The mixed-wettability microchannel and in-channel water introduction used in this study simulate a polymer electrolyte fuel cell cathode air flow channel.

PASTA in Penicillin Binding Proteins and Serine/Threonine Kinases: A Recipe of Structural, Dynamic and Binding Properties.

Science.gov (United States)

Calvanese, Luisa; Falcigno, Lucia; Squeglia, Flavia; D'Auria, Gabriella; Berisio, Rita

2017-11-24

Penicillin binding proteins (PBPs) and Serine Threonine kinases (STPKs) are two classes of bacterial enzymes whose involvement in a series of vital processes in bacterial growth and division is well assessed. Many PBPs and STPKs show linked an ancillary domain named PASTA, whose functional role is not completely deciphered so far. It has been proposed that PASTAs are sensor modules that by binding opportune ligands (i.e. muropeptides) activate the cognate proteins to their functions. However, based on recent data, the sensor annotation sounds true for PASTA from STPKs, and false for PASTA from PBPs. Different PASTA domains, belonging or not to different protein classes, sharing or not appreciable sequence identities, always show identical folds. This survey of the structural, binding and dynamic properties of PASTA domains pursues the reasons why identical topologies may turn in different roles. Amino acid compositions, total charges and distribution of the hydrophobic/hydrophilic patches on the surface, significantly vary among PASTAs from STPKs and PBPs and appear to correlate with different functions. A possible criterion to discriminate between PASTA modules of STPKs or PBPs solely based on their sequences is proposed. Possibly reflecting different species as well as functional roles and evolutionary profile, our routine represents a fast even though approximate method to distinguish between PASTA belonging to different classes. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

On the evaluation of debris flows dynamics by means of mathematical models

Directory of Open Access Journals (Sweden)

M. Arattano

2003-01-01

Full Text Available The prediction of debris flow dynamic characteristics in a debris flow prone torrent is generally made through the investigation of past events. This investigation can be carried out through a survey of the marks left by past debris flows along the channel and through a detailed analysis of the type and shape of the deposits found on the debris fan. The rheological behaviour of future debris flows can then be inferred from the results of these surveys and their dynamic characteristics can be estimated applying well known formulas proposed in literature. These latter will make use of the assumptions on the rheological behaviour previously made. This type of estimation has been performed for a debris flow occurred in an instrumented basin, on the North-Eastern Italian Alps, in 1996 and the results have been compared to those obtained by means of a mathematical simulation. For the calibration of the mathematical model the limnographs recorded by three different ultrasonic gauges installed along a torrent reach on the fan were used. The comparison evidenced the importance of time data recordings for a correct prediction of the debris flows dynamics. Without the availability of data recordings, the application of formulas based only on assumptions derived from field analysis could be misleading.

Water Flow in Karst Aquifer Considering Dynamically Variable Saturation Conduit

Science.gov (United States)

Tan, Chaoqun; Hu, Bill X.

2017-04-01

The karst system is generally conceptualized as dual-porosity system, which is characterized by low conductivity and high storage continuum matrix and high conductivity and quick flow conduit networks. And so far, a common numerical model for simulating flow in karst aquifer is MODFLOW2005-CFP, which is released by USGS in 2008. However, the steady-state approach for conduit flow in CFP is physically impractical when simulating very dynamic hydraulics with variable saturation conduit. So, we adopt the method proposed by Reimann et al. (2011) to improve current model, in which Saint-Venant equations are used to model the flow in conduit. Considering the actual background that the conduit is very big and varies along flow path and the Dirichlet boundary varies with rainfall in our study area in Southwest China, we further investigate the influence of conduit diameter and outflow boundary on numerical model. And we also analyze the hydraulic process in multi-precipitation events. We find that the numerical model here corresponds well with CFP for saturated conduit, and it could depict the interaction between matrix and conduit during very dynamic hydraulics pretty well compare with CFP.

Dynamic flow control strategies of vehicle SCR Urea Dosing System

Science.gov (United States)

Lin, Wei; Zhang, Youtong; Asif, Malik

2015-03-01

Selective Catalyst Reduction(SCR) Urea Dosing System(UDS) directly affects the system accuracy and the dynamic response performance of a vehicle. However, the UDS dynamic response is hard to keep up with the changes of the engine's operating conditions. That will lead to low NO X conversion efficiency or NH3 slip. In order to optimize the injection accuracy and the response speed of the UDS in dynamic conditions, an advanced control strategy based on an air-assisted volumetric UDS is presented. It covers the methods of flow compensation and switching working conditions. The strategy is authenticated on an UDS and tested in different dynamic conditions. The result shows that the control strategy discussed results in higher dynamic accuracy and faster dynamic response speed of UDS. The inject deviation range is improved from being between -8% and 10% to -4% and 2% and became more stable than before, and the dynamic response time was shortened from 200 ms to 150 ms. The ETC cycle result shows that after using the new strategy the NH3 emission is reduced by 60%, and the NO X emission remains almost unchanged. The trade-off between NO X conversion efficiency and NH3 slip is mitigated. The studied flow compensation and switching working conditions can improve the dynamic performance of the UDS significantly and make the UDS dynamic response keep up with the changes of the engine's operating conditions quickly.

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

International Nuclear Information System (INIS)

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

2006-01-01

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

Dynamics of polymers in elongational flow studied by the neutron spin-echo technique

International Nuclear Information System (INIS)

Rheinstaedter, Maikel C.; Sattler, Rainer; Haeussler, Wolfgang; Wagner, Christian

2010-01-01

The nanoscale fluctuation dynamics of semidilute high molecular weight polymer solutions of polyethylenoxide (PEO) in D 2 O under non-equilibrium flow conditions were studied by the neutron spin-echo technique. The sample cell was in contraction flow geometry and provided a pressure driven flow with a high elongational component that stretched the polymers most efficiently. Neutron scattering experiments in dilute polymer solutions are challenging because of the low polymer concentration and corresponding small quasi-elastic signals. A relaxation process with relaxation times of about 10 ps was observed, which shows anisotropic dynamics with applied flow.

Chaos in a dynamic model of urban transportation network flow based on user equilibrium states

International Nuclear Information System (INIS)

Xu Meng; Gao Ziyou

2009-01-01

In this study, we investigate the dynamical behavior of network traffic flow. We first build a two-stage mathematical model to analyze the complex behavior of network flow, a dynamical model, which is based on the dynamical gravity model proposed by Dendrinos and Sonis [Dendrinos DS, Sonis M. Chaos and social-spatial dynamic. Berlin: Springer-Verlag; 1990] is used to estimate the number of trips. Considering the fact that the Origin-Destination (O-D) trip cost in the traffic network is hard to express as a functional form, in the second stage, the user equilibrium network assignment model was used to estimate the trip cost, which is the minimum cost of used path when user equilibrium (UE) conditions are satisfied. It is important to use UE to estimate the O-D cost, since a connection is built among link flow, path flow, and O-D flow. The dynamical model describes the variations of O-D flows over discrete time periods, such as each day and each week. It is shown that even in a system with dimensions equal to two, chaos phenomenon still exists. A 'Chaos Propagation' phenomenon is found in the given model.

DNA-magnetic Particle Binding Analysis by Dynamic and Electrophoretic Light Scattering.

Science.gov (United States)

Haddad, Yazan; Dostalova, Simona; Kudr, Jiri; Zitka, Ondrej; Heger, Zbynek; Adam, Vojtech

2017-11-09

Isolation of DNA using magnetic particles is a field of high importance in biotechnology and molecular biology research. This protocol describes the evaluation of DNA-magnetic particles binding via dynamic light scattering (DLS) and electrophoretic light scattering (ELS). Analysis by DLS provides valuable information on the physicochemical properties of particles including particle size, polydispersity, and zeta potential. The latter describes the surface charge of the particle which plays major role in electrostatic binding of materials such as DNA. Here, a comparative analysis exploits three chemical modifications of nanoparticles and microparticles and their effects on DNA binding and elution. Chemical modifications by branched polyethylenimine, tetraethyl orthosilicate and (3-aminopropyl)triethoxysilane are investigated. Since DNA exhibits a negative charge, it is expected that zeta potential of particle surface will decrease upon binding of DNA. Forming of clusters should also affect particle size. In order to investigate the efficiency of these particles in isolation and elution of DNA, the particles are mixed with DNA in low pH (~6), high ionic strength and dehydration environment. Particles are washed on magnet and then DNA is eluted by Tris-HCl buffer (pH = 8). DNA copy number is estimated using quantitative polymerase chain reaction (PCR). Zeta potential, particle size, polydispersity and quantitative PCR data are evaluated and compared. DLS is an insightful and supporting method of analysis that adds a new perspective to the process of screening of particles for DNA isolation.

Tokamak turbulence in self-regulated differentially rotating flow and L-H transition dynamics

International Nuclear Information System (INIS)

Terry, P.W.; Carreras, B.A.; Sidikman, K.

1992-01-01

An analytical study of turbulence in the presence of turbulently generated differentially rotating flow is presented as a paradigm for fluctuation dynamics in L- and H-mode plasmas. Using a drift wave model, the role of both flow shear and flow curvature (second radial derivative of the poloidal ExB flow) is detailed in linear and saturated turbulence phases. In the strong turbulence saturated state, finite amplitude-induced modification of the fluctuation structure near low order rational surfaces strongly inhibits flow shear suppression. Suppression by curvature is not diminished, but it occurs through a frequency shift. A description of L-H mode transition dynamics based on the self-consistent linking of turbulence suppression by differentially rotating flow and generation of flow by turbulent momentum transport is presented. In this model, rising edge temperature triggers a transition characterized by spontaneous generation of differentially rotating flow and decreasing turbulence intensity

Dynamic Factors Affecting Gaseous Ligand Binding in an Artificial Oxygen Transport Protein‡

Science.gov (United States)

Zhang, Lei; Andersen, Eskil M.E.; Khajo, Abdelahad; Magliozzo, Richard S.; Koder, Ronald L.

2013-01-01

We report the functional analysis of an artificial hexacoordinate oxygen transport protein, HP7, which operates via a mechanism similar to that of human neuroglobin and cytoglobin: the destabilization of one of two heme-ligating histidine residues. In the case of HP7 this is the result of the coupling of histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Here we compare gaseous ligand binding, including rates, affinities and oxyferrous state lifetimes, of both heme binding sites in HP7. We find that despite the identical sequence of helices in both binding sites, there are differences in oxygen affinity and oxyferrous state lifetime which may be the result of differences in the freedom of motion imposed by the candelabra fold on the two sites of the protein. We further examine the effect of mutational removal of the buried glutamates on function. Heme iron in the ferrous state of this mutant is rapidly oxidized when when exposed to oxygen. Compared to HP7, distal histidine affinity is increased by a 22-fold decrease in the histidine ligand off-rate. EPR comparison of these ferric hemoproteins demonstrates that the mutation increases disorder at the heme binding site. NMR-detected deuterium exchange demonstrates that the mutation greatly increases water penetration into the protein core. The inability of the mutant protein to bind oxygen may be due to increased water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors. Together these data underline the importance of the control of protein dynamics in the design of functional artificial proteins. PMID:23249163

Dynamically Partitionable Autoassociative Networks as a Solution to the Neural Binding Problem

Directory of Open Access Journals (Sweden)

Kenneth Jeffrey Hayworth

2012-09-01

Full Text Available An outstanding question in theoretical neuroscience is how the brain solves the neural binding problem. In vision, binding can be summarized as the ability to represent that certain properties belong to one object while other properties belong to a different object. I review the binding problem in visual and other domains, and review its simplest proposed solution – the anatomical binding hypothesis. This hypothesis has traditionally been rejected as a true solution because it seems to require a type of one-to-one wiring of neurons that would be impossible in a biological system (as opposed to an engineered system like a computer. I show that this requirement for one-to-one wiring can be loosened by carefully considering how the neural representation is actually put to use by the rest of the brain. This leads to a solution where a symbol is represented not as a particular pattern of neural activation but instead as a piece of a global stable attractor state. I introduce the Dynamically Partitionable AutoAssociative Network (DPAAN as an implementation of this solution and show how DPANNs can be used in systems which perform perceptual binding and in systems that implement syntax-sensitive rules. Finally I show how the core parts of the cognitive architecture ACT-R can be neurally implemented using a DPAAN as ACT-R’s global workspace. Because the DPAAN solution to the binding problem requires only ‘flat’ neural representations (as opposed to the phase encoded representation hypothesized in neural synchrony solutions it is directly compatible with the most well developed neural models of learning, memory, and pattern recognition.

Structure, dynamics and RNA binding of the multi-domain splicing factor TIA-1

Science.gov (United States)

Wang, Iren; Hennig, Janosch; Jagtap, Pravin Kumar Ankush; Sonntag, Miriam; Valcárcel, Juan; Sattler, Michael

2014-01-01

Alternative pre-messenger ribonucleic acid (pre-mRNA) splicing is an essential process in eukaryotic gene regulation. The T-cell intracellular antigen-1 (TIA-1) is an apoptosis-promoting factor that modulates alternative splicing of transcripts, including the pre-mRNA encoding the membrane receptor Fas. TIA-1 is a multi-domain ribonucleic acid (RNA) binding protein that recognizes poly-uridine tract RNA sequences to facilitate 5′ splice site recognition by the U1 small nuclear ribonucleoprotein (snRNP). Here, we characterize the RNA interaction and conformational dynamics of TIA-1 by nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC) and small angle X-ray scattering (SAXS). Our NMR-derived solution structure of TIA-1 RRM2–RRM3 (RRM2,3) reveals that RRM2 adopts a canonical RNA recognition motif (RRM) fold, while RRM3 is preceded by an non-canonical helix α0. NMR and SAXS data show that all three RRMs are largely independent structural modules in the absence of RNA, while RNA binding induces a compact arrangement. RRM2,3 binds to pyrimidine-rich FAS pre-mRNA or poly-uridine (U9) RNA with nanomolar affinities. RRM1 has little intrinsic RNA binding affinity and does not strongly contribute to RNA binding in the context of RRM1,2,3. Our data unravel the role of binding avidity and the contributions of the TIA-1 RRMs for recognition of pyrimidine-rich RNAs. PMID:24682828

Dynamic conformational change regulates the protein-DNA recognition: an investigation on binding of a Y-family polymerase to its target DNA.

Directory of Open Access Journals (Sweden)

Xiakun Chu

2014-09-01

Full Text Available Protein-DNA recognition is a central biological process that governs the life of cells. A protein will often undergo a conformational transition to form the functional complex with its target DNA. The protein conformational dynamics are expected to contribute to the stability and specificity of DNA recognition and therefore may control the functional activity of the protein-DNA complex. Understanding how the conformational dynamics influences the protein-DNA recognition is still challenging. Here, we developed a two-basin structure-based model to explore functional dynamics in Sulfolobus solfataricus DNA Y-family polymerase IV (DPO4 during its binding to DNA. With explicit consideration of non-specific and specific interactions between DPO4 and DNA, we found that DPO4-DNA recognition is comprised of first 3D diffusion, then a short-range adjustment sliding on DNA and finally specific binding. Interestingly, we found that DPO4 is under a conformational equilibrium between multiple states during the binding process and the distributions of the conformations vary at different binding stages. By modulating the strength of the electrostatic interactions, the flexibility of the linker, and the conformational dynamics in DPO4, we drew a clear picture on how DPO4 dynamically regulates the DNA recognition. We argue that the unique features of flexibility and conformational dynamics in DPO4-DNA recognition have direct implications for low-fidelity translesion DNA synthesis, most of which is found to be accomplished by the Y-family DNA polymerases. Our results help complete the description of the DNA synthesis process for the Y-family polymerases. Furthermore, the methods developed here can be widely applied for future investigations on how various proteins recognize and bind specific DNA substrates.

Vesicle dynamics in a confined Poiseuille flow: from steady state to chaos.

Science.gov (United States)

Aouane, Othmane; Thiébaud, Marine; Benyoussef, Abdelilah; Wagner, Christian; Misbah, Chaouqi

2014-09-01

Red blood cells (RBCs) are the major component of blood, and the flow of blood is dictated by that of RBCs. We employ vesicles, which consist of closed bilayer membranes enclosing a fluid, as a model system to study the behavior of RBCs under a confined Poiseuille flow. We extensively explore two main parameters: (i) the degree of confinement of vesicles within the channel and (ii) the flow strength. Rich and complex dynamics for vesicles are revealed, ranging from steady-state shapes (in the form of parachute and slipper shapes) to chaotic dynamics of shape. Chaos occurs through a cascade of multiple periodic oscillations of the vesicle shape. We summarize our results in a phase diagram in the parameter plane (degree of confinement and flow strength). This finding highlights the level of complexity of a flowing vesicle in the small Reynolds number where the flow is laminar in the absence of vesicles and can be rendered turbulent due to elasticity of vesicles.

Dynamics of nuclear fuel assemblies in vertical flow channels

International Nuclear Information System (INIS)

Mason, V.A.

1988-01-01

DYNMOD is a computer program designed to predict the dynamic behaviour of nuclear fuel assemblies in axial flow. The calculations performed by DYNMOD and the input data required by the program are described in this report. Examples of DYNMOD usage and a brief assessment of the accuracy of the dynamic model are also presented. It is intended that the report will be used as a reference manual by users of DYNMOD

Dynamics of renal blood flow autoregulation in rats

DEFF Research Database (Denmark)

Holstein-Rathlou, N H; Wagner, A J; Marsh, D J

1991-01-01

Two separate components could be resolved in tests of the dynamic autoregulation of renal blood flow. The slow component corresponds to the frequency at which spontaneous proximal tubular pressure oscillations are found, and are most likely due to the operation of the TGF. The high frequency...

Translanguaging as Dynamic Activity Flows in CLIL Classrooms

Science.gov (United States)

Lin, Angel M. Y.; He, Peichang

2017-01-01

In this article, the role of translanguaging in facilitating content and language integrated learning (CLIL) is examined in connection with the notion of academic language across the curriculum in multilingual contexts. Ethnographic naturalistic observations and interviews were conducted to analyse translanguaging in the dynamic flow of…

How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations.

Science.gov (United States)

Xu, Yechun; Shen, Jianhua; Luo, Xiaomin; Silman, Israel; Sussman, Joel L; Chen, Kaixian; Jiang, Hualiang

2003-09-17

The entering and leaving processes of Huperzine A (HupA) binding with the long active-site gorge of Torpedo californica acetylcholinesterase (TcAChE) have been investigated by using steered molecular dynamics simulations. The analysis of the force required along the pathway shows that it is easier for HupA to bind to the active site of AChE than to disassociate from it, which for the first time interprets at the atomic level the previous experimental result that unbinding process of HupA is much slower than its binding process to AChE. The direct hydrogen bonds, water bridges, and hydrophobic interactions were analyzed during two steered molecular dynamics (SMD) simulations. Break of the direct hydrogen bond needs a great pulling force. The steric hindrance of bottleneck might be the most important factor to produce the maximal rupture force for HupA to leave the binding site but it has a little effect on the binding process of HupA with AChE. Residue Asp72 forms a lot of water bridges with HupA leaving and entering the AChE binding gorge, acting as a clamp to take out HupA from or put HupA into the active site. The flip of the peptide bond between Gly117 and Gly118 has been detected during both the conventional MD and SMD simulations. The simulation results indicate that this flip phenomenon could be an intrinsic property of AChE and the Gly117-Gly118 peptide bond in both HupA bound and unbound AChE structures tends to adopt the native enzyme structure. At last, in a vacuum the rupture force is increased up to 1500 pN while in water solution the greatest rupture force is about 800 pN, which means water molecules in the binding gorge act as lubricant to facilitate HupA entering or leaving the binding gorge.

The Dynamics of Controlled Flow Separation within a Diverter Duct Diffuser

Science.gov (United States)

Peterson, C. J.; Vukasinovic, B.; Glezer, A.

2016-11-01

The evolution and receptivity to fluidic actuation of the flow separation within a rectangular, constant-width, diffuser that is branched off of a primary channel is investigated experimentally at speeds up to M = 0.4. The coupling between the diffuser's adverse pressure gradient and the internal separation that constricts nearly half of the flow passage through the duct is controlled using a spanwise array of fluidic actuators on the surface upstream of the diffuser's inlet plane. The dynamics of the separating surface vorticity layer in the absence and presence of actuation are investigated using high-speed particle image velocimetry combined with surface pressure measurements and total pressure distributions at the primary channel's exit plane. It is shown that the actuation significantly alters the incipient dynamics of the separating vorticity layer as the characteristic cross stream scales of the boundary layer upstream of separation and of the ensuing vorticity concentrations within the separated flow increase progressively with actuation level. It is argued that the dissipative (high frequency) actuation alters the balance between large- and small-scale motions near separation by intensifying the large-scale motions and limiting the small-scale dynamics. Controlling separation within the diffuser duct also has a profound effect on the global flow. In the presence of actuation, the mass flow rate in the primary duct increases 10% while the fraction of the diverted mass flow rate in the diffuser increases by more than 45% at 0.7% actuation mass fraction. Supported by the Boeing Company.

The role of ice dynamics in shaping vegetation in flowing waters.

Science.gov (United States)

Lind, Lovisa; Nilsson, Christer; Polvi, Lina E; Weber, Christine

2014-11-01

Ice dynamics is an important factor affecting vegetation in high-altitude and high-latitude streams and rivers. During the last few decades, knowledge about ice in streams and rivers has increased significantly and a respectable body of literature is now available. Here we review the literature on how ice dynamics influence riparian and aquatic vegetation. Traditionally, plant ecologists have focused their studies on the summer period, largely ignoring the fact that processes during winter also impact vegetation dynamics. For example, the freeze-up period in early winter may result in extensive formation of underwater ice that can restructure the channel, obstruct flow, and cause flooding and thus formation of more ice. In midwinter, slow-flowing reaches develop a surface-ice cover that accumulates snow, protecting habitats under the ice from formation of underwater ice but also reducing underwater light, thus suppressing photosynthesis. Towards the end of winter, ice breaks up and moves downstream. During this transport, ice floes can jam up and cause floods and major erosion. The magnitudes of the floods and their erosive power mainly depend on the size of the watercourse, also resulting in different degrees of disturbance to the vegetation. Vegetation responds both physically and physiologically to ice dynamics. Physical action involves the erosive force of moving ice and damage caused by ground frost, whereas physiological effects - mostly cell damage - happen as a result of plants freezing into the ice. On a community level, large magnitudes of ice dynamics seem to favour species richness, but can be detrimental for individual plants. Human impacts, such as flow regulation, channelisation, agriculturalisation and water pollution have modified ice dynamics; further changes are expected as a result of current and predicted future climate change. Human impacts and climate change can both favour and disfavour riverine vegetation dynamics. Restoration of streams

Modeling Day-to-day Flow Dynamics on Degradable Transport Network

Science.gov (United States)

Gao, Bo; Zhang, Ronghui; Lou, Xiaoming

2016-01-01

Stochastic link capacity degradations are common phenomena in transport network which can cause travel time variations and further can affect travelers’ daily route choice behaviors. This paper formulates a deterministic dynamic model, to capture the day-to-day (DTD) flow evolution process in the presence of degraded link capacity degradations. The aggregated network flow dynamics are driven by travelers’ study of uncertain travel time and their choice of risky routes. This paper applies the exponential-smoothing filter to describe travelers’ study of travel time variations, and meanwhile formulates risk attitude parameter updating equation to reflect travelers’ endogenous risk attitude evolution schema. In addition, this paper conducts theoretical analyses to investigate several significant mathematical characteristics implied in the proposed DTD model, including fixed point existence, uniqueness, stability and irreversibility. Numerical experiments are used to demonstrate the effectiveness of the DTD model and verify some important dynamic system properties. PMID:27959903

The Src SH2 domain interacts dynamically with the focal adhesion kinase binding site as demonstrated by paramagnetic NMR spectroscopy.

Science.gov (United States)

Lindfors, Hanna E; Drijfhout, Jan Wouter; Ubbink, Marcellus

2012-06-01

The interaction between the tyrosine kinases Src and focal adhesion kinase (FAK) is a key step in signaling processes from focal adhesions. The phosphorylated tyrosine residue 397 in FAK is able to bind the Src SH2 domain. To establish the extent of the FAK binding motif, the binding affinity of the SH2 domain for phosphorylated and unphosphorylated FAK-derived peptides of increasing length was determined and compared with that of the internal Src SH2 binding site. It is shown that the FAK peptides have higher affinity than the internal binding site and that seven negative residues adjacent to the core SH2 binding motif increase the binding constant 30-fold. A rigid spin-label incorporated in the FAK peptides was used to establish on the basis of paramagnetic relaxation enhancement whether the peptide-protein complex is well defined. A large spread of the paramagnetic effects on the surface of the SH2 domain suggests that the peptide-protein complex exhibits dynamics, despite the high affinity of the peptide. The strong electrostatic interaction between the positive side of the SH2 domain and the negative peptide results in a high affinity but may also favor a dynamic interaction. Copyright © 2012 Wiley Periodicals, Inc.

Dynamic factors affecting gaseous ligand binding in an artificial oxygen transport protein.

Science.gov (United States)

Zhang, Lei; Andersen, Eskil M E; Khajo, Abdelahad; Magliozzo, Richard S; Koder, Ronald L

2013-01-22

We report the functional analysis of an artificial hexacoordinate oxygen transport protein, HP7, which operates via a mechanism similar to that of human neuroglobin and cytoglobin: the destabilization of one of two heme-ligating histidine residues. In the case of HP7, this is the result of the coupling of histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Here we compare gaseous ligand binding, including rates, affinities, and oxyferrous state lifetimes, of both heme binding sites in HP7. We find that despite the identical sequence of helices in both binding sites, there are differences in oxygen affinity and oxyferrous state lifetime that may be the result of differences in the freedom of motion imposed by the candelabra fold on the two sites of the protein. We further examine the effect of mutational removal of the buried glutamates on function. Heme iron in the ferrous state of this mutant is rapidly oxidized when exposed to oxygen. Compared to that of HP7, the distal histidine affinity is increased by a 22-fold decrease in the histidine ligand off rate. Electron paramagnetic resonance comparison of these ferric hemoproteins demonstrates that the mutation increases the level of disorder at the heme binding site. Nuclear magnetic resonance-detected deuterium exchange demonstrates that the mutation greatly increases the degree of penetration of water into the protein core. The inability of the mutant protein to bind oxygen may be due to an increased level of water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors. Together, these data underline the importance of the control of protein dynamics in the design of functional artificial proteins.

Understanding binding affinity : A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

NARCIS (Netherlands)

Talhout, Reinskje; Villa, Alessandra; Mark, AE; Engberts, JBFN

2003-01-01

The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para

THE EFFECTS OF ACCRETION FLOW DYNAMICS ON THE BLACK HOLE SHADOW OF SAGITTARIUS A*

Energy Technology Data Exchange (ETDEWEB)

Pu, Hung-Yi; Asada, Keiichi [Institute of Astronomy and Astrophysics, Academia Sinica, 11F of Astronomy-Mathematics Building, AS/NTU No. 1, Taipei 10617, Taiwan (China); Akiyama, Kazunori [Massachusetts Institute of Technology, Haystack Observatory, Route 40, Westford, MA 01886 (United States)

2016-11-01

A radiatively inefficient accretion flow (RIAF), which is commonly characterized by its sub-Keplerian nature, is a favored accretion model for the supermassive black hole at the Galactic center, Sagittarius A*. To investigate the observable features of an RIAF, we compare the modeled shadow images, visibilities, and spectra of three flow models with dynamics characterized by (i) a Keplerian shell that is rigidly rotating outside the innermost stable circular orbit (ISCO) and infalling with a constant angular momentum inside ISCO, (ii) a sub-Keplerian motion, and (iii) a free-falling motion with zero angular momentum at infinity. At near-millimeter wavelengths, the emission is dominated by the flow within several Schwarzschild radii. The energy shift due to these flow dynamics becomes important and distinguishable, suggesting that the flow dynamics are an important model parameter for interpreting the millimeter/sub-millimeter very long baseline interferometric observations with the forthcoming, fully assembled Event Horizon Telescope (EHT). As an example, we demonstrate that structural variations of Sagittarius A* on event horizon-scales detected in previous EHT observations can be explained by the non-stationary dynamics of an RIAF.

Dynamics and rheology under continuous shear flow studied by x-ray photon correlation spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Fluerasu, Andrei [Brookhaven National Laboratory, NSLS-II, Upton, NY 11973 (United States); Kwasniewski, Pawel; Caronna, Chiara; Madsen, Anders [European Synchrotron Radiation Facility, ID10 (Troika), Grenoble 38043 (France); Destremaut, Fanny; Salmon, Jean-Baptiste [LOF, UMR 5258 CNRS-Rhodia Bordeaux 1, 33608 Pessac (France)], E-mail: fluerasu@bnl.gov

2010-03-15

X-ray photon correlation spectroscopy (XPCS) has emerged as a unique technique allowing the measurement of dynamics of materials on mesoscopic lengthscales. One of the most common problems associated with the use of bright x-ray beams is beam-induced radiation damage, and this is likely to become an even more limiting factor at future synchrotron and free-electron laser sources. Flowing the sample during data acquisition is one of the simplest methods allowing the radiation damage to be limited. In addition to distributing the dose over many different scatterers, the method also enables new functionalities such as time-resolved studies. Here, we further develop a recently proposed experimental technique that combines XPCS and continuously flowing samples. More specifically, we use a model colloidal suspension to show how the macroscopic advective response to flow and the microscopic dissipative dynamics (diffusion) can be quantified from the x-ray data. Our results show very good quantitative agreement with a Poisseuille-flow hydrodynamical model combined with Brownian mechanics. The method has many potential applications, e.g. in the study of dynamics of glasses and gels under continuous shear/flow, protein aggregation processes and the interplay between dynamics and rheology in complex fluids.

Mode decomposition and Lagrangian structures of the flow dynamics in orbitally shaken bioreactors

Science.gov (United States)

Weheliye, Weheliye Hashi; Cagney, Neil; Rodriguez, Gregorio; Micheletti, Martina; Ducci, Andrea

2018-03-01

In this study, two mode decomposition techniques were applied and compared to assess the flow dynamics in an orbital shaken bioreactor (OSB) of cylindrical geometry and flat bottom: proper orthogonal decomposition and dynamic mode decomposition. Particle Image Velocimetry (PIV) experiments were carried out for different operating conditions including fluid height, h, and shaker rotational speed, N. A detailed flow analysis is provided for conditions when the fluid and vessel motions are in-phase (Fr = 0.23) and out-of-phase (Fr = 0.47). PIV measurements in vertical and horizontal planes were combined to reconstruct low order models of the full 3D flow and to determine its Finite-Time Lyapunov Exponent (FTLE) within OSBs. The combined results from the mode decomposition and the FTLE fields provide a useful insight into the flow dynamics and Lagrangian coherent structures in OSBs and offer a valuable tool to optimise bioprocess design in terms of mixing and cell suspension.

Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

Science.gov (United States)

Brand, Luise H.; Fischer, Nina M.; Harter, Klaus; Kohlbacher, Oliver; Wanke, Dierk

2013-01-01

WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the ‘TTGACY’ W-box consensus. We speculated that the W-box consensus might be more degenerate and yet undetected differences in the W-box consensus of WRKYs of different evolutionary descent exist. The phylogenetic analysis of WRKY DBDs suggests that they evolved from an ancestral group IIc-like WRKY early in the eukaryote lineage. A direct descent of group IIc WRKYs supports a monophyletic origin of all other group II and III WRKYs from group I by loss of an N-terminal DBD. Group I WRKYs are of paraphyletic descent and evolved multiple times independently. By homology modeling, molecular dynamics simulations and in vitro DNA–protein interaction-enzyme-linked immunosorbent assay with AtWRKY50 (IIc), AtWRKY33 (I) and AtWRKY11 (IId) DBDs, we revealed differences in DNA-binding specificities. Our data imply that other components are essentially required besides the W-box-specific binding to DNA to facilitate a stimulus-specific WRKY function. PMID:23975197

Modeling dynamic stall on wind turbine blades under rotationally augmented flow fields

Energy Technology Data Exchange (ETDEWEB)

Guntur, S. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Schreck, S. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Sorensen, N. N. [Technical Univ. of Denmark, Lyngby (Denmark); Bergami, L. [Technical Univ. of Denmark, Lyngby (Denmark)

2015-04-22

It is well known that airfoils under unsteady flow conditions with a periodically varying angle of attack exhibit aerodynamic characteristics different from those under steady flow conditions, a phenomenon commonly known as dynamic stall. It is also well known that the steady aerodynamic characteristics of airfoils in the inboard region of a rotating blade differ from those under steady two-dimensional (2D) flow conditions, a phenomenon commonly known as rotational augmentation. This paper presents an investigation of these two phenomena together in the inboard parts of wind turbine blades. This analysis is carried out using data from three sources: (1) the National Renewable Energy Laboratory’s Unsteady Aerodynamics Experiment Phase VI experimental data, including constant as well as continuously pitching blade conditions during axial operation, (2) data from unsteady Delayed Detached Eddy Simulations (DDES) carried out using the Technical University of Denmark’s in-house flow solver Ellipsys3D, and (3) data from a simplified model based on the blade element momentum method with a dynamic stall subroutine that uses rotationally augmented steady-state polars obtained from steady Phase VI experimental sequences, instead of the traditional 2D nonrotating data. The aim of this work is twofold. First, the blade loads estimated by the DDES simulations are compared to three select cases of the N sequence experimental data, which serves as a validation of the DDES method. Results show reasonable agreement between the two data in two out of three cases studied. Second, the dynamic time series of the lift and the moment polars obtained from the experiments are compared to those from the dynamic stall subroutine that uses the rotationally augmented steady polars. This allowed the differences between the stall phenomenon on the inboard parts of harmonically pitching blades on a rotating wind turbine and the classic dynamic stall representation in 2D flow to be

Mimicking the Interfacial Dynamics of Flowing White Blood Cells

Science.gov (United States)

Santore, Maria

2015-03-01

The rolling of particles on surfaces, facilitated by hydrodynamic forces combined with localized surface interactions of the appropriate strengths, spatial arrangements, and ranges, is a technologically useful means of transporting and manipulating particles. One's intuition for the rolling of a marble or a car tire cannot be extrapolated down to microparticle length scales because the microparticle interactions are dominated by electrostatic, van der Waals, and hydrogen bonding interactions rather than a friction that depends on an imposed normal force. Indeed, our microparticle rolling systems are inspired by the rolling of white blood cells on the inner walls of venules as part of the innate immune response: Selectin molecules engage with their counterparts on the opposing surfaces to slow cell motion relative to that for freely flowing cells. In the resulting rolling signature, ligand-receptor binding and crack closing on the front of the cell are balanced with molecular dis-bonding and crack opening at the rear. The contact region is relatively static, allowing other interactions (for instance signaling) to occur for a finite duration. Thus, achieving particle rolling in synthetic systems is important because it facilitates particle-surface interactions in a continuous nonfouling fashion where the contact surface is continually renewed. In developing a synthetic model for this system, we employ polymers to modify flowing particles and /or planar collectors, producing heterogeneous interfaces which can support rolling or produce other motion signatures such as skipping, arrest, or free flow. We identify, in the synthetic system, combinations of variables that produce rolling and demonstrate how the distinction between rolling and arrest is not a simple matter of the adhesion strength between the particles and the collector. Rolling is a cooperative process and the coordination of binding in one location with dis-bonding in another requires appropriate length

Nuclear receptor ligand-binding domains: reduction of helix H12 dynamics to favour crystallization

Energy Technology Data Exchange (ETDEWEB)

Nahoum, Virginie; Lipski, Alexandra; Quillard, Fabien; Guichou, Jean-François [INSERM, U554, 34090 Montpellier (France); Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale (CBS), 34090 Montpellier (France); Boublik, Yvan [CNRS, UMR5237, Centre de Recherche de Biochimie Macromoléculaire (CRBM), 34293 Montpellier (France); Pérez, Efrèn [Universidade de Vigo, Departamento de Quimica Organica, Facultad de Química, 36310 Vigo (Spain); Germain, Pierre [Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), BP 10142, 67404 Illkirch CEDEX (France); Lera, Angel R. de [Universidade de Vigo, Departamento de Quimica Organica, Facultad de Química, 36310 Vigo (Spain); Bourguet, William, E-mail: bourguet@cbs.cnrs.fr [INSERM, U554, 34090 Montpellier (France); Université de Montpellier, CNRS, UMR5048, Centre de Biochimie Structurale (CBS), 34090 Montpellier (France)

2008-07-01

Attempts have been made to crystallize the ligand-binding domain of the human retinoid X receptor in complex with a variety of newly synthesized ligands. An inverse correlation was observed between the ‘crystallizability’ and the structural dynamics of the various receptor–ligand complexes. Crystallization trials of the human retinoid X receptor α ligand-binding domain (RXRα LBD) in complex with various ligands have been carried out. Using fluorescence anisotropy, it has been found that when compared with agonists these small-molecule effectors enhance the dynamics of the RXRα LBD C-terminal helix H12. In some cases, the mobility of this helix could be dramatically reduced by the addition of a 13-residue co-activator fragment (CoA). In keeping with these observations, crystals have been obtained of the corresponding ternary RXRα LBD–ligand–CoA complexes. In contrast, attempts to crystallize complexes with a highly mobile H12 remained unsuccessful. These experimental observations substantiate the previously recognized role of co-regulator fragments in facilitating the crystallization of nuclear receptor LBDs.

Two-dimensional fluid dynamics in a sharply bent channel: Laminar flow, separation bubble, and vortex dynamics

Science.gov (United States)

Matsumoto, Daichi; Fukudome, Koji; Wada, Hirofumi

2016-10-01

Understanding the hydrodynamic properties of fluid flow in a curving pipe and channel is important for controlling the flow behavior in technologies and biomechanics. The nature of the resulting flow in a bent pipe is extremely complicated because of the presence of a cross-stream secondary flow. In an attempt to disentangle this complexity, we investigate the fluid dynamics in a bent channel via the direct numerical simulation of the Navier-Stokes equation in two spatial dimensions. We exploit the absence of secondary flow from our model and systematically investigate the flow structure along the channel as a function of both the bend angle and Reynolds number of the laminar-to-turbulent regime. We numerically suggest a scaling relation between the shape of the separation bubble and the flow conductance, and construct an integrated phase diagram.

Lactose Binding Induces Opposing Dynamics Changes in Human Galectins Revealed by NMR-Based Hydrogen-Deuterium Exchange.

Science.gov (United States)

Chien, Chih-Ta Henry; Ho, Meng-Ru; Lin, Chung-Hung; Hsu, Shang-Te Danny

2017-08-16

Galectins are β-galactoside-binding proteins implicated in a myriad of biological functions. Despite their highly conserved carbohydrate binding motifs with essentially identical structures, their affinities for lactose, a common galectin inhibitor, vary significantly. Here, we aimed to examine the molecular basis of differential lactose affinities amongst galectins using solution-based techniques. Consistent dissociation constants of lactose binding were derived from nuclear magnetic resonance (NMR) spectroscopy, intrinsic tryptophan fluorescence, isothermal titration calorimetry and bio-layer interferometry for human galectin-1 (hGal1), galectin-7 (hGal7), and the N-terminal and C-terminal domains of galectin-8 (hGal8 NTD and hGal8 CTD , respectively). Furthermore, the dissociation rates of lactose binding were extracted from NMR lineshape analyses. Structural mapping of chemical shift perturbations revealed long-range perturbations upon lactose binding for hGal1 and hGal8 NTD . We further demonstrated using the NMR-based hydrogen-deuterium exchange (HDX) that lactose binding increases the exchange rates of residues located on the opposite side of the ligand-binding pocket for hGal1 and hGal8 NTD , indicative of allostery. Additionally, lactose binding induces significant stabilisation of hGal8 CTD across the entire domain. Our results suggested that lactose binding reduced the internal dynamics of hGal8 CTD on a very slow timescale (minutes and slower) at the expense of reduced binding affinity due to the unfavourable loss of conformational entropy.

Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein.

Science.gov (United States)

Bertaccini, Edward J; Lindahl, Erik; Sixma, Titia; Trudell, James R

2008-04-01

Recent crystal structures of the acetylcholine binding protein (AChBP) have revealed surprisingly small structural alterations upon ligand binding. Here we investigate the extent to which ligand binding may affect receptor dynamics. AChBP is a homologue of the extracellular component of ligand-gated ion channels (LGICs). We have previously used an elastic network normal-mode analysis to propose a gating mechanism for the LGICs and to suggest the effects of various ligands on such motions. However, the difficulties with elastic network methods lie in their inability to account for the modest effects of a small ligand or mutation on ion channel motion. Here, we report the successful application of an elastic network normal mode technique to measure the effects of large ligand binding on receptor dynamics. The present calculations demonstrate a clear alteration in the native symmetric motions of a protein due to the presence of large protein cobratoxin ligands. In particular, normal-mode analysis revealed that cobratoxin binding to this protein significantly dampened the axially symmetric motion of the AChBP that may be associated with channel gating in the full nAChR. The results suggest that alterations in receptor dynamics could be a general feature of ligand binding.

Visualization and PIV measurement of unsteady flow around a darrieus wind turbine in dynamic stall

Energy Technology Data Exchange (ETDEWEB)

Shibuya, Satoshi; Fujisawa, Nobuyuki; Takano, Tsuyoshi [Dept. of Mechanical and Production Engineering, Niigata Univ., Niigata (Japan)

1999-07-01

Flow around a Darrieus wind turbine in dynamic stall is studied by flow visualization and PIV (particle image velocimeter) measurement in a rotating frame of reference, which allows the successive observation of the dynamic stall over the blade. The qualitative features of the flow field in dynamic stall observed by the flow visualization, such as the formation and shedding of the stall vortices, are quantitatively reproduced in the instantaneous velocity distributions near the blade by using PIV. These results indicate that two pairs of stall vortices are generated from the blade during one rotation of the blade and that the size and the generating blade angle of the stall vortices are enlarged as the tip-speed ratio decreases. These stall vortices are produced by the in-flow motion from the outer surface to the inner surface through the trailing edge of the blade and the flow separation over the inner surface of the blade. (author)

Conformational dynamics and ligand binding in the multi-domain protein PDC109.

Directory of Open Access Journals (Sweden)

Hyun Jin Kim

2010-02-01

Full Text Available PDC109 is a modular multi-domain protein with two fibronectin type II (Fn2 repeats joined by a linker. It plays a major role in bull sperm binding to the oviductal epithelium through its interactions with phosphorylcholines (PhCs, a head group of sperm cell membrane lipids. The crystal structure of the PDC109-PhC complex shows that each PhC binds to the corresponding Fn2 domain, while the two domains are on the same face of the protein. Long timescale explicit solvent molecular dynamics (MD simulations of PDC109, in the presence and absence of PhC, suggest that PhC binding strongly correlates with the relative orientation of choline-phospholipid binding sites of the two Fn2 domains; unless the two domains tightly bind PhCs, they tend to change their relative orientation by deforming the flexible linker. The effective PDC109-PhC association constant of 28 M(-1, estimated from their potential of mean force is consistent with the experimental result. Principal component analysis of the long timescale MD simulations was compared to the significantly less expensive normal mode analysis of minimized structures. The comparison indicates that difference between relative domain motions of PDC109 with bound and unbound PhC is captured by the first principal component in the principal component analysis as well as the three lowest normal modes in the normal mode analysis. The present study illustrates the use of detailed MD simulations to clarify the energetics of specific ligand-domain interactions revealed by a static crystallographic model, as well as their influence on relative domain motions in a multi-domain protein.

PIV-measured versus CFD-predicted flow dynamics in anatomically realistic cerebral aneurysm models.

Science.gov (United States)

Ford, Matthew D; Nikolov, Hristo N; Milner, Jaques S; Lownie, Stephen P; Demont, Edwin M; Kalata, Wojciech; Loth, Francis; Holdsworth, David W; Steinman, David A

2008-04-01

Computational fluid dynamics (CFD) modeling of nominally patient-specific cerebral aneurysms is increasingly being used as a research tool to further understand the development, prognosis, and treatment of brain aneurysms. We have previously developed virtual angiography to indirectly validate CFD-predicted gross flow dynamics against the routinely acquired digital subtraction angiograms. Toward a more direct validation, here we compare detailed, CFD-predicted velocity fields against those measured using particle imaging velocimetry (PIV). Two anatomically realistic flow-through phantoms, one a giant internal carotid artery (ICA) aneurysm and the other a basilar artery (BA) tip aneurysm, were constructed of a clear silicone elastomer. The phantoms were placed within a computer-controlled flow loop, programed with representative flow rate waveforms. PIV images were collected on several anterior-posterior (AP) and lateral (LAT) planes. CFD simulations were then carried out using a well-validated, in-house solver, based on micro-CT reconstructions of the geometries of the flow-through phantoms and inlet/outlet boundary conditions derived from flow rates measured during the PIV experiments. PIV and CFD results from the central AP plane of the ICA aneurysm showed a large stable vortex throughout the cardiac cycle. Complex vortex dynamics, captured by PIV and CFD, persisted throughout the cardiac cycle on the central LAT plane. Velocity vector fields showed good overall agreement. For the BA, aneurysm agreement was more compelling, with both PIV and CFD similarly resolving the dynamics of counter-rotating vortices on both AP and LAT planes. Despite the imposition of periodic flow boundary conditions for the CFD simulations, cycle-to-cycle fluctuations were evident in the BA aneurysm simulations, which agreed well, in terms of both amplitudes and spatial distributions, with cycle-to-cycle fluctuations measured by PIV in the same geometry. The overall good agreement

Magnetic resonance velocity mapping of 3D cerebrospinal fluid flow dynamics in hydrocephalus: preliminary results

International Nuclear Information System (INIS)

Stadlbauer, Andreas; Salomonowitz, Erich; Brenneis, Christian; Ungersboeck, Karl; Riet, Wilma van der; Buchfelder, Michael; Ganslandt, Oliver

2012-01-01

To investigate the detectability of CSF flow alterations in the ventricular system of patients with hydrocephalus using time-resolved 3D MR velocity mapping. MR velocity mapping was performed in 21 consecutive hydrocephalus patients and 21 age-matched volunteers using a 3D phase-contrast (PC) sequence. Velocity vectors and particle path lines were calculated for visualisation of flow dynamics. CSF flow was classified as ''hypomotile flow'' if it showed attenuated dynamics and as ''hypermotile flow'' if it showed increased dynamics compared with volunteers. Diagnostic efficacy was compared with routine 2D cine PC-MRI. Seven patients showed hypomotile CSF flow: six had non-communicating hydrocephalus due to aqueductal stenosis. One showed oscillating flow between the lateral ventricles after craniotomy for intracranial haemorrhage. Seven patients showed normal flow: six had hydrocephalus ex vacuo due to brain atrophy. One patient who underwent ventriculostomy 10 years ago showed a flow path through the opening. Seven patients showed hypermotile flow: three had normal pressure hydrocephalus, three had dementia, and in one the diagnosis remained unclear. The diagnostic efficacy of velocity mapping was significantly higher except for that of aqueductal stenosis. Our approach may be useful for diagnosis, therapy planning, and follow-up of different kinds of hydrocephalus. (orig.)

Magnetic resonance velocity mapping of 3D cerebrospinal fluid flow dynamics in hydrocephalus: preliminary results

Energy Technology Data Exchange (ETDEWEB)

Stadlbauer, Andreas [Landesklinikum St. Poelten, MR Physics Group, Department of Radiology, St. Poelten (Austria); University of Erlangen-Nuremberg, Department of Neurosurgery, Erlangen (Germany); Salomonowitz, Erich [Landesklinikum St. Poelten, MR Physics Group, Department of Radiology, St. Poelten (Austria); Brenneis, Christian [Landesklinikum St. Poelten, Department of Neurology, St. Poelten (Austria); Ungersboeck, Karl [Landesklinikum St. Poelten, Department of Neurosurgery, St. Poelten (Austria); Riet, Wilma van der [European MRI Consultancy (EMRIC), Strasbourg (France); Buchfelder, Michael; Ganslandt, Oliver [University of Erlangen-Nuremberg, Department of Neurosurgery, Erlangen (Germany)

2012-01-15

To investigate the detectability of CSF flow alterations in the ventricular system of patients with hydrocephalus using time-resolved 3D MR velocity mapping. MR velocity mapping was performed in 21 consecutive hydrocephalus patients and 21 age-matched volunteers using a 3D phase-contrast (PC) sequence. Velocity vectors and particle path lines were calculated for visualisation of flow dynamics. CSF flow was classified as ''hypomotile flow'' if it showed attenuated dynamics and as ''hypermotile flow'' if it showed increased dynamics compared with volunteers. Diagnostic efficacy was compared with routine 2D cine PC-MRI. Seven patients showed hypomotile CSF flow: six had non-communicating hydrocephalus due to aqueductal stenosis. One showed oscillating flow between the lateral ventricles after craniotomy for intracranial haemorrhage. Seven patients showed normal flow: six had hydrocephalus ex vacuo due to brain atrophy. One patient who underwent ventriculostomy 10 years ago showed a flow path through the opening. Seven patients showed hypermotile flow: three had normal pressure hydrocephalus, three had dementia, and in one the diagnosis remained unclear. The diagnostic efficacy of velocity mapping was significantly higher except for that of aqueductal stenosis. Our approach may be useful for diagnosis, therapy planning, and follow-up of different kinds of hydrocephalus. (orig.)

Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Zeynab Mohammad Hosseini Naveh

Full Text Available Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP, a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD and Temperature Accelerated Molecular Dynamics (TAMD simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit.

Outlook of the world steel cycle based on the stock and flow dynamics.

Science.gov (United States)

Hatayama, Hiroki; Daigo, Ichiro; Matsuno, Yasunari; Adachi, Yoshihiro

2010-08-15

We present a comprehensive analysis of steel use in the future compiled using dynamic material flow analysis (MFA). A dynamic MFA for 42 countries depicted the global in-use stock and flow up to the end of 2005. On the basis of the transition of steel stock for 2005, the growth of future steel stock was then estimated considering the economic growth for every country. Future steel demand was estimated using dynamic analysis under the new concept of "stocks drive flows". The significant results follow. World steel stock reached 12.7 billion t in 2005, and has doubled in the last 25 years. The world stock in 2005 mainly consisted of construction (60%) and vehicles (10%). Stock in these end uses will reach 55 billion t in 2050, driven by a 10-fold increase in Asia. Steel demand will reach 1.8 billion t in 2025, then slightly decrease, and rise again by replacement of buildings. The forecast of demand clearly represents the industrial shift; at first the increase is dominated by construction, and then, after 2025, demand for construction decreases and demand for vehicles increases instead. This study thus provides the dynamic mechanism of steel stock and flow toward the future, which contributes to the design of sustainable steel use.

Partitioning dynamics of unsaturated flows in fractured porous media: Laboratory studies and three-dimensional multi-scale smoothed particle hydrodynamics simulations of gravity-driven flow in fractures

Science.gov (United States)

Kordilla, J.; Bresinsky, L. T.; Shigorina, E.; Noffz, T.; Dentz, M.; Sauter, M.; Tartakovsky, A. M.

2017-12-01

Preferential flow dynamics in unsaturated fractures remain a challenging topic on various scales. On pore- and fracture-scales the highly erratic gravity-driven flow dynamics often provoke a strong deviation from classical volume-effective approaches. Against the common notion that flow in fractures (or macropores) can only occur under equilibrium conditions, i.e., if the surrounding porous matrix is fully saturated and capillary pressures are high enough to allow filling of the fracture void space, arrival times suggest the existence of rapid preferential flow along fractures, fracture networks, and fault zones, even if the matrix is not fully saturated. Modeling such flows requires efficient numerical techniques to cover various flow-relevant physics, such as surface tension, static and dynamic contact angles, free-surface (multi-phase) interface dynamics, and formation of singularities. Here we demonstrate the importance of such flow modes on the partitioning dynamics at simple fracture intersections, with a combination of laboratory experiments, analytical solutions and numerical simulations using our newly developed massively parallel smoothed particle hydrodynamics (SPH) code. Flow modes heavily influence the "bypass" behavior of water flowing along a fracture junction. Flows favoring the formation of droplets exhibit a much stronger bypass capacity compared to rivulet flows, where nearly the whole fluid mass is initially stored within the horizontal fracture. This behavior is demonstrated for a multi-inlet laboratory setup where the inlet-specific flow rate is chosen so that either a droplet or rivulet flow persists. The effect of fluid buffering within the horizontal fracture is presented in terms of dimensionless fracture inflow so that characteristic scaling regimes can be recovered. For both cases (rivulets and droplets), flow within the horizontal fracture transitions into a Washburn regime until a critical threshold is reached and the bypass efficiency

Discrete Adjoint-Based Design Optimization of Unsteady Turbulent Flows on Dynamic Unstructured Grids

Science.gov (United States)

Nielsen, Eric J.; Diskin, Boris; Yamaleev, Nail K.

2009-01-01

An adjoint-based methodology for design optimization of unsteady turbulent flows on dynamic unstructured grids is described. The implementation relies on an existing unsteady three-dimensional unstructured grid solver capable of dynamic mesh simulations and discrete adjoint capabilities previously developed for steady flows. The discrete equations for the primal and adjoint systems are presented for the backward-difference family of time-integration schemes on both static and dynamic grids. The consistency of sensitivity derivatives is established via comparisons with complex-variable computations. The current work is believed to be the first verified implementation of an adjoint-based optimization methodology for the true time-dependent formulation of the Navier-Stokes equations in a practical computational code. Large-scale shape optimizations are demonstrated for turbulent flows over a tiltrotor geometry and a simulated aeroelastic motion of a fighter jet.

Prediction of flow- induced dynamic stress in an axial pump impeller using FEM

International Nuclear Information System (INIS)

Gao, J Y; Hou, Y S; Xi, S Z; Cai, Z H; Yao, P P; Shi, H L

2013-01-01

Axial pumps play an important role in water supply and flood control projects. Along with growing requirements for high reliability and large capacity, the dynamic stress of axial pumps has become a key problem. Unsteady flow is a significant reason which results structural dynamic stress of a pump. This paper reports on a flow-induced dynamic stress simulation in an axial pump impeller at three flow conditions by using FEM code. The pressure pulsation obtained from flow simulation using CFD code was set as the force boundary condition. The results show that the maximum stress of impeller appeared at joint between blade and root flange near trailing edge or joint between blade and root flange near leading edge. The dynamic stress of the two zones was investigated under three flow conditions (0.8Q d , 1.0Q d , 1.1Q d ) in time domain and frequency domain. The frequencies of stress at zones of maximum stress are 22.9Hz and 37.5Hz as the fundamental frequency and its harmonics. The fundamental frequencies are nearly equal to vane passing frequency (22.9 Hz) and 3 times blade passing frequency (37.5Hz). The first dominant frequency at zones of maximum stress is equal to the vane passing frequency due to rotor-stator interaction between the vane and the blade. This study would be helpful for axial pumps in reducing stress, improving structure design and fatigue life

Dynamic modeling of renal blood flow in Dahl hypertensive and normotensive rats

DEFF Research Database (Denmark)

Knudsen, Torben; Elmer, Henrik; Knudsen, Morten H

2004-01-01

A method is proposed in this paper which allows characterization of renal autoregulatory dynamics and efficiency using quantitative mathematical methods. Based on data from rat experiments, where arterial blood pressure and renal blood flow are measured, a quantitative model for renal blood flow...

Conformational Entropy of FK506 Binding to FKBP12 Determined by Nuclear Magnetic Resonance Relaxation and Molecular Dynamics Simulations.

Science.gov (United States)

Solomentsev, Gleb; Diehl, Carl; Akke, Mikael

2018-03-06

FKBP12 (FK506 binding protein 12 kDa) is an important drug target. Nuclear magnetic resonance (NMR) order parameters, describing amplitudes of motion on the pico- to nanosecond time scale, can provide estimates of changes in conformational entropy upon ligand binding. Here we report backbone and methyl-axis order parameters of the apo and FK506-bound forms of FKBP12, based on 15 N and 2 H NMR relaxation. Binding of FK506 to FKBP12 results in localized changes in order parameters, notably for the backbone of residues E54 and I56 and the side chains of I56, I90, and I91, all positioned in the binding site. The order parameters increase slightly upon FK506 binding, indicating an unfavorable entropic contribution to binding of TΔ S = -18 ± 2 kJ/mol at 293 K. Molecular dynamics simulations indicate a change in conformational entropy, associated with all dihedral angles, of TΔ S = -26 ± 9 kJ/mol. Both these values are significant compared to the total entropy of binding determined by isothermal titration calorimetry and referenced to a reactant concentration of 1 mM ( TΔ S = -29 ± 1 kJ/mol). Our results reveal subtle differences in the response to ligand binding compared to that of the previously studied rapamycin-FKBP12 complex, despite the high degree of structural homology between the two complexes and their nearly identical ligand-FKBP12 interactions. These results highlight the delicate dependence of protein dynamics on drug interactions, which goes beyond the view provided by static structures, and reinforce the notion that protein conformational entropy can make important contributions to the free energy of ligand binding.

Comparison of cerebral blood flow and metabolism to flumazenil binding potential in patients with hemodynamic ischemia

International Nuclear Information System (INIS)

Yukawa, Hirotsugu; Ogasawara, Kuniaki

2003-01-01

Because benzodiazepine receptors (BZR) are abundant in the cortex, an accumulation of 11 C-flumazenil which selectively bind to BZR may be useful as markers of neuron density. The aims of this study were to clarify the relationship between neuron density and cerebral oxygen metabolism and to investigate the usefulness of 11 C-flumazenil PET for detecting misery perfusion. The subjects were 16 patients with either internal carotid or middle cerebral arterial occlusive disease who underwent PET. Regional cerebral blood flow (CBF), regional cerebral oxygen extraction fraction (OEF), regional cerebral metabolic rate for oxygen (CMRO 2 ) and regional cerebrovascular reserve capacity (CVRC) to acetazolamide were calculated. After CBF study, flumazenil binding potential was measured using the [ 11 C] flumazenil bolus injection method. Forty-eight regions of interests (ROIs) were obtained in 16 patients. Flumazenil binding potential was correlated to CMRO 2 (r=0.337, p=0.0069), but in 7 of 48 ROIs, CMRO 2 decreased, whereas flumazenil binding potential did not change. Seventeen of 29 ROIs with decreased CVRC showed high OEF and the remaining 12 showed normal OEF. Flumazenil binding potential in ROIs with normal OEF was significantly lower than in those with high OEF (p=0.0003). This study demonstrated that 11 C-flumazenil PET is useful for detecting misery perfusion in patients with hemodynamic ischemia. (author)

DFTBaby: A software package for non-adiabatic molecular dynamics simulations based on long-range corrected tight-binding TD-DFT(B)

Science.gov (United States)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of tight-binding DFT. A long-range correction is incorporated to avoid spurious charge transfer states. Excited state energies, their analytic gradients and scalar non-adiabatic couplings are computed using tight-binding TD-DFT. These quantities are fed into a molecular dynamics code, which integrates Newton's equations of motion for the nuclei together with the electronic Schrödinger equation. Non-adiabatic effects are included by surface hopping. As an example, the program is applied to the optimization of excited states and non-adiabatic dynamics of polyfluorene. The python and Fortran source code is available at http://www.dftbaby.chemie.uni-wuerzburg.de.

Flow cytometry analysis of FITC-labeled concanavalin A binding to human blood cells as an indicator of radiation-induced membrane alterations

International Nuclear Information System (INIS)

Donnadieu-Claraz, M.; Paillole, N.; Voisin, P.

1995-01-01

The 3 H concanavalin-A binding to human blood cells have been described as a promising biological indicator of radiation overexposure. Flow cytometry adaptation of this technique using fluorescein-labelled concanavalin-A were performed to estimate time-dependent changes in binding on human blood cells membranes after in vitro γ irradiation ( 60 Co). Result revealed significant enhanced lectin-binding to platelets and erythrocytes in a dose range of 0,5-5 Gy, 1 and 3 hours after irradiation. However for both platelets and erythrocytes, it was impossible to discriminate between the different doses. Further studies are necessary to confirm the suitability of lectin-binding as a biological indicator for radiation dose assessment. (authors). 5 refs., 1 fig

Comparative molecular dynamics study of neuromyelitis optica-immunoglobulin G binding to aquaporin-4 extracellular domains.

Science.gov (United States)

Alberga, Domenico; Trisciuzzi, Daniela; Lattanzi, Gianluca; Bennett, Jeffrey L; Verkman, Alan S; Mangiatordi, Giuseppe Felice; Nicolotti, Orazio

2017-08-01

Neuromyelitis optica (NMO) is an inflammatory demyelinating disease of the central nervous system in which most patients have serum autoantibodies (called NMO-IgG) that bind to astrocyte water channel aquaporin-4 (AQP4). A potential therapeutic strategy in NMO is to block the interaction of NMO-IgG with AQP4. Building on recent observation that some single-point and compound mutations of the AQP4 extracellular loop C prevent NMO-IgG binding, we carried out comparative Molecular Dynamics (MD) investigations on three AQP4 mutants, TP 137-138 AA, N 153 Q and V 150 G, whose 295-ns long trajectories were compared to that of wild type human AQP4. A robust conclusion of our modeling is that loop C mutations affect the conformation of neighboring extracellular loop A, thereby interfering with NMO-IgG binding. Analysis of individual mutations suggested specific hydrogen bonding and other molecular interactions involved in AQP4-IgG binding to AQP4. Copyright © 2017 Elsevier B.V. All rights reserved.

Charging and Transport Dynamics of a Flow-Through Electrode Capacitive Deionization System.

Science.gov (United States)

Qu, Yatian; Campbell, Patrick G; Hemmatifar, Ali; Knipe, Jennifer M; Loeb, Colin K; Reidy, John J; Hubert, Mckenzie A; Stadermann, Michael; Santiago, Juan G

2018-01-11

We present a study of the interplay among electric charging rate, capacitance, salt removal, and mass transport in "flow-through electrode" capacitive deionization (CDI) systems. We develop two models describing coupled transport and electro-adsorption/desorption which capture salt removal dynamics. The first model is a simplified, unsteady zero-dimensional volume-averaged model which identifies dimensionless parameters and figures of merits associated with cell performance. The second model is a higher fidelity area-averaged model which captures both spatial and temporal responses of charging. We further conducted an experimental study of these dynamics and considered two salt transport regimes: (1) advection-limited regime and (2) dispersion-limited regime. We use these data to validate models. The study shows that, in the advection-limited regime, differential charge efficiency determines the salt adsorption at the early stage of the deionization process. Subsequently, charging transitions to a quasi-steady state where salt removal rate is proportional to applied current scaled by the inlet flow rate. In the dispersion-dominated regime, differential charge efficiency, cell volume, and diffusion rates govern adsorption dynamics and flow rate has little effect. In both regimes, the interplay among mass transport rate, differential charge efficiency, cell capacitance, and (electric) charging current governs salt removal in flow-through electrode CDI.

Computational fluid dynamics simulations of light water reactor flows

International Nuclear Information System (INIS)

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

1999-01-01

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

Dynamic characteristics of a perforated cylindrical shell for flow distribution in SMART

Energy Technology Data Exchange (ETDEWEB)

Lim, Seungho; Choi, Youngin; Ha, Kyungrok [Department of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749 (Korea, Republic of); Park, Kyoung-Su, E-mail: pks6348@yonsei.ac.kr [Department of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749 (Korea, Republic of); Park, No-Cheol; Park, Young-Pil [Department of Mechanical Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749 (Korea, Republic of); Jeong, Kyeong-Hoon; Park, Jin-Seok [Korea Atomic Energy Research Institute, 1045 Daedeokdaero, Yuseong, Daejeon 305-303 (Korea, Republic of)

2011-10-15

Highlights: > A 1/12 scaled-down flow skirt is manufactured and a modal test is performed. > A finite element model predicts the added mass effect of the perforated cylindrical shell. > Modal characteristics are extracted by considering the fluid-structure interaction. - Abstract: The System-integrated Modular Advanced ReacTor (SMART) is a small nuclear reactor under development in Korea. It is equipped with a perforated cylindrical shell, which is called a flow skirt, in the lower plenum of the reactor for uniform flow distribution and to prevent inflow of debris into the core. This perforated cylindrical shell can be excited by external forces such as seismic or pump pulsation loads. The dynamic characteristics of the perforated cylindrical shell must be identified for further dynamic analysis. This research explores the modal analysis of the scaled-down flow skirt model submerged in coolant water. For the numerical simulation, finite element analysis is carried out to extract modal characteristics of the structure considering the fluid-structure interaction and we introduce the NAVMI factor for similarity analysis. In the finite element model, the whole shape of the perforated cylindrical shell is simulated instead of using the effective material properties. In addition, a 1/12 scaled-down flow skirt is manufactured, and an experiment is designed using an exciter and waterproof accelerometers for the modal test. Due to excellent agreement between the modal test results and the finite element analysis results such as natural frequencies and mode shapes, the finite element model is validated and can be used to predict the dynamic characteristics of the real flow skirt. Moreover, the natural frequency of the real flow skirt can be calculated from the NAVMI factor and is in good agreement with the FEM result.

Quantifying Km-scale Hydrological Exchange Flows under Dynamic Flows and Their Influences on River Corridor Biogeochemistry

Science.gov (United States)

Chen, X.; Song, X.; Shuai, P.; Hammond, G. E.; Ren, H.; Zachara, J. M.

2017-12-01

Hydrologic exchange flows (HEFs) in rivers play vital roles in watershed ecological and biogeochemical functions due to their strong capacity to attenuate contaminants and process significant quantities of carbon and nutrients. While most of existing HEF studies focus on headwater systems with the assumption of steady-state flow, there is lack of understanding of large-scale HEFs in high-order regulated rivers that experience high-frequency stage fluctuations. The large variability of HEFs is a result of interactions between spatial heterogeneity in hydrogeologic properties and temporal variation in river discharge induced by natural or anthropogenic perturbations. Our 9-year spatially distributed dataset (water elevation, specific conductance, and temperature) combined with mechanistic hydrobiogeochemical simulations have revealed complex spatial and temporal dynamics in km-scale HEFs and their significant impacts on contaminant plume mobility and hyporheic biogeochemical processes along the Hanford Reach. Extended multidirectional flow behaviors of unconfined, river corridor groundwater were observed hundreds of meters inland from the river shore resulting from discharge-dependent HEFs. An appropriately sized modeling domain to capture the impact of regional groundwater flow as well as knowledge of subsurface structures controlling intra-aquifer hydrologic connectivity were essential to realistically model transient storage in this large-scale river corridor. This work showed that both river water and mobile groundwater contaminants could serve as effective tracers of HEFs, thus providing valuable information for evaluating and validating the HEF models. Multimodal residence time distributions with long tails were resulted from the mixture of long and short exchange pathways, which consequently impact the carbon and nutrient cycling within the river corridor. Improved understanding of HEFs using integrated observational and modeling approaches sheds light on

Millisecond dynamics in glutaredoxin during catalytic turnover is dependent on substrate binding and absent in the resting states

DEFF Research Database (Denmark)

Jensen, Kristine Steen; Winther, Jakob R; Teilum, Kaare

2011-01-01

to the glutathione exchange rate was observed for 23 residues. Binding of reduced glutathione resulted in competitive inhibition of the reduced enzyme having kinetics similar to that of the reaction. This observation couples the motions observed during catalysis directly to substrate binding. Backbone motions......Conformational dynamics is important for enzyme function. Which motions of enzymes determine catalytic efficiency and whether the same motions are important for all enzymes, however, are not well understood. Here we address conformational dynamics in glutaredoxin during catalytic turnover...... with a combination of NMR magnetization transfer, R(2) relaxation dispersion, and ligand titration experiments. Glutaredoxins catalyze a glutathione exchange reaction, forming a stable glutathinoylated enzyme intermediate. The equilibrium between the reduced state and the glutathionylated state was biochemically...

An autonomous dynamical system captures all LCSs in three-dimensional unsteady flows.

Science.gov (United States)

Oettinger, David; Haller, George

2016-10-01

Lagrangian coherent structures (LCSs) are material surfaces that shape the finite-time tracer patterns in flows with arbitrary time dependence. Depending on their deformation properties, elliptic and hyperbolic LCSs have been identified from different variational principles, solving different equations. Here we observe that, in three dimensions, initial positions of all variational LCSs are invariant manifolds of the same autonomous dynamical system, generated by the intermediate eigenvector field, ξ 2 (x 0 ), of the Cauchy-Green strain tensor. This ξ 2 -system allows for the detection of LCSs in any unsteady flow by classical methods, such as Poincaré maps, developed for autonomous dynamical systems. As examples, we consider both steady and time-aperiodic flows, and use their dual ξ 2 -system to uncover both hyperbolic and elliptic LCSs from a single computation.

Finite element simulation of dynamic wetting flows as an interface formation process

KAUST Repository

Sprittles, J.E.

2013-01-01

A mathematically challenging model of dynamic wetting as a process of interface formation has been, for the first time, fully incorporated into a numerical code based on the finite element method and applied, as a test case, to the problem of capillary rise. The motivation for this work comes from the fact that, as discovered experimentally more than a decade ago, the key variable in dynamic wetting flows - the dynamic contact angle - depends not just on the velocity of the three-phase contact line but on the entire flow field/geometry. Hence, to describe this effect, it becomes necessary to use the mathematical model that has this dependence as its integral part. A new physical effect, termed the \\'hydrodynamic resist to dynamic wetting\\', is discovered where the influence of the capillary\\'s radius on the dynamic contact angle, and hence on the global flow, is computed. The capabilities of the numerical framework are then demonstrated by comparing the results to experiments on the unsteady capillary rise, where excellent agreement is obtained. Practical recommendations on the spatial resolution required by the numerical scheme for a given set of non-dimensional similarity parameters are provided, and a comparison to asymptotic results available in limiting cases confirms that the code is converging to the correct solution. The appendix gives a user-friendly step-by-step guide specifying the entire implementation and allowing the reader to easily reproduce all presented results, including the benchmark calculations. © 2012 Elsevier Inc.

Improved dynamic CT angiography visualization by flow territory masking

Directory of Open Access Journals (Sweden)

Søren Christensen

2015-01-01

Full Text Available Backgound and Purpose: Computerized tomography (CT perfusion (or CTP source images from CT scanners with small detector widths can be used to create a dynamic CT angiogram (CTA similar to digital subtraction angiography (DSA. Because CTP studies use a single intravenous injection, all arterial territories enhance simultaneously, and individual arterial territories [i.e., anterior cerebral artery (ACA, middle cerebral artery (MCA, and posterior cerebral artery (PCA] cannot be delineated. This limits the ability to assess collateral flow patterns on dynamic CTAs. The aim of this study was to devise and test a postprocessing method to selectively color-label the major arterial territories on dynamic CTA. Materials and Methods: We identified 22 acute-stroke patients who underwent CTP on a 320-slice CT scanner within 6 h from symptom onset. For each case, two investigators independently generated an arterial territory map from CTP bolus arrival maps using a semiautomated method. The volumes of the arterial territories were calculated for each map and the average relative difference between these volumes was calculated for each case as a measure of interrater agreement. Arterial territory maps were superimposed on the dynamic CTA to create a vessel-selective dynamic CTA with color-coding of the main arterial territories. Two experts rated the arterial territory maps and the color-coded CTAs for consistency with expected arterial territories on a 3-point scale (excellent, moderate, poor. Results: Arterial territory maps were generated for all 22 patients. The median difference in arterial territory volumes between investigators was 2.2% [interquartile range (IQR 0.6-8.5%]. Based on expert review, the arterial territory maps and the vessel-selective dynamic CTAs showed excellent consistency with the expected arterial territories in 18 of 22 patients, moderate consistency in 2 patients, and poor consistency in another 2 patients. Conclusion: Using a

Low-angle dunes in the Changjiang (Yangtze) Estuary: Flow and sediment dynamics under tidal influence

Science.gov (United States)

Hu, Hao; Wei, Taoyuan; Yang, Zhongyong; Hackney, Christopher R.; Parsons, Daniel R.

2018-05-01

It has long been highlighted that important feedbacks exist between river bed morphology, sediment transport and the turbulent flow field and that these feedbacks change in response to forcing mechanisms. However, our current understanding of bedform dynamics is largely based on studies of steady flow environments and cohesionless bed conditions. Few investigations have been made under rapidly changing flows. Here, we examine flow and sediment dynamics over low-angle dunes in unsteady flows in the Changjiang (Yangtze) Estuary, China. Topography, flow and sediment data were collected over a reach ca 1.8 km long through a semi-diurnal tidal cycle in a moderate tide of flood season. The results show that: (1) roughness length derived from the upper flow changes little with the flow reversing and displays the same value on both the ebb and flood tide. Moreover, the variability of individual bedform features plays an important role in roughness length variation. (2) Shear stress over the crest of low-angle dunes roughly represents the total spatially averaged stress over dunes in this study area, which has significant implications for advancing numerical models. (3) Changes in morphology, flow and sediment dynamics over dunes through time reveal how low-angle dunes evolve within a tidal cycle. (4) The clockwise hysteresis loops between flow dynamics and bedform features (height and aspect ratio) are also observed. The combination of suspended sediment transport and bedload transport on dune transformation and migration attributes to the clockwise hysteresis. The specific sediment composition of the riverbed, in some extent, affects the mechanism of sediment transport related to the exchange between suspended sediment and riverbed, but further investigation is needed to figure out the mechanism behind this for extended series of tides, such as spring/neap tide and tides in flooding and dry season.

Computational fluid dynamics simulations of single-phase flow in a filter-press flow reactor having a stack of three cells

International Nuclear Information System (INIS)

Sandoval, Miguel A.; Fuentes, Rosalba; Walsh, Frank C.; Nava, José L.; Ponce de León, Carlos

2016-01-01

Highlights: • Computational fluid dynamic simulations in a filter-press stack of three cells. • The fluid velocity was different in each cell due to local turbulence. • The upper cell link pipe of the filter press cell acts as a fluid mixer. • The fluid behaviour tends towards a continuous mixing flow pattern. • Close agreement between simulations and experimental data was achieved. - Abstract: Computational fluid dynamics (CFD) simulations were carried out for single-phase flow in a pre-pilot filter press flow reactor with a stack of three cells. Velocity profiles and streamlines were obtained by solving the Reynolds-Averaged Navier-Stokes (RANS) equations with a standard k − ε turbulence model. The flow behaviour shows the appearance of jet flow at the entrance to each cell. At lengths from 12 to 15 cm along the cells channels, a plug flow pattern is developed at all mean linear flow rates studied here, 1.2 ≤ u ≤ 2.1 cm s −1 . The magnitude of the velocity profiles in each cell was different, due to the turbulence generated by the change of flow direction in the last fluid manifold. Residence time distribution (RTD) simulations indicated that the fluid behaviour tends towards a continuous mixing flow pattern, owing to flow at the output of each cell across the upper cell link pipe, which acts as a mixer. Close agreement between simulations and experimental RTD was obtained.

Estimation of vessel diameter and blood flow dynamics from laser speckle images

DEFF Research Database (Denmark)

Postnov, Dmitry D.; Tuchin, Valery V.; Sosnovtseva, Olga

2016-01-01

Laser speckle imaging is a rapidly developing method to study changes of blood velocity in the vascular networks. However, to assess blood flow and vascular responses it is crucial to measure vessel diameter in addition to blood velocity dynamics. We suggest an algorithm that allows for dynamical...

Dynamic Model for the Stocks and Release Flows of Engineered Nanomaterials.

Science.gov (United States)

Song, Runsheng; Qin, Yuwei; Suh, Sangwon; Keller, Arturo A

2017-11-07

Most existing life-cycle release models for engineered nanomaterials (ENM) are static, ignoring the dynamics of stock and flows of ENMs. Our model, nanoRelease, estimates the annual releases of ENMs from manufacturing, use, and disposal of a product explicitly taking stock and flow dynamics into account. Given the variabilities in key parameters (e.g., service life of products and annual release rate during use) nanoRelease is designed as a stochastic model. We apply nanoRelease to three ENMs (TiO 2 , SiO 2 and FeO x ) used in paints and coatings through seven product applications, including construction and building, household and furniture, and automotive for the period from 2000 to 2020 using production volume and market projection information. We also consider model uncertainties using Monte Carlo simulation. Compared with 2016, the total annual releases of ENMs in 2020 will increase by 34-40%, and the stock will increase by 28-34%. The fraction of the end-of-life release among total release flows will increase from 11% in 2002 to 43% in 2020. As compared to static models, our dynamic model predicts about an order of magnitude lower values for the amount of ENM released from this sector in the near-term while stock continues to build up in the system.

A note on the theory of fast money flow dynamics

Science.gov (United States)

Sokolov, A.; Kieu, T.; Melatos, A.

2010-08-01

The gauge theory of arbitrage was introduced by Ilinski in [K. Ilinski, preprint arXiv:hep-th/9710148 (1997)] and applied to fast money flows in [A. Ilinskaia, K. Ilinski, preprint arXiv:cond-mat/9902044 (1999); K. Ilinski, Physics of finance: gauge modelling in non-equilibrium pricing (Wiley, 2001)]. The theory of fast money flow dynamics attempts to model the evolution of currency exchange rates and stock prices on short, e.g. intra-day, time scales. It has been used to explain some of the heuristic trading rules, known as technical analysis, that are used by professional traders in the equity and foreign exchange markets. A critique of some of the underlying assumptions of the gauge theory of arbitrage was presented by Sornette in [D. Sornette, Int. J. Mod. Phys. C 9, 505 (1998)]. In this paper, we present a critique of the theory of fast money flow dynamics, which was not examined by Sornette. We demonstrate that the choice of the input parameters used in [K. Ilinski, Physics of finance: gauge modelling in non-equilibrium pricing (Wiley, 2001)] results in sinusoidal oscillations of the exchange rate, in conflict with the results presented in [K. Ilinski, Physics of finance: gauge modelling in non-equilibrium pricing (Wiley, 2001)]. We also find that the dynamics predicted by the theory are generally unstable in most realistic situations, with the exchange rate tending to zero or infinity exponentially.

Petrological Geodynamics of Mantle Melting II. AlphaMELTS + Multiphase Flow: Dynamic Fractional Melting

Science.gov (United States)

Tirone, Massimiliano

2018-03-01

In this second installment of a series that aims to investigate the dynamic interaction between the composition and abundance of the solid mantle and its melt products, the classic interpretation of fractional melting is extended to account for the dynamic nature of the process. A multiphase numerical flow model is coupled with the program AlphaMELTS, which provides at the moment possibly the most accurate petrological description of melting based on thermodynamic principles. The conceptual idea of this study is based on a description of the melting process taking place along a 1-D vertical ideal column where chemical equilibrium is assumed to apply in two local sub-systems separately on some spatial and temporal scale. The solid mantle belongs to a local sub-system (ss1) that does not interact chemically with the melt reservoir which forms a second sub-system (ss2). The local melt products are transferred in the melt sub-system ss2 where the melt phase eventually can also crystallize into a different solid assemblage and will evolve dynamically. The main difference with the usual interpretation of fractional melting is that melt is not arbitrarily and instantaneously extracted from the mantle, but instead remains a dynamic component of the model, hence the process is named dynamic fractional melting (DFM). Some of the conditions that may affect the DFM model are investigated in this study, in particular the effect of temperature, mantle velocity at the boundary of the mantle column. A comparison is made with the dynamic equilibrium melting (DEM) model discussed in the first installment. The implications of assuming passive flow or active flow are also considered to some extent. Complete data files of most of the DFM simulations, four animations and two new DEM simulations (passive/active flow) are available following the instructions in the supplementary material.

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.

Directory of Open Access Journals (Sweden)

Kota Kasahara

Full Text Available Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML, which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/.

Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes

Science.gov (United States)

Collepardo-Guevara, Rosana; Schlick, Tamar

2012-01-01

Monte Carlo simulations of a mesoscale model of oligonucleosomes are analyzed to examine the role of dynamic-linker histone (LH) binding/unbinding in high monovalent salt with divalent ions, and to further interpret noted chromatin fiber softening by dynamic LH in monovalent salt conditions. We find that divalent ions produce a fiber stiffening effect that competes with, but does not overshadow, the dramatic softening triggered by dynamic-LH behavior. Indeed, we find that in typical in vivo conditions, dynamic-LH binding/unbinding reduces fiber stiffening dramatically (by a factor of almost 5, as measured by the elasticity modulus) compared with rigidly fixed LH, and also the force needed to initiate chromatin unfolding, making it consistent with those of molecular motors. Our data also show that, during unfolding, divalent ions together with LHs induce linker-DNA bending and DNA–DNA repulsion screening, which guarantee formation of heteromorphic superbeads-on-a-string structures that combine regions of loose and compact fiber independently of the characteristics of the LH–core bond. These structures might be important for gene regulation as they expose regions of the DNA selectively. Dynamic control of LH binding/unbinding, either globally or locally, in the presence of divalent ions, might constitute a mechanism for regulation of gene expression. PMID:22790986

Reduction of gas flow nonuniformity in gas turbine engines by means of gas-dynamic methods

Science.gov (United States)

Matveev, V.; Baturin, O.; Kolmakova, D.; Popov, G.

2017-08-01

Gas flow nonuniformity is one of the main sources of rotor blade vibrations in the gas turbine engines. Usually, the flow circumferential nonuniformity occurs near the annular frames, located in the flow channel of the engine. This leads to the increased dynamic stresses in blades and as a consequence to the blade damage. The goal of the research was to find an acceptable method of reducing the level of gas flow nonuniformity as the source of dynamic stresses in the rotor blades. Two different methods were investigated during this research. Thus, this study gives the ideas about methods of improving the flow structure in gas turbine engine. On the basis of existing conditions (under development or existing engine) it allows the selection of the most suitable method for reducing gas flow nonuniformity.

Stability of Intelligent Transportation Network Dynamics: A Daily Path Flow Adjustment considering Travel Time Differentiation

Directory of Open Access Journals (Sweden)

Ming-Chorng Hwang

2015-01-01

Full Text Available A theoretic formulation on how traffic time information distributed by ITS operations influences the trajectory of network flows is presented in this paper. The interactions between users and ITS operator are decomposed into three parts: (i travel time induced path flow dynamics (PFDTT; (ii demand induced path flow dynamics (PFDD; and (iii predicted travel time dynamics for an origin-destination (OD pair (PTTDOD. PFDTT describes the collective results of user’s daily route selection by pairwise comparison of path travel time provided by ITS services. The other two components, PTTDOD and PFDD, are concentrated on the evolutions of system variables which are predicted and observed, respectively, by ITS operators to act as a benchmark in guiding the target system towards an expected status faster. In addition to the delivered modelings, the stability theorem of the equilibrium solution in the sense of Lyapunov stability is also provided. A Lyapunov function is developed and employed to the proof of stability theorem to show the asymptotic behavior of the aimed system. The information of network flow dynamics plays a key role in traffic control policy-making. The evaluation of ITS-based strategies will not be reasonable without a well-established modeling of network flow evolutions.

Analysis of liver blood flow by dynamic hepatic scintigraphy

International Nuclear Information System (INIS)

Xie Tianhao; Jia Shiquan

1996-01-01

Liver blood flow was studied in 45 patients with solitary malignant liver cancer, 17 patients with multiple liver metastases, 18 patients with benign liver tumor and 20 control subjects by dynamic hepatic scintigraphy. The hepatic perfusion index (HPI) in control subjects, patients with liver malignant cancer and benign tumor was 0.33 +- 0.069, 0.589 +- 0.084, 0.384 +-0.046 respectively, and the mesenteric fraction (MF) was 0.56 +- 0.054, 0.246 +- 0.064, 0.524 +- 0.086 respectively. In conclusion, flow scintigraphy is a non-invasive, sensitive and repeatable method for detection of liver tumor

Effect of short-chain branching on interfacial polymer structure and dynamics under shear flow.

Science.gov (United States)

Jeong, Sohdam; Kim, Jun Mo; Cho, Soowon; Baig, Chunggi

2017-11-22

We present a detailed analysis on the effect of short-chain branches on the structure and dynamics of interfacial chains using atomistic nonequilibrium molecular dynamics simulations of confined polyethylene melts in a wide range of shear rates. The intrinsically fast random motions of the short branches constantly disturb the overall chain conformation, leading to a more compact and less deformed chain structure of the short-chain branched (SCB) polymer against the imposed flow field in comparison with the corresponding linear polymer. Moreover, such highly mobile short branches along the backbone of the SCB polymer lead to relatively weaker out-of-plane wagging dynamics of interfacial chains, with highly curvy backbone structures in the intermediate flow regime. In conjunction with the contribution of short branches (as opposed to that of the backbone) to the total interfacial friction between the chains and the wall, the SCB polymer shows a nearly constant behavior in the degree of slip (d s ) with respect to shear rate in the weak-to-intermediate flow regimes. On the contrary, in the strong flow regime where irregular chain rotation and tumbling dynamics occur via intensive dynamical collisions between interfacial chains and the wall, an enhancement effect on the chain detachment from the wall, caused by short branches, leads to a steeper increase in d s for the SCB polymer than for the linear polymer. Remarkably, the SCB chains at the interface exhibit two distinct types of rolling mechanisms along the backbone, with a half-dumbbell mesoscopic structure at strong flow fields, in addition to the typical hairpin-like tumbling behavior displayed by the linear chains.

Increasing blood flow to exercising muscle attenuates systemic cardiovascular responses during dynamic exercise in humans.

Science.gov (United States)

Ichinose, Masashi; Ichinose-Kuwahara, Tomoko; Kondo, Narihiko; Nishiyasu, Takeshi

2015-11-15

Reducing blood flow to working muscles during dynamic exercise causes metabolites to accumulate within the active muscles and evokes systemic pressor responses. Whether a similar cardiovascular response is elicited with normal blood flow to exercising muscles during dynamic exercise remains unknown, however. To address that issue, we tested whether cardiovascular responses are affected by increases in blood flow to active muscles. Thirteen healthy subjects performed dynamic plantarflexion exercise for 12 min at 20%, 40%, and 60% of peak workload (EX20, EX40, and EX60) with their lower thigh enclosed in a negative pressure box. Under control conditions, the box pressure was the same as the ambient air pressure. Under negative pressure conditions, beginning 3 min after the start of the exercise, the box pressure was decreased by 20, 45, and then 70 mmHg in stepwise fashion with 3-min step durations. During EX20, the negative pressure had no effect on blood flow or the cardiovascular responses measured. However, application of negative pressure increased blood flow to the exercising leg during EX40 and EX60. This increase in blood flow had no significant effect on systemic cardiovascular responses during EX40, but it markedly attenuated the pressor responses otherwise seen during EX60. These results demonstrate that during mild exercise, normal blood flow to exercising muscle is not a factor eliciting cardiovascular responses, whereas it elicits an important pressor effect during moderate exercise. This suggests blood flow to exercising muscle is a major determinant of cardiovascular responses during dynamic exercise at higher than moderate intensity. Copyright © 2015 the American Physiological Society.

Nephron blood flow dynamics measured by laser speckle contrast imaging

DEFF Research Database (Denmark)

von Holstein-Rathlou, Niels-Henrik; Sosnovtseva, Olga V; Pavlov, Alexey N

2011-01-01

Tubuloglomerular feedback (TGF) has an important role in autoregulation of renal blood flow and glomerular filtration rate (GFR). Because of the characteristics of signal transmission in the feedback loop, the TGF undergoes self-sustained oscillations in single-nephron blood flow, GFR, and tubular...... simultaneously. The interacting nephron fields are likely to be more extensive. We have turned to laser speckle contrast imaging to measure the blood flow dynamics of 50-100 nephrons simultaneously on the renal surface of anesthetized rats. We report the application of this method and describe analytic...... pressure and flow. Nephrons interact by exchanging electrical signals conducted electrotonically through cells of the vascular wall, leading to synchronization of the TGF-mediated oscillations. Experimental studies of these interactions have been limited to observations on two or at most three nephrons...

Flow vibrations and dynamic instability of heat exchanger tube bundles

International Nuclear Information System (INIS)

Granger, S.; Langre, E. de

1995-01-01

This paper presents a review of external-flow-induced vibration of heat exchanger tube bundles. Attention is focused on a dynamic instability, known as ''fluidelastic instability'', which can develop when flow is transverse to the tube axis. The main physical models proposed in the literature are successively reviewed in a critical way. As a consequence, some concepts are clarified, some a priori plausible misinterpretations are rejected and finally, certain basic mechanisms, induced by the flow-structure interaction and responsible for the ultimate onset of fluidelastic instability, are elucidated. Design tools and methods for predictive analysis of industrial cases are then presented. The usual design tool is the ''stability map'', i.e. an empirical correlation which must be interpreted in a conservative way. Of course, when using this approach, the designer must also consider reasonable safety margins. In the area of predictive analysis, the ''unsteady semi-analytical models'' seem to be a promising and efficient methodology. A modern implementation of these ideas mix an original experimental approach for taking fluid dynamic forces into account, together with non-classical numerical methods of mechanical vibration. (authors). 20 refs., 9 figs

Coarse-grained debris flow dynamics on erodible beds

Science.gov (United States)

Lanzoni, Stefano; Gregoretti, Carlo; Stancanelli, Laura Maria

2017-03-01

A systematic set of flume experiments is used to investigate the features of velocity profiles within the body of coarse-grained debris flows and the dependence of the transport sediment concentration on the relevant parameters (runoff discharge, bed slope, grain size, and form). The flows are generated in a 10 m long laboratory flume, initially filled with a layer consisting of loose debris. After saturation, a prescribed water discharge is suddenly supplied over the granular bed, and the runoff triggers a debris flow wave that reaches nearly steady conditions. Three types of material have been used in the tests: gravel with mean grain size of 3 and 5 mm, and 3 mm glass spheres. Measured parameters included: triggering water discharge, volumetric sediment discharge, sediment concentration, flow depth, and velocity profiles. The dynamic similarity with full-sized debris flows is discussed on the basis of the relevant dimensionless parameters. Concentration data highlight the dependence on the slope angle and the importance of the quasi-static friction angle. The effects of flow rheology on the shape of velocity profiles are analyzed with attention to the role of different stress-generating mechanisms. A remarkable collapse of the dimensionless profiles is obtained by scaling the debris flow velocity with the runoff velocity, and a power law characterization is proposed following a heuristic approach. The shape of the profiles suggests a smooth transition between the different rheological regimes (collisional and frictional) that establish in the upper and lower regions of the flow and is compatible with the presence of multiple length scales dictated by the type of contacts (instantaneous or long lasting) between grains.

Computational modeling of lava domes using particle dynamics to investigate the effect of conduit flow mechanics on flow patterns

Science.gov (United States)

Husain, Taha Murtuza

Large (1--4 x 106 m3) to major (> 4 x 106 m3) dome collapses for andesitic lava domes such as Soufriere Hills Volcano, Montserrat are observed for elevated magma discharge rates (6--13 m3/s). The gas rich magma pulses lead to pressure build up in the lava dome that result in structural failure of the over steepened canyon-like walls which may lead to rockfall or pyroclastic flow. This indicates that dome collapse intimately related to magma extrusion rate. Variation in magma extrusion rate for open-system magma chambers is observed to follow alternating periods of high and low activity. Periodic behavior of magma exhibits a rich diversity in the nature of its eruptive history due to variation in magma chamber size, total crystal content, linear crystal growth rate and magma replenishment rate. Distinguished patterns of growth were observed at different magma flow rates ranging from endogenous to exogenous dome growth for magma with varying strengths. Determining the key parameters that control the transition in flow pattern of the magma during its lava dome building eruption is the main focus. This dissertation examines the mechanical effects on the morphology of the evolving lava dome on the extrusion of magma from a central vent using a 2D particle dynamics model. The particle dynamics model is coupled with a conduit flow model that incorporates the kinetics of crystallization and rheological stiffening to investigate important mechanisms during lava dome building eruptions. Chapter I of this dissertation explores lava dome growth and failure mechanics using a two-dimensional particle-dynamics model. The model follows the evolution of fractured lava, with solidification driven by degassing induced crystallization of magma. The particle-dynamics model emulates the natural development of dome growth and rearrangement of the lava dome which is difficult in mesh-based analyses due to mesh entanglement effects. The deformable talus evolves naturally as a frictional

Experimental study of poloidal flow effect on magnetic island dynamics in LHD and TJ-II

International Nuclear Information System (INIS)

Narushima, Y.; Sakakibara, S.; Castejon, F.

2010-11-01

The dynamics of a magnetic island are studied by focusing on the poloidal flows in the helical devices LHD and TJ-II. The temporal increment of the ExB poloidal flow prior to the magnetic island transition from growth to healing is observed. The direction of the poloidal flow is in the electron-diamagnetic direction in LHD and in the ion-diamagnetic direction in TJ-II. From the magnetic diagnostics, it is observed that a current structure flowing in the plasma moves ∼π rad poloidally in the electron-diamagnetic direction during the transition in LHD experiments. These experimental observations from LHD and TJ-II show that the temporal increment of the poloidal flow is followed by the transition (growth to healing) of the magnetic island regardless of the flow direction and clarify the fact that significant poloidal flow affects the magnetic island dynamics. (author)

Functionalized Magnetic Resonance Contrast Agent Selectively Binds to Glycoprotein IIb/IIIa on Activated Human Platelets under Flow Conditions and Is Detectable at Clinically Relevant Field Strengths

Directory of Open Access Journals (Sweden)

Constantin von zur Mühlen

2008-03-01

Full Text Available Recent progress in molecular magnetic resonance imaging (MRI provides the opportunity to image cells and cellular receptors using microparticles of iron oxide (MPIOs. However, imaging targets on vessel walls remains challenging owing to the quantity of contrast agents delivered to areas of interest under shear stress conditions. We evaluated ex vivo binding characteristics of a functional MRI contrast agent to ligand-induced binding sites (LIBSs on activated glycoprotein IIb/IIIa receptors of human platelets, which were lining rupture-prone atherosclerotic plaques and could therefore facilitate detection of platelet-mediated pathology in atherothrombotic disease. MPIOs were conjugated to anti-LIBS single-chain antibodies (LIBS-MPIO or control antibodies (control MPIO. Ex vivo binding to human platelet-rich clots in a dose-dependent manner was confirmed on a 3 T clinical MRI scanner and by histology (p < .05 for LIBS-MPIO vs control MPIO. By using a flow chamber setup, significant binding of LIBS-MPIO to a platelet matrix was observed under venous and arterial flow conditions, but not for control MPIO (p < .001. A newly generated MRI contrast agent detects activated human platelets at clinically relevant magnetic field strengths and binds to platelets under venous and arterial flow conditions, conveying high payloads of contrast to specific molecular targets. This may provide the opportunity to identify vulnerable, rupture-prone atherosclerotic plaques via noninvasive MRI.

Modeling dynamic stall on wind turbine blades under rotationally augmented flow fields

DEFF Research Database (Denmark)

Guntur, Srinivas; Sørensen, Niels N.; Schreck, Scott

2016-01-01

a reduced order dynamic stall model that uses rotationally augmented steady-state polars obtained from steady Phase VI experimental sequences, instead of the traditional two-dimensional, non-rotating data. The aim of this work is twofold. First, the blade loads estimated by the DDES simulations are compared...... Experiment Phase VI experimental data, including constant as well as continuously pitching blade conditions during axial operation; (2) data from unsteady delayed detached eddy simulations (DDES) carried out using the Technical University of Denmark’s in-house flow solver Ellipsys3D; and (3) data from...... with those from the dynamic stall model. This allowed the differences between the stall phenomenon on the inboard parts of harmonically pitching blades on a rotating wind turbine and the classic dynamic stall representation in two-dimensional flow to be investigated. Results indicated a good qualitative...

Dynamic Flow Management Problems in Air Transportation

Science.gov (United States)

Patterson, Sarah Stock

1997-01-01

In 1995, over six hundred thousand licensed pilots flew nearly thirty-five million flights into over eighteen thousand U.S. airports, logging more than 519 billion passenger miles. Since demand for air travel has increased by more than 50% in the last decade while capacity has stagnated, congestion is a problem of undeniable practical significance. In this thesis, we will develop optimization techniques that reduce the impact of congestion on the national airspace. We start by determining the optimal release times for flights into the airspace and the optimal speed adjustment while airborne taking into account the capacitated airspace. This is called the Air Traffic Flow Management Problem (TFMP). We address the complexity, showing that it is NP-hard. We build an integer programming formulation that is quite strong as some of the proposed inequalities are facet defining for the convex hull of solutions. For practical problems, the solutions of the LP relaxation of the TFMP are very often integral. In essence, we reduce the problem to efficiently solving large scale linear programming problems. Thus, the computation times are reasonably small for large scale, practical problems involving thousands of flights. Next, we address the problem of determining how to reroute aircraft in the airspace system when faced with dynamically changing weather conditions. This is called the Air Traffic Flow Management Rerouting Problem (TFMRP) We present an integrated mathematical programming approach for the TFMRP, which utilizes several methodologies, in order to minimize delay costs. In order to address the high dimensionality, we present an aggregate model, in which we formulate the TFMRP as a multicommodity, integer, dynamic network flow problem with certain side constraints. Using Lagrangian relaxation, we generate aggregate flows that are decomposed into a collection of flight paths using a randomized rounding heuristic. This collection of paths is used in a packing integer

Measurement of Liquid-Metal Two-Phase Flow with a Dynamic Neutron Radiography

International Nuclear Information System (INIS)

Cha, J. E.; Lim, I. C.; Kim, H. R.; Kim, C. M.; Nam, H. Y.; Saito, Y.

2005-01-01

The dynamic neutron radiography(DNR) has complementary characteristics to X-ray radiography and is suitable to visualization and measurement of a multi-phase flow research in a metallic duct and liquid metal flow. The flow-field information of liquid metal system is very important for the safety analysis of fast breeder reactor and the design of the spallation target of accelerator driven system. A DNR technique was applied to visualize the flow field in the gas-liquid metal two-phase flow with the HANARO-beam facility. The lead bismuth eutectic and the nitrogen gas were used to construct the two-phase flow field in the natural circulation U-channel. The two-phase flow images in the riser were taken at various combinations of the liquid flow and gas flow with high frame-rate neutron radiography at 1000 fps

The RNA-Binding Site of Poliovirus 3C Protein Doubles as a Phosphoinositide-Binding Domain.

Science.gov (United States)

Shengjuler, Djoshkun; Chan, Yan Mei; Sun, Simou; Moustafa, Ibrahim M; Li, Zhen-Lu; Gohara, David W; Buck, Matthias; Cremer, Paul S; Boehr, David D; Cameron, Craig E

2017-12-05

Some viruses use phosphatidylinositol phosphate (PIP) to mark membranes used for genome replication or virion assembly. PIP-binding motifs of cellular proteins do not exist in viral proteins. Molecular-docking simulations revealed a putative site of PIP binding to poliovirus (PV) 3C protein that was validated using nuclear magnetic resonance spectroscopy. The PIP-binding site was located on a highly dynamic α helix, which also functions in RNA binding. Broad PIP-binding activity was observed in solution using a fluorescence polarization assay or in the context of a lipid bilayer using an on-chip, fluorescence assay. All-atom molecular dynamics simulations of the 3C protein-membrane interface revealed PIP clustering and perhaps PIP-dependent conformations. PIP clustering was mediated by interaction with residues that interact with the RNA phosphodiester backbone. We conclude that 3C binding to membranes will be determined by PIP abundance. We suggest that the duality of function observed for 3C may extend to RNA-binding proteins of other viruses. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamic methods of air traffic flow management

Directory of Open Access Journals (Sweden)

Jacek SKORUPSKI

2011-01-01

Full Text Available Air traffic management is a complex hierarchical system. Hierarchy levels can be defined according to decision making time horizon or to analyze area volume. For medium time horizon and wide analysis area, the air traffic flow management services were established. Their main task is to properly co-ordinate air traffic in European airspace, so as to minimize delays arising in congested sectors. Those services have to assure high safety level at the same time. Thus it is a very complex task, with many goals, many decision variables and many constraints.In the paper review of the methods developed for aiding air traffic flow management services is presented. More detailed description of a dynamic method is given. This method is based on stochastic capacity and scenario analysis. Some problems in utilization of presented methods are also pointed out, so are the next research possibilities.

Fundamental considerations in ski binding analysis.

Science.gov (United States)

Mote, C D; Hull, M L

1976-01-01

1. The static adjustment of a ski binding by hand or by available machines is only an adjustment and is neither a static nor a dynamic evaluation of the binding design. Bindings of different design with identical static adjustments will perform differently in environments in which the forces are static or dynamic. 2. The concept of binding release force is a useful measure of binding adjustment, but it is inappropriate as a criterion for binding evaluation. First, it does not direct attention toward the injury causing mechanism, strain, or displacement in the leg. Second, it is only part of the evaluation in dynamic problems. 3. The binding release decision in present bindings is displacement controlled. The relative displacement of the boot and ski is the system variable. For any specified relative displacement the binding force can be any of an infinite number of possibilities determined by the loading path. 4. The response of the leg-ski system to external impulses applied to the ski is independent of the boot-ski relative motion as long as the boot recenters quickly in the binding. Response is dependent upon the external impulse plus system inertia, damping and stiffness. 5. When tested under half sinusoidal forces applied to a test ski, all bindings will demonstrate static and impulse loading regions. In the static region the force drives the binding to a relative release displacement. In the impulse region the initial velocity of the ski drives the binding to a release displacement. 6. The transition between the static and impulse loading regions is determined by the binding's capacity to store and dissipate energy along the principal loading path. Increased energy capacity necessitates larger external impulses to produce release. 7. In all bindings examined to date, the transmitted leg displacement or strain at release under static loading exceeds leg strain under dynamic or impact loading. Because static loading is responsible for many injuries, a skier

Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations.

Science.gov (United States)

Zhang, Yuxin; Huang, Xiaoqin; Han, Keli; Zheng, Fang; Zhan, Chang-Guo

2016-11-25

The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (∼5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of ∼5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (∼0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental K M values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Dynamics of three-tori in a periodically forced navier-stokes flow

Science.gov (United States)

Lopez; Marques

2000-07-31

Three-tori solutions of the Navier-Stokes equations and their dynamics are elucidated by use of a global Poincare map. The flow is contained in a finite annular gap between two concentric cylinders, driven by the steady rotation and axial harmonic oscillations of the inner cylinder. The three-tori solutions undergo global bifurcations, including a new gluing bifurcation, associated with homoclinic and heteroclinic connections to unstable solutions (two-tori). These unstable two-tori act as organizing centers for the three-tori dynamics. A discrete space-time symmetry influences the dynamics.

Improving flow distribution in influent channels using computational fluid dynamics.

Science.gov (United States)

Park, No-Suk; Yoon, Sukmin; Jeong, Woochang; Lee, Seungjae

2016-10-01

Although the flow distribution in an influent channel where the inflow is split into each treatment process in a wastewater treatment plant greatly affects the efficiency of the process, and a weir is the typical structure for the flow distribution, to the authors' knowledge, there is a paucity of research on the flow distribution in an open channel with a weir. In this study, the influent channel of a real-scale wastewater treatment plant was used, installing a suppressed rectangular weir that has a horizontal crest to cross the full channel width. The flow distribution in the influent channel was analyzed using a validated computational fluid dynamics model to investigate (1) the comparison of single-phase and two-phase simulation, (2) the improved procedure of the prototype channel, and (3) the effect of the inflow rate on flow distribution. The results show that two-phase simulation is more reliable due to the description of the free-surface fluctuations. It should first be considered for improving flow distribution to prevent a short-circuit flow, and the difference in the kinetic energy with the inflow rate makes flow distribution trends different. The authors believe that this case study is helpful for improving flow distribution in an influent channel.

Approaching multiphase flows from the perspective of computational fluid dynamics

International Nuclear Information System (INIS)

Banas, A.O.

1992-01-01

Thermalhydraulic simulation methodologies based on subchannel and porous-medium concepts are briefly reviewed and contrasted with the general approach of Computational Fluid Dynamics (CFD). An outline of the advanced CFD methods for single-phase turbulent flows is followed by a short discussion of the unified formulation of averaged equations for turbulent and multiphase flows. Some of the recent applications of CFD at Chalk River Laboratories are discussed, and the complementary role of CFD with regard to the established thermalhydraulic methods of analysis is indicated. (author). 8 refs

Numerical simulation of 3D unsteady flow in a rotating pump by dynamic mesh technique

International Nuclear Information System (INIS)

Huang, S; Guo, J; Yang, F X

2013-01-01

In this paper, the numerical simulation of unsteady flow for three kinds of typical rotating pumps, roots blower, roto-jet pump and centrifugal pump, were performed using the three-dimensional Dynamic Mesh technique. In the unsteady simulation, all the computational domains, as stationary, were set in one inertial reference frame. The motions of the solid boundaries were defined by the Profile file in FLUENT commercial code, in which the rotational orientation and speed of the rotors were specified. Three methods (Spring-based Smoothing, Dynamic Layering and Local Re-meshing) were used to achieve mesh deformation and re-meshing. The unsteady solutions of flow field and pressure distribution were solved. After a start-up stage, the flow parameters exhibit time-periodic behaviour corresponding to blade passing frequency of rotor. This work shows that Dynamic Mesh technique could achieve numerical simulation of three-dimensional unsteady flow field in various kinds of rotating pumps and have a strong versatility and broad application prospects

Dynamic fluid connectivity during steady-state multiphase flow in a sandstone.

Science.gov (United States)

Reynolds, Catriona A; Menke, Hannah; Andrew, Matthew; Blunt, Martin J; Krevor, Samuel

2017-08-01

The current conceptual picture of steady-state multiphase Darcy flow in porous media is that the fluid phases organize into separate flow pathways with stable interfaces. Here we demonstrate a previously unobserved type of steady-state flow behavior, which we term "dynamic connectivity," using fast pore-scale X-ray imaging. We image the flow of N 2 and brine through a permeable sandstone at subsurface reservoir conditions, and low capillary numbers, and at constant fluid saturation. At any instant, the network of pores filled with the nonwetting phase is not necessarily connected. Flow occurs along pathways that periodically reconnect, like cars controlled by traffic lights. This behavior is consistent with an energy balance, where some of the energy of the injected fluids is sporadically converted to create new interfaces.

Dynamics of an elastic capsule in moderate Reynolds number Poiseuille flow

International Nuclear Information System (INIS)

Shin, Soo Jai; Sung, Hyung Jin

2012-01-01

Highlights: ► Dynamics of a capsule in moderate Re Poiseuille flow were explored numerically. ► Capsule tends to tumbling motion for larger membrane elasticity and higher Re flow. ► Capsule undergoes swinging motion for larger size and aspect ratio of the capsule. ► Capsule tends to migrate to a specific lateral equilibrium as Re increases. ► Equilibrium position varies differently around the transition of the dynamic motion. - Abstract: The dynamic motions and lateral equilibrium positions of a two-dimensional elastic capsule in a Poiseuille flow were explored at moderate Reynolds number (10 ⩽ Re ⩽ 100) as a function of the initial lateral position (y 0 ), Re, aspect ratio (ε), size ratio (λ), membrane stretching coefficient (φ) and bending coefficient (γ). The transition between tank-treading (TT) and swinging (SW) to tumbling (TU) motions was observed and the lateral equilibrium positions of the capsules varied according to the conditions. The initial behavior of the elastic capsule was influenced by variation in the initial lateral position (y 0 ), but the equilibrium position and dynamic motion of the capsule were not affected by such variation. The capsules had a stronger tendency toward TU motion at higher values of Re, φ and γ, whereas the capsules underwent TT or SW motion as the values of ε and λ increased. Under moderate Re Poiseuille flows, capsules tended to migrate across streamlines to a specific equilibrium position. The lateral equilibrium position shifted toward the centerline at larger λ and migrated toward the wall at larger ε,φandγ. As Re increased, the equilibrium position first shifted toward the bottom wall, then toward the channel center. However, different equilibrium position trends were obtained around the SW–TU transition. The capsule undergoing TU motion tended to migrate downward toward the bottom wall more than the capsule undergoing SW motion, all other conditions being similar.

Investigation of the Binding Site of CCR2 using 4-Azetidinyl-1-aryl-cyclohexane Derivatives: A Membrane Modeling and Molecular Dynamics Study

Energy Technology Data Exchange (ETDEWEB)

Kothandan, Gugan; Gadhe, Changdev G.; Cho, Seung Joo [Chosun Univ., Gwangju (Korea, Republic of)

2013-11-15

Chemokine receptor (CCR2) is a G protein-coupled receptor that contains seven transmembrane helices. Recent pharmaceutical research has focused on the antagonism of CCR2 and candidate drugs are currently undergoing clinical studies for the treatment of diseases like arthritis, multiple sclerosis, and type 2 diabetes. In this study, we analyzed the time dependent behavior of CCR2 docked with a potent 4-azetidinyl-1-aryl-cyclohexane (4AAC) derivative using molecular dynamics simulations (MDS) for 20 nanoseconds (ns). Homology modeling of CCR2 was performed and the 4AAC derivative was docked into this binding site. The docked model of selected conformations was then utilized to study the dynamic behavior of the 4AAC enzyme complexes inside lipid membrane. MDS of CCR2-16b of 4AAC complexes allowed us to refine the system since binding of an inhibitor to a receptor is a dynamic process and identify stable structures and better binding modes. Structure activity relationships (SAR) for 4AAC derivatives were investigated and reasons for the activities were determined. Probable binding pose for some CCR2 antagonists were determined from the perspectives of binding site. Initial modeling showed that Tyr49, Trp98, Ser101, Glu291, and additional residues are crucial for 4AAC binding, but MDS analysis showed that Ser101 may not be vital. 4AAC moved away from Ser101 and the hydrogen bonding between 4AAC and Ser101 vanished. The results of this study provide useful information regarding the structure-based drug design of CCR2 antagonists and additionally suggest key residues for further study by mutagenesis.

Flow dynamic study of a single-phase square NCL using recurrence ...

Indian Academy of Sciences (India)

Department of Mechanical Engineering, Jadavpur University, Kolkata 700 032, India ... With increase in heater power, a change in loop fluid flow dynamics has been observed. For ... reactor core cooling, solar water heaters, gas turbine.

Assessment of Electromagnetic Stirrer Agitated Liquid Metal Flows by Dynamic Neutron Radiography

Science.gov (United States)

Ščepanskis, Mihails; Sarma, Mārtiņš; Vontobel, Peter; Trtik, Pavel; Thomsen, Knud; Jakovičs, Andris; Beinerts, Toms

2017-04-01

This paper presents qualitative and quantitative characterization of two-phase liquid metal flows agitated by the stirrer on rotating permanent magnets. The stirrer was designed to fulfill various eddy flows, which may have different rates of solid particle entrapment from the liquid surface and their homogenization. The flow was characterized by visualization of the tailored tracer particles by means of dynamic neutron radiography, an experimental method well suited for liquid metal flows due to low opacity of some metals for neutrons. The rather high temporal resolution of the image acquisition (32 Hz image acquisition rate) allows for the quantitative investigation of the flows up to 30 cm/s using neutron particle image velocimetry. In situ visualization of the two-phase liquid metal flow is also demonstrated.

Instantaneous aerosol dynamics in a turbulent flow

KAUST Repository

Zhou, Kun

2012-01-01

Dibutyl phthalate aerosol particles evolution dynamics in a turbulent mixing layer is simulated by means of direct numerical simulation for the flow field and the direct quadrature method of moments for the aerosol evolution. Most par-ticles are nucleated in a thin layer region corresponding to a specific narrow temperature range near the cool stream side. However, particles undergo high growth rate on the hot stream side due to condensation. Coagulation decreases the total particle number density at a rate which is highly correlated to the in-stantaneous number density.

Dynamics of a confined dusty fluid in a sheared ion flow

Energy Technology Data Exchange (ETDEWEB)

Laishram, Modhuchandra; Sharma, Devendra; Kaw, Predhiman K. [Institute for Plasma Research, Bhat, Gandhinagar 382428 (India)

2014-07-15

Dynamics of an isothermally driven dust fluid is analyzed which is confined in an azimuthally symmetric cylindrical setup by an effective potential and is in equilibrium with an unconfined sheared flow of a streaming plasma. Cases are analyzed where the confining potential constitutes a barrier for the driven fluid, limiting its spatial extension and boundary velocity. The boundary effects entering the formulation are characterized by applying the appropriate boundary conditions and a range of solutions exhibiting single and multiple vortex are obtained. The equilibrium solutions considered in the cylindrical setup feature a transition from single to multiple vortex state of the driven flow. Effects of (i) the variation in dust viscosity, (ii) coupling between the driving and the driven fluid, and (iii) a friction determining the equilibrium dynamics of the driven system are characterized.

Alignment dynamics of diffusive scalar gradient in a two-dimensional model flow

Science.gov (United States)

Gonzalez, M.

2018-04-01

The Lagrangian two-dimensional approach of scalar gradient kinematics is revisited accounting for molecular diffusion. Numerical simulations are performed in an analytic, parameterized model flow, which enables considering different regimes of scalar gradient dynamics. Attention is especially focused on the influence of molecular diffusion on Lagrangian statistical orientations and on the dynamics of scalar gradient alignment.

Identifying the Interaction of Vancomycin With Novel pH-Responsive Lipids as Antibacterial Biomaterials Via Accelerated Molecular Dynamics and Binding Free Energy Calculations.

Science.gov (United States)

Ahmed, Shaimaa; Vepuri, Suresh B; Jadhav, Mahantesh; Kalhapure, Rahul S; Govender, Thirumala

2018-06-01

Nano-drug delivery systems have proven to be an efficient formulation tool to overcome the challenges with current antibiotics therapy and resistance. A series of pH-responsive lipid molecules were designed and synthesized for future liposomal formulation as a nano-drug delivery system for vancomycin at the infection site. The structures of these lipids differ from each other in respect of hydrocarbon tails: Lipid1, 2, 3 and 4 have stearic, oleic, linoleic, and linolenic acid hydrocarbon chains, respectively. The impact of variation in the hydrocarbon chain in the lipid structure on drug encapsulation and release profile, as well as mode of drug interaction, was investigated using molecular modeling analyses. A wide range of computational tools, including accelerated molecular dynamics, normal molecular dynamics, binding free energy calculations and principle component analysis, were applied to provide comprehensive insight into the interaction landscape between vancomycin and the designed lipid molecules. Interestingly, both MM-GBSA and MM-PBSA binding affinity calculations using normal molecular dynamics and accelerated molecular dynamics trajectories showed a very consistent trend, where the order of binding affinity towards vancomycin was lipid4 > lipid1 > lipid2 > lipid3. From both normal molecular dynamics and accelerated molecular dynamics, the interaction of lipid3 with vancomycin is demonstrated to be the weakest (∆G binding  = -2.17 and -11.57, for normal molecular dynamics and accelerated molecular dynamics, respectively) when compared to other complexes. We believe that the degree of unsaturation of the hydrocarbon chain in the lipid molecules may impact on the overall conformational behavior, interaction mode and encapsulation (wrapping) of the lipid molecules around the vancomycin molecule. This thorough computational analysis prior to the experimental investigation is a valuable approach to guide for predicting the encapsulation

Influence of cerebrovascular resistance on the dynamic relationship between blood pressure and cerebral blood flow in humans.

Science.gov (United States)

Smirl, J D; Tzeng, Y C; Monteleone, B J; Ainslie, P N

2014-06-15

We examined the hypothesis that changes in the cerebrovascular resistance index (CVRi), independent of blood pressure (BP), will influence the dynamic relationship between BP and cerebral blood flow in humans. We altered CVRi with (via controlled hyperventilation) and without [via indomethacin (INDO, 1.2 mg/kg)] changes in PaCO2. Sixteen subjects (12 men, 27 ± 7 yr) were tested on two occasions (INDO and hypocapnia) separated by >48 h. Each test incorporated seated rest (5 min), followed by squat-stand maneuvers to increase BP variability and improve assessment of the pressure-flow dynamics using linear transfer function analysis (TFA). Beat-to-beat BP, middle cerebral artery velocity (MCAv), posterior cerebral artery velocity (PCAv), and end-tidal Pco2 were monitored. Dynamic pressure-flow relations were quantified using TFA between BP and MCAv/PCAv in the very low and low frequencies through the driven squat-stand maneuvers at 0.05 and 0.10 Hz. MCAv and PCAv reductions by INDO and hypocapnia were well matched, and CVRi was comparably elevated (P flow dynamics. These findings are consistent with the concept of CVRi being a key factor that should be considered in the correct interpretation of cerebral pressure-flow dynamics as indexed using TFA metrics. Copyright © 2014 the American Physiological Society.

Dynamic electro-thermal modeling of all-vanadium redox flow battery with forced cooling strategies

International Nuclear Information System (INIS)

Wei, Zhongbao; Zhao, Jiyun; Xiong, Binyu

2014-01-01

Highlights: • A dynamic electro-thermal model is proposed for VRB with forced cooling. • The Foster network is adopted to model the battery cooling process. • Both the electrolyte temperature and terminal voltage can be accurately predicted. • The flow rate of electrolyte and coolant significantly impact battery performance. - Abstract: The present study focuses on the dynamic electro-thermal modeling for the all-vanadium redox flow battery (VRB) with forced cooling strategies. The Foster network is adopted to dynamically model the heat dissipation of VRB with heat exchangers. The parameters of Foster network are extracted by fitting the step response of it to the results of linearized CFD model. Then a complete electro-thermal model is proposed by coupling the heat generation model, Foster network and electrical model. Results show that the established model has nearly the same accuracy with the nonlinear CFD model in electrolyte temperature prediction but drastically improves the computational efficiency. The modeled terminal voltage is also benchmarked with the experimental data under different current densities. The electrolyte temperature is found to be significantly influenced by the flow rate of coolant. As compared, although the electrolyte flow rate has unremarkable impact on electrolyte temperature, its effect on system pressure drop and battery efficiency is significant. Increasing the electrolyte flow rate improves the coulombic efficiency, voltage efficiency and energy efficiency simultaneously but at the expense of higher pump power demanded. An optimal flow rate exists for each operating condition to maximize the system efficiency

Single-molecule analysis reveals the kinetics and physiological relevance of MutL-ssDNA binding.

Directory of Open Access Journals (Sweden)

Jonghyun Park

2010-11-01

Full Text Available DNA binding by MutL homologs (MLH/PMS during mismatch repair (MMR has been considered based on biochemical and genetic studies. Bulk studies with MutL and its yeast homologs Mlh1-Pms1 have suggested an integral role for a single-stranded DNA (ssDNA binding activity during MMR. We have developed single-molecule Förster resonance energy transfer (smFRET and a single-molecule DNA flow-extension assays to examine MutL interaction with ssDNA in real time. The smFRET assay allowed us to observe MutL-ssDNA association and dissociation. We determined that MutL-ssDNA binding required ATP and was the greatest at ionic strength below 25 mM (K(D = 29 nM while it dramatically decreases above 100 mM (K(D>2 µM. Single-molecule DNA flow-extension analysis suggests that multiple MutL proteins may bind ssDNA at low ionic strength but this activity does not enhance stability at elevated ionic strengths. These studies are consistent with the conclusion that a stable MutL-ssDNA interaction is unlikely to occur at physiological salt eliminating a number of MMR models. However, the activity may infer some related dynamic DNA transaction process during MMR.

Ligand receptor dynamics at streptavidin-coated particle surfaces: A flow cytometric and spectrofluorimetric study

Energy Technology Data Exchange (ETDEWEB)

Buranda, T. [Univ. of New Mexico School of Medicine, Albuquerque, NM (United States)]|[Univ. of New Mexico, Albuquerque, NM (United States); Jones, G.M. [Univ. of New Mexico School of Medicine, Albuquerque, NM (United States); Nolan, J.P.; Keij, J. [Los Alamos National Labs., NM (United States); Lopez, G.P. [Univ. of New Mexico, Albuquerque, NM (United States); Sklar, L.A. [Univ. of New Mexico School of Medicine, Albuquerque, NM (United States)]|[Los Alamos National Lab., NM (United States)

1999-04-29

The authors have studied the binding of 5-((N-(5-(N-(6-(biotinoyl)amino)hexanoyl)amino)pentyl)thioureidyl)fluorescein (fluorescein biotin) to 6.2 {micro}m diameter, streptavidin-coated polystyrene beads using a combination of fluorimetric and flow cytometric methods. They have determined the average number of binding sites per bead, the extent of fluorescein quenching upon binding to the bead, and the association and dissociation kinetics. The authors estimate the site number to be {approx}1 million per bead. The binding of the fluorescein biotin ligand occurs in steps where the insertion of the biotin moiety into one receptor pocket is followed immediately by the capture of the fluorescein moiety by a neighboring binding pocket; fluorescence quenching is a consequence of this secondary binding. At high surface coverage, the dominant mechanism of quenching appears to be via the formation of nonfluorescent nearest-neighbor aggregates. At early times, the binding process is characterized by biphasic association and dissociation kinetics which are remarkably dependent on the initial concentration of the ligand. The rate constant for binding to the first receptor pocket of a streptavidin molecule is {approx}(1.3 {+-} 0.3) {times} 10{sup 7} 1{sup {minus}1} S{sup {minus}1}. The rate of binding of a second biotin may be reduced due to steric interference. The early time dissociative behavior is in sharp contrast to the typical stability associated with this system. The early time dissociative behavior is in sharp contrast to the typical stability associated with this system. The dissociation rate constant is as high as 0.05 s{sup {minus}1} shortly after binding, but decreases by 3 orders of magnitude after 3 h of binding. Potential sources for the time dependence of the dissociation rate constant are discussed.

Computational Fluid Dynamic Pressure Drop Estimation of Flow between Parallel Plates

Energy Technology Data Exchange (ETDEWEB)

Son, Hyung Min; Yang, Soo Hyung; Park, Jong Hark [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2014-10-15

Many pool type reactors have forced downward flows inside the core during normal operation; there is a chance of flow inversion when transients occur. During this phase, the flow undergo transition between turbulent and laminar regions where drastic changes take place in terms of momentum and heat transfer, and the decrease in safety margin is usually observed. Additionally, for high Prandtl number fluids such as water, an effect of the velocity profile inside the channel on the temperature distribution is more pronounced over the low Prandtl number ones. This makes the checking of its pressure drop estimation accuracy less important, assuming the code verification is complete. With an advent of powerful computer hardware, engineering applications of computational fluid dynamics (CFD) methods have become quite common these days. Especially for a fully-turbulent and single phase convective heat transfer, the predictability of the commercial codes has matured enough so that many well-known companies adopt those to accelerate a product development cycle and to realize an increased profitability. In contrast to the above, the transition models for the CFD code are still under development, and the most of the models show limited generality and prediction accuracy. Unlike the system codes, the CFD codes estimate the pressure drop from the velocity profile which is obtained by solving momentum conservation equations, and the resulting friction factor can be a representative parameter for a constant cross section channel flow. In addition, the flow inside a rectangular channel with a high span to gap ratio can be approximated by flow inside parallel plates. The computational fluid dynamics simulation on the flow between parallel plates showed reasonable prediction capability for the laminar and the turbulent regime.

Wake flow control using a dynamically controlled wind turbine

Science.gov (United States)

Castillo, Ricardo; Wang, Yeqin; Pol, Suhas; Swift, Andy; Hussain, Fazle; Westergaard, Carsten; Texas Tech University Team

2016-11-01

A wind tunnel based "Hyper Accelerated Wind Farm Kinematic-Control Simulator" (HAWKS) is being built at Texas Tech University to emulate controlled wind turbine flow physics. The HAWKS model turbine has pitch, yaw and speed control which is operated in real model time, similar to that of an equivalent full scale turbine. Also, similar to that of a full scale wind turbine, the controls are developed in a Matlab Simulink environment. The current diagnostic system consists of power, rotor position, rotor speed measurements and PIV wake characterization with four cameras. The setup allows up to 7D downstream of the rotor to be mapped. The purpose of HAWKS is to simulate control strategies at turnaround times much faster than CFD and full scale testing. The fundamental building blocks of the simulator have been tested, and demonstrate wake steering for both static and dynamic turbine actuation. Parameters which have been studied are yaw, rotor speed and combinations hereof. The measured wake deflections for static yaw cases are in agreement with previously reported research implying general applicability of the HAWKS platform for the purpose of manipulating the wake. In this presentation the general results will be introduced followed by an analysis of the wake turbulence and coherent structures when comparing static and dynamic flow cases. The outcome of such studies could ultimately support effective wind farm wake flow control strategies. Texas Emerging Technology Fund (ETF).

Characterization of cardiac flow in heart disease patients by computational fluid dynamics and 4D flow MRI

Science.gov (United States)

Lantz, Jonas; Gupta, Vikas; Henriksson, Lilian; Karlsson, Matts; Persson, Ander; Carhall, Carljohan; Ebbers, Tino

2017-11-01

In this study, cardiac blood flow was simulated using Computational Fluid Dynamics and compared to in vivo flow measurements by 4D Flow MRI. In total, nine patients with various heart diseases were studied. Geometry and heart wall motion for the simulations were obtained from clinical CT measurements, with 0.3x0.3x0.3 mm spatial resolution and 20 time frames covering one heartbeat. The CFD simulations included pulmonary veins, left atrium and ventricle, mitral and aortic valve, and ascending aorta. Mesh sizes were on the order of 6-16 million cells, depending on the size of the heart, in order to resolve both papillary muscles and trabeculae. The computed flow field agreed visually very well with 4D Flow MRI, with characteristic vortices and flow structures seen in both techniques. Regression analysis showed that peak flow rate as well as stroke volume had an excellent agreement for the two techniques. We demonstrated the feasibility, and more importantly, fidelity of cardiac flow simulations by comparing CFD results to in vivo measurements. Both qualitative and quantitative results agreed well with the 4D Flow MRI measurements. Also, the developed simulation methodology enables ``what if'' scenarios, such as optimization of valve replacement and other surgical procedures. Funded by the Wallenberg Foundation.

Efficient and dynamic nuclear localization of green fluorescent protein via RNA binding

Energy Technology Data Exchange (ETDEWEB)

Kitamura, Akira; Nakayama, Yusaku; Kinjo, Masataka, E-mail: kinjo@sci.hokudai.ac.jp

2015-07-31

Classical nuclear localization signal (NLS) sequences have been used for artificial localization of green fluorescent protein (GFP) in the nucleus as a positioning marker or for measurement of the nuclear-cytoplasmic shuttling rate in living cells. However, the detailed mechanism of nuclear retention of GFP-NLS remains unclear. Here, we show that a candidate mechanism for the strong nuclear retention of GFP-NLS is via the RNA-binding ability of the NLS sequence. GFP tagged with a classical NLS derived from Simian virus 40 (GFP-NLS{sup SV40}) localized not only in the nucleoplasm, but also to the nucleolus, the nuclear subdomain in which ribosome biogenesis takes place. GFP-NLS{sup SV40} in the nucleolus was mobile, and intriguingly, the diffusion coefficient, which indicates the speed of diffusing molecules, was 1.5-fold slower than in the nucleoplasm. Fluorescence correlation spectroscopy (FCS) analysis showed that GFP-NLS{sup SV40} formed oligomers via RNA binding, the estimated molecular weight of which was larger than the limit for passive nuclear export into the cytoplasm. These findings suggest that the nuclear localization of GFP-NLS{sup SV40} likely results from oligomerization mediated via RNA binding. The analytical technique used here can be applied for elucidating the details of other nuclear localization mechanisms, including those of several types of nuclear proteins. In addition, GFP-NLS{sup SV40} can be used as an excellent marker for studying both the nucleoplasm and nucleolus in living cells. - Highlights: • Nuclear localization signal-tagged GFP (GFP-NLS) showed clear nuclear localization. • The GFP-NLS dynamically localized not only in the nucleoplasm, but also to the nucleolus. • The nuclear localization of GFP-NLS results from transient oligomerization mediated via RNA binding. • Our NLS-tagging procedure is ideal for use in artificial sequestration of proteins in the nucleus.

Efficient and dynamic nuclear localization of green fluorescent protein via RNA binding

International Nuclear Information System (INIS)

Kitamura, Akira; Nakayama, Yusaku; Kinjo, Masataka

2015-01-01

Classical nuclear localization signal (NLS) sequences have been used for artificial localization of green fluorescent protein (GFP) in the nucleus as a positioning marker or for measurement of the nuclear-cytoplasmic shuttling rate in living cells. However, the detailed mechanism of nuclear retention of GFP-NLS remains unclear. Here, we show that a candidate mechanism for the strong nuclear retention of GFP-NLS is via the RNA-binding ability of the NLS sequence. GFP tagged with a classical NLS derived from Simian virus 40 (GFP-NLS SV40 ) localized not only in the nucleoplasm, but also to the nucleolus, the nuclear subdomain in which ribosome biogenesis takes place. GFP-NLS SV40 in the nucleolus was mobile, and intriguingly, the diffusion coefficient, which indicates the speed of diffusing molecules, was 1.5-fold slower than in the nucleoplasm. Fluorescence correlation spectroscopy (FCS) analysis showed that GFP-NLS SV40 formed oligomers via RNA binding, the estimated molecular weight of which was larger than the limit for passive nuclear export into the cytoplasm. These findings suggest that the nuclear localization of GFP-NLS SV40 likely results from oligomerization mediated via RNA binding. The analytical technique used here can be applied for elucidating the details of other nuclear localization mechanisms, including those of several types of nuclear proteins. In addition, GFP-NLS SV40 can be used as an excellent marker for studying both the nucleoplasm and nucleolus in living cells. - Highlights: • Nuclear localization signal-tagged GFP (GFP-NLS) showed clear nuclear localization. • The GFP-NLS dynamically localized not only in the nucleoplasm, but also to the nucleolus. • The nuclear localization of GFP-NLS results from transient oligomerization mediated via RNA binding. • Our NLS-tagging procedure is ideal for use in artificial sequestration of proteins in the nucleus

Channel Geometry and Flood Flows: Quantifying over-bank flow dynamics during high-flow events in North Carolina's floodplains

Science.gov (United States)

Lovette, J. P.; Duncan, J. M.; Vimal, S.; Band, L. E.

2015-12-01

Natural riparian areas play numerous roles in the maintenance and improvement of stream water quality. Both restoration of riparian areas and improvement of hydrologic connectivity to the stream are often key goals of river restoration projects. These management actions are designed to improve nutrient removal by slowing and treating overland flow delivered from uplands and by storing, treating, and slowly releasing streamwater from overbank inundation during flood events. A major question is how effective this storage of overbank flow is at treating streamwater based on the cumulative time stream discharge at a downstream location has spent in shallower, slower overbank flow. The North Carolina Floodplain Mapping Program maintains a detailed statewide Flood Risk Information System (FRIS) using HEC-RAS modeling, lidar, and detailed surveyed river cross-sections. FRIS provides extensive information regarding channel geometry on approximately 39,000 stream reaches (a slightly coarser spatial resolution than the NHD+v2 dataset) with tens of cross-sections for each reach. We use this FRIS data to calculate volume and discharge from floodplain riparian areas separately from in-channel flow during overbank events. Preliminary results suggest that a small percentage of total annual discharge interacts with the full floodplain extent along a stream reach due to the infrequency of overbank flow events. However, with the significantly different physical characteristics of the riparian area when compared to the channel itself, this overbank flow can provide unique services to water quality. Our project aims to use this information in conjunction with data from the USGS SPARROW program to target non-point source hotspots of Nitrogen and Phosphorus addition and removal. By better understanding the flow dynamics within riparian areas during high flow events, riparian restoration projects can be carried out with improved efficacy.

Statistical state dynamics-based analysis of the physical mechanisms sustaining and regulating turbulence in Couette flow

Science.gov (United States)

Farrell, Brian F.; Ioannou, Petros J.

2017-08-01

This paper describes a study of the self-sustaining process in wall turbulence. The study is based on a second order statistical state dynamics model of Couette flow in which the state variables are the streamwise mean flow (first cumulant) and perturbation covariance (second cumulant). This statistical state dynamics model is closed by either setting the third cumulant to zero or by replacing it with a stochastic parametrization. Statistical state dynamics models with this form are referred to as S3T models. S3T models have been shown to self-sustain turbulence with a mean flow and second order perturbation structure similar to that obtained by direct numerical simulation of the equations of motion. The use of a statistical state dynamics model to study the physical mechanisms underlying turbulence has important advantages over the traditional approach of studying the dynamics of individual realizations of turbulence. One advantage is that the analytical structure of S3T statistical state dynamics models isolates the interaction between the mean flow and the perturbation components of the turbulence. Isolation of the interaction between these components reveals how this interaction underlies both the maintenance of the turbulence variance by transfer of energy from the externally driven flow to the perturbation components as well as the enforcement of the observed statistical mean turbulent state by feedback regulation between the mean and perturbation fields. Another advantage of studying turbulence using statistical state dynamics models of S3T form is that the analytical structure of S3T turbulence can be completely characterized. For example, the perturbation component of turbulence in the S3T system is demonstrably maintained by a parametric perturbation growth mechanism in which fluctuation of the mean flow maintains the perturbation field which in turn maintains the mean flow fluctuations in a synergistic interaction. Furthermore, the equilibrium

On the Mutual Dynamics of Interregional Gross Migration Flows in Space and Time

DEFF Research Database (Denmark)

Mitze, Timo

2016-01-01

This paper applies spatial dynamic panel data models to analyse the labor market dimension of interregional population flows among German federal states in the period 1993–2009. Making use of recent improvements in the estimation of space-time dynamic panel data models and the computation of mean...

Modeling the Structure and Effectiveness of Intelligence Organizations: Dynamic Information Flow Simulation

National Research Council Canada - National Science Library

Behrman, Robert; Carley, Kathleen

2003-01-01

This paper describes the Dynamic Information Flow Simulation (DIFS), an abstract model for analyzing the structure and function of intelligence support organizations and the activities of entities within...

Probing of possible olanzapine binding site on human serum albumin: Combination of spectroscopic methods and molecular dynamics simulation

International Nuclear Information System (INIS)

Shahlaei, Mohsen; Rahimi, Behnoosh; Ashrafi-Kooshk, Mohammad Reza; Sadrjavadi, Komail; Khodarahmi, Reza

2015-01-01

Human serum albumin (HSA)-drug binding affinity is one of the major factors that determine the pharmacokinetics, halftime and bioavailability of drugs in various tissues. In the present study, the interaction of olanzapine (OLZ), a thienobenzodiazepine drug, administered for the treatment of schizophrenia and bipolar disorder, with HSA has been studied using spectroscopic methods such as ultraviolet absorbance, fluorescence and FTIR combined with computational procedures. Analyzing of the Stern–Volmer quenching data showed only one primary binding site on HSA with a binding constant of 4.12×10 4 M −1 at 298 K. Thermodynamic analyses showed enthalpy change (ΔH°) and entropy change (ΔS°) were 28.03±3.42 kJ mol −1 and −25.52±11.52 J mol −1 K −1 , respectively. Molecular docking results suggested the hydrophobic residues such as Val 216 , Leu 327 , Ala 350 and polar residues such as Glu 354 play an important role in the drug binding. Decrement in α-helix content of the protein upon OLZ binding was also confirmed by evidences provided by molecular dynamics simulation as well as FTIR spectroscopy. - Highlights: • Leu 327 , Ala 350 as well as hydrophilic residues of HSA play an important role in the binding reaction. • The drug has only one primary binding site on HSA with a binding constant of 4.12×10 4 M −1 at 298 K. • The drug binds near to site I

Evaluation of steady flow torques and pressure losses in a rotary flow control valve by means of computational fluid dynamics

International Nuclear Information System (INIS)

Okhotnikov, Ivan; Noroozi, Siamak; Sewell, Philip; Godfrey, Philip

2017-01-01

Highlights: • A novel design of a rotary flow control valve driven by a stepper motor is proposed. • The intended use of the valve in the high flow rate independent metering hydraulic system is suggested. • Pressure drops, steady flow torques of the valve for various flow rates and orifice openings are studied by means of computational fluid dynamics. • The discharge coefficient and flow jet angles dependencies on the orifice opening are obtained. • A design method to decrease the flow forces without reducing the flow rate in single-staged valves is demonstrated. - Abstract: In this paper, a novel design of a rotary hydraulic flow control valve has been presented for high flow rate fluid power systems. High flow rates in these systems account for substantial flow forces acting on the throttling elements of the valves and cause the application of mechanically sophisticated multi-staged servo valves for flow regulation. The suggested design enables utilisation of single-stage valves in power hydraulics operating at high flow rates regimes. A spool driver and auxiliary mechanisms of the proposed valve design were discussed and selection criteria were suggested. Analytical expressions for metering characteristics as well as steady flow torques have been derived. Computational fluid dynamics (CFD) analysis of steady state flow regimes was conducted to evaluate the hydraulic behaviour of the proposed valve. This study represents a special case of an independent metering concept applied to the design of power hydraulic systems with direct proportional valve control operating at flow rates above 150 litres per minute. The result gained using parametric CFD simulations predicted the induced torque and the pressure drops due to a steady flow. Magnitudes of these values prove that by minimising the number of spool's mobile metering surfaces it is possible to reduce the flow-generated forces in the new generation of hydraulic valves proposed in this study

A Computational Fluid Dynamics Study of Swirling Flow Reduction by Using Anti-Vortex Baffle

Science.gov (United States)

Yang, H. Q.; Peugeot, John W.; West, Jeff S.

2017-01-01

An anti-vortex baffle is a liquid propellant management device placed adjacent to an outlet of the propellant tank. Its purpose is to substantially reduce or eliminate the formation of free surface dip and vortex, as well as prevent vapor ingestion into the outlet, as the liquid drains out through the flight. To design an effective anti-vortex baffle, Computational Fluid Dynamic (CFD) simulations were undertaken for the NASA Ares I vehicle LOX tank subjected to the simulated flight loads with and without the anti-vortex baffle. The Six Degree-Of-Freedom (6-DOF) dynamics experienced by the Crew Launch Vehicle (CLV) during ascent were modeled by modifying the momentum equations in a CFD code to accommodate the extra body forces from the maneuvering in a non-inertial frame. The present analysis found that due to large moments, the CLV maneuvering has a significant impact on the vortical flow generation inside the tank. Roll maneuvering and side loading due to pitch and yaw are shown to induce swirling flow. The vortical flow due to roll is symmetrical with respect to the tank centerline, while those induced by pitch and yaw maneuverings showed two vortices side by side. The study found that without the anti-vortex baffle, the swirling flow caused surface dip during the late stage of drainage and hence early vapor ingestion. The flow can also be non-uniform in the drainage pipe as the secondary swirling flow velocity component can be as high as 10% of the draining velocity. An analysis of the vortex dynamics shows that the swirling flow in the drainage pipe during the Upper Stage burn is mainly the result of residual vortices inside the tank due to the conservation of angular momentum. The study demonstrated that the swirling flow in the drainage pipe can be effectively suppressed by employing the anti-vortex baffle.

Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated......Many questions about the nature of aggregation and the proteins that are involved in these events are still left unanswered. One of the proteins that is known to form amyloids is Transthyretine (TTR), the secondary transporter of thyroxine and transporter of retinol-binding-protein. Several...

Hepatic blood flow mapping by dynamic CT method in liver diseases

International Nuclear Information System (INIS)

Sugano, Shigeo; Mizuyosi, Hideo; Okajima, Tsugio; Ishii, Kouji; Abei, Tohru; Machida, Keiichi

1986-01-01

Two parameters of dynamic CT, peak time (PT) and first moment (M1), were compared among healthy control, chronic hepatitis (CH) and liver cirrhosis (LC). The means of PT and M1 in each 9 (3 x 3) pixels on a slice of hepatic CT were computed and converted to gray spots by gray scale, so that deep gray represented high values and light gray low values of these parameters. The distribution of these gray spots in each pixels was depicted on the slice as a blood flow mapping, and it was compared among the groups. In normal control, dynamic CT showed the shortest PT and deep gray spots were distributed diffusely in the slice. In CH, where PT was longer than control, lighter gray spots were diffusely seen. LC had the longest PT and its mapping showed mottles of light gray and black, the latter indicating the presence of spots with scanty blood flow, scattering throughout the slice. The mapping of M1 gave almost the same picture as PT for each group, revieling that the disappearring time of the media in CH and LC was impaired in the same manner as in PT. This method of hepatic blood flow mapping was thought to be useful to add evidences for the understanding of abnormal blood flow in liver diseases. (author)

Fluid dynamics following flow shut-off in bottle filling

Science.gov (United States)

Thete, Sumeet; Appathurai, Santosh; Gao, Haijing; Basaran, Osman

2012-11-01

Bottle filling is ubiquitous in industry. Examples include filling of bottles with shampoos and cleaners, engine oil and pharmaceuticals. In these examples, fluid flows out of a nozzle to fill bottles in an assembly line. Once the required volume of fluid has flowed out of the nozzle, the flow is shut off. However, an evolving fluid thread or string may remain suspended from the nozzle following flow shut-off and persist. This stringing phenomenon can be detrimental to a bottle filling operation because it can adversely affect line speed and filling accuracy by causing uncertainty in fill volume, product loss and undesirable marring of the bottles' exterior surfaces. The dynamics of stringing are studied numerically primarily by using the 1D, slender-jet approximation of the flow equations. A novel feature entails development and use of a new boundary condition downstream of the nozzle exit to expedite the computations. While the emphasis is on stringing of Newtonian fluids and use of 1D approximations, results will also be presented for situations where (a) the fluids are non-Newtonian and (b) the full set of equations are solved without invoking the 1D approximation. Phase diagrams will be presented that identify conditions for which stringing can be problematic.

Renal blood flow regulation and arterial pressure fluctuations: a case study in nonlinear dynamics

DEFF Research Database (Denmark)

Holstein-Rathlou, N H; Marsh, D J

1994-01-01

in which the kidney is obliged to operate. Were it not for renal blood flow autoregulation, it would be difficult to regulate renal excretory processes so as to maintain whole body variables within narrow bounds. Autoregulation is the noise filter on which other renal processes depend for maintaining...... a relatively noise-free environment in which to work. Because of the time-varying nature of the blood pressure, we have concentrated in this review on the now substantial body of work on the dynamics of renal blood flow regulation and the underlying mechanisms. Renal vascular control mechanisms are not simply....... The significance of deterministic chaos in the context of renal blood flow regulation is that the system regulating blood flow undergoes a physical change to a different dynamical state, and because the change is deterministic, there is every expectation that the critical change will yield itself to experimental...

Debris flow analysis with a one dimensional dynamic run-out model that incorporates entrained material

Science.gov (United States)

Luna, Byron Quan; Remaître, Alexandre; van Asch, Theo; Malet, Jean-Philippe; van Westen, Cees

2010-05-01

Estimating the magnitude and the intensity of rapid landslides like debris flows is fundamental to evaluate quantitatively the hazard in a specific location. Intensity varies through the travelled course of the flow and can be described by physical features such as deposited volume, velocities, height of the flow, impact forces and pressures. Dynamic run-out models are able to characterize the distribution of the material, its intensity and define the zone where the elements will experience an impact. These models can provide valuable inputs for vulnerability and risk calculations. However, most dynamic run-out models assume a constant volume during the motion of the flow, ignoring the important role of material entrained along its path. Consequently, they neglect that the increase of volume enhances the mobility of the flow and can significantly influence the size of the potential impact area. An appropriate erosion mechanism needs to be established in the analyses of debris flows that will improve the results of dynamic modeling and consequently the quantitative evaluation of risk. The objective is to present and test a simple 1D debris flow model with a material entrainment concept based on limit equilibrium considerations and the generation of excess pore water pressure through undrained loading of the in situ bed material. The debris flow propagation model is based on a one dimensional finite difference solution of a depth-averaged form of the Navier-Stokes equations of fluid motions. The flow is treated as a laminar one phase material, which behavior is controlled by a visco-plastic Coulomb-Bingham rheology. The model parameters are evaluated and the model performance is tested on a debris flow event that occurred in 2003 in the Faucon torrent (Southern French Alps).

Fluid flow dynamics in MAS systems

Science.gov (United States)

Wilhelm, Dirk; Purea, Armin; Engelke, Frank

2015-08-01

The turbine system and the radial bearing of a high performance magic angle spinning (MAS) probe with 1.3 mm-rotor diameter has been analyzed for spinning rates up to 67 kHz. We focused mainly on the fluid flow properties of the MAS system. Therefore, computational fluid dynamics (CFD) simulations and fluid measurements of the turbine and the radial bearings have been performed. CFD simulation and measurement results of the 1.3 mm-MAS rotor system show relatively low efficiency (about 25%) compared to standard turbo machines outside the realm of MAS. However, in particular, MAS turbines are mainly optimized for speed and stability instead of efficiency. We have compared MAS systems for rotor diameter of 1.3-7 mm converted to dimensionless values with classical turbomachinery systems showing that the operation parameters (rotor diameter, inlet mass flow, spinning rate) are in the favorable range. This dimensionless analysis also supports radial turbines for low speed MAS probes and diagonal turbines for high speed MAS probes. Consequently, a change from Pelton type MAS turbines to diagonal turbines might be worth considering for high speed applications. CFD simulations of the radial bearings have been compared with basic theoretical values proposing considerably smaller frictional loss values. The discrepancies might be due to the simple linear flow profile employed for the theoretical model. Frictional losses generated inside the radial bearings result in undesired heat-up of the rotor. The rotor surface temperature distribution computed by CFD simulations show a large temperature gradient over the rotor.

Hydrodynamically Coupled Brownian Dynamics simulations for flow on non-Newtonian fluids

NARCIS (Netherlands)

Ahuja, Vishal Raju

2018-01-01

This thesis deals with model development for particle-based flow simulations of non-Newtonian fluids such as polymer solutions. A novel computational technique called Hydrodynamically Coupled Brownian Dynamics (HCBD) is presented in this thesis. This technique essentially couples the Brownian motion

Analysis of phase dynamics in two-phase flow using latticegas automata

International Nuclear Information System (INIS)

Ohashi, H.; Hashimoto, Y.; Tsumaya, A.; Chen, Y.; Akiyama, M.

1998-01-01

In this paper, we describe lattice gas automaton models appropriate for two-phase flow simulation and their applications to study various phase dynamics of two-fluid mixtures. Several algorithms are added to the original immiscible Lattice Gas model to adjust surface tension and to introduce density difference between two fluids. Surface tension is controlled by the collision rules an difference in density is due to nonlocal forces between automaton particles. We simulate the relative motion of the dispersed phase in another continuous fluid. Deformation and disintegration of rising drops are reproduced. The interaction between multiple drops is also observed in calculations. Furutre, we obtain the transition of the two-phase flow pattern from bubbly, slug to annular flow. Density difference of two phase is one of the key ingredients to generate the annular flow pattern

Numerical modeling of turbulent swirling flow in a multi-inlet vortex nanoprecipitation reactor using dynamic DDES

Science.gov (United States)

Hill, James C.; Liu, Zhenping; Fox, Rodney O.; Passalacqua, Alberto; Olsen, Michael G.

2015-11-01

The multi-inlet vortex reactor (MIVR) has been developed to provide a platform for rapid mixing in the application of flash nanoprecipitation (FNP) for manufacturing functional nanoparticles. Unfortunately, commonly used RANS methods are unable to accurately model this complex swirling flow. Large eddy simulations have also been problematic, as expensive fine grids to accurately model the flow are required. These dilemmas led to the strategy of applying a Delayed Detached Eddy Simulation (DDES) method to the vortex reactor. In the current work, the turbulent swirling flow inside a scaled-up MIVR has been investigated by using a dynamic DDES model. In the DDES model, the eddy viscosity has a form similar to the Smagorinsky sub-grid viscosity in LES and allows the implementation of a dynamic procedure to determine its coefficient. The complex recirculating back flow near the reactor center has been successfully captured by using this dynamic DDES model. Moreover, the simulation results are found to agree with experimental data for mean velocity and Reynolds stresses.

Post-operative ventricular flow dynamics following atrioventricular valve surgical and device therapies: A review.

Science.gov (United States)

Nguyen, Yen Ngoc; Ismail, Munirah; Kabinejadian, Foad; Tay, Edgar Lik Wui; Leo, Hwa Liang

2018-04-01

Intra-ventricular flow dynamics has recently emerged as an important evaluation and diagnosis tool in different cardiovascular conditions. The formation of vortex pattern during the cardiac cycle has been suggested to play important epigenetic and energy-modulation roles in cardiac remodelling, adaptations and mal-adaptations. In this new perspective, flow alterations due to different cardiovascular procedures can affect the long-term outcome of those procedures. Especially, repairs and replacements performed on atrioventricular valves are likely to exert direct impact on intra-ventricular flow pattern. In this review, current consensus around the roles of vortex dynamics in cardiac function is discussed. An overview of physiological vortex patterns found in healthy left and right ventricles as well as post-operative ventricular flow phenomenon owing to different atrioventricular valvular procedures are reviewed, followed by the summary of different vortex identification schemes used to characterise intraventricular flow. This paper also emphasises on future research directions towards a comprehensive understanding of intra-cardiac flow and its clinical relevance. The knowledge could encourage more effective pre-operative planning and better outcomes for current clinical practices. Copyright © 2018. Published by Elsevier Ltd.

Mapping of barley alpha-amylases and outer subsite mutants reveals dynamic high-affinity subsites and barriers in the long substrate binding cleft

DEFF Research Database (Denmark)

Kandra, L.; Abou Hachem, Maher; Gyemant, G.

2006-01-01

Subsite affinity maps of long substrate binding clefts in barley alpha-amylases, obtained using a series of maltooligosaccharides of degree of polymerization of 3-12, revealed unfavorable binding energies at the internal subsites -3 and -5 and at subsites -8 and +3/+4 defining these subsites...... as binding barriers. Barley a-amylase I mutants Y105A and T212Y at subsite -6 and +4 resulted in release or anchoring of bound substrate, thus modifying the affinities of other high-affinity subsites (-2 and +2) and barriers. The double mutant Y105A-T212Y displayed a hybrid subsite affinity profile......, converting barriers to binding areas. These findings highlight the dynamic binding energy distribution and the versatility of long maltooligosaccharide derivatives in mapping extended binding clefts in a-amylases....

Understanding Ion Binding Affinity and Selectivity in β-Parvalbumin Using Molecular Dynamics and Mean Spherical Approximation Theory.

Science.gov (United States)

Kucharski, Amir N; Scott, Caitlin E; Davis, Jonathan P; Kekenes-Huskey, Peter M

2016-08-25

Parvalbumin (PV) is a globular calcium (Ca(2+))-selective protein expressed in a variety of biological tissues. Our computational studies of the rat β-parvalbumin (β-PV) isoform seek to elucidate the molecular thermodynamics of Ca(2+) versus magnesium (Mg(2+)) binding at the protein's two EF-hand motifs. Specifically, we have utilized molecular dynamics (MD) simulations and a mean-field electrolyte model (mean spherical approximation (MSA) theory) to delineate how the EF-hand scaffold controls the "local" thermodynamics of Ca(2+) binding selectivity over Mg(2+). Our MD simulations provide the probability density of metal-chelating oxygens within the EF-hand scaffolds for both Ca(2+) and Mg(2+), as well the conformational strain induced by Mg(2+) relative to Ca(2+) binding. MSA theory utilizes the binding domain oxygen and charge distributions to predict the chemical potential of ion binding, as well as their corresponding concentrations within the binding domain. We find that the electrostatic and steric contributions toward ion binding were similar for Mg(2+) and Ca(2+), yet the latter was 5.5 kcal/mol lower in enthalpy when internal strain within the EF hand was considered. We therefore speculate that beyond differences in dehydration energies for the Ca(2+) versus Mg(2+), strain induced in the β-PV EF hand by cation binding significantly contributes to the nearly 10,000-fold difference in binding affinity reported in the literature. We further complemented our analyses of local factors governing cation binding selectivity with whole-protein (global) contributions, such as interhelical residue-residue contacts and solvent exposure of hydrophobic surface. These contributions were found to be comparable for both Ca(2+)- and Mg(2+)-bound β-PV, which may implicate local factors, EF-hand strain, and dehydration, in providing the primary means of selectivity. We anticipate these methods could be used to estimate metal binding thermodynamics across a broad range of

Hydro-dynamic Solute Transport under Two-Phase Flow Conditions.

Science.gov (United States)

Karadimitriou, Nikolaos K; Joekar-Niasar, Vahid; Brizuela, Omar Godinez

2017-07-26

There are abundant examples of natural, engineering and industrial applications, in which "solute transport" and "mixing" in porous media occur under multiphase flow conditions. Current state-of-the-art understanding and modelling of such processes are established based on flawed and non-representative models. Moreover, there is no direct experimental result to show the true hydrodynamics of transport and mixing under multiphase flow conditions while the saturation topology is being kept constant for a number of flow rates. With the use of a custom-made microscope, and under well-controlled flow boundary conditions, we visualized directly the transport of a tracer in a Reservoir-on-Chip (RoC) micromodel filled with two immiscible fluids. This study provides novel insights into the saturation-dependency of transport and mixing in porous media. To our knowledge, this is the first reported pore-scale experiment in which the saturation topology, relative permeability, and tortuosity were kept constant and transport was studied under different dynamic conditions in a wide range of saturation. The critical role of two-phase hydrodynamic properties on non-Fickian transport and saturation-dependency of dispersion are discussed, which highlight the major flaws in parametrization of existing models.

Open-end tube dynamic flow model with an oscillatory extortion

Directory of Open Access Journals (Sweden)

Tulwin Tytus

2017-01-01

Full Text Available This paper presents a derivation of dynamic 2d mathematical model for open end tube with oscillatory extortion in the region of the closed end. The aim the research is to investigate possible uses of the increased pressure in the enclosed tube chamber, especially for energy efficient lift generation. The mathematical model allows to test and predict how flow modifications impact the resultant lifting force. A derivation of the proposed mathematical model is shown. The mathematical model is then compared to the computational fluid dynamics discrete model. The results prove the accuracy of the mathematical physical model.

A dynamic global-coefficient mixed subgrid-scale model for large-eddy simulation of turbulent flows

International Nuclear Information System (INIS)

Singh, Satbir; You, Donghyun

2013-01-01

Highlights: ► A new SGS model is developed for LES of turbulent flows in complex geometries. ► A dynamic global-coefficient SGS model is coupled with a scale-similarity model. ► Overcome some of difficulties associated with eddy-viscosity closures. ► Does not require averaging or clipping of the model coefficient for stabilization. ► The predictive capability is demonstrated in a number of turbulent flow simulations. -- Abstract: A dynamic global-coefficient mixed subgrid-scale eddy-viscosity model for large-eddy simulation of turbulent flows in complex geometries is developed. In the present model, the subgrid-scale stress is decomposed into the modified Leonard stress, cross stress, and subgrid-scale Reynolds stress. The modified Leonard stress is explicitly computed assuming a scale similarity, while the cross stress and the subgrid-scale Reynolds stress are modeled using the global-coefficient eddy-viscosity model. The model coefficient is determined by a dynamic procedure based on the global-equilibrium between the subgrid-scale dissipation and the viscous dissipation. The new model relieves some of the difficulties associated with an eddy-viscosity closure, such as the nonalignment of the principal axes of the subgrid-scale stress tensor and the strain rate tensor and the anisotropy of turbulent flow fields, while, like other dynamic global-coefficient models, it does not require averaging or clipping of the model coefficient for numerical stabilization. The combination of the global-coefficient eddy-viscosity model and a scale-similarity model is demonstrated to produce improved predictions in a number of turbulent flow simulations

Membrane dynamics of γ-secretase provides a molecular basis for Aβ binding and processing

DEFF Research Database (Denmark)

Somavarapu, Arun Kumar; Kepp, Kasper Planeta

2017-01-01

and explicit dynamics relevant to substrate processing remain unknown. We report a modeled structure utilizing the optimal multi-template information available, including loops and missing side chains, account of maturation cleavage, and explicit all-atom molecular dynamics in the membrane. We observe three...... interactions and induces shorter residence time and by inference releases Aβ peptides of longer lengths. Our simulations thus provide a molecular basis for substrate processing and changes in the Aβ42/Aβ40 ratio. Accordingly, selective binding to protect the semi-open “innocent” conformation provides......γ-secretase produces β-amyloid (Aβ) within its presenilin (PS1) subunit, mutations in which cause Alzheimer’s disease, and current therapies thus seek to modulate its activity. While the general structure is known from recent electron microscopy studies, direct loop- and membrane-interactions...

A total pressure-saturation formulation of two-phase flow incorporating dynamic effects in the capillary-pressure-saturation relationship

Energy Technology Data Exchange (ETDEWEB)

Dahle, H K; Celia, M A; Hassanizadeh, S M; Karlsen, K H

2002-07-01

New theories suggest that the relationship between capillary pressure and saturation should be enhanced by a dynamic term that is proportional to the time rate of change of saturation. This so-called dynamic capillary pressure formulation is supported by laboratory experiments, and can be included in various forms of the governing equations for two-phase flow in porous media. An extended model of two-phase flow in porous media may be developed based on fractional flow curves and a total pressure - saturation description that includes the dynamic capillary pressure terms. A dimensionless form of the resulting equation set provides an ideal tool to study the relative importance of the dynamic capillary pressure effect. This equation provides a rich set of mathematical research questions, and numerical solutions to the equation provide insights into the behavior of two-phase immiscible flow. For typical two-phase flow systems, dynamic capillary pressure acts to retard infiltration fronts, with responses dependent on system parameters including boundary conditions. Recent theoretical work suggests that the traditional algebraic relationship between capillary pressure and saturation may be inadequate. Instead, a so-called dynamic capillary pressure formulation is needed, where capillary pressure is defined as a thermodynamic variable, and the difference between phase pressures is only equal to the capillary pressure at equilibrium. Under dynamic conditions, the disequilibrium between phase-pressure differences and the capillary pressure is taken to be proportional to the time rate of change of saturation. A recent study by Hassanizadeh et al. presents experimental evidence, culled from the literature, to support this claim. Numerical simulations using dynamic pore-scale network models and upscaling also support the claim. Hassanizadeh et al. also presented numerical solutions for an enhanced version of Richards' equation that included the dynamic terms. A preliminary

Probing of possible olanzapine binding site on human serum albumin: Combination of spectroscopic methods and molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Shahlaei, Mohsen, E-mail: mohsenshahlaei@yahoo.com [Nano drug delivery research Center, Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Rahimi, Behnoosh [Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Student research committee, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Ashrafi-Kooshk, Mohammad Reza [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Sadrjavadi, Komail [Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Khodarahmi, Reza, E-mail: rkhodarahmi@mbrc.ac.ir [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

2015-02-15

Human serum albumin (HSA)-drug binding affinity is one of the major factors that determine the pharmacokinetics, halftime and bioavailability of drugs in various tissues. In the present study, the interaction of olanzapine (OLZ), a thienobenzodiazepine drug, administered for the treatment of schizophrenia and bipolar disorder, with HSA has been studied using spectroscopic methods such as ultraviolet absorbance, fluorescence and FTIR combined with computational procedures. Analyzing of the Stern–Volmer quenching data showed only one primary binding site on HSA with a binding constant of 4.12×10{sup 4} M{sup −1} at 298 K. Thermodynamic analyses showed enthalpy change (ΔH°) and entropy change (ΔS°) were 28.03±3.42 kJ mol{sup −1} and −25.52±11.52 J mol{sup −1} K{sup −1}, respectively. Molecular docking results suggested the hydrophobic residues such as Val{sub 216}, Leu{sub 327}, Ala{sub 350} and polar residues such as Glu{sub 354} play an important role in the drug binding. Decrement in α-helix content of the protein upon OLZ binding was also confirmed by evidences provided by molecular dynamics simulation as well as FTIR spectroscopy. - Highlights: • Leu{sub 327}, Ala{sub 350} as well as hydrophilic residues of HSA play an important role in the binding reaction. • The drug has only one primary binding site on HSA with a binding constant of 4.12×10{sup 4} M{sup −1} at 298 K. • The drug binds near to site I.

Information Flow Through Stages of Complex Engineering Design Projects: A Dynamic Network Analysis Approach

DEFF Research Database (Denmark)

Parraguez, Pedro; Eppinger, Steven D.; Maier, Anja

2015-01-01

The pattern of information flow through the network of interdependent design activities is thought to be an important determinant of engineering design process results. A previously unexplored aspect of such patterns relates to the temporal dynamics of information transfer between activities...... design process and thus support theory-building toward the evolution of information flows through systems engineering stages. Implications include guidance on how to analyze and predict information flows as well as better planning of information flows in engineering design projects according...

Hybrid Approximate Dynamic Programming Approach for Dynamic Optimal Energy Flow in the Integrated Gas and Power Systems

DEFF Research Database (Denmark)

Shuai, Hang; Ai, Xiaomeng; Wen, Jinyu

2017-01-01

This paper proposes a hybrid approximate dynamic programming (ADP) approach for the multiple time-period optimal power flow in integrated gas and power systems. ADP successively solves Bellman's equation to make decisions according to the current state of the system. So, the updated near future...

Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

Energy Technology Data Exchange (ETDEWEB)

Cheng, Xiaofei [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036 (China); Deng, Ping; Cui, Hongguang [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); Wang, Aiming, E-mail: aiming.wang@agr.gc.ca [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada)

2015-11-15

Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

International Nuclear Information System (INIS)

Cheng, Xiaofei; Deng, Ping; Cui, Hongguang; Wang, Aiming

2015-01-01

Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

Dynamic properties of blood flow and leukocyte mobilization in infected flaps

International Nuclear Information System (INIS)

Feng, L.J.; Price, D.C.; Mathes, S.J.; Hohn, D.

1990-01-01

Two aspects of the inflammatory response to infection--blood flow alteration and leukocyte mobilization--are investigated in the canine model. The elevation of paired musculocutaneous (MC) and random pattern (RP) flaps allowed comparison of healing flaps with significant differences in blood flow (lower in random pattern flaps) and resistance to infection (greater in musculocutaneous flaps). Blood flow changes as determined by radioactive xenon washout were compared in normal skin and distal flap skin both after elevation and following bacterial inoculation. Simultaneous use of In-111 labeled leukocytes allowed determination of leukocyte mobilization and subsequent localization in response to flap infection. Blood flow significantly improved in the musculocutaneous flap in response to infection. Although total leukocyte mobilization in the random pattern flap was greater, the leukocytes in the musculocutaneous flap were localized around the site of bacterial inoculation within the dermis. Differences in the dynamic blood flow and leukocyte mobilization may, in part, explain the greater reliability of musculocutaneous flaps when transposed in the presence of infection

Irreversible energy flow in forced Vlasov dynamics

KAUST Repository

Plunk, Gabriel G.; Parker, Joseph T.

2014-01-01

© EDP Sciences, Società Italiana di Fisica, Springer-Verlag. The recent paper of Plunk [G.G. Plunk, Phys. Plasmas 20, 032304 (2013)] considered the forced linear Vlasov equation as a model for the quasi-steady state of a single stable plasma wavenumber interacting with a bath of turbulent fluctuations. This approach gives some insight into possible energy flows without solving for nonlinear dynamics. The central result of the present work is that the forced linear Vlasov equation exhibits asymptotically zero (irreversible) dissipation to all orders under a detuning of the forcing frequency and the characteristic frequency associated with particle streaming. We first prove this by direct calculation, tracking energy flow in terms of certain exact conservation laws of the linear (collisionless) Vlasov equation. Then we analyze the steady-state solutions in detail using a weakly collisional Hermite-moment formulation, and compare with numerical solution. This leads to a detailed description of the Hermite energy spectrum, and a proof of no dissipation at all orders, complementing the collisionless Vlasov result.

Irreversible energy flow in forced Vlasov dynamics

KAUST Repository

Plunk, Gabriel G.

2014-10-01

© EDP Sciences, Società Italiana di Fisica, Springer-Verlag. The recent paper of Plunk [G.G. Plunk, Phys. Plasmas 20, 032304 (2013)] considered the forced linear Vlasov equation as a model for the quasi-steady state of a single stable plasma wavenumber interacting with a bath of turbulent fluctuations. This approach gives some insight into possible energy flows without solving for nonlinear dynamics. The central result of the present work is that the forced linear Vlasov equation exhibits asymptotically zero (irreversible) dissipation to all orders under a detuning of the forcing frequency and the characteristic frequency associated with particle streaming. We first prove this by direct calculation, tracking energy flow in terms of certain exact conservation laws of the linear (collisionless) Vlasov equation. Then we analyze the steady-state solutions in detail using a weakly collisional Hermite-moment formulation, and compare with numerical solution. This leads to a detailed description of the Hermite energy spectrum, and a proof of no dissipation at all orders, complementing the collisionless Vlasov result.

A simple delay model for two-phase flow dynamics

Energy Technology Data Exchange (ETDEWEB)

Clausse, A.; Delmastro, D.F.; Juanico`, L.E. [Centro Atomico Bariloche (Argentina)

1995-09-01

A model based in delay equations for density-wave oscillations is presented. High Froude numbers and moderate ones were considered. The equations were numerically analyzed and compared with more sophisticated models. The influence of the gravity term was studied. Different kinds of behavior were found, particularly sub-critical and super-critical Hopf bifurcations. Moreover the present approach can be used to better understand the complicated dynamics of boiling flows systems.

Probing the 3-D Structure, Dynamics, and Stability of Bacterial Collagenase Collagen Binding Domain (apo- versus holo-) by Limited Proteolysis MALDI-TOF MS

Science.gov (United States)

Sides, Cynthia R.; Liyanage, Rohana; Lay, Jackson O.; Philominathan, Sagaya Theresa Leena; Matsushita, Osamu; Sakon, Joshua

2012-03-01

Pairing limited proteolysis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to probe clostridial collagenase collagen binding domain (CBD) reveals the solution dynamics and stability of the protein, as these factors are crucial to CBD effectiveness as a drug-delivery vehicle. MS analysis of proteolytic digests indicates initial cleavage sites, thereby specifying the less stable and highly accessible regions of CBD. Modulation of protein structure and stability upon metal binding is shown through MS analysis of calcium-bound and cobalt-bound CBD proteolytic digests. Previously determined X-ray crystal structures illustrate that calcium binding induces secondary structure transformation in the highly mobile N-terminal arm and increases protein stability. MS-based detection of exposed residues confirms protein flexibility, accentuates N-terminal dynamics, and demonstrates increased global protein stability exported by calcium binding. Additionally, apo- and calcium-bound CBD proteolysis sites correlate well with crystallographic B-factors, accessibility, and enzyme specificity. MS-observed cleavage sites with no clear correlations are explained either by crystal contacts of the X-ray crystal structures or by observed differences between Molecules A and B in the X-ray crystal structures. The study newly reveals the absence of the βA strand and thus the very dynamic N-terminal linker, as corroborated by the solution X-ray scattering results. Cobalt binding has a regional effect on the solution phase stability of CBD, as limited proteolysis data implies the capture of an intermediate-CBD solution structure when cobalt is bound.

State diagram for adhesion dynamics of deformable capsules under shear flow.

Science.gov (United States)

Luo, Zheng Yuan; Bai, Bo Feng

2016-08-17

Due to the significance of understanding the underlying mechanisms of cell adhesion in biological processes and cell capture in biomedical applications, we numerically investigate the adhesion dynamics of deformable capsules under shear flow by using a three-dimensional computational fluid dynamic model. This model is based on the coupling of the front tracking-finite element method for elastic mechanics of the capsule membrane and the adhesion kinetics simulation for adhesive interactions between capsules and functionalized surfaces. Using this model, three distinct adhesion dynamic states are predicted, such as detachment, rolling and firm-adhesion. Specifically, the effects of capsule deformability quantified by the capillary number on the transitions of these three dynamic states are investigated by developing an adhesion dynamic state diagram for the first time. At low capillary numbers (e.g. Ca state no longer appears, since capsules exhibit large deviation from the spherical shape.

Research on Dynamic Dissolving Model and Experiment for Rock Salt under Different Flow Conditions

Directory of Open Access Journals (Sweden)

Xinrong Liu

2015-01-01

Full Text Available Utilizing deep rock salt cavern is not only a widely recognized energy reserve method but also a key development direction for implementing the energy strategic reserve plan. And rock salt cavern adopts solution mining techniques to realize building cavity. In view of this, the paper, based on the dissolving properties of rock salt, being simplified and hypothesized the dynamic dissolving process of rock salt, combined conditions between dissolution effect and seepage effect in establishing dynamic dissolving models of rock salt under different flow quantities. Devices were also designed to test the dynamic dissolving process for rock salt samples under different flow quantities and then utilized the finite-difference method to find the numerical solution of the dynamic dissolving model. The artificial intelligence algorithm, Particle Swarm Optimization algorithm (PSO, was finally introduced to conduct inverse analysis of parameters on the established model, whose calculation results coincide with the experimental data.

The dynamic behavior of chemically "stiffened" red blood cells in microchannel flows.

Science.gov (United States)

Forsyth, Alison M; Wan, Jiandi; Ristenpart, William D; Stone, Howard A

2010-07-01

The rigidity of red blood cells (RBCs) plays an important role in whole blood viscosity and is correlated with several cardiovascular diseases. Two chemical agents that are commonly used to study cell deformation are diamide and glutaraldehyde. Despite diamide's common usage, there are discrepancies in the literature surrounding diamide's effect on the deformation of RBCs in shear and pressure-driven flows; in particular, shear flow experiments have shown that diamide stiffens cells, while pressure-driven flow in capillaries did not give this result. We performed pressure-driven flow experiments with RBCs in a microfluidic constriction and quantified the cell dynamics using high-speed imaging. Diamide, which affects RBCs by cross-linking spectrin skeletal membrane proteins, did not reduce deformation and showed an unchanged effective strain rate when compared to healthy cells. In contrast, glutaraldehyde, which is a non-specific fixative that acts on all components of the cell, did reduce deformation and showed increased instances of tumbling, both of which are characteristic features of stiffened, or rigidified, cells. Because glutaraldehyde increases the effective viscosity of the cytoplasm and lipid membrane while diamide does not, one possible explanation for our results is that viscous effects in the cytoplasm and/or lipid membrane are a dominant factor in dictating dynamic responses of RBCs in pressure-driven flows. Finally, literature on the use of diamide as a stiffening agent is summarized, and provides supporting evidence for our conclusions. Copyright 2010 Elsevier Inc. All rights reserved.

Quantitative flow analysis of swimming dynamics with coherent Lagrangian vortices.

Science.gov (United States)

Huhn, F; van Rees, W M; Gazzola, M; Rossinelli, D; Haller, G; Koumoutsakos, P

2015-08-01

Undulatory swimmers flex their bodies to displace water, and in turn, the flow feeds back into the dynamics of the swimmer. At moderate Reynolds number, the resulting flow structures are characterized by unsteady separation and alternating vortices in the wake. We use the flow field from simulations of a two-dimensional, incompressible viscous flow of an undulatory, self-propelled swimmer and detect the coherent Lagrangian vortices in the wake to dissect the driving momentum transfer mechanisms. The detected material vortex boundary encloses a Lagrangian control volume that serves to track back the vortex fluid and record its circulation and momentum history. We consider two swimming modes: the C-start escape and steady anguilliform swimming. The backward advection of the coherent Lagrangian vortices elucidates the geometry of the vorticity field and allows for monitoring the gain and decay of circulation and momentum transfer in the flow field. For steady swimming, momentum oscillations of the fish can largely be attributed to the momentum exchange with the vortex fluid. For the C-start, an additionally defined jet fluid region turns out to balance the high momentum change of the fish during the rapid start.

Predicting Flow Reversals in a Computational Fluid Dynamics Simulated Thermosyphon Using Data Assimilation.

Science.gov (United States)

Reagan, Andrew J; Dubief, Yves; Dodds, Peter Sheridan; Danforth, Christopher M

2016-01-01

A thermal convection loop is a annular chamber filled with water, heated on the bottom half and cooled on the top half. With sufficiently large forcing of heat, the direction of fluid flow in the loop oscillates chaotically, dynamics analogous to the Earth's weather. As is the case for state-of-the-art weather models, we only observe the statistics over a small region of state space, making prediction difficult. To overcome this challenge, data assimilation (DA) methods, and specifically ensemble methods, use the computational model itself to estimate the uncertainty of the model to optimally combine these observations into an initial condition for predicting the future state. Here, we build and verify four distinct DA methods, and then, we perform a twin model experiment with the computational fluid dynamics simulation of the loop using the Ensemble Transform Kalman Filter (ETKF) to assimilate observations and predict flow reversals. We show that using adaptively shaped localized covariance outperforms static localized covariance with the ETKF, and allows for the use of less observations in predicting flow reversals. We also show that a Dynamic Mode Decomposition (DMD) of the temperature and velocity fields recovers the low dimensional system underlying reversals, finding specific modes which together are predictive of reversal direction.

Predicting Flow Reversals in a Computational Fluid Dynamics Simulated Thermosyphon Using Data Assimilation.

Directory of Open Access Journals (Sweden)

Andrew J Reagan

Full Text Available A thermal convection loop is a annular chamber filled with water, heated on the bottom half and cooled on the top half. With sufficiently large forcing of heat, the direction of fluid flow in the loop oscillates chaotically, dynamics analogous to the Earth's weather. As is the case for state-of-the-art weather models, we only observe the statistics over a small region of state space, making prediction difficult. To overcome this challenge, data assimilation (DA methods, and specifically ensemble methods, use the computational model itself to estimate the uncertainty of the model to optimally combine these observations into an initial condition for predicting the future state. Here, we build and verify four distinct DA methods, and then, we perform a twin model experiment with the computational fluid dynamics simulation of the loop using the Ensemble Transform Kalman Filter (ETKF to assimilate observations and predict flow reversals. We show that using adaptively shaped localized covariance outperforms static localized covariance with the ETKF, and allows for the use of less observations in predicting flow reversals. We also show that a Dynamic Mode Decomposition (DMD of the temperature and velocity fields recovers the low dimensional system underlying reversals, finding specific modes which together are predictive of reversal direction.

Quantitative chemical exchange saturation transfer with hyperpolarized nuclei (qHyper-CEST): sensing xenon-host exchange dynamics and binding affinities by NMR.

Science.gov (United States)

Kunth, M; Witte, C; Schröder, L

2014-11-21

The reversible binding of xenon to host molecules has found numerous applications in nuclear magnetic resonance studies. Quantitative characterization of the Xe exchange dynamics is important to understand and optimize the physico-chemical behavior of such Xe hosts, but is often challenging to achieve at low host concentrations. We have investigated a sensitive quantification technique based on chemical exchange saturation transfer with hyperpolarized nuclei, qHyper-CEST. Using simulated signals we demonstrated that qHyper-CEST yielded accurate and precise results and was robust in the presence of large amounts of noise (10%). This is of particular importance for samples with completely unknown exchange rates. Using these findings we experimentally determined the following exchange parameters for the Xe host cryptophane-A monoacid in dimethyl sulfoxide in one type of experiment: the ratio of bound and free Xe, the Xe exchange rate, the resonance frequencies of free and bound Xe, the Xe host occupancy, and the Xe binding constant. Taken together, qHyper-CEST facilitates sensitive quantification of the Xe exchange dynamics and binding to hydrophobic cavities and has the potential to analyze many different host systems or binding sites. This makes qHyper-CEST an indispensable tool for the efficient design of highly specific biosensors.

Combinatorial computational chemistry approach of tight-binding quantum chemical molecular dynamics method to the design of the automotive catalysts

International Nuclear Information System (INIS)

Ito, Yuki; Jung, Changho; Luo, Yi; Koyama, Michihisa; Endou, Akira; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

2006-01-01

Recently, we have developed a new tight-binding quantum chemical molecular dynamics program 'Colors' for combinatorial computational chemistry approach. This methodology is based on our original tight-binding approximation and realized over 5000 times acceleration compared to the conventional first-principles molecular dynamics method. In the present study, we applied our new program to the simulations on various realistic large-scale models of the automotive three-way catalysts, ultrafine Pt particle/CeO 2 (111) support. Significant electron transfer from the Pt particle to the CeO 2 (111) surface was observed and it was found to strongly depend on the size of the Pt particle. Furthermore, our simulation results suggest that the reduction of the Ce atom due to the electron transfer from the Pt particle to the CeO 2 surface is a main reason for the strong interaction of the Pt particle and CeO 2 (111) support

A sequential binding mechanism in a PDZ domain

DEFF Research Database (Denmark)

Chi, Celestine N; Bach, Anders; Engström, Åke

2009-01-01

that ligand binding involves at least a two-step process. By using an ultrarapid continuous-flow mixer, we then detected a hyperbolic dependence of binding rate constants on peptide concentration, corroborating the two-step binding mechanism. Furthermore, we found a similar dependence of the rate constants...

Determination of Noncovalent Binding Using a Continuous Stirred Tank Reactor as a Flow Injection Device Coupled to Electrospray Ionization Mass Spectrometry

Science.gov (United States)

Santos, Inês C.; Waybright, Veronica B.; Fan, Hui; Ramirez, Sabra; Mesquita, Raquel B. R.; Rangel, António O. S. S.; Fryčák, Petr; Schug, Kevin A.

2015-07-01

Described is a new method based on the concept of controlled band dispersion, achieved by hyphenating flow injection analysis with ESI-MS for noncovalent binding determinations. A continuous stirred tank reactor (CSTR) was used as a FIA device for exponential dilution of an equimolar host-guest solution over time. The data obtained was treated for the noncovalent binding determination using an equimolar binding model. Dissociation constants between vancomycin and Ac-Lys(Ac)-Ala-Ala-OH peptide stereoisomers were determined using both the positive and negative ionization modes. The results obtained for Ac- L-Lys(Ac)- D-Ala- D-Ala (a model for a Gram-positive bacterial cell wall) binding were in reasonable agreement with literature values made by other mass spectrometry binding determination techniques. Also, the developed method allowed the determination of dissociation constants for vancomycin with Ac- L-Lys(Ac)- D-Ala- L-Ala, Ac- L-Lys(Ac)- L-Ala- D-Ala, and Ac- L-Lys(Ac)- L-Ala- L-Ala. Although some differences in measured binding affinities were noted using different ionization modes, the results of each determination were generally consistent. Differences are likely attributable to the influence of a pseudo-physiological ammonium acetate buffer solution on the formation of positively- and negatively-charged ionic complexes.

Axial-Flow Turbine Rotor Discharge-Flow Overexpansion and Limit-Loading Condition, Part I: Computational Fluid Dynamics (CFD) Investigation

Science.gov (United States)

Chen, Shu-Cheng S.

2017-01-01

A Computational Fluid Dynamic (CFD) investigation is conducted over a two-dimensional axial-flow turbine rotor blade row to study the phenomena of turbine rotor discharge flow overexpansion at subcritical, critical, and supercritical conditions. Quantitative data of the mean-flow Mach numbers, mean-flow angles, the tangential blade pressure forces, the mean-flow mass flux, and the flow-path total pressure loss coefficients, averaged or integrated across the two-dimensional computational domain encompassing two blade-passages, are obtained over a series of 14 inlet-total to exit-static pressure ratios, from 1.5 (un-choked; subcritical condition) to 10.0 (supercritical with excessively high pressure ratio.) Detailed flow features over the full domain-of-computation, such as the streamline patterns, Mach contours, pressure contours, blade surface pressure distributions, etc. are collected and displayed in this paper. A formal, quantitative definition of the limit loading condition based on the channel flow theory is proposed and explained. Contrary to the comments made in the historical works performed on this subject, about the deficiency of the theoretical methods applied in analyzing this phenomena, using modern CFD method for the study of this subject appears to be quite adequate and successful. This paper describes the CFD work and its findings.

Inertia-dependent dynamics of three-dimensional vesicles and red blood cells in shear flow.

Science.gov (United States)

Luo, Zheng Yuan; Wang, Shu Qi; He, Long; Xu, Feng; Bai, Bo Feng

2013-10-28

A three-dimensional (3D) simulation study of the effect of inertia on the dynamics of vesicles and red blood cells (RBCs) has not been reported. Here, we developed a 3D model based on the front tracking method to investigate how inertia affects the dynamics of spherical/non-spherical vesicles and biconcave-shaped RBCs with the Reynolds number ranging from 0.1 to 10. The results showed that inertia induced non-spherical vesicles transitioned from tumbling to swinging, which was not observed in previous 2D models. The critical viscosity ratio of inner/outer fluids for the tumbling–swinging transition remarkably increased with an increasing Reynolds number. The deformation of vesicles was greatly enhanced by inertia, and the frequency of tumbling and tank-treading was significantly decreased by inertia. We also found that RBCs can transit from tumbling to steady tank-treading through the swinging regime when the Reynolds number increased from 0.1 to 10. These results indicate that inertia needs to be considered at moderate Reynolds number (Re ~ 1) in the study of blood flow in the human body and the flow of deformable particle suspension in inertial microfluidic devices. The developed 3D model provided new insights into the dynamics of RBCs under shear flow, thus holding great potential to better understand blood flow behaviors under normal/disease conditions.

Emerging insights into the dynamics of submarine debris flows

Directory of Open Access Journals (Sweden)

A. Elverhøi

2005-01-01

Full Text Available Recent experimental and theoretical work on the dynamics of submarine debris flows is summarized. Hydroplaning was first discovered in laboratory flows and later shown to likely occur in natural debris flows as well. It is a prime mechanism for explaining the extremely long runout distances observed in some natural debris flows even of over-consolidated clay materials. Moreover, the accelerations and high velocities reached by the flow head in a short time appear to fit well with the required initial conditions of observed tsunamis as obtained from back-calculations. Investigations of high-speed video recordings of laboratory debris flows were combined with measurements of total and pore pressure. The results are pointing towards yet another important role of ambient water: Water that intrudes from the water cushion underneath the hydroplaning head and through cracks in the upper surface of the debris flow may drastically soften initially stiff clayey material in the 'neck' of the flow, where significant stretching occurs due to the reduced friction at the bottom of the hydroplaning head. This self-reinforcing process may lead to the head separating from the main body and becoming an 'outrunner' block as clearly observed in several natural debris flows. Comparison of laboratory flows with different material composition indicates a gradual transition from hydroplaning plug flows of stiff clay-rich material, with a very low suspension rate, to the strongly agitated flow of sandy materials that develop a pronounced turbidity current. Statistical analysis of the great number of distinguishable lobes in the Storegga slide complex reveals power-law scaling behavior of the runout distance with the release mass over many orders of magnitude. Mathematical flow models based on viscoplastic material behavior (e.g. BING successfully reproduce the observed scaling behavior only for relatively small clay-rich debris flows while granular (frictional models

Tight-binding molecular dynamics simulation of charge state effects in semiconductors

CERN Document Server

Khakimov, Z M; Sulaymonov, N T; Kiv, A E; Levin, A A

2002-01-01

New model of Si-H bond dissociation has been proposed and tested in the cluster Si sub 1 sub 0 H sub 1 sub 6 by the simulation approach that combines classical molecular dynamics method and the self-consistent tight-binding electronic and total energy calculation one. It is shown that the monohydride Si-H bond is unstable with respect to formation of silicon dangling bond and bend bridge Si-H-Si bond when this cluster traps the single positive charge. In this case hydrogen atom migrates rather rotating around Si-Si bond than crossing the center of this bond (the bond-centered position). The model can be useful for understanding hydrogen related phenomena at surfaces, interfaces, internal voids of various hydrogenated silicon systems: electronic devices, silicon solar cells, and nanocrystalline and porous silicon. (author)

Statistical dynamical subgrid-scale parameterizations for geophysical flows

International Nuclear Information System (INIS)

O'Kane, T J; Frederiksen, J S

2008-01-01

Simulations of both atmospheric and oceanic circulations at given finite resolutions are strongly dependent on the form and strengths of the dynamical subgrid-scale parameterizations (SSPs) and in particular are sensitive to subgrid-scale transient eddies interacting with the retained scale topography and the mean flow. In this paper, we present numerical results for SSPs of the eddy-topographic force, stochastic backscatter, eddy viscosity and eddy-mean field interaction using an inhomogeneous statistical turbulence model based on a quasi-diagonal direct interaction approximation (QDIA). Although the theoretical description on which our model is based is for general barotropic flows, we specifically focus on global atmospheric flows where large-scale Rossby waves are present. We compare and contrast the closure-based results with an important earlier heuristic SSP of the eddy-topographic force, based on maximum entropy or statistical canonical equilibrium arguments, developed specifically for general ocean circulation models (Holloway 1992 J. Phys. Oceanogr. 22 1033-46). Our results demonstrate that where strong zonal flows and Rossby waves are present, such as in the atmosphere, maximum entropy arguments are insufficient to accurately parameterize the subgrid contributions due to eddy-eddy, eddy-topographic and eddy-mean field interactions. We contrast our atmospheric results with findings for the oceans. Our study identifies subgrid-scale interactions that are currently not parameterized in numerical atmospheric climate models, which may lead to systematic defects in the simulated circulations.

Analysis of compressible light dynamic stall flow at transitional Reynolds numbers

DEFF Research Database (Denmark)

Dyken, R.D. Van; Ekaterinaris, John A.; Chandrasekhara, M.S.

1996-01-01

Numerical and experimental results of steady and light dynamic stall flow over an oscillating NACA 0012 airfoil at a freestream Mach number of 0.3 and Reynolds number of 0.54 x 10(6) are compared, The experimental observation that dynamic stall is induced from the bursting of a laminar separation...... point is specified suitably and a simple transition length model is incorporated to determine the extent of the laminar separation bubble. The thin-layer approximations of compressible, Reynolds-averaged, Navier-Stokes equations are used for the numerical solution, with an implicit, upwind-biased, third...

Molecular Dynamics Simulations to Investigate the Binding Mode of the Natural Product Liphagal with Phosphoinositide 3-Kinase α

Directory of Open Access Journals (Sweden)

Yanjuan Gao

2016-06-01

Full Text Available Phosphatidylinositol 3-kinase α (PI3Kα is an attractive target for anticancer drug design. Liphagal, isolated from the marine sponge Aka coralliphaga, possesses the special “liphagane” meroterpenoid carbon skeleton and has been demonstrated as a PI3Kα inhibitor. Molecular docking and molecular dynamics simulations were performed to explore the dynamic behaviors of PI3Kα binding with liphagal, and free energy calculations and energy decomposition analysis were carried out by use of molecular mechanics/Poisson-Boltzmann (generalized Born surface area (MM/PB(GBSA methods. The results reveal that the heteroatom rich aromatic D-ring of liphagal extends towards the polar region of the binding site, and the D-ring 15-hydroxyl and 16-hydroxyl form three hydrogen bonds with Asp810 and Tyr836. The cyclohexyl A-ring projects up into the upper pocket of the lipophilic region, and the hydrophobic/van der Waals interactions with the residues Met772, Trp780, Ile800, Ile848, Val850, Met922, Phe930, Ile932 could be the key interactions for the affinity of liphagal to PI3Kα. Thus, a new strategy for the rational design of more potent analogs of liphagal against PI3Kα is provided. Our proposed PI3Kα/liphagal binding mode would be beneficial for the discovery of new active analogs of liphagal against PI3Kα.

Large eddy simulation of spanwise rotating turbulent channel flow with dynamic variants of eddy viscosity model

Science.gov (United States)

Jiang, Zhou; Xia, Zhenhua; Shi, Yipeng; Chen, Shiyi

2018-04-01

A fully developed spanwise rotating turbulent channel flow has been numerically investigated utilizing large-eddy simulation. Our focus is to assess the performances of the dynamic variants of eddy viscosity models, including dynamic Vreman's model (DVM), dynamic wall adapting local eddy viscosity (DWALE) model, dynamic σ (Dσ ) model, and the dynamic volumetric strain-stretching (DVSS) model, in this canonical flow. The results with dynamic Smagorinsky model (DSM) and direct numerical simulations (DNS) are used as references. Our results show that the DVM has a wrong asymptotic behavior in the near wall region, while the other three models can correctly predict it. In the high rotation case, the DWALE can get reliable mean velocity profile, but the turbulence intensities in the wall-normal and spanwise directions show clear deviations from DNS data. DVSS exhibits poor predictions on both the mean velocity profile and turbulence intensities. In all three cases, Dσ performs the best.

Nonlinear transport processes and fluid dynamics: Cylindrical Couette flow of Lennard-Jones fluids

International Nuclear Information System (INIS)

Khayat, R.E.; Eu, B.C.

1988-01-01

In this paper we report on calculations of flow profiles for cylindrical Couette flow of a Lennard-Jones fluid. The flow is subjected to a temperature gradient and thermoviscous effects are taken into consideration. We apply the generalized fluid dynamic equations which are provided by the modified moment method for the Boltzmann equation reported previously. The results of calculations are in good agreement with the Monte Carlo direct simulation method by K. Nanbu [Phys. Fluids 27, 2632 (1984)] for most of Knudsen numbers for which the simulation data are available

In-vivo imaging of blood flow dynamics using color Doppler optical coherence tomography

Science.gov (United States)

Yazdanfar, Siavash; Rollins, Andrew M.; Izatt, Joseph A.

2000-04-01

Noninvasive quantitation of blood flow in the retinal micro circulation may elucidate the progression and treatment of ocular disorders including diabetic retinopathy, age-related degeneration, and glaucoma. Color Doppler optical coherence tomography was recently introduced as a technique allowing simultaneous micron-scale resolution cross-sectional imaging of tissue micro structure and blood flow in the human retina. Here, time-resolved imaging of dynamics of blood flow profiles was performed to measure cardiac pulsatility within retinal vessels. Retinal pulsatility has been shown to decrease throughout the progression of diabetic retinopathy.

Dynamic interaction between myocardial contraction and coronary flow.

Science.gov (United States)

Beyar, R; Sideman, S

1997-01-01

Phasic coronary flow is determined by the dynamic interaction between central hemodynamics and myocardial and ventricular mechanics. Various models, including the waterfall, intramyocardial pump and myocardial structural models, have been proposed for the coronary circulation. Concepts such as intramyocardial pressure, local elastance and others have been proposed to help explain the coronary compression by the myocardium. Yet some questions remain unresolved, and a new model has recently been proposed, linking a muscle collagen fibrous model to a physiologically based coronary model, and accounting for transport of fluids across the capillaries and lymphatic flow between the interstitial space and the venous system. One of the unique features of this model is that the intramyocardial pressure (IMP) in the interstitial space is calculated from the balance of forces and fluid transport in the system, and is therefore dependent on the coronary pressure conditions, the myocardial function and the transport properties of the system. The model predicts a wide range of experimentally observed phenomena associated with coronary compression.

Simulation-Based Dynamic Passenger Flow Assignment Modelling for a Schedule-Based Transit Network

Directory of Open Access Journals (Sweden)

Xiangming Yao

2017-01-01

Full Text Available The online operation management and the offline policy evaluation in complex transit networks require an effective dynamic traffic assignment (DTA method that can capture the temporal-spatial nature of traffic flows. The objective of this work is to propose a simulation-based dynamic passenger assignment framework and models for such applications in the context of schedule-based rail transit systems. In the simulation framework, travellers are regarded as individual agents who are able to obtain complete information on the current traffic conditions. A combined route selection model integrated with pretrip route selection and entrip route switch is established for achieving the dynamic network flow equilibrium status. The train agent is operated strictly with the timetable and its capacity limitation is considered. A continuous time-driven simulator based on the proposed framework and models is developed, whose performance is illustrated through a large-scale network of Beijing subway. The results indicate that more than 0.8 million individual passengers and thousands of trains can be simulated simultaneously at a speed ten times faster than real time. This study provides an efficient approach to analyze the dynamic demand-supply relationship for large schedule-based transit networks.

Experimental Measurements and Mathematical Modeling of Static and Dynamic Characteristics of Water Flow in a Long Pipe

Science.gov (United States)

Jablonska, J.; Kozubkova, M.

2017-08-01

Static and dynamic characteristics of flow in technical practice are very important and serious problem and can be solved by experimental measurement or mathematical modeling. Unsteady flow presents time changes of the flow and water hammer can be an example of this phenomenon. Water hammer is caused by rapid changes in the water flow by means the closure or opening of the control valve. The authors deal with by hydraulic hammer at the multiphase flow (water and air), its one-dimensional modeling (Matlab SimHydraulics) and modeling with the use of the finite volume method (Ansys Fluent) in article. The circuit elements are defined by static and dynamic characteristics. The results are verified with measurements. The article evaluates different approaches, their advantages, disadvantages and specifics in solving of water hammer.

Absolute quantification of regional renal blood flow in swine by dynamic contrast-enhanced magnetic resonance imaging using a blood pool contrast agent.

Science.gov (United States)

Lüdemann, Lutz; Nafz, Benno; Elsner, Franz; Grosse-Siestrup, Christian; Meissler, Michael; Kaufels, Nicola; Rehbein, Hagen; Persson, Pontus B; Michaely, Henrik J; Lengsfeld, Philipp; Voth, Matthias; Gutberlet, Matthias

2009-03-01

To evaluate for the first time in an animal model the possibility of absolute regional quantification of renal medullary and cortical perfusion by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) using a blood pool contrast agent. A total of 18 adult female pigs (age, 16-22 weeks; body weight, 45-65 kg; no dietary restrictions) were investigated by DCE-MRI. Absolute renal blood flow (RBF) measured by an ultrasound transit time flow probe around the renal vein was used as the standard of reference. An inflatable stainless cuff placed around the renal artery near its origin from the abdominal aorta was used to reduce RBF to 60%, 40%, and 20% of the baseline flow. The last measurement was performed with the cuff fully reopened. Absolute RBF values during these 4 perfusion states were compared with the results of DCE-MRI performed on a 1.5-T scanner with an 8-channel phased-array surface coil. All scans were acquired in breath-hold technique in the coronal plane using a field of view of 460 mm.Each dynamic scan commenced with a set of five 3D T1-weighted gradient echo sequences with different flip angles (alpha = 2 degrees, 5 degrees, 10 degrees, 20 degrees, 30 degrees): TE, 0.88 milliseconds; TR, 2.65 milliseconds; slice thickness, 8.8 mm for 4 slices; acquisition matrix, 128 x 128; and acquisitions, 4. These data served to calculate 3D intrinsic longitudinal relaxation rate maps (R10) and magnetization (M0). Immediately after these images, the dynamic 3D T1-weighted gradient echo images were acquired with the same parameters and a constant alpha = 30 degrees, half Fourier, 1 acquisition, 64 frames, a time interval of 1.65 seconds between each frame, and a total duration of 105.6. Three milliliters of an albumin-binding blood pool contrast agent (0.25 mmol/mL gadofosveset trisodium, Vasovist, Bayer Schering Pharma AG, Berlin, Germany) was injected at a rate of 3 mL/s. Perfusion was calculated using the arterial input function from the aorta, which was

Spatiotemporal evolution of cavitation dynamics exhibited by flowing microbubbles during ultrasound exposure.

Science.gov (United States)

Choi, James J; Coussios, Constantin-C

2012-11-01

Ultrasound and microbubble-based therapies utilize cavitation to generate bioeffects, yet cavitation dynamics during individual pulses and across consecutive pulses remain poorly understood under physiologically relevant flow conditions. SonoVue(®) microbubbles were made to flow (fluid velocity: 10-40 mm/s) through a vessel in a tissue-mimicking material and were exposed to ultrasound [frequency: 0.5 MHz, peak-rarefactional pressure (PRP): 150-1200 kPa, pulse length: 1-100,000 cycles, pulse repetition frequency (PRF): 1-50 Hz, number of pulses: 10-250]. Radiated emissions were captured on a linear array, and passive acoustic mapping was used to spatiotemporally resolve cavitation events. At low PRPs, stable cavitation was maintained throughout several pulses, thus generating a steady rise in energy with low upstream spatial bias within the focal volume. At high PRPs, inertial cavitation was concentrated in the first 6.3 ± 1.3 ms of a pulse, followed by an energy reduction and high upstream bias. Multiple pulses at PRFs below a flow-dependent critical rate (PRF(crit)) produced predictable and consistent cavitation dynamics. Above the PRF(crit), energy generated was unpredictable and spatially biased. In conclusion, key parameters in microbubble-seeded flow conditions were matched with specific types, magnitudes, distributions, and durations of cavitation; this may help in understanding empirically observed in vivo phenomena and guide future pulse sequence designs.

Detecting dynamic causal inference in nonlinear two-phase fracture flow

Science.gov (United States)

Faybishenko, Boris

2017-08-01

Identifying dynamic causal inference involved in flow and transport processes in complex fractured-porous media is generally a challenging task, because nonlinear and chaotic variables may be positively coupled or correlated for some periods of time, but can then become spontaneously decoupled or non-correlated. In his 2002 paper (Faybishenko, 2002), the author performed a nonlinear dynamical and chaotic analysis of time-series data obtained from the fracture flow experiment conducted by Persoff and Pruess (1995), and, based on the visual examination of time series data, hypothesized that the observed pressure oscillations at both inlet and outlet edges of the fracture result from a superposition of both forward and return waves of pressure propagation through the fracture. In the current paper, the author explores an application of a combination of methods for detecting nonlinear chaotic dynamics behavior along with the multivariate Granger Causality (G-causality) time series test. Based on the G-causality test, the author infers that his hypothesis is correct, and presents a causation loop diagram of the spatial-temporal distribution of gas, liquid, and capillary pressures measured at the inlet and outlet of the fracture. The causal modeling approach can be used for the analysis of other hydrological processes, for example, infiltration and pumping tests in heterogeneous subsurface media, and climatic processes, for example, to find correlations between various meteorological parameters, such as temperature, solar radiation, barometric pressure, etc.

Unified solver for fluid dynamics and aeroacoustics in isentropic gas flows

Science.gov (United States)

Pont, Arnau; Codina, Ramon; Baiges, Joan; Guasch, Oriol

2018-06-01

The high computational cost of solving numerically the fully compressible Navier-Stokes equations, together with the poor performance of most numerical formulations for compressible flow in the low Mach number regime, has led to the necessity for more affordable numerical models for Computational Aeroacoustics. For low Mach number subsonic flows with neither shocks nor thermal coupling, both flow dynamics and wave propagation can be considered isentropic. Therefore, a joint isentropic formulation for flow and aeroacoustics can be devised which avoids the need for segregating flow and acoustic scales. Under these assumptions density and pressure fluctuations are directly proportional, and a two field velocity-pressure compressible formulation can be derived as an extension of an incompressible solver. Moreover, the linear system of equations which arises from the proposed isentropic formulation is better conditioned than the homologous incompressible one due to the presence of a pressure time derivative. Similarly to other compressible formulations the prescription of boundary conditions will have to deal with the backscattering of acoustic waves. In this sense, a separated imposition of boundary conditions for flow and acoustic scales which allows the evacuation of waves through Dirichlet boundaries without using any tailored damping model will be presented.

Unsteady Flow Dynamics and Acoustics of Two-Outlet Centrifugal Fan Design

Science.gov (United States)

Wong, I. Y. W.; Leung, R. C. K.; Law, A. K. Y.

2011-09-01

In this study, a centrifugal fan design with two flow outlets is investigated. This design aims to provide high mass flow rate but low noise performance. Two dimensional unsteady flow simulation with CFD code (FLUENT 6.3) is carried out to analyze the fan flow dynamics and its acoustics. The calculations were done using the unsteady Reynolds averaged Navier Stokes (URANS) approach in which effects of turbulence were accounted for using κ-ɛ model. This work aims to provide an insight how the dominant noise source mechanisms vary with a key fan geometrical paramters, namely, the ratio between cutoff distance and the radius of curvature of the fan housing. Four new fan designs were calculated. Simulation results show that the unsteady flow-induced forces on the fan blades are found to be the main noise sources. The blade force coefficients are then used to build the dipole source terms in Ffowcs Williams and Hawkings (FW-H) Equation for estimating their noise effects. It is found that one design is able to deliver a mass flow 34% more, but with sound pressure level (SPL) 10 dB lower, than the existing design .

Debris flow run-out simulation and analysis using a dynamic model

Science.gov (United States)

Melo, Raquel; van Asch, Theo; Zêzere, José L.

2018-02-01

Only two months after a huge forest fire occurred in the upper part of a valley located in central Portugal, several debris flows were triggered by intense rainfall. The event caused infrastructural and economic damage, although no lives were lost. The present research aims to simulate the run-out of two debris flows that occurred during the event as well as to calculate via back-analysis the rheological parameters and the excess rain involved. Thus, a dynamic model was used, which integrates surface runoff, concentrated erosion along the channels, propagation and deposition of flow material. Afterwards, the model was validated using 32 debris flows triggered during the same event that were not considered for calibration. The rheological and entrainment parameters obtained for the most accurate simulation were then used to perform three scenarios of debris flow run-out on the basin scale. The results were confronted with the existing buildings exposed in the study area and the worst-case scenario showed a potential inundation that may affect 345 buildings. In addition, six streams where debris flow occurred in the past and caused material damage and loss of lives were identified.

Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

Science.gov (United States)

Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

2017-02-22

Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.

Nonlinear dynamics of an elliptic vortex embedded in an oscillatory shear flow.

Science.gov (United States)

Ryzhov, Eugene A

2017-11-01

The nonlinear dynamics of an elliptic vortex subjected to a time-periodic linear external shear flow is studied numerically. Making use of the ideas from the theory of nonlinear resonance overlaps, the study focuses on the appearance of chaotic regimes in the ellipse dynamics. When the superimposed flow is stationary, two general types of the steady-state phase portrait are considered: one that features a homoclinic separatrix delineating bounded and unbounded phase trajectories and one without a separatrix (all the phase trajectories are bounded in a periodic domain). When the external flow is time-periodic, the ensuing nonlinear dynamics differs significantly in both cases. For the case with a separatrix and two distinct types of phase trajectories: bounded and unbounded, the effect of the most influential nonlinear resonance with the winding number of 1:1 is analyzed in detail. Namely, the process of occupying the central stability region associated with the steady-state elliptic critical point by the stability region associated with the nonlinear resonance of 1:1 as the perturbation frequency gradually varies is investigated. A stark increase in the persistence of the central regular dynamics region against perturbation when the resonance of 1:1 associated stability region occupies the region associated with the steady-state elliptic critical point is observed. An analogous persistence of the regular motion occurs for higher perturbation frequencies when the corresponding stability islands reach the central stability region associated with the steady-state elliptic point. An analysis for the case with the resonance of 1:2 is presented. For the second case with only bounded phase trajectories and, therefore, no separatrix, the appearance of much bigger stability islands associated with nonlinear resonances compared with the case with a separatrix is reported.

The promising gas-dynamic schemes of vacuum deposition from the supersonic gas mixture flows

International Nuclear Information System (INIS)

Maltsev, R V; Rebrov, A K

2008-01-01

Gas jet deposition (GJD) becomes promising method of thin film and nanoparticle deposition. This paper is focused on elaboration of new methods of GJD based on different gas dynamic schemes of flow formation and interaction with substrate. Using direct statistical simulation method, the analysis was performed for: a) interaction of the jet from the sonic nozzle with a substrate; b) fan flow in the result of interaction of two opposite jets; c) convergent flow from the ring nozzle, directional to the axis; d) interaction of the jet after convergent flow with the substrate; e) fan flow in the result of interaction of two opposite jets after convergent expansion

Chaotic state to self-organized critical state transition of serrated flow dynamics during brittle-to-ductile transition in metallic glass

Energy Technology Data Exchange (ETDEWEB)

Wang, C.; Wang, W. H.; Bai, H. Y., E-mail: hybai@aphy.iphy.ac.cn [Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Sun, B. A. [Centre for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Kowloon (Hong Kong)

2016-02-07

We study serrated flow dynamics during brittle-to-ductile transition induced by tuning the sample aspect ratio in a Zr-based metallic glass. The statistical analysis reveals that the serrated flow dynamics transforms from a chaotic state characterized by Gaussian-distribution serrations corresponding to stick-slip motion of randomly generated and uncorrelated single shear band and brittle behavior, into a self-organized critical state featured by intermittent scale-free distribution of shear avalanches corresponding to a collective motion of multiple shear bands and ductile behavior. The correlation found between serrated flow dynamics and plastic deformation might shed light on the plastic deformation dynamic and mechanism in metallic glasses.

Low-order dynamical system model of a fully developed turbulent channel flow

Science.gov (United States)

Hamilton, Nicholas; Tutkun, Murat; Cal, Raúl Bayoán

2017-06-01

A reduced order model of a turbulent channel flow is composed from a direct numerical simulation database hosted at the Johns Hopkins University. Snapshot proper orthogonal decomposition (POD) is used to identify the Hilbert space from which the reduced order model is obtained, as the POD basis is defined to capture the optimal energy content by mode. The reduced order model is defined by coupling the evolution of the dynamic POD mode coefficients through their respective time derivative with a least-squares polynomial fit of terms up to third order. Parameters coupling the dynamics of the POD basis are defined in analog to those produced in the classical Galerkin projection. The resulting low-order dynamical system is tested for a range of basis modes demonstrating that the non-linear mode interactions do not lead to a monotonic decrease in error propagation. A basis of five POD modes accounts for 50% of the integrated turbulence kinetic energy but captures only the largest features of the turbulence in the channel flow and is not able to reflect the anticipated flow dynamics. Using five modes, the low-order model is unable to accurately reproduce Reynolds stresses, and the root-mean-square error of the predicted stresses is as great as 30%. Increasing the basis to 28 modes accounts for 90% of the kinetic energy and adds intermediate scales to the dynamical system. The difference between the time derivatives of the random coefficients associated with individual modes and their least-squares fit is amplified in the numerical integration leading to unstable long-time solutions. Periodic recalibration of the dynamical system is undertaken by limiting the integration time to the range of the sampled data and offering the dynamical system new initial conditions. Renewed initial conditions are found by pushing the mode coefficients in the end of the integration time toward a known point along the original trajectories identified through a least-squares projection. Under

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

Science.gov (United States)

Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

2017-05-01

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

Traffic flow dynamics. Data, models and simulation

Energy Technology Data Exchange (ETDEWEB)

Treiber, Martin [Technische Univ. Dresden (Germany). Inst. fuer Wirtschaft und Verkehr; Kesting, Arne [TomTom Development Germany GmbH, Berlin (Germany)

2013-07-01

First comprehensive textbook of this fascinating interdisciplinary topic which explains advances in a way that it is easily accessible to engineering, physics and math students. Presents practical applications of traffic theory such as driving behavior, stability analysis, stop-and-go waves, and travel time estimation. Presents the topic in a novel and systematic way by addressing both microscopic and macroscopic models with a focus on traffic instabilities. Revised and extended edition of the German textbook ''Verkehrsdynamik und -simulation''. This textbook provides a comprehensive and instructive coverage of vehicular traffic flow dynamics and modeling. It makes this fascinating interdisciplinary topic, which to date was only documented in parts by specialized monographs, accessible to a broad readership. Numerous figures and problems with solutions help the reader to quickly understand and practice the presented concepts. This book is targeted at students of physics and traffic engineering and, more generally, also at students and professionals in computer science, mathematics, and interdisciplinary topics. It also offers material for project work in programming and simulation at college and university level. The main part, after presenting different categories of traffic data, is devoted to a mathematical description of the dynamics of traffic flow, covering macroscopic models which describe traffic in terms of density, as well as microscopic many-particle models in which each particle corresponds to a vehicle and its driver. Focus chapters on traffic instabilities and model calibration/validation present these topics in a novel and systematic way. Finally, the theoretical framework is shown at work in selected applications such as traffic-state and travel-time estimation, intelligent transportation systems, traffic operations management, and a detailed physics-based model for fuel consumption and emissions.

Chaotic-Dynamical Conceptual Model to Describe Fluid Flow and Contaminant Transport in a Fractured Vadose Zone

International Nuclear Information System (INIS)

Faybishenko, Boris; Doughty, Christine; Geller, Jil T.

1999-01-01

DOE faces the remediation of numerous contaminated sites, such as those at Hanford, INEEL, LLNL, and LBNL, where organic and/or radioactive wastes were intentionally or accidentally released to the vadose zone from surface spills, underground tanks, cribs, shallow ponds, and deep wells. Migration of these contaminants through the vadose zone has led to the contamination of (or threatens to contaminate) underlying groundwater. A key issue in choosing a corrective action plan to clean up contaminated sites is the determination of the location, total mass, mobility and travel time to receptors for contaminants moving in the vadose zone. These problems are difficult to solve in a technically defensible and accurate manner because contaminants travel downward intermittently, through narrow pathways, driven by variations in environmental conditions. These preferential flow pathways can be difficult to find and predict. The primary objective of this project is to determine if and when dynamical chaos theory can be used to investigate infiltration of fluid and contaminant transport in heterogeneous soils and fractured rocks. The objective of this project is being achieved through the following activities: Development of multi scale conceptual models and mathematical and numerical algorithms for flow and transport, which incorporate both (a) the spatial variability of heterogeneous porous and fractured media and (b) the temporal dynamics of flow and transport; Development of appropriate experimental field and laboratory techniques needed to detect diagnostic parameters for chaotic behavior of flow; Evaluation of chaotic behavior of flow in laboratory and field experiments using methods from non-linear dynamics; Evaluation of the impact these dynamics may have on contaminant transport through heterogeneous fractured rocks and soils and remediation efforts. This approach is based on the consideration of multi scale spatial heterogeneity and flow phenomena that are affected by

Free-Surface flow dynamics and its effect on travel time distribution in unsaturated fractured zones - findings from analogue percolation experiments

Science.gov (United States)

Noffz, Torsten; Kordilla, Jannes; Dentz, Marco; Sauter, Martin

2017-04-01

Flow in unsaturated fracture networks constitutes a high potential for rapid mass transport and can therefore possibly contributes to the vulnerability of aquifer systems. Numerical models are generally used to predict flow and transport and have to reproduce various complex effects of gravity-driven flow dynamics. However, many classical volume-effective modelling approaches often do not grasp the non-linear free surface flow dynamics and partitioning behaviour at fracture intersections in unsaturated fracture networks. Better process understanding can be obtained by laboratory experiments, that isolate single aspects of the mass partitioning process, which influence travel time distributions and allow possible cross-scale applications. We present a series of percolation experiments investigating partitioning dynamics of unsaturated multiphase flow at an individual horizontal fracture intersection. A high precision multichannel dispenser is used to establish gravity-driven free surface flow on a smooth and vertical PMMA (poly(methyl methacrylate)) surface at rates ranging from 1.5 to 4.5 mL/min to obtain various flow modes (droplets; rivulets). Cubes with dimensions 20 x 20 x 20 cm are used to create a set of simple geometries. A digital balance provides continuous real-time cumulative mass bypassing the network. The influence of variable flow rate, atmospheric pressure and temperature on the stability of flow modes is shown in single-inlet experiments. Droplet and rivulet flow are delineated and a transition zone exhibiting mixed flow modes can be determined. Furthermore, multi-inlet setups with constant total inflow rates are used to reduce variance and the effect of erratic free-surface flow dynamics. Investigated parameters include: variable aperture widths df, horizontal offsets dv of the vertical fracture surface and alternating injection methods for both droplet and rivulet flow. Repetitive structures with several horizontal fractures extend arrival times

Droplet sizes, dynamics and deposition in vertical annular flow

International Nuclear Information System (INIS)

Lopes, J.C.B.; Dukler, A.E.

1985-10-01

The role of droplets in vertical upwards annular flow is investigated, focusing on the droplet size distributions, dynamics, and deposition phenomena. An experimental program was performed based on a new laser optical technique developed in these laboratories and implemented here for annular flow. This permitted the simultaneous measurement of droplet size, axial and radial velocity. The dependence of droplet size distributions on flow conditions is analyzed. The Upper-Log Normal function proves to be a good model for the size distribution. The mechanism controlling the maximum stable drop size was found to result from the interaction of the pressure fluctuations of the turbulent flow of the gas core with the droplet. The average axial droplet velocity showed a weak dependence on gas rates. This can be explained once the droplet size distribution and droplet size-velocity relationship are analyzed simultaneously. The surprising result from the droplet conditional analysis is that larger droplet travel faster than smaller ones. This dependence cannot be explained if the drag curves used do not take into account the high levels of turbulence present in the gas core in annular flow. If these are considered, then interesting new situations of multiplicity and stability of droplet terminal velocities are encountered. Also, the observed size-velocity relationship can be explained. A droplet deposition is formulated based on the particle inertia control. This permitted the calculation of rates of drop deposition directly from the droplet size and velocities data

Dynamic behaviour of high-pressure natural-gas flow in pipelines

International Nuclear Information System (INIS)

Gato, L.M.C.; Henriques, J.C.C.

2005-01-01

The aim of the present study is the numerical modelling of the dynamic behaviour of high-pressure natural-gas flow in pipelines. The numerical simulation was performed by solving the conservation equations, for one-dimensional compressible flow, using the Runge-Kutta discontinuous Galerkin method, with third-order approximation in space and time. The boundary conditions were imposed using a new weak formulation based on the characteristic variables. The occurrence of pressure oscillations in natural-gas pipelines was studied as a result of the compression wave originated by the rapid closure of downstream shut-off valves. The effect of the partial reflection of pressure waves was also analyzed in the transition between pipes of different cross-sectional areas

Dynamic behaviour of high-pressure natural-gas flow in pipelines

Energy Technology Data Exchange (ETDEWEB)

Gato, L.M.C. [Department of Mechanical Engineering, Instituto Superior Tecnico, Technical University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon (Portugal)]. E-mail: lgato@mail.ist.utl.pt; Henriques, J.C.C. [Department of Mechanical Engineering, Instituto Superior Tecnico, Technical University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon (Portugal)]. E-mail: jcch@mail.ist.utl.pt

2005-10-01

The aim of the present study is the numerical modelling of the dynamic behaviour of high-pressure natural-gas flow in pipelines. The numerical simulation was performed by solving the conservation equations, for one-dimensional compressible flow, using the Runge-Kutta discontinuous Galerkin method, with third-order approximation in space and time. The boundary conditions were imposed using a new weak formulation based on the characteristic variables. The occurrence of pressure oscillations in natural-gas pipelines was studied as a result of the compression wave originated by the rapid closure of downstream shut-off valves. The effect of the partial reflection of pressure waves was also analyzed in the transition between pipes of different cross-sectional areas.

Dynamics of fragments and associated phenomena in heavy-ion collisions using a modified secondary algorithm

Energy Technology Data Exchange (ETDEWEB)

Kumar, Rohit [Department of Physics, Panjab University, Chandigarh-160014 (India)

2016-05-06

We discuss the stability of fragments identified by secondary algorithms used to construct fragments within quantum molecular dynamics model. For this purpose we employ three different algorithms for fragment identification. 1) The conventional minimum spanning tree (MST) method based on the spatial correlations, 2) an improved version of MST with additional binding energy constraints of cold nuclear matter, 3) and that of hot matter. We find significant role of thermal binding energies over cold matter binding energies. Significant role is observed for fragment multiplicities and stopping of fragments. Whereas insignificant effect is observed on fragment’s flow.

Stopped-flow studies of spectral changes in bilirubin-human serum albumin following an alkaline pH jump and following binding of bilirubin

DEFF Research Database (Denmark)

Honoré, B

1987-01-01

A stopped-flow technique was used to study the spectral changes occurring in bilirubin-albumin following a pH jump as well as following binding of bilirubin at 25 degrees C. The changes were studied in two wavelength ranges, 280-310 nm (tyrosine residues) and 400-510 nm (bound bilirubin). The cha......A stopped-flow technique was used to study the spectral changes occurring in bilirubin-albumin following a pH jump as well as following binding of bilirubin at 25 degrees C. The changes were studied in two wavelength ranges, 280-310 nm (tyrosine residues) and 400-510 nm (bound bilirubin......). The changes were analyzed according to a scheme of consecutive unimolecular reactions. Spectral monitoring of a pH jump from 11.3 to 11.8 reveals that the bilirubin-albumin complex changes its structure in several steps. The UV absorption spectra show that 3.8 tyrosine residues ionize in the first step, 2...

Dynamic interaction of two-phase debris flow with pyramidal defense structures: An optimal strategy to efficiently protecting the desired area

Science.gov (United States)

Kattel, Parameshwari; Kafle, Jeevan; Fischer, Jan-Thomas; Mergili, Martin; Tuladhar, Bhadra Man; Pudasaini, Shiva P.

2017-04-01

In this work we analyze the dynamic interaction of two phase debris flows with pyramidal obstacles. To simulate the dynamic interaction of two-phase debris flow (a mixture of solid particles and viscous fluid) with obstacles of different dimensions and orientations, we employ the general two-phase mass flow model (Pudasaini, 2012). The model consists of highly non-linear partial differential equations representing the mass and momentum conservations for both solid and fluid. Besides buoyancy, the model includes some dominant physical aspects of the debris flows such as generalized drag, virtual mass and non-Newtonian viscous stress as induced by the gradient of solid-volume-fraction. Simulations are performed with high-resolution numerical schemes to capture essential dynamics, including the strongly re-directed flow with multiple stream lines, mass arrest and debris-vacuum generation when the rapidly cascading debris mass suddenly encounters the obstacle. The solid and fluid phases show fundamentally different interactions with obstacles, flow spreading and dispersions, run-out dynamics, and deposition morphology. A forward-facing pyramid deflects the mass wider, and a rearward-facing pyramid arrests a portion of solid-mass at its front. Our basic study reveals that appropriately installed obstacles, their dimensions and orientations have a significant influence on the flow dynamics, material redistribution and redirection. The precise knowledge of the change in dynamics is of great importance for the optimal and effective protection of designated areas along the mountain slopes and the runout zones. Further important results are, that specific installations lead to redirect either solid, or fluid, or both, in the desired amounts and directions. The present method of the complex interactions of real two-phase mass flows with the obstacles may help us to construct defense structures and to design advanced and physics-based engineering solutions for the prevention

Forecasting Multivariate Road Traffic Flows Using Bayesian Dynamic Graphical Models, Splines and Other Traffic Variables

NARCIS (Netherlands)

Anacleto, Osvaldo; Queen, Catriona; Albers, Casper J.

Traffic flow data are routinely collected for many networks worldwide. These invariably large data sets can be used as part of a traffic management system, for which good traffic flow forecasting models are crucial. The linear multiregression dynamic model (LMDM) has been shown to be promising for

Exploring the Relationship of Exit Flow and Jam Density in Panic Scenarios Using Animal Dynamics

NARCIS (Netherlands)

Sobhani, A.; Sarvi, M.; Duives, D.C.; Ejtemai, O.; Aghabayk, K.; Hoogendoorn, S.P.

2014-01-01

There are few studies investigating crowd dynamics in panic situations. They used measures such as exit flow rate to explore the exit performance in evacuation scenarios. However, there is limited research exploring the relationship of exit flow rate and density behind the exit for panic scenarios.

Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA.

Science.gov (United States)

Hardianto, Ari; Liu, Fei; Ranganathan, Shoba

2018-02-26

(-)-Balanol is an adenosine triphosphate mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is known as a tumor promoter, PKC isozymes can be tumor promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood. Interestingly, in contrast to PKA, PKCε is more sensitive to this fluorine effect. Here we investigate the global fluorine effect on the different binding responses of PKCε and PKA to balanoids using molecular dynamics (MD) simulations. For the first time to the best of our knowledge, we found that a structurally equivalent residue in each kinase, Thr184 in PKA and Ala549 in PKCε, is essential for the different binding responses. Furthermore, the study revealed that the invariant Lys, Lys73 in PKA and Lys437 in PKCε, already known to have a crucial role in the catalytic activity of kinases, serves as the main anchor for balanol binding. Overall, while Thr184 in PKA attenuates the effect of fluorination, Ala549 permits remote response of PKCε to fluorine substitution, with implications for rational design of future balanol-based PKCε inhibitors.

Dynamics of blood flow and thrombus formation in a multi-bypass microfluidic ladder network.

Science.gov (United States)

Zilberman-Rudenko, Jevgenia; Sylman, Joanna L; Lakshmanan, Hari H S; McCarty, Owen J T; Maddala, Jeevan

2017-02-01

The reaction dynamics of a complex mixture of cells and proteins, such as blood, in branched circulatory networks within the human microvasculature or extravascular therapeutic devices such as extracorporeal oxygenation machine (ECMO) remains ill-defined. In this report we utilize a multi-bypass microfluidics ladder network design with dimensions mimicking venules to study patterns of blood platelet aggregation and fibrin formation under complex shear. Complex blood fluid dynamics within multi-bypass networks under flow were modeled using COMSOL. Red blood cells and platelets were assumed to be non-interacting spherical particles transported by the bulk fluid flow, and convection of the activated coagulation factor II, thrombin, was assumed to be governed by mass transfer. This model served as the basis for predicting formation of local shear rate gradients, stagnation points and recirculation zones as dictated by the bypass geometry. Based on the insights from these models, we were able to predict the patterns of blood clot formation at specific locations in the device. Our experimental data was then used to adjust the model to account for the dynamical presence of thrombus formation in the biorheology of blood flow. The model predictions were then compared to results from experiments using recalcified whole human blood. Microfluidic devices were coated with the extracellular matrix protein, fibrillar collagen, and the initiator of the extrinsic pathway of coagulation, tissue factor. Blood was perfused through the devices at a flow rate of 2 µL/min, translating to physiologically relevant initial shear rates of 300 and 700 s -1 for main channels and bypasses, respectively. Using fluorescent and light microscopy, we observed distinct flow and thrombus formation patterns near channel intersections at bypass points, within recirculation zones and at stagnation points. Findings from this proof-of-principle ladder network model suggest a specific correlation between

Dynamic alteration of regional cerebral blood flow during carotid compression and proof of reversibility

International Nuclear Information System (INIS)

Asahi, Kouichi; Hori, M; Hamasaki, N; Sato, S; Nakanishi, H; Kuwatsuru, R; Sasai, K; Aoki, S

2012-01-01

It is difficult to non-invasively visualize changes in regional cerebral blood flow caused by manual compression of the carotid artery. To visualize dynamic changes in regional cerebral blood flow during and after manual compression of the carotid artery. Two healthy volunteers were recruited. Anatomic features and flow directions in the circle of Willis were evaluated with time-of-flight magnetic resonance angiography (MRA) and two-dimensional phase-contrast (2DPC) MRA, respectively. Regional cerebral blood flow was visualized with territorial arterial spin-labeling magnetic resonance imaging (TASL-MRI). TASL-MRI and 2DPC-MRA were performed in three states: at rest, during manual compression of the right carotid artery, and after decompression. In one volunteer, time-space labeling inversion pulse (Time-SLIP) MRA was performed to confirm collateral flow. During manual carotid compression, in one volunteer, the right thalamus changed to be fed only by the vertebrobasilar system, and the right basal ganglia changed to be fed by the left internal carotid artery. In the other volunteer, the right basal ganglia changed to be fed by the vertebrobasilar system. 2DPC-MRA showed that the flow direction changed in the right A1 segment of the anterior cerebral artery and the right posterior communicating artery. Perfusion patterns and flow directions recovered after decompression. Time-SLIP MRA showed pial vessels and dural collateral circulation when the right carotid artery was manually compressed. Use of TASL-MRI and 2DPC-MRA was successful for non-invasive visualization of the dynamic changes in regional cerebral blood flow during and after manual carotid compression

IN-CYLINDER MASS FLOW ESTIMATION AND MANIFOLD PRESSURE DYNAMICS FOR STATE PREDICTION IN SI ENGINES

Directory of Open Access Journals (Sweden)

Wojnar Sławomir

2014-06-01

Full Text Available The aim of this paper is to present a simple model of the intake manifold dynamics of a spark ignition (SI engine and its possible application for estimation and control purposes. We focus on pressure dynamics, which may be regarded as the foundation for estimating future states and for designing model predictive control strategies suitable for maintaining the desired air fuel ratio (AFR. The flow rate measured at the inlet of the intake manifold and the in-cylinder flow estimation are considered as parts of the proposed model. In-cylinder flow estimation is crucial for engine control, where an accurate amount of aspired air forms the basis for computing the manipulated variables. The solutions presented here are based on the mean value engine model (MVEM approach, using the speed-density method. The proposed in-cylinder flow estimation method is compared to measured values in an experimental setting, while one-step-ahead prediction is illustrated using simulation results.

Affinity enhancement of nanobody binding to EGFR: in silico site-directed mutagenesis and molecular dynamics simulation approaches.

Science.gov (United States)

Farasat, Alireza; Rahbarizadeh, Fatemeh; Hosseinzadeh, Ghader; Sajjadi, Sharareh; Kamali, Mehdi; Keihan, Amir Homayoun

2017-06-01

Epidermal growth factor receptor (EGFR), a transmembrane glycoprotein, is overexpressed in many cancers such as head-neck, breast, prostate, and skin cancers for this reason it is a good target in cancer therapy and diagnosis. In nanobody-based cancer diagnosis and treatment, nanobodies with high affinity toward receptor (e.g. EGFR) results in effective treatment or diagnosis of cancer. In this regard, the main aim of this study is to develop a method based on molecular dynamic (MD) simulations for designing of 7D12 based nanobody with high affinity compared with wild-type nanobody. By surveying electrostatic and desolvation interactions between different residues of 7D12 and EGFR, the critical residues of 7D12 that play the main role in the binding of 7D12 to EGFR were elucidated and based on these residues, five logical variants were designed. Following the 50 ns MD simulations, pull and umbrella sampling simulation were performed for 7D12 and all its variants in complex with EGFR. Binding free energy of 7D12 (and all its variants) with EGFR was obtained by weighted histogram analysis method. According to binding free energy results, GLY101 to GLU mutation showed the highest binding affinity but this variant is unstable after 50 ns MD simulations. ALA100 to GLU mutation shows suitable binding enhancement with acceptable structural stability. Suitable position and orientation of GLU in residue 100 of 7D12 against related amino acids of EGFR formed some extra hydrogen and electrostatic interactions which resulted in binding enhancement.

Dynamic Gas Flow Effects on the ESD of Aerospace Vehicle Surfaces

Science.gov (United States)

Hogue, Michael D.; Kapat, Jayanta; Ahmed, Kareem; Cox, Rachel E.; Wilson, Jennifer G.; Calle, Luz M.; Mulligan, Jaysen

2016-01-01

The purpose of this work is to develop a dynamic version of Paschen's Law that takes into account the flow of ambient gas past aerospace vehicle surfaces. However, the classic Paschen's Law does not take into account the flow of gas of an aerospace vehicle, whose surfaces may be triboelectrically charged by dust or ice crystal impingement, traversing the atmosphere. The basic hypothesis of this work is that the number of electron-ion pairs created per unit distance by the electric field between the electrodes is mitigated by the electron-ion pairs removed per unit distance by the flow of gas. The revised Paschen equation must be a function of the mean velocity, v(sub xm), of the ambient gas and reduces to the classical version of Paschen's law when the gas mean velocity, v(sub xm) = 0. New formulations of Paschen's Law, taking into account Mach number and dynamic pressure, derived by the authors, will be discussed. These equations will be evaluated by wind tunnel experimentation later this year. Based on the results of this work, it is hoped that the safety of aerospace vehicles will be enhanced with a redefinition of electrostatic launch commit criteria. It is also possible that new products, such as new anti-static coatings, may be formulated from this data.

Dynamics of blood flow: twenty years of achievement

International Nuclear Information System (INIS)

Rosendorff, C.

1988-01-01

The physiology of blood circulation has evolved from the descriptive phenomenology of William Harvey's time to an interdisciplinary science, involving elements of fluid dynamics, vessel wall mechanics, electrophysiology, cell biology, biochemistry and molecular biology. Most of these new developments have occured during the lifetime of the South African Medical Research Council. Highlights of the research undertaken by the Council regarding circulatory physiology are given. In the 1960s the use of xenon-133 to study the flow of blood to the brain resulted in the first systematic description of cerebral blood flow and its control by sympathetic nerves. During the 1970s this technique was refined and the use of radioactive microspheres for the measurement of tissue blood flow was developed. Research concerning the control of blood vessels in the kidney was also carried out, and this showed that the sympathetic nerves control renal blood flow by releasing a local hormone called renin. The renal release of renin was later recognised as being important in the control of blood pressure. Another development was the discovery that vascular sensitivity to noradrenaline was increased in certain types of liver diseases. An analysis of the blood of patients with obstructive jaundice showed that the substance responsible for this noradrenaline effect was a combination of cholesterol and lipo-protein. This led to the theory that excessive cholesterol in the blood may be dangerous. In the late 1970s a shift in research emphasis to coronary artery physiology occurred and the 1980s saw research move into the area of cell biology

Ultrafast dynamic computed tomography myelography for the precise identification of high-flow cerebrospinal fluid leaks caused by spiculated spinal osteophytes.

Science.gov (United States)

Thielen, Kent R; Sillery, John C; Morris, Jonathan M; Hoxworth, Joseph M; Diehn, Felix E; Wald, John T; Rosebrock, Richard E; Yu, Lifeng; Luetmer, Patrick H

2015-03-01

Precise localization and understanding of the origin of spontaneous high-flow spinal CSF leaks is required prior to targeted treatment. This study demonstrates the utility of ultrafast dynamic CT myelography for the precise localization of high-flow CSF leaks caused by spiculated spinal osteophytes. This study reports a series of 14 patients with high-flow CSF leaks caused by spiculated spinal osteophytes who underwent ultrafast dynamic CT myelography between March 2009 and December 2010. There were 10 male and 4 female patients, with an average age of 49 years (range 37-74 years). The value of ultrafast dynamic CT myelography in depicting the CSF leak site was qualitatively assessed. In all 14 patients, ultrafast dynamic CT myelography was technically successful at precisely demonstrating the site of the CSF leak, the causative spiculated osteophyte piercing the dura, and the relationship of the implicated osteophyte to adjacent structures. Leak sites included 3 cervical, 11 thoracic, and 0 lumbar levels, with 86% of the leaks occurring from C-5 to T-7. Information obtained from the ultrafast dynamic CT myelogram was considered useful in all treated CSF leaks. Spinal osteophytes piercing the dura are a more frequent cause of high-flow CSF leaks than previously recognized. Ultrafast dynamic CT myelography adds value beyond standard dynamic myelography or digital subtraction myelography in the diagnosis and anatomical characterization of high-flow spinal CSF leaks caused by these osteophytes. This information allows for appropriate planning for percutaneous or surgical treatment.

Exploring the binding sites and binding mechanism for hydrotrope encapsulated griseofulvin drug on γ-tubulin protein.

Directory of Open Access Journals (Sweden)

Shubhadip Das

Full Text Available The protein γ-tubulin plays an important role in centrosomal clustering and this makes it an attractive therapeutic target for treating cancers. Griseofulvin, an antifungal drug, has recently been used to inhibit proliferation of various types of cancer cells. It can also affect the microtubule dynamics by targeting the γ-tubulin protein. So far, the binding pockets of γ-tubulin protein are not properly identified and the exact mechanism by which the drug binds to it is an area of intense speculation and research. The aim of the present study is to investigate the binding mechanism and binding affinity of griseofulvin on γ-tubulin protein using classical molecular dynamics simulations. Since the drug griseofulvin is sparingly soluble in water, here we also present a promising approach for formulating and achieving delivery of hydrophobic griseofulvin drug via hydrotrope sodium cumene sulfonate (SCS cluster. We observe that the binding pockets of γ-tubulin protein are mainly formed by the H8, H9 helices and S7, S8, S14 strands and the hydrophobic interactions between the drug and γ-tubulin protein drive the binding process. The release of the drug griseofulvin from the SCS cluster is confirmed by the coordination number analysis. We also find hydrotrope-induced alteration of the binding sites of γ-tubulin protein and the weakening of the drug-protein interactions.

Dynamic modeling of Shell entrained flow gasifier in an integrated gasification combined cycle process

International Nuclear Information System (INIS)

Lee, Hyeon-Hui; Lee, Jae-Chul; Joo, Yong-Jin; Oh, Min; Lee, Chang-Ha

2014-01-01

Highlights: • Detailed dynamic model for the Shell entrained flow gasifier was developed. • The model included sub-models of reactor, membrane wall, gas quench and slag flow. • The dynamics of each zone including membrane wall in the gasifier were analyzed. • Cold gas efficiency (81.82%), gas fraction and temperature agreed with Shell data. • The model could be used as part of the overall IGCC simulation. - Abstract: The Shell coal gasification system is a single-stage, up-flow, oxygen-blown gasifier which utilizes dry pulverized coal with an entrained flow mechanism. Moreover, it has a membrane wall structure and operates in the slagging mode. This work provides a detailed dynamic model of the 300 MW Shell gasifier developed for use as part of an overall IGCC (integrated gasification combined cycle) process simulation. The model consists of several sub-models, such as a volatilization zone, reaction zone, quench zone, slag zone, and membrane wall zone, including heat transfers between the wall layers and steam generation. The dynamic results were illustrated and the validation of the gasifier model was confirmed by comparing the results in the steady state with the reference data. The product gases (H 2 and CO) began to come out from the exit of the reaction zone within 0.5 s, and nucleate boiling heat transfer was dominant in the water zone of the membrane wall due to high heat fluxes. The steady state of the process was reached at nearly t = 500 s, and our simulation data for the steady state, such as the temperature and composition of the syngas, the cold gas efficiency (81.82%), and carbon conversion (near 1.0) were in good agreement with the reference data

Multiphase Flow Dynamics 4 Turbulence, Gas Adsorption and Release, Diesel Fuel Properties

CERN Document Server

Kolev, Nikolay Ivanov

2012-01-01

The present Volume 4 of the successful monograh package “Multiphase Flow Dynamics”is devoted to selected Chapters of the multiphase fluid dynamics that are important for practical applications but did not find place in the previous volumes. The state of the art of the turbulence modeling in multiphase flows is presented. As introduction, some basics of the single phase boundary layer theory including some important scales and flow oscillation characteristics in pipes and rod bundles are presented. Then the scales characterizing the dispersed flow systems are presented. The description of the turbulence is provided at different level of complexity: simple algebraic models for eddy viscosity, simple algebraic models based on the Boussinesq hypothesis, modification of the boundary layer share due to modification of the bulk turbulence, modification of the boundary layer share due to nucleate boiling. The role of the following forces on the mathematical description of turbulent flows is discussed: the lift fo...

Dietary flavonoid fisetin binds to β-tubulin and disrupts microtubule dynamics in prostate cancer cells.

Science.gov (United States)

Mukhtar, Eiman; Adhami, Vaqar Mustafa; Sechi, Mario; Mukhtar, Hasan

2015-10-28

Microtubule targeting based therapies have revolutionized cancer treatment; however, resistance and side effects remain a major limitation. Therefore, novel strategies that can overcome these limitations are urgently needed. We made a novel discovery that fisetin, a hydroxyflavone, is a microtubule stabilizing agent. Fisetin binds to tubulin and stabilizes microtubules with binding characteristics far superior than paclitaxel. Surface plasmon resonance and computational docking studies suggested that fisetin binds to β-tubulin with superior affinity compared to paclitaxel. Fisetin treatment of human prostate cancer cells resulted in robust up-regulation of microtubule associated proteins (MAP)-2 and -4. In addition, fisetin treated cells were enriched in α-tubulin acetylation, an indication of stabilization of microtubules. Fisetin significantly inhibited PCa cell proliferation, migration, and invasion. Nudc, a protein associated with microtubule motor dynein/dynactin complex that regulates microtubule dynamics, was inhibited with fisetin treatment. Further, fisetin treatment of a P-glycoprotein overexpressing multidrug-resistant cancer cell line NCI/ADR-RES inhibited the viability and colony formation. Our results offer in vitro proof-of-concept for fisetin as a microtubule targeting agent. We suggest that fisetin could be developed as an adjuvant for treatment of prostate and other cancer types. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Putting the "Ecology" into Environmental Flows: Ecological Dynamics and Demographic Modelling

Science.gov (United States)

Shenton, Will; Bond, Nicholas R.; Yen, Jian D. L.; Mac Nally, Ralph

2012-07-01

There have been significant diversions of water from rivers and streams around the world; natural flow regimes have been perturbed by dams, barriers and excessive extractions. Many aspects of the ecological `health' of riverine systems have declined due to changes in water flows, which has stimulated the development of thinking about the maintenance and restoration of these systems, which we refer to as environmental flow methodologies (EFMs). Most existing EFMs cannot deliver information on the population viability of species because they: (1) use habitat suitability as a proxy for population status; (2) use historical time series (usually of short duration) to forecast future conditions and flow sequences; (3) cannot, or do not, handle extreme flow events associated with climate variability; and (4) assume process stationarity for flow sequences, which means the past sequences are treated as good indicators of the future. These assumptions undermine the capacity of EFMs to properly represent risks associated with different flow management options; assumption (4) is untenable given most climate-change predictions. We discuss these concerns and advocate the use of demographic modelling as a more appropriate tool for linking population dynamics to flow regime change. A `meta-species' approach to demographic modelling is discussed as a useful step from habitat based models towards modelling strategies grounded in ecological theory when limited data are available on flow-demographic relationships. Data requirements of demographic models will undoubtedly expose gaps in existing knowledge, but, in so doing, will strengthen future efforts to link changes in river flows with their ecological consequences.

Putting the "ecology" into environmental flows: ecological dynamics and demographic modelling.

Science.gov (United States)

Shenton, Will; Bond, Nicholas R; Yen, Jian D L; Mac Nally, Ralph

2012-07-01

There have been significant diversions of water from rivers and streams around the world; natural flow regimes have been perturbed by dams, barriers and excessive extractions. Many aspects of the ecological 'health' of riverine systems have declined due to changes in water flows, which has stimulated the development of thinking about the maintenance and restoration of these systems, which we refer to as environmental flow methodologies (EFMs). Most existing EFMs cannot deliver information on the population viability of species because they: (1) use habitat suitability as a proxy for population status; (2) use historical time series (usually of short duration) to forecast future conditions and flow sequences; (3) cannot, or do not, handle extreme flow events associated with climate variability; and (4) assume process stationarity for flow sequences, which means the past sequences are treated as good indicators of the future. These assumptions undermine the capacity of EFMs to properly represent risks associated with different flow management options; assumption (4) is untenable given most climate-change predictions. We discuss these concerns and advocate the use of demographic modelling as a more appropriate tool for linking population dynamics to flow regime change. A 'meta-species' approach to demographic modelling is discussed as a useful step from habitat based models towards modelling strategies grounded in ecological theory when limited data are available on flow-demographic relationships. Data requirements of demographic models will undoubtedly expose gaps in existing knowledge, but, in so doing, will strengthen future efforts to link changes in river flows with their ecological consequences.

Dynamics of a fluid flow on Mars: Lava or mud?

Science.gov (United States)

Wilson, Lionel; Mouginis-Mark, Peter J.

2014-05-01

A distinctive flow deposit southwest of Cerberus Fossae on Mars is analyzed. The flow source is a ∼20 m deep, ∼12 × 1.5 km wide depression within a yardang associated with the Medusae Fossae Formation. The flow traveled for ∼40 km following topographic lows to leave a deposit on average 3-4 km wide. The surface morphology of the deposit suggests that it was produced by the emplacement of a fluid flowing in a laminar fashion and possessing a finite yield strength. We use topographic data from a digital elevation model (DEM) to model the dynamics of the motion and infer that the fluid had a Bingham rheology with a plastic viscosity of ∼1 Pa s and a yield strength of ∼185 Pa. Although the low viscosity is consistent with the properties of komatiite-like lava, the combination of values of viscosity and yield strength, as well as the surface morphology of the flow, suggests that this was a mud flow. Comparison with published experimental data implies a solids content close to 60% by volume and a grain size dominated by silt-size particles. Comparison of the ∼1.5 km3 deposit volume with the ∼0.03 km3 volume of the source depression implies that ∼98% of the flow material was derived from depth in the crust. There are similarities between the deposit studied here, which we infer to be mud, and other flow deposits on Mars currently widely held to be lavas. This suggests that a re-appraisal of many of these deposits is now in order.

Preferential flow in the vadose zone and interface dynamics: Impact of microbial exudates

Science.gov (United States)

Li, Biting; Pales, Ashley R.; Clifford, Heather M.; Kupis, Shyla; Hennessy, Sarah; Liang, Wei-Zhen; Moysey, Stephen; Powell, Brian; Finneran, Kevin T.; Darnault, Christophe J. G.

2018-03-01

In the hydrological cycle, the infiltration process is a critical component in the distribution of water into the soil and in the groundwater system. The nonlinear dynamics of the soil infiltration process yield preferential flow which affects the water distribution in soil. Preferential flow is influenced by the interactions between water, soil, plants, and microorganisms. Although the relationship among the plant roots, their rhizodeposits and water transport in soil has been the subject of extensive study, the effect of microbial exudates has been studied in only a few cases. Here the authors investigated the influence of two artificial microbial exudates-catechol and riboflavin-on the infiltration process, particularly unstable fingered flow, one form of preferential flow. Flow experiments investigating the effects of types and concentrations of microbial exudates on unstable fingered flow were conducted in a two-dimensional tank that was filled with ASTM

Inertial-particle dynamics in turbulent flows: caustics, concentration fluctuations and random uncorrelated motion

International Nuclear Information System (INIS)

Gustavsson, K; Mehlig, B; Meneguz, E; Reeks, M

2012-01-01

We have performed numerical simulations of inertial particles in random model flows in the white-noise limit (at zero Kubo number, Ku = 0) and at finite Kubo numbers. Our results for the moments of relative inertial-particle velocities are in good agreement with recent theoretical results (Gustavsson and Mehlig 2011a) based on the formation of phase-space singularities in the inertial-particle dynamics (caustics). We discuss the relation between three recent approaches describing the dynamics and spatial distribution of inertial particles suspended in turbulent flows: caustic formation, real-space singularities of the deformation tensor and random uncorrelated motion. We discuss how the phase- and real-space singularities are related. Their formation is well understood in terms of a local theory. We summarise the implications for random uncorrelated motion. (paper)

Muscle blood flow at onset of dynamic exercise in humans.

Science.gov (United States)

Rådegran, G; Saltin, B

1998-01-01

To evaluate the temporal relationship between blood flow, blood pressure, and muscle contractions, we continuously measured femoral arterial inflow with ultrasound Doppler at onset of passive exercise and voluntary, one-legged, dynamic knee-extensor exercise in humans. Blood velocity and inflow increased (P dicrotic and diastolic blood pressure notches, respectively. Mechanical hindrance occurred (P dicrotic notch. The increase in blood flow (Q) was characterized by a one-component (approximately 15% of peak power output), two-component (approximately 40-70% of peak power output), or three-component exponential model (> or = 75% of peak power output), where Q(t) = Qpassive + delta Q1.[1 - e-(t - TD1/tau 1)]+ delta Q2.[1 - e-(t - TD2/tau 2)]+ delta Q3.[1 - e-(t - TD3/tau 3)]; Qpassive, the blood flow during passive leg movement, equals 1.17 +/- 0.11 l/min; TD is the onset latency; tau is the time constant; delta Q is the magnitude of blood flow rise; and subscripts 1-3 refer to the first, second, and third components of the exponential model, respectively. The time to reach 50% of the difference between passive and voluntary asymptotic blood flow was approximately 2.2-8.9 s. The blood flow leveled off after approximately 10-150 s, related to the power outputs. It is concluded that the elevation in blood flow with the first duty cycle(s) is due to muscle mechanical factors, but vasodilators initiate a more potent amplification within the second to fourth contraction.

Identification of the hot spot residues for pyridine derivative inhibitor CCT251455 and ATP substrate binding on monopolar spindle 1 (MPS1) kinase by molecular dynamic simulation.

Science.gov (United States)

Chen, Kai; Duan, Wenxiu; Han, Qianqian; Sun, Xuan; Li, Wenqian; Hu, Shuangyun; Wan, Jiajia; Wu, Jiang; Ge, Yushu; Liu, Dan

2018-03-08

Protein kinase monopolar spindle 1 plays an important role in spindle assembly checkpoint at the onset of mitosis. Over expression of MPS1 correlated with a wide range of human tumors makes it an attractive target for finding an effective and specific inhibitor. In this work, we performed molecular dynamics simulations of protein MPS1 itself as well as protein bound systems with the inhibitor and natural substrate based on crystal structures. The reported orally bioavailable 1 h-pyrrolo [3,2-c] pyridine inhibitors of MPS1 maintained stable binding in the catalytic site, while natural substrate ATP could not stay. Comparative study of stability and flexibility of three systems reveals position shifting of β-sheet region within the catalytic site, which indicates inhibition mechanism was through stabilizing the β-sheet region. Binding free energies calculated with MM-GB/PBSA method shows different binding affinity for inhibitor and ATP. Finally, interactions between protein and inhibitor during molecular dynamic simulations were measured and counted. Residue Gly605 and Leu654 were suggested as important hot spots for stable binding of inhibitor by molecular dynamic simulation. Our results reveal an important position shifting within catalytic site for non-inhibited proteins. Together with hot spots found by molecular dynamic simulation, the results provide important information of inhibition mechanism and will be referenced for designing novel inhibitors.

Vortex dynamics and heat transfer behind self-oscillating inverted flags of various lengths in channel flow

Science.gov (United States)

Yu, Yuelong; Liu, Yingzheng; Chen, Yujia

2018-04-01

The influence of an inverted flag's length-to-channel-width ratio (C* = L/W) on its oscillating behavior in a channel flow and the resultant vortex dynamics and heat transfer are determined experimentally. Three systems with C* values of 0.125, 0.250, and 0.375 were chosen for comparison. The interaction of highly unsteady flow with the inverted flag is measured with time-resolved particle image velocimetry. Variations in the underlying flow physics are discussed in terms of the statistical flow quantities, flag displacement, phase-averaged flow field, and vortex dynamics. The results show that the increase in C* shifts the occurrence of the flapping regime at high dimensionless bending stiffness. With the flag in the flapping region, three distinct vortex dynamics—the von Kármán vortex street, the G mode, and the singular mode—are identified at C* values of 0.375, 0.250, and 0.125, respectively. Finally, the heat transfer enhancement from the self-oscillating inverted flag is measured to serve as complementary information to quantify the cause-and-effect relationship between vortex dynamics and wall heat transfer. The increase in C* strongly promotes wall heat removal because disruption of the boundary layer by the energetic vortices is substantially intensified. Among all systems, wall heat transfer removal is most efficient at the intermediate C* value of 0.250.

Spontaneous and Flow-Driven Interfacial Phase Change: Dynamics of Microemulsion Formation at the Pore Scale.

Science.gov (United States)

Tagavifar, Mohsen; Xu, Ke; Jang, Sung Hyun; Balhoff, Matthew T; Pope, Gary A

2017-11-14

The dynamic behavior of microemulsion-forming water-oil-amphiphiles mixtures is investigated in a 2.5D micromodel. The equilibrium phase behavior of such mixtures is well-understood in terms of macroscopic phase transitions. However, what is less understood and where experimental data are lacking is the coupling between the phase change and the bulk flow. Herein, we study the flow of an aqueous surfactant solution-oil mixture in porous media and analyze the dependence of phase formation and spatial phase configurations on the bulk flow rate. We find that a microemulsion forms instantaneously as a boundary layer at the initial surface of contact between the surfactant solution and oil. The boundary layer is temporally continuous because of the imposed convection. In addition to the imposed flow, we observe spontaneous pulsed Marangoni flows that drag the microemulsion and surfactant solution into the oil stream, forming large (macro)emulsion droplets. The formation of the microemulsion phase at the interface distinguishes the situation from that of the more common Marangoni flow with only two phases present. Additionally, an emulsion forms via liquid-liquid nucleation or the Ouzo effect (i.e., spontaneous emulsification) at low flow rates and via mechanical mixing at high flow rates. With regard to multiphase flow, contrary to the common belief that the microemulsion is the wetting liquid, we observe that the minor oil phase wets the solid surface. We show that a layered flow pattern is formed because of the out-of-equilibrium phase behavior at high volumetric flow rates (order of 2 m/day) where advection is much faster than the diffusive interfacial mass transfer and transverse mixing, which promote equilibrium behavior. At lower flow rates (order of 30 cm/day), however, the dynamic and equilibrium phase behaviors are well-correlated. These results clearly show that the phase change influences the macroscale flow behavior.

Molecular insights into the specific recognition between the RNA binding domain qRRM2 of hnRNP F and G-tract RNA: A molecular dynamics study.

Science.gov (United States)

Wang, Lingyun; Yan, Feng

2017-12-09

Heterogeneous nuclear ribonucleoprotein F (hnRNP F) controls the expression of various genes through regulating the alternative splicing of pre-mRNAs in the nucleus. It uses three quasi-RNA recognition motifs (qRRMs) to recognize G-tract RNA which contains at least three consecutive guanines. The structures containing qRRMs of hnRNP F in complex with G-tract RNA have been determined by nuclear magnetic resonance (NMR) spectroscopy, shedding light on the recognition mechanism of qRRMs with G-tract RNA. However, knowledge of the recognition details is still lacking. To investigate how qRRMs specifically bind with G-tract RNA and how the mutations of any guanine to an adenine in the G-tract affect the binding, molecular dynamics simulations with binding free energy analysis were performed based on the NMR structure of qRRM2 in complex with G-tract RNA. Simulation results demonstrate that qRRM2 binds strongly with G-tract RNA, but any mutation of the G-tract leads to a drastic reduction of the binding free energy. Further comparisons of the energetic components reveal that van der Waals and non-polar interactions play essential roles in the binding between qRRM2 and G-tract RNA, but the interactions are weakened by the effect of RNA mutations. Structural and dynamical analyses indicate that when qRRM2 binds with G-tract RNA, both qRRM2 and G-tract maintain stabilized structures and dynamics; however, the stability is disrupted by the mutations of the G-tract. These results provide novel insights into the recognition mechanism of qRRM2 with G-tract RNA that are not elucidated by the NMR technique. Copyright © 2017 Elsevier Inc. All rights reserved.

Solution structure, copper binding and backbone dynamics of recombinant Ber e 1-the major allergen from Brazil nut.

Directory of Open Access Journals (Sweden)

Louise Rundqvist

Full Text Available BACKGROUND: The 2S albumin Ber e 1 is the major allergen in Brazil nuts. Previous findings indicated that the protein alone does not cause an allergenic response in mice, but the addition of components from a Brazil nut lipid fraction were required. Structural details of Ber e 1 may contribute to the understanding of the allergenic properties of the protein and its potential interaction partners. METHODOLOGY/PRINCIPAL FINDINGS: The solution structure of recombinant Ber e 1 was solved using NMR spectroscopy and measurements of the protein back bone dynamics at a residue-specific level were extracted using (15N-spin relaxation. A hydrophobic cavity was identified in the structure of Ber e 1. Using the paramagnetic relaxation enhancement property of Cu(2+ in conjunction with NMR, it was shown that Ber e 1 is able to specifically interact with the divalent copper ion and the binding site was modeled into the structure. The IgE binding region as well as the copper binding site show increased dynamics on both fast ps-ns timescale as well as slower µs-ms timescale. CONCLUSIONS/SIGNIFICANCE: The overall fold of Ber e 1 is similar to other 2S albumins, but the hydrophobic cavity resembles that of a homologous non-specific lipid transfer protein. Ber e 1 is the first 2S albumin shown to interact with Cu(2+ ions. This Cu(2+ binding has minimal effect on the electrostatic potential on the surface of the protein, but the charge distribution within the hydrophobic cavity is significantly altered. As the hydrophobic cavity is likely to be involved in a putative lipid interaction the Cu(2+ can in turn affect the interaction that is essential to provoke an allergenic response.

Evaluations of CSF flow dynamics in elderly with dementia by metrizamide CT cisternography

International Nuclear Information System (INIS)

Nokura, Kazuya; Kabasawa, Hidehiro; Matsubara, Mitsutaka; Yamamoto, Masahiko; Nagai, Hajime

1988-01-01

We have investigated Metrizamide CT-cisternography in multi-infarct dementia (MID): 29 cases, senile dementia of the Alzheimer type (SDAT): 7 cases, normal pressure hydrocephalus (NPH): 8 cases and spinocerebellar degeneration (SCD): 3 cases. By quantitative manner the differences of cerebrospinal fluid (CSF) flowdynamics in each group have been evaluated. In comparison with SCD which show normal CSF flow, MID show tendency to ventricular reflux and convexity stasis. No difference was seen between MID and SDAT. Though NPH shows stronger ventricular reflux than that or MID, the stasis in MID is more severe than that of NPH. In MID group subject of older than 70 years show more severe SCF flow disturbances. When divided into two groups by ADL (Activities of daily living) scale (full of 15 points) the group of less than 6 points show slight disturbances in comparison with that of more than 6 points. And the same is true in Hasegawas dementia rating scales, namely the group of less than 21 points (full of 32.5) shows slight disturbances in comparison with that of more than 21 points. The flow dynamics pattern of slight ventricular reflux in 24 hours and stasis in convexity from 24 to 48 hours seems to be typical in either MID or SDAT. But such a pattern has never been reported in SCF flow dynamics studies. These findings may suggest that CSF flow disturbances have a close relation with aging and dementia. (author)

Evaluations of CSF flow dynamics in elderly with dementia by metrizamide CT cisternography

Energy Technology Data Exchange (ETDEWEB)

Nokura, Kazuya; Kabasawa, Hidehiro; Matsubara, Mitsutaka; Yamamoto, Masahiko; Nagai, Hajime

1988-06-01

We have investigated Metrizamide CT-cisternography in multi-infarct dementia (MID): 29 cases, senile dementia of the Alzheimer type (SDAT): 7 cases, normal pressure hydrocephalus (NPH): 8 cases and spinocerebellar degeneration (SCD): 3 cases. By quantitative manner the differences of cerebrospinal fluid (CSF) flowdynamics in each group have been evaluated. In comparison with SCD which show normal CSF flow, MID show tendency to ventricular reflux and convexity stasis. No difference was seen between MID and SDAT. Though NPH shows stronger ventricular reflux than that or MID, the stasis in MID is more severe than that of NPH. In MID group subject of older than 70 years show more severe SCF flow disturbances. When divided into two groups by ADL (Activities of daily living) scale (full of 15 points) the group of less than 6 points show slight disturbances in comparison with that of more than 6 points. And the same is true in Hasegawas dementia rating scales, namely the group of less than 21 points (full of 32.5) shows slight disturbances in comparison with that of more than 21 points. The flow dynamics pattern of slight ventricular reflux in 24 hours and stasis in convexity from 24 to 48 hours seems to be typical in either MID or SDAT. But such a pattern has never been reported in SCF flow dynamics studies. These findings may suggest that CSF flow disturbances have a close relation with aging and dementia.

Measurements of granular flow dynamics with high speed digital images

Energy Technology Data Exchange (ETDEWEB)

Lee, Jingeol [Univ. of Florida, Gainesville, FL (United States)

1994-01-01

The flow of granular materials is common to many industrial processes. This dissertation suggests and validates image processing algorithms applied to high speed digital images to measure the dynamics (velocity, temperature and volume fraction) of dry granular solids flowing down an inclined chute under the action of gravity. Glass and acrylic particles have been used as granular solids in the experiment. One technique utilizes block matching for spatially averaged velocity measurements of the glass particles. This technique is compared with the velocity measurement using an optic probe which is a conventional granular flow velocity measurement device. The other technique for measuring the velocities of individual acrylic particles is developed with correspondence using a Hopfield network. This technique first locates the positions of particles with pattern recognition techniques, followed by a clustering technique, which produces point patterns. Also, several techniques are compared for particle recognition: synthetic discriminant function (SDF), minimum average correlation energy (MACE) filter, modified minimum average correlation energy (MMACE) filter and variance normalized correlation. The author proposes an MMACE filter which improves generalization of the MACE filter by adjusting the amount of averaged spectrum of training images in the spectrum whitening stages of the MACE filter. Variance normalized correlation is applied to measure the velocity and temperature of flowing glass particles down the inclined chute. The measurements are taken for the steady and wavy flow and qualitatively compared with a theoretical model of granular flow.

Effect of river flow fluctuations on riparian vegetation dynamics: Processes and models

Science.gov (United States)

Vesipa, Riccardo; Camporeale, Carlo; Ridolfi, Luca

2017-12-01

Several decades of field observations, laboratory experiments and mathematical modelings have demonstrated that the riparian environment is a disturbance-driven ecosystem, and that the main source of disturbance is river flow fluctuations. The focus of the present work has been on the key role that flow fluctuations play in determining the abundance, zonation and species composition of patches of riparian vegetation. To this aim, the scientific literature on the subject, over the last 20 years, has been reviewed. First, the most relevant ecological, morphological and chemical mechanisms induced by river flow fluctuations are described from a process-based perspective. The role of flow variability is discussed for the processes that affect the recruitment of vegetation, the vegetation during its adult life, and the morphological and nutrient dynamics occurring in the riparian habitat. Particular emphasis has been given to studies that were aimed at quantifying the effect of these processes on vegetation, and at linking them to the statistical characteristics of the river hydrology. Second, the advances made, from a modeling point of view, have been considered and discussed. The main models that have been developed to describe the dynamics of riparian vegetation have been presented. Different modeling approaches have been compared, and the corresponding advantages and drawbacks have been pointed out. Finally, attention has been paid to identifying the processes considered by the models, and these processes have been compared with those that have actually been observed or measured in field/laboratory studies.

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

Correlation Networks from Flows. The Case of Forced and Time-Dependent Advection-Diffusion Dynamics.

Directory of Open Access Journals (Sweden)

Liubov Tupikina

Full Text Available Complex network theory provides an elegant and powerful framework to statistically investigate different types of systems such as society, brain or the structure of local and long-range dynamical interrelationships in the climate system. Network links in climate networks typically imply information, mass or energy exchange. However, the specific connection between oceanic or atmospheric flows and the climate network's structure is still unclear. We propose a theoretical approach for verifying relations between the correlation matrix and the climate network measures, generalizing previous studies and overcoming the restriction to stationary flows. Our methods are developed for correlations of a scalar quantity (temperature, for example which satisfies an advection-diffusion dynamics in the presence of forcing and dissipation. Our approach reveals that correlation networks are not sensitive to steady sources and sinks and the profound impact of the signal decay rate on the network topology. We illustrate our results with calculations of degree and clustering for a meandering flow resembling a geophysical ocean jet.

Dynamic Multi-Component Covalent Assembly for the Reversible Binding of Secondary Alcohols and Chirality Sensing

Science.gov (United States)

You, Lei; Berman, Jeffrey S.; Anslyn, Eric V.

2011-01-01

Reversible covalent bonding is often employed for the creation of novel supramolecular structures, multi-component assemblies, and sensing ensembles. In spite of remarkable success of dynamic covalent systems, the reversible binding of a mono-alcohol with high strength is challenging. Here we show that a strategy of carbonyl activation and hemiaminal ether stabilization can be embodied in a four-component reversible assembly that creates a tetradentate ligand and incorporates secondary alcohols with exceptionally high affinity. Evidence is presented that the intermediate leading to binding and exchange of alcohols is an iminium ion. Further, to demonstrate the use of this assembly process we explored chirality sensing and enantiomeric excess determinations. An induced twist in the ligand by a chiral mono-ol results in large Cotton effects in the circular dichroism spectra indicative of the alcohol’s handedness. The strategy revealed in this study should prove broadly applicable for the incorporation of alcohols into supramolecular architecture construction. PMID:22109274

POD- Mapping and analysis of hydroturbine exit flow dynamics

Science.gov (United States)

Kjeldsen, Morten; Finstad, Pal Henrik

2012-11-01

Pairwise radial dynamic measurements of the swirling draft tube flow have been made at the 25 MW Svorka power plant in Surnadal operating at 48% load at 6 radial and 7 angular positions. The data is analyzed with traditional methods as well as with POD. The measurements were made in the turbine draft tube/exit flow in an axial measurement plane about 1200mm downstream the turbine runner. The draft tube diameter in the measurement plane is about 1300mm. The flow rate during measurements was close to 5.8m3/s. Two probes were used; both of length Le=700 mm and made of stainless steel with an outer diameter of Do=20 mm and inner diameter Di=4mm. At the end of each probe a full bridge cylindrical KULITE xcl152, 0-3.5, was mounted. 90 seconds samples at 10 kS/s were taken. The POD analysis largely follows that of Tutkun et al. (see e.g. AIAA J., 45,5,2008). The analysis shows that 26% of the pressure pulsation energy can be addressed to azimuthal mode 1. The work has been supported by Energy Norway.

Visualization and analysis of flow patterns of human carotid bifurcation by computational fluid dynamics

International Nuclear Information System (INIS)

Xue Yunjing; Gao Peiyi; Lin Yan

2007-01-01

Objective: To investigate flow patterns at carotid bifurcation in vivo by combining computational fluid dynamics (CFD)and MR angiography imaging. Methods: Seven subjects underwent contrast-enhanced MR angiography of carotid artery in Siemens 3.0 T MR. Flow patterns of the carotid artery bifurcation were calculated and visualized by combining MR vascular imaging post-processing and CFD. Results: The flow patterns of the carotid bifurcations in 7 subjects were varied with different phases of a cardiac cycle. The turbulent flow and back flow occurred at bifurcation and proximal of internal carotid artery (ICA) and external carotid artery (ECA), their occurrence and conformation were varied with different phase of a cardiac cycle. The turbulent flow and back flow faded out quickly when the blood flow to the distal of ICA and ECA. Conclusion: CFD combined with MR angiography can be utilized to visualize the cyclical change of flow patterns of carotid bifurcation with different phases of a cardiac cycle. (authors)

Three-Dimensional Smoothed Particle Hydrodynamics Modeling of Preferential Flow Dynamics at Fracture Intersections on a High-Performance Computing Platform

Science.gov (United States)

Kordilla, J.; Bresinsky, L. T.

2017-12-01

The physical mechanisms that govern preferential flow dynamics in unsaturated fractured rock formations are complex and not well understood. Fracture intersections may act as an integrator of unsaturated flow, leading to temporal delay, intermittent flow and partitioning dynamics. In this work, a three-dimensional Pairwise-Force Smoothed Particle Hydrodynamics (PF-SPH) model is being applied in order to simulate gravity-driven multiphase flow at synthetic fracture intersections. SPH, as a meshless Lagrangian method, is particularly suitable for modeling deformable interfaces, such as three-phase contact dynamics of droplets, rivulets and free-surface films. The static and dynamic contact angle can be recognized as the most important parameter of gravity-driven free-surface flow. In SPH, surface tension and adhesion naturally emerges from the implemented pairwise fluid-fluid (sff) and solid-fluid (ssf) interaction force. The model was calibrated to a contact angle of 65°, which corresponds to the wetting properties of water on Poly(methyl methacrylate). The accuracy of the SPH simulations were validated against an analytical solution of Poiseuille flow between two parallel plates and against laboratory experiments. Using the SPH model, the complex flow mode transitions from droplet to rivulet flow of an experimental study were reproduced. Additionally, laboratory dimensionless scaling experiments of water droplets were successfully replicated in SPH. Finally, SPH simulations were used to investigate the partitioning dynamics of single droplets into synthetic horizontal fractures with various apertures (Δdf = 0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0 mm) and offsets (Δdoff = -1.5, -1.0, -0.5, 0, 1.0, 2.0, 3.0 mm). Fluid masses were measured in the domains R1, R2 and R3. The perfect conditions of ideally smooth surfaces and the SPH inherent advantage of particle tracking allow the recognition of small scale partitioning mechanisms and its importance for bulk flow

Experimental evaluation of the use of homogeneous and slip-flow two-phase dynamic models in evaporator modelling

DEFF Research Database (Denmark)

Jakobsen, Arne; Antonius, Jesper; Knudsen, Hans Jørgen Høgaard

1999-01-01

of the homogeneous model is approximately a factor 3 less than the charge calculated using the slip-flow model.The overall conclusion is that when one wants to investigate the dynamic behaviour due to the movement and amount of the refrigerant in the evaporator, then it is needed to use a slip-flow two-phase model...... shows that the dynamic response of the homogeneous model is too fast whereas the simulation results based on the slip-flow model agrees very well with the experimental results. Another difference in the results from the two types of models is the estimation of charge. The charge calculated by the use...

Blood flow and oxygenation in peritendinous tissue and calf muscle during dynamic exercise in humans

DEFF Research Database (Denmark)

Boushel, Robert Christopher; Langberg, H; Green, Sara Marie Ehrenreich

2000-01-01

1. Circulation around tendons may act as a shunt for muscle during exercise. The perfusion and oxygenation of Achilles' peritendinous tissue was measured in parallel with that of calf muscle during exercise to determine (1) whether blood flow is restricted in peritendinous tissue during exercise......, and (2) whether blood flow is coupled to oxidative metabolism. 2. Seven individuals performed dynamic plantar flexion from 1 to 9 W. Radial artery and popliteal venous blood were sampled for O2, peritendinous blood flow was determined by 133Xe-washout, calf blood flow by plethysmography, cardiac output...

DYNAM, Once Through Boiling Flow with Steam Superheat, Laplace Transformation

International Nuclear Information System (INIS)

Schlueter, G.; Efferding, L.E.

1973-01-01

1 - Description of problem or function: DYNAM performs a dynamic analysis of once-through boiling flow oscillations with steam superheat. The model describing the superheat regime (single- phase, variable density fluid) for subcritical pressure operation is also applicable to the study of once-through operation using supercritical pressure water. 2 - Method of solution: Linearized partial differential conservation equations are solved using Laplace transformation of the temporal terms and integration of the spatial variations. DYNAM is written in complex variable notation. 3 - Restrictions on the complexity of the problem - Maxima of: 30 intervals used to describe the power distribution in the non-boiling and boiling regions, 29 boiling nodes, 7 intervals and corresponding friction multipliers read in per case, 14 exit qualities read in per case, 40 superheat nodes, 10 coefficients read in for the phi 2 vs, x-polynomial fit, 48 frequencies at which open-loop frequency response is desired, 48 frequencies at which signal output is desired

A dynamic model of gas flow in a non-uniform pipe

International Nuclear Information System (INIS)

Mensah, S.; Lepp, R.M.

1979-08-01

A gas-line model, based on the analysis of compressible flow with friction, has been developed to describe the dynamics of gas flow in a non-uniform line, i.e. one comprising segments of different lengths and diameters. Acoustic wave analysis was used in a novel way, by considering the line as a cascaded connection of uniform pipes separated by discontinuities. The transmission matrix representing this non-uniform line is the product of the matrices for each element in the system. To facilitate implementation of the theoretical model on a hybrid computer, modal approximatons to its transfer functions were derived. Both models were validated against experimental data. (author)

Nonequilibrium Langevin dynamics: A demonstration study of shear flow fluctuations in a simple fluid

Science.gov (United States)

Belousov, Roman; Cohen, E. G. D.; Rondoni, Lamberto

2017-08-01

The present paper is based on a recent success of the second-order stochastic fluctuation theory in describing time autocorrelations of equilibrium and nonequilibrium physical systems. In particular, it was shown to yield values of the related deterministic parameters of the Langevin equation for a Couette flow in a microscopic molecular dynamics model of a simple fluid. In this paper we find all the remaining constants of the stochastic dynamics, which then is simulated numerically and compared directly with the original physical system. By using these data, we study in detail the accuracy and precision of a second-order Langevin model for nonequilibrium physical systems theoretically and computationally. We find an intriguing relation between an applied external force and cumulants of the resulting flow fluctuations. This is characterized by a linear dependence of an athermal cumulant ratio, an apposite quantity introduced here. In addition, we discuss how the order of a given Langevin dynamics can be raised systematically by introducing colored noise.

Structural and dynamic studies of the dimerization and DNA-binding domains of the transcription factors v-Myc and Max

International Nuclear Information System (INIS)

Fieber, W.

2001-05-01

In the present work, solution structural and dynamic properties of the dimerization and DNA binding domains of the transcription factors v-Myc and Max were characterized by NMR and CD spectroscopy. It could be demonstrated that v-Myc in the absence of its authentic binding partner Max does not homodimerize, but exists in a monomeric and prestructured form. Two separated α-helical regions in the leucine zipper region and in the basic-H1 region, respectively, could be identified, while the latter appeared to be less stable. Both helices lack stabilizing tertiary side chain interactions and represent exceptional examples for loosely coupled, structured segments in a native protein. The structure of v-Myc is dynamic and can be described as a distribution of conformational substates. Motion within the substates comprise fast (picosecond to nanosecond) local backbone fluctuations like helical fraying, whereas motion between the substates comprise the relative orientation of the two helices and occur at larger time scales (microsecond to millisecond). The preformation of the specific protein and DNA binding sites, leucine zipper and the basic region, presumably allows rapid and accurate recognition of the respective binding partners. v-Myc-Max and Max-Max protein preparations were shown to form stable dimers. Thermodynamic analysis of the dissociation reactions of v-Myc-Max revealed a significant higher stability of the heterodimer than of the Max-Max homodimer over the whole temperature range. It could be demonstrated that the restricted conformational space of the v-Myc bHLHZip domain reduces the entropy penalty associated with dimerization and contributes to the preference of Max to form heterodimers with v-Myc rather than homodimers. (author)

Two-phase flow dynamics in a model steam generator under vertical acceleration oscillation field

International Nuclear Information System (INIS)

Ishida, T.; Teshima, N.; Sakurai, S.

1992-01-01

The influence of periodically varying acceleration on hydrodynamic response has been studied experimentally using an experimental rig which models a marine reactor subject to vertical motion. The effect on the primary loop is small, but the effect on the secondary loop is large. The variables of the secondary loop, such as circulation flow rate and water level, oscillate with acceleration. The variation of gains in frequency response is analysed. The variations of flow in the secondary loop and in the downcome water level, increase in proportion to the acceleration. The effect of the flow resistance in the secondary loop on the two-phase flow dynamics is clarified. (7 figures) (Author)

Dynamics of cold helium flow inside a cryoline used for large cryogenic distribution system

International Nuclear Information System (INIS)

Kumar, Uday; Jadon, Mohit; Choukekar, Ketan; Shukla, Vinit; Patel, Pratik; Kapoor, Himanshu; Shah, Nitin; Muralidhara, Srinivasa; Sarkar, Biswanath

2015-01-01

The Cryolines, which by definition transfers cryogens from the source, normally a cryogenic plant, to several systems requiring cooling at cryogenic temperature to the level of 4 K and 80 K. The operations of cryolines are normally assumed to be steady state following a cool down from room temperature to the cryogenic temperature. It is to be noted that in a distributed cryogenic system, especially in a nuclear facility such as ITER having confinement definition due to the regulatory requirements, do also attract the attention in the system design that the release from safety valves cannot be allowed inside a building. Therefore, all safety valves need to be discharged inside a confined space, which is a specific space requiring fulfillment of definition for a cryogenic line. The specificity in such cases is that such cryogenic lines will realize dynamic conditions for each release of safety valves or a combination of safety valves in terms of pressure, temperature and flow, leading to unexpected failures. Such operating scenarios also lead to serious impact on fatigue with a question mark on the reliability. Therefore, one can define such cryolines as Relief Collection Header (RCH) which collects discharged helium and transport it to the appropriate place as defined in the system design. The discharges of cold helium from safety relief discharge ports of equipment can result into significantly unsteady and compressible flow in RCH. The proper design of the RCH has to be supported by detailed dynamic of expected flow phenomena for specific cases. The paper presents the dynamics of cold helium flow inside the typical RCH that has been performed to investigate the variation in flow parameters (pressure, temperature, velocity and density) along the axis of RCH and predictions on its reliability. (author)

Gas flow characteristics of a time modulated APPJ: the effect of gas heating on flow dynamics

International Nuclear Information System (INIS)

Zhang, S; Sobota, A; Van Veldhuizen, E M; Bruggeman, P J

2015-01-01

This work investigates the flow dynamics of a radio-frequency (RF) non-equilibrium argon atmospheric pressure plasma jet. The RF power is at a frequency of 50 Hz or 20 kHz. Combined flow pattern visualizations (obtained by shadowgraphy) and gas temperature distributions (obtained by Rayleigh scattering) are used to study the formation of transient vortex structures in initial flow field shortly after the plasma is switched on and off in the case of 50 Hz modulation. The transient vortex structures correlate well with observed temperature differences. Experimental results of the fast modulated (20 kHz) plasma jet that does not induce changes of the gas temperature are also presented. The latter result suggests that momentum transfer by ions does not have dominant effect on the flow pattern close to the tube. It is argued that the increased gas temperature and corresponding gas velocity increase at the tube exit due to the plasma heating increases the admixing of surrounding air and reduces the effective potential core length. With increasing plasma power a reduction of the effective potential core length is observed with a minimum length for 5.6 W after which the length extends again. Possible mechanisms related to viscosity effects and ionic momentum transfer are discussed. (paper)

Reversal of flow in the inferior vena cava and hepatic veins on dynamic CT

International Nuclear Information System (INIS)

Lelij, H. van der; Mallens, W.M.C.

1988-01-01

A tricuspid insufficiency may not be clinically evident and may remain unknown to the clinician. The phenomenon of a reversal of inferior vena caval blood flow and hepatic veins is known to occur in tricuspid regurgitation from right ventricular angiography and duplex scanning. Demonstration of such a reversal flow on a dynamic CT scan, as in our case, has, to our knowledge, not as yet been reported

Turbulent Flow and Sand Dune Dynamics: Identifying Controls on Aeolian Sediment Transport

Science.gov (United States)

Weaver, C. M.; Wiggs, G.

2007-12-01

Sediment transport models are founded on cubic power relationships between the transport rate and time averaged flow parameters. These models have achieved limited success and recent aeolian and fluvial research has focused on the modelling and measurement of sediment transport by temporally varying flow conditions. Studies have recognised turbulence as a driving force in sediment transport and have highlighted the importance of coherent flow structures in sediment transport systems. However, the exact mechanisms are still unclear. Furthermore, research in the fluvial environment has identified the significance of turbulent structures for bedform morphology and spacing. However, equivalent research in the aeolian domain is absent. This paper reports the findings of research carried out to characterise the importance of turbulent flow parameters in aeolian sediment transport and determine how turbulent energy and turbulent structures change in response to dune morphology. The relative importance of mean and turbulent wind parameters on aeolian sediment flux was examined in the Skeleton Coast, Namibia. Measurements of wind velocity (using sonic anemometers) and sand transport (using grain impact sensors) at a sampling frequency of 10 Hz were made across a flat surface and along transects on a 9 m high barchan dune. Mean wind parameters and mass sand flux were measured using cup anemometers and wedge-shaped sand traps respectively. Vertical profile data from the sonic anemometers were used to compute turbulence and turbulent stress (Reynolds stress; instantaneous horizontal and vertical fluctuations; coherent flow structures) and their relationship with respect to sand transport and evolving dune morphology. On the flat surface time-averaged parameters generally fail to characterise sand transport dynamics, particularly as the averaging interval is reduced. However, horizontal wind speed correlates well with sand transport even with short averaging times. Quadrant

Particle and Blood Cell Dynamics in Oscillatory Flows Final Report

International Nuclear Information System (INIS)

Restrepo, Juan M.

2008-01-01

Our aim has been to uncover fundamental aspects of the suspension and dislodgement of particles in wall-bounded oscillatory flows, in flows characterized by Reynolds numbers encompassing the situation found in rivers and near shores (and perhaps in some industrial processes). Our research tools are computational and our coverage of parameter space fairly broad. Computational means circumvent many complications that make the measurement of the dynamics of particles in a laboratory setting an impractical task, especially on the broad range of parameter space we plan to report upon. The impact of this work on the geophysical problem of sedimentation is boosted considerably by the fact that the proposed calculations can be considered ab-initio, in the sense that little to no modeling is done in generating dynamics of the particles and of the moving fluid: we use a three-dimensional Navier Stokes solver along with straightforward boundary conditions. Hence, to the extent that Navier Stokes is a model for an ideal incompressible isotropic Newtonian fluid, the calculations yield benchmark values for such things as the drag, buoyancy, and lift of particles, in a highly controlled environment. Our approach will be to make measurements of the lift, drag, and buoyancy of particles, by considering progressively more complex physical configurations and physics.

Synchronized renal blood flow dynamics mapped with wavelet analysis of laser speckle flowmetry data

DEFF Research Database (Denmark)

Brazhe, Alexey R; Marsh, Donald J; von Holstein-Rathlou, Niels-Henrik

2014-01-01

of rat kidneys. The regulatory mechanism in the renal microcirculation generates oscillations in arterial blood flow at several characteristic frequencies. Our approach to laser speckle image processing allows detection of frequency and phase entrainments, visualization of their patterns, and estimation......Full-field laser speckle microscopy provides real-time imaging of superficial blood flow rate. Here we apply continuous wavelet transform to time series of speckle-estimated blood flow from each pixel of the images to map synchronous patterns in instantaneous frequency and phase on the surface...... of the extent of synchronization in renal cortex dynamics....

Turbulent flow structure at a discordant river confluence: Asymmetric jet dynamics with implications for channel morphology

Science.gov (United States)

Sukhodolov, Alexander N.; Krick, Julian; Sukhodolova, Tatiana A.; Cheng, Zhengyang; Rhoads, Bruce L.; Constantinescu, George S.

2017-06-01

Only a handful of field studies have examined turbulent flow structure at discordant confluences; the dynamics of flow at such confluences have mainly been examined in the laboratory. This paper reports results of a field-based investigation of turbulent flow structure at a discordant river confluence. These results support the hypothesis that flow at a discordant alluvial confluence with a velocity ratio greater than 2 exhibits jet-like characteristics. Scaling analysis shows that the dynamics of the jet core are quite similar to those of free jets but that the complex structure of flow at the confluence imposes strong effects that can locally suppress or enhance the spreading rate of the jet. This jet-like behavior of the flow has important implications for morphodynamic processes at these types of confluences. The highly energetic core of the jet at this discordant confluence is displaced away from the riverbed, thereby inhibiting scour; however, helical motion develops adjacent to the jet, particularly at high flows, which may promote scour. Numerical experiments demonstrate that the presence or absence of a depositional wedge at the mouth of the tributary can strongly influence detachment of the jet from the bed and the angle of the jet within the confluence.

DYNAMICAL EVOLUTION OF AGN HOST GALAXIES-GAS IN/OUT-FLOW RATES IN SEVEN NUGA GALAXIES

International Nuclear Information System (INIS)

Haan, Sebastian; Schinnerer, Eva; Rix, Hans-Walter; Emsellem, Eric; GarcIa-Burillo, Santiago; Combes, Francoise; Mundell, Carole G.

2009-01-01

To examine the role of the host galaxy structure in fueling nuclear activity, we estimated gas flow rates from several kpc down to the inner few 10 pc for seven nearby spiral galaxies, selected from the NUclei of GAlaxies sample. We calculated gravitational torques from near-infrared images and determined gas in/out-flow rates as a function of radius and location within the galactic disks, based on high angular resolution interferometric observations of molecular (CO using Plateau de Bure interferometer) and atomic (H I using the Very Large Array) gas. The results are compared with kinematic evidence for radial gas flows and the dynamical state of the galaxies (via resonances) derived from several different methods. We show that gravitational torques are very efficient at transporting gas from the outer disk all the way into the galaxies centers at ∼100 pc; previously assumed dynamical barriers to gas transport, such as the corotation resonance of stellar bars, seem to be overcome by gravitational torque induced gas flows from other nonaxisymmetric structures. The resulting rates of gas mass inflow range from 0.01 to 50 M sun yr -1 and are larger for the galaxy center than for the outer disk. Our gas flow maps show the action of nested bars within larger bars for three galaxies. Noncircular streaming motions found in the kinematic maps are larger in the center than in the outer disk and appear to correlate only loosely with the in/out-flow rates as a function of radius. We demonstrate that spiral gas disks are very dynamic systems that undergo strong radial evolution on timescales of a few rotation periods (e.g., 5 x 10 8 yrs at a radius of 5 kpc), due to the effectiveness of gravitational torques in redistributing the cold galactic gas.

[Application of optical flow dynamic texture in land use/cover change detection].

Science.gov (United States)

Yan, Li; Gong, Yi-Long; Zhang, Yi; Duan, Wei

2014-11-01

In the present study, a novel change detection approach for high resolution remote sensing images is proposed based on the optical flow dynamic texture (OFDT), which could achieve the land use & land cover change information automatically with a dynamic description of ground-object changes. This paper describes the ground-object gradual change process from the principle using optical flow theory, which breaks the ground-object sudden change hypothesis in remote sensing change detection methods in the past. As the steps of this method are simple, it could be integrated in the systems and software such as Land Resource Management and Urban Planning software that needs to find ground-object changes. This method takes into account the temporal dimension feature between remote sensing images, which provides a richer set of information for remote sensing change detection, thereby improving the status that most of the change detection methods are mainly dependent on the spatial dimension information. In this article, optical flow dynamic texture is the basic reflection of changes, and it is used in high resolution remote sensing image support vector machine post-classification change detection, combined with spectral information. The texture in the temporal dimension which is considered in this article has a smaller amount of data than most of the textures in the spatial dimensions. The highly automated texture computing has only one parameter to set, which could relax the onerous manual evaluation present status. The effectiveness of the proposed approach is evaluated with the 2011 and 2012 QuickBird datasets covering Duerbert Mongolian Autonomous County of Daqing City, China. Then, the effects of different optical flow smooth coefficient and the impact on the description of the ground-object changes in the method are deeply analyzed: The experiment result is satisfactory, with an 87.29% overall accuracy and an 0.850 7 Kappa index, and the method achieves better

Investigating the flow dynamics in the obstructed and stented ureter by means of a biomimetic artificial model.

Directory of Open Access Journals (Sweden)

Francesco Clavica

Full Text Available Double-J stenting is the most common clinical method employed to restore the upper urinary tract drainage, in the presence of a ureteric obstruction. After implant, stents provide an immediate pain relief by decreasing the pressure in the renal pelvis (P. However, their long-term usage can cause infections and encrustations, due to bacterial colonization and crystal deposition on the stent surface, respectively. The performance of double-J stents - and in general of all ureteric stents - is thought to depend significantly on urine flow field within the stented ureter. However very little fundamental research about the role played by fluid dynamic parameters on stent functionality has been conducted so far. These parameters are often difficult to assess in-vivo, requiring the implementation of laborious and expensive experimental protocols. The aim of the present work was therefore to develop an artificial model of the ureter (i.e. ureter model, UM to mimic the fluid dynamic environment in a stented ureter. The UM was designed to reflect the geometry of pig ureters, and to investigate the values of fluid dynamic viscosity (μ, volumetric flow rate (Q and severity of ureteric obstruction (OB% which may cause critical pressures in the renal pelvis. The distributed obstruction derived by the sole stent insertion was also quantified. In addition, flow visualisation experiments and computational simulations were performed in order to further characterise the flow field in the UM. Unique characteristics of the flow dynamics in the obstructed and stented ureter have been revealed with using the developed UM.

Validation of a Multimodality Flow Phantom and Its Application for Assessment of Dynamic SPECT and PET Technologies.

Science.gov (United States)

Gabrani-Juma, Hanif; Clarkin, Owen J; Pourmoghaddas, Amir; Driscoll, Brandon; Wells, R Glenn; deKemp, Robert A; Klein, Ran

2017-01-01

Simple and robust techniques are lacking to assess performance of flow quantification using dynamic imaging. We therefore developed a method to qualify flow quantification technologies using a physical compartment exchange phantom and image analysis tool. We validate and demonstrate utility of this method using dynamic PET and SPECT. Dynamic image sequences were acquired on two PET/CT and a cardiac dedicated SPECT (with and without attenuation and scatter corrections) systems. A two-compartment exchange model was fit to image derived time-activity curves to quantify flow rates. Flowmeter measured flow rates (20-300 mL/min) were set prior to imaging and were used as reference truth to which image derived flow rates were compared. Both PET cameras had excellent agreement with truth ( [Formula: see text]). High-end PET had no significant bias (p > 0.05) while lower-end PET had minimal slope bias (wash-in and wash-out slopes were 1.02 and 1.01) but no significant reduction in precision relative to high-end PET ( 0.3). SPECT (without scatter and attenuation corrections) slope biases were noted (0.85 and 1.32) and attributed to camera saturation in early time frames. Analysis of wash-out rates from non-saturated, late time frames resulted in excellent agreement with truth ( [Formula: see text], slope = 0.97). Attenuation and scatter corrections did not significantly impact SPECT performance. The proposed phantom, software and quality assurance paradigm can be used to qualify imaging instrumentation and protocols for quantification of kinetic rate parameters using dynamic imaging.

Void fraction measurement in two-phase flow processes via symbolic dynamic filtering of ultrasonic signals

International Nuclear Information System (INIS)

Chakraborty, Subhadeep; Keller, Eric; Talley, Justin; Srivastav, Abhishek; Ray, Asok; Kim, Seungjin

2009-01-01

This communication introduces a non-intrusive method for void fraction measurement and identification of two-phase flow regimes, based on ultrasonic sensing. The underlying algorithm is built upon the recently reported theory of a statistical pattern recognition method called symbolic dynamic filtering (SDF). The results of experimental validation, generated on a laboratory test apparatus, show a one-to-one correspondence between the flow measure derived from SDF and the void fraction measured by a conductivity probe. A sharp change in the slope of flow measure is found to be in agreement with a transition from fully bubbly flow to cap-bubbly flow. (rapid communication)

An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features.

Directory of Open Access Journals (Sweden)

Renata De Paris

Full Text Available Protein receptor conformations, obtained from molecular dynamics (MD simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering algorithms have been widely used as a means to reduce such ensembles to a manageable size. Most studies investigate different algorithms using pairwise Root-Mean Square Deviation (RMSD values for all, or part of the MD conformations. Nevertheless, the RMSD only may not be the most appropriate gauge to cluster conformations when the target receptor has a plastic active site, since they are influenced by changes that occur on other parts of the structure. Hence, we have applied two partitioning methods (k-means and k-medoids and four agglomerative hierarchical methods (Complete linkage, Ward's, Unweighted Pair Group Method and Weighted Pair Group Method to analyze and compare the quality of partitions between a data set composed of properties from an enzyme receptor substrate-binding cavity and two data sets created using different RMSD approaches. Ensembles of representative MD conformations were generated by selecting a medoid of each group from all partitions analyzed. We investigated the performance of our new method for evaluating binding conformation of drug candidates to the InhA enzyme, which were performed by cross-docking experiments between a 20 ns MD trajectory and 20 different ligands. Statistical analyses showed that the novel ensemble, which is represented by only 0.48% of the MD conformations, was able to reproduce 75% of all dynamic behaviors within the binding cavity for the docking experiments performed. Moreover, this new approach not only outperforms the other two RMSD-clustering solutions, but it also shows to be a promising strategy to

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

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Paul D. Morris, PhD

2017-08-01

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

Complete energetic description of hydrokinetic turbine impact on flow channel dynamics

Science.gov (United States)

Brasseale, E.; Kawase, M.

2016-02-01

Energy budget analysis on tidal channels quantifies and demarcates the impacts of marine renewables on environmental fluid dynamics. Energy budget analysis assumes the change in total kinetic energy within a volume of fluid can be described by the work done by each force acting on the flow. In a numerically simulated channel, the balance between energy change and work done has been validated up to 5% error.The forces doing work on the flow include pressure, turbulent dissipation, and stress from the estuary floor. If hydrokinetic turbines are installed in an estuarine channel to convert tidal energy into usable power, the dynamics of the channel change. Turbines provide additional pressure work against the flow of the channel which will slow the current and lessen turbulent dissipation and bottom stress. These losses may negatively impact estuarine circulation, seafloor scour, and stratification.The environmental effects of turbine deployment have been quantified using a three dimensional, Reynolds-averaged, Navier-Stokes model of an idealized flow channel situated between the ocean and a large estuarine basin. The channel is five kilometers wide, twenty kilometers long and fifty meters deep, and resolved to a grid size of 10 meters by 10 meters by 1 meter. Tidal currents are simulated by an initial difference in sea surface height across the channel of 160 centimeters from the channel entrance to the channel exit. This creates a pressure gradient which drives flow through the channel. Tidal power turbines are represented as disks that force the channel in proportion to the strength of the current. Three tidal turbines twenty meters in diameters have been included in the model to simulate the impacts of a pilot scale test deployment.This study is the first to appreciate the energetic impact of marine renewables in a three dimensional model through the energy equation's constituent terms. This study provides groundwork for understanding and predicting the

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

Energy Technology Data Exchange (ETDEWEB)

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

2015-07-28

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

In-Vivo High Dynamic Range Vector Flow Imaging

DEFF Research Database (Denmark)

Villagómez Hoyos, Carlos Armando; Stuart, Matthias Bo; Jensen, Jørgen Arendt

2015-01-01

example with a high dynamic velocity range. Velocities with an order of magnitude apart are detected on the femoral artery of a 41 years old healthy individual. Three distinct heart cycles are captured during a 3 secs acquisition. The estimated vector velocities are compared against each other within...... the heart cycle. The relative standard deviation of the measured velocity magnitude between the three peak systoles was found to be 5.11% with a standard deviation on the detected angle of 1.06◦ . In the diastole, it was 1.46% and 6.18◦ , respectively. Results proves that the method is able to estimate flow...

Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation.

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David J Huggins

2010-08-01

Full Text Available The Polo-Like Kinase 1 (PLK1 acts as a central regulator of mitosis and is over-expressed in a wide range of human tumours where high levels of expression correlate with a poor prognosis. PLK1 comprises two structural elements, a kinase domain and a polo-box domain (PBD. The PBD binds phosphorylated substrates to control substrate phosphorylation by the kinase domain. Although the PBD preferentially binds to phosphopeptides, it has a relatively broad sequence specificity in comparison with other phosphopeptide binding domains. We analysed the molecular determinants of recognition by performing molecular dynamics simulations of the PBD with one of its natural substrates, CDC25c. Predicted binding free energies were calculated using a molecular mechanics, Poisson-Boltzmann surface area approach. We calculated the per-residue contributions to the binding free energy change, showing that the phosphothreonine residue and the mainchain account for the vast majority of the interaction energy. This explains the very broad sequence specificity with respect to other sidechain residues. Finally, we considered the key role of bridging water molecules at the binding interface. We employed inhomogeneous fluid solvation theory to consider the free energy of water molecules on the protein surface with respect to bulk water molecules. Such an analysis highlights binding hotspots created by elimination of water molecules from hydrophobic surfaces. It also predicts that a number of water molecules are stabilized by the presence of the charged phosphate group, and that this will have a significant effect on the binding affinity. Our findings suggest a molecular rationale for the promiscuous binding of the PBD and highlight a role for bridging water molecules at the interface. We expect that this method of analysis will be very useful for probing other protein surfaces to identify binding hotspots for natural binding partners and small molecule inhibitors.

Lattice Boltzmann simulations for wall-flow dynamics in porous ceramic diesel particulate filters

Science.gov (United States)

Lee, Da Young; Lee, Gi Wook; Yoon, Kyu; Chun, Byoungjin; Jung, Hyun Wook

2018-01-01

Flows through porous filter walls of wall-flow diesel particulate filter are investigated using the lattice Boltzmann method (LBM). The microscopic model of the realistic filter wall is represented by randomly overlapped arrays of solid spheres. The LB simulation results are first validated by comparison to those from previous hydrodynamic theories and constitutive models for flows in porous media with simple regular and random solid-wall configurations. We demonstrate that the newly designed randomly overlapped array structures of porous walls allow reliable and accurate simulations for the porous wall-flow dynamics in a wide range of solid volume fractions from 0.01 to about 0.8, which is beyond the maximum random packing limit of 0.625. The permeable performance of porous media is scrutinized by changing the solid volume fraction and particle Reynolds number using Darcy's law and Forchheimer's extension in the laminar flow region.

Development of subchannel void measurement sensor and multidimensional two-phase flow dynamics in rod bundle

International Nuclear Information System (INIS)

Arai, T.; Furuya, M.; Kanai, T.; Shirakawa, K.

2011-01-01

An accurate subchannel database is crucial for modeling the multidimensional two-phase flow in a rod bundle and for validating subchannel analysis codes. Based on available reference, it can be said that a point-measurement sensor for acquiring void fractions and bubble velocity distributions do not infer interactions of the subchannel flow dynamics, such as a cross flow and flow distribution, etc. In order to acquire multidimensional two-phase flow in a 10×10 rod bundle with an o.d. of 10 mm and 3110 mm length, a new sensor consisting of 11-wire by 11-wire and 10-rod by 10-rod electrodes was developed. Electric potential in the proximity region between two wires creates a void fraction in the center subchannel region, like a so-called wire mesh sensor. A unique aspect of the devised sensor is that the void fraction near the rod surface can be estimated from the electric potential in the proximity region between one wire and one rod. The additional 400 points of void fraction and phasic velocity in 10×10 bundle can therefore be acquired. The devised sensor exhibits the quasi three-dimensional flow structures, i.e. void fraction, phasic velocity and bubble chord length distributions. These quasi three-dimensional structures exhibit the complexity of two-phase flow dynamics, such as coalescence and the breakup of bubbles in transient phasic velocity distributions. (author)

Demand dynamic bio-girdling in heart failure: improved efficacy of dynamic cardiomyoplasty by LD contraction during aortic out-flow.

Science.gov (United States)

Carraro, U; Rigatelli, G; Rossini, K; Barbiero, M; Rigatelli, G

2003-03-01

The value of dynamic cardiomyoplasty has been brought into question by the disappointing results produced by slow contraction-relaxation cycle and possibly degeneration of the latissimus dorsi muscle (LD) secondary to temporary tenotomy and chronic daily electrical stimulation. Objective of our study is to determine whether daily periods of rest introduced by demand stimulation in the continuous contraction protocol produce systolic assistance and improve clinical results. Twelve dynamic cardiomyoplasty patients (mean age 58.2 +/- 5.8 years, M/F=11/1, sinus rhythm/atrial fibrillation=11/1) with dilated myocardiopathy were enrolled in an unrandomized trial of Demand Dynamic Heart Bio-Girdling in a public regional teaching hospital. Periods of LD inactivity, each lasting several hours, were introduced daily on a heart rate-based demand regime. To avoid full transformation of LD, fewer impulses per day were delivered, daily providing the LD with long periods of rest (Demand light stimulation). The contractile properties were measured by transcutaneous non-invasive LD tensiomyogram interrogation (LD tensiomyogram). Bio-Girdle activation was synchronized to heart beat by combining tensiomyogram and echocardiography. Clinical, echocardiographic and hemodynamic records, as well as aortic flow measurements by Doppler aortic flow wire were taken during the follow-up. Mean duration of the demand stimulation follow-up was 40.2+13.8 months. At five years, "Demand stimulation" shows: 1) no operative death; 2) 83% actuarial survival; 3) highly significant 47.4% decrease of the NYHA class (from 3.17 +/- 0.38 to 1.67 +/- 0.77, p=0.0001); 4) 41.6% improvement of LVEF (from 22.6 +/- 4.38 to 32.0 +/- 7.0, p=0.001); 5) 7.5 +/- 3.0% increase in aortic flow velocity peak in assisted vs. unassisted beats, and 6) preservation of LD from slowness (TFF value 33 +/- 7.86 at follow-up versus 15.8 +/- 11.1 Hz just before switching from continuous to demand stimulation, p=0.0001) and muscle

Molecular dynamics simulations of oscillatory flows in microfluidic channels

DEFF Research Database (Denmark)

Hansen, J.S.; Ottesen, Johnny T.

2006-01-01

In this paper we apply the direct non-equilibrium molecular dynamics technique to oscillatory flows of fluids in microscopic channels. Initially, we show that the microscopic simulations resemble the macroscopic predictions based on the Navier–Stokes equation very well for large channel width, high...... density and low temperature. Further simulations for high temperature and low density show that the non-slip boundary condition traditionally used in the macroscopic equation is greatly compromised when the fluid–wall interactions are the same as the fluid–fluid interactions. Simulations of a system...

Predicting the onset of dynamic instability of a cylindrical plate under axial flow conditions

Energy Technology Data Exchange (ETDEWEB)

Marcum, W.R., E-mail: marcumw@engr.orst.edu [Oregon State University, Department of Nuclear Engineering and Radiation Health Physics, 116 Radiation Center, Corvallis, OR 97330 (United States); Woods, B.G. [Oregon State University, Department of Nuclear Engineering and Radiation Health Physics, 116 Radiation Center, Corvallis, OR 97330 (United States)

2012-09-15

Highlights: Black-Right-Pointing-Pointer A semi-numerical flow induced vibration model is developed of a cylindrical plate. Black-Right-Pointing-Pointer Test case results are presented and agree well with previous studies data. Black-Right-Pointing-Pointer The model identifies a relationship between forces and the plate natural frequency. - Abstract: The dynamic mechanical stability of a single cylindrical plate under flow conditions is considered herein. Numerous plate-type research reactors such as the Advanced Test Reactor (ATR) located at the Idaho National Laboratory (INL) comprise fuel elements which contain arrays of concentrically aligned cylindrical plates. Several of these reactors are licensed to operate at extreme heat fluxes; as a corollary their hydraulic designs require large flow rates sufficient to remove this heat. These flow rates may reach superficial velocities upwards of 15 m/s through individual flow channels. Given that fuel plates typically found in such research reactors are relatively long ({approx}1.2573 m), wide ({approx}0.1397 m), and extremely thin ({approx}0.00127 m) concern is drawn toward the susceptibility of flow induced vibration (FIV). In an attempt to gain a more comprehensive understanding toward the dynamic mechanical limit of stability of cylindrical plates, a FIV model was developed using semi-numerical methods. The FIV model was developed in two separate modules; a plate stability module, and a flow module. These modules were then coupled together to produce a FIV model. In this study, a set of test cases are presented on the plate stability module under free vibration conditions, comparing well against known available information from previous studies. Results are similarly presented on the flow module and compared against a RELAP5-3D model. Lastly, results of these coupled modules are presented and discussion is given toward the relationship between plate natural frequency, geometry, and plate membrane pressures.

Asymmetric Flow Field Flow Fractionation of Aqueous C60 Nanoparticles with Size Determination by Dynamic Light Scattering and Quantification by Liquid Chromatography Atmospheric Pressure Photo-Ionization Mass Spectrometry

Science.gov (United States)

A size separation method was developed for aqueous C60 fullerene aggregates (aqu/C60) using asymmetric flow field flow fractionation (AF4) coupled to a dynamic light scattering detector in flow through mode. Surfactants, which are commonly used in AF4, were avoided as they may al...

Final accepted paper. Effects of turbulence near a free surface on the dynamics of two-phase flow

International Nuclear Information System (INIS)

Uzawa, Ken; Watanabe, Tadashi

2011-01-01

The effect of turbulence on the dynamics of three-dimensional dam break flow is numerically investigated based on the incompressible Reynolds-averaged Navier- Stokes (RANS) equations with the Volume Of Fluid (VOF) function. It is found that the tip velocity over the ground and the impact pressure against the vertical wall in the Launder- Gibson (LG) model are in good agreement with experimental results. The dynamics of the dam break flow is subject to the viscous dissipation during the collapse of the flow, which is underestimated in the laminar model and overestimated in the realizable k - ε (RKE) model. The turbulent viscous dissipation near the free surface is comparable to that inside the water in the LG model. (author)

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

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Yu-Ru Zhang

Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

Quantitative analysis of the aqueductal CSF flow dynamics with FLASH sequence

International Nuclear Information System (INIS)

Seki, Kouji; Tsuji, Shoji; Yuasa, Tatsuhiko; Miyatake, Tadashi.

1993-01-01

Aqueductal cerebrospinal fluid (CSF) flow image and its dynamics were analyzed with 1.5 T MR system using ECG-gated Fast Low Flip Angle Shot (FLASH). High flip angle (90 degree) and short echo time (10 ms) were applicated. Seventeen ECG gated nine images were obtained in one cardiac cycle from the inferior midbrain. Axial imaging plane (across at 60 degree to the aqueduct) and 6 mm of slice thickness is available. The CSF flow velocity was estimated by a standard curve of signal intensity ratio, obtained by the running water in model tubes. Examinations of five normal subjects (male/female=2/3, 48.4±15 years old) were performed. The aqueductal flow signal had two peaks in one cardiac cycle. The latter oval signals within the diastolic phase represent the caudal (downward) CSF flow, and the former wedge shaped signals represent the cephalad (reverse) flow. The peak velocity of the caudal CSF flow is about 6.5 mm/s, the cephalad flow is about 4.5 mm/s. We defined two zero points of the to-and-fro curve as turning points, the first (caudal to cephalad) zero point as the 'first turning point', the second (cephalad to caudal) zero point as the 'second turning point'. In normal subjects, the first turning points are at 236±28 ms (±SD), the second turning points are at 723±67 ms (±SD) after ECG R wave. This new method is highly useful for the analyzing disorders with CSF flow abnormalities. (author)

Computational Fluid Dynamics and Visualisation of Coastal Flows in Tidal Channels Supporting Ocean Energy Development

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Enayatollah Zangiabadi

2015-06-01

Full Text Available Flow characteristics in coastal regions are strongly influenced by the topography of the seabed and understanding the fluid dynamics is necessary before installation of tidal stream turbines (TST. In this paper, the bathymetry of a potential TST deployment site is used in the development of the a CFD (Computational Fluid Dynamics model. The steady state k-ϵ and transient Large Eddy Simulation (LES turbulence methods are employed and compared. The simulations are conducted with a fixed representation of the ocean surface, i.e., a rigid lid representation. In the vicinity of Horse Rock a study of the pressure difference shows that the small change in height of the water column is negligible, providing confidence in the simulation results. The stream surface method employed to visualise the results has important inherent characteristics that can enhance the visual perception of complex flow structures. The results of all cases are compared with the flow data transect gathered by an Acoustic Doppler Current Profiler (ADCP. It has been understood that the k-ϵ method can predict the flow pattern relatively well near the main features of the domain and the LES model has the ability to simulate some important flow patterns caused by the bathymetry.

Movable shark scales act as a passive dynamic micro-roughness to control flow separation

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