Physics of Bacterial Morphogenesis

PubMed Central

Sun, Sean X.; Jiang, Hongyuan

2011-01-01

Summary: Bacterial cells utilize three-dimensional (3D) protein assemblies to perform important cellular functions such as growth, division, chemoreception, and motility. These assemblies are composed of mechanoproteins that can mechanically deform and exert force. Sometimes, small-nucleotide hydrolysis is coupled to mechanical deformations. In this review, we describe the general principle for an understanding of the coupling of mechanics with chemistry in mechanochemical systems. We apply this principle to understand bacterial cell shape and morphogenesis and how mechanical forces can influence peptidoglycan cell wall growth. We review a model that can potentially reconcile the growth dynamics of the cell wall with the role of cytoskeletal proteins such as MreB and crescentin. We also review the application of mechanochemical principles to understand the assembly and constriction of the FtsZ ring. A number of potential mechanisms are proposed, and important questions are discussed. PMID:22126993

Mechanical influences in bacterial morphogenesis and cell division

NASA Astrophysics Data System (ADS)

Sun, Sean

2010-03-01

Bacterial cells utilize a ring-like organelle (the Z-ring) to accomplish cell division. The Z-ring actively generates a contractile force and influences cell wall growth. We will discuss a general model of bacterial morphogenesis where mechanical forces are coupled to the growth dynamics of the cell wall. The model suggests a physical mechanism that determines the shapes of bacteria cells. The roles of several bacterial cytoskeletal proteins and the Z-ring are discussed. We will also explore molecular mechanisms of force generation by the Z-ring and how cells can generate mechanical forces without molecular motors.

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

PubMed Central

Somogyi, Endre; Glazier, James A.

2017-01-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment. PMID:29303160

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

PubMed

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

Extra-embryonic tissue spreading directs early embryo morphogenesis in killifish

PubMed Central

Reig, Germán; Cerda, Mauricio; Sepúlveda, Néstor; Flores, Daniela; Castañeda, Victor; Tada, Masazumi; Härtel, Steffen; Concha, Miguel L.

2017-01-01

The spreading of mesenchymal-like cell layers is critical for embryo morphogenesis and tissue repair, yet we know little of this process in vivo. Here we take advantage of unique developmental features of the non-conventional annual killifish embryo to study the principles underlying tissue spreading in a simple cellular environment, devoid of patterning signals and major morphogenetic cell movements. Using in vivo experimentation and physical modelling we reveal that the extra-embryonic epithelial enveloping cell layer, thought mainly to provide protection to the embryo, directs cell migration and the spreading of embryonic tissue during early development. This function relies on the ability of embryonic cells to couple their autonomous random motility to non-autonomous signals arising from the expansion of the extra-embryonic epithelium, mediated by cell membrane adhesion and tension. Thus, we present a mechanism of extra-embryonic control of embryo morphogenesis that couples the mechanical properties of adjacent tissues in the early killifish embryo. PMID:28580937

Coordinated Beating of Algal Flagella is Mediated by Basal Coupling

NASA Astrophysics Data System (ADS)

Wan, Kirsty; Goldstein, Raymond

Cilia or flagella often exhibit synchronized behavior. This includes phase-locking, as seen in Chlamydomonas, and metachronal wave formation in the respiratory cilia of higher organisms. Since the observations by Gray and Rothschild of phase synchrony of nearby swimming spermatozoa, it has been a working hypothesis that synchrony arises from hydrodynamic interactions between beating filaments. Recent work on the dynamics of physically separated pairs of flagella isolated from the multicellular alga Volvox has shown that hydrodynamic coupling alone is sufficient for synchrony. However, the situation is more complex when considering multiple flagella on a single cell. We suggest that a mechanism, internal to the cell, provides an additional flagellar coupling. For instance, flagella of Chlamydomonas mutants deficient in filamentary connections between basal bodies are found to display markedly different synchronization from the wildtype. Diverse flagellar coordination strategies found in quadri-, octo- and hexadecaflagellates reveal further evidence that intracellular couplings between flagellar basal bodies compete with hydrodynamic interactions to determine the precise form of flagellar synchronization in unicellular algae.

Electrochemical-mechanical coupled modeling and parameterization of swelling and ionic transport in lithium-ion batteries

NASA Astrophysics Data System (ADS)

Sauerteig, Daniel; Hanselmann, Nina; Arzberger, Arno; Reinshagen, Holger; Ivanov, Svetlozar; Bund, Andreas

2018-02-01

The intercalation and aging induced volume changes of lithium-ion battery electrodes lead to significant mechanical pressure or volume changes on cell and module level. As the correlation between electrochemical and mechanical performance of lithium ion batteries at nano and macro scale requires a comprehensive and multidisciplinary approach, physical modeling accounting for chemical and mechanical phenomena during operation is very useful for the battery design. Since the introduced fully-coupled physical model requires proper parameterization, this work also focuses on identifying appropriate mathematical representation of compressibility as well as the ionic transport in the porous electrodes and the separator. The ionic transport is characterized by electrochemical impedance spectroscopy (EIS) using symmetric pouch cells comprising LiNi1/3Mn1/3Co1/3O2 (NMC) cathode, graphite anode and polyethylene separator. The EIS measurements are carried out at various mechanical loads. The observed decrease of the ionic conductivity reveals a significant transport limitation at high pressures. The experimentally obtained data are applied as input to the electrochemical-mechanical model of a prismatic 10 Ah cell. Our computational approach accounts intercalation induced electrode expansion, stress generation caused by mechanical boundaries, compression of the electrodes and the separator, outer expansion of the cell and finally the influence of the ionic transport within the electrolyte.

Shc and the mechanotransduction of cellular anchorage and metastasis.

PubMed

Terada, Lance S

2017-02-17

Tissue cells continually monitor anchorage conditions by gauging the physical properties of their underlying matrix and surrounding environment. The Rho and Ras GTPases are essential components of these mechanosensory pathways. These molecular switches control both cytoskeletal as well as cell fate responses to anchorage conditions and are thus critical to our understanding of how cells respond to their physical environment and, by extension, how malignant cells gainsay these regulatory pathways. Recent studies indicate that 2 proteins produced by the SHC1 gene, thought for the most part to functionally oppose each other, collaborate in their ability to respond to mechanical force by initiating respective Rho and Ras signals. In this review, we focus on the coupling of Shc and GTPases in the cellular response to mechanical anchorage signals, with emphasis on its relevance for cancer.

A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation

NASA Astrophysics Data System (ADS)

Delile, Julien; Herrmann, Matthieu; Peyriéras, Nadine; Doursat, René

2017-01-01

The study of multicellular development is grounded in two complementary domains: cell biomechanics, which examines how physical forces shape the embryo, and genetic regulation and molecular signalling, which concern how cells determine their states and behaviours. Integrating both sides into a unified framework is crucial to fully understand the self-organized dynamics of morphogenesis. Here we introduce MecaGen, an integrative modelling platform enabling the hypothesis-driven simulation of these dual processes via the coupling between mechanical and chemical variables. Our approach relies upon a minimal `cell behaviour ontology' comprising mesenchymal and epithelial cells and their associated behaviours. MecaGen enables the specification and control of complex collective movements in 3D space through a biologically relevant gene regulatory network and parameter space exploration. Three case studies investigating pattern formation, epithelial differentiation and tissue tectonics in zebrafish early embryogenesis, the latter with quantitative comparison to live imaging data, demonstrate the validity and usefulness of our framework.

Arnold Tongues in Cell Dynamics

NASA Astrophysics Data System (ADS)

Jensen, Mogens

In a recent work with Leo Kadanoff we studied the synchronization between an internal and an external frequency. One obtains a highly structured diagram with details that in essence are related to the difference between rational and irrational number. The synchronized regions appear as Arnold tongues that widen as the coupling between the frequencies increases. Such tongues have been observed in many physical systems, like in the Libchaber convective cell in the basement of the University of Chicago. In biological systems, where oscillators appear in in a broad variety, very little research on Arnold tongues has been performed. We discuss single cell oscillating dynamics triggered by an external cytokine signal. When this signal is overlaid by an oscillating variation, the two oscillators might couple leading to Arnold tongue diagram. When the tongues overlap, the cell dynamics can shift between the tongues eventually leading to a chaotic response. We quantify such switching in single cell experiments and in model systems based on Gillespie simulations. Kadanoff session.

Interactive coupling of electronic and optical man-made devices to biological systems

NASA Astrophysics Data System (ADS)

Ozden, Ilker

Fireflies blink synchronously, lasers are "mode-locked" for amplification, cardiac pacemaker cells maintain a steady heartbeat, and crickets chirps get in step. These are examples of coupled oscillators. Coupled non-linear limit-cycle oscillator models are used extensively to provide information about the collective behavior of many physical and biological systems. Depending on the system parameters, namely, the coupling coefficient and the time delay in the coupling, these coupled limit-cycle oscillator exhibit several interesting phenomena; they either synchronize to a common frequency, or oscillate completely independent of each other, or drag each other to a standstill i.e., show "amplitude death". Many neuronal systems exhibit synchronized limit-cycle oscillations in network of electrically coupled cells. The inferior olivary (IO) neuron is an example of such a system. The inferior olive has been widely studied by neuroscientists as it exhibits spontaneous oscillations in its membrane potential, typically in the range of 1--10 Hz. Located in the medulla, the inferior olive is believed to form the neural basis for precise timing and learning in motor circuits by making strong synaptic connections onto Purkinjee cells in the cerebellum. In this thesis work, we report on work, which focuses on the implementation and study of coupling of a biological circuit, which is the inferior olivary system, with a man-made electronic oscillator, the so-called Chua's circuit. We were able to study the interaction between the two oscillators over a wide range coupling conditions. With increasing coupling strength, the oscillators become phase-locked, or synchronized, but with a phase relationship which is either in- or out-of-phase depending on the detailed adjustment in the coupling. Finally, the coupled system reaches the conditions for amplitude death, a rather fundamental result given that the interaction has taken place between purely biological and man-made circuit elements.

Ultrathin lightweight plate-type acoustic metamaterials with positive lumped coupling resonant

NASA Astrophysics Data System (ADS)

Ma, Fuyin; Huang, Meng; Wu, Jiu Hui

2017-01-01

The experimental realization and theoretical understanding of a two-dimensional multiple cells lumped ultrathin lightweight plate-type acoustic metamaterials structures have been presented, wherein broadband excellent sound attenuation ability at low frequencies is realized by employing a lumped element coupling resonant effect. The basic unit cell of the metamaterials consists of an ultrathin stiff nylon plate clamped by two elastic ethylene-vinyl acetate copolymer or acrylonitrile butadiene styrene frames. The strong sound attenuation (up to nearly 99%) at low frequencies is experimentally revealed by the precisely designed metamaterials, for which the physical mechanism of the sound attenuation could be explicitly understood using the finite element simulations. As to the designed samples, the lumped effect from the frame compliance leads to a coupling flexural resonance at designable low frequencies. As a result, the whole composite structure become strongly anti-resonant with the incident sound waves, followed by a higher sound attenuation, i.e., the lumped resonant effect has been effectively reversed to be positive from negative for sound attenuation, and the acoustic metamaterial design could be extended to the lumped element containing multiple cells, rather than confined to a single cell.

Global Three-dimensional Simulation of the Solar Wind-Magnetosphere Interaction Using a Two-way Coupled Magnetohydrodynamics with Embedded Particle-in-Cell Model

NASA Astrophysics Data System (ADS)

Chen, Y.; Toth, G.; Cassak, P.; Jia, X.; Gombosi, T. I.; Slavin, J. A.; Welling, D. T.; Markidis, S.; Peng, I. B.; Jordanova, V. K.; Henderson, M. G.

2017-12-01

We perform a three-dimensional (3D) global simulation of Earth's magnetosphere with kinetic reconnection physics to study the interaction between the solar wind and Earth's magnetosphere. In this global simulation with magnetohydrodynamics with embedded particle-in-cell model (MHD-EPIC), both the dayside magnetopause reconnection region and the magnetotail reconnection region are covered with a kinetic particle-in-cell code iPIC3D, which is two-way coupled with the global MHD model BATS-R-US. We will describe the dayside reconnection related phenomena, such as the lower hybrid drift instability (LHDI) and the evolution of the flux transfer events (FTEs) along the magnetopause, and compare the simulation results with observations. We will also discuss the response of the magnetotail to the southward IMF. The onset of the tail reconnection and the properties of the magnetotail flux ropes will be discussed.

Messenger RNA Detection in Leukemia Cell lines by Novel Metal-Tagged in situ Hybridization using Inductively Coupled Plasma Mass Spectrometry.

PubMed

Ornatsky, Olga I; Baranov, Vladimir I; Bandura, Dmitry R; Tanner, Scott D; Dick, John

2006-01-01

Conventional gene expression profiling relies on using fluorescent detection of hybridized probes. Physical characteristics of fluorophores impose limitations on achieving a highly multiplex gene analysis of single cells. Our work demonstrates the feasibility of using metal-tagged in situ hybridization for mRNA detection by inductively coupled plasma mass spectrometry (ICP-MS). ICP-MS as an analytical detector has a number of unique and relevant properties: 1) metals and their stable isotopes generate non-overlapping distinct signals that can be detected simultaneously; 2) these signals can be measured over a wide dynamic range; 3) ICP-MS is quantitative and very sensitive. We used commercial antibodies conjugated to europium (Eu) and gold together with biotinylated oligonucleotide probes reacted with terbium-labeled streptavidin to demonstrate simultaneous mRNA and protein detection by ICP-MS in leukemia cells.

Messenger RNA Detection in Leukemia Cell lines by Novel Metal-Tagged in situ Hybridization using Inductively Coupled Plasma Mass Spectrometry

PubMed Central

Ornatsky, Olga I.; Baranov, Vladimir I.; Bandura, Dmitry R.; Tanner, Scott D.; Dick, John

2006-01-01

Conventional gene expression profiling relies on using fluorescent detection of hybridized probes. Physical characteristics of fluorophores impose limitations on achieving a highly multiplex gene analysis of single cells. Our work demonstrates the feasibility of using metal-tagged in situ hybridization for mRNA detection by inductively coupled plasma mass spectrometry (ICP-MS). ICP-MS as an analytical detector has a number of unique and relevant properties: 1) metals and their stable isotopes generate non-overlapping distinct signals that can be detected simultaneously; 2) these signals can be measured over a wide dynamic range; 3) ICP-MS is quantitative and very sensitive. We used commercial antibodies conjugated to europium (Eu) and gold together with biotinylated oligonucleotide probes reacted with terbium-labeled streptavidin to demonstrate simultaneous mRNA and protein detection by ICP-MS in leukemia cells. PMID:23662035

Regulation of Cell Cytoskeleton and Membrane Mechanics by Electric Field: Role of Linker Proteins

PubMed Central

Titushkin, Igor; Cho, Michael

2009-01-01

Abstract Cellular mechanics is known to play an important role in the cell homeostasis including proliferation, motility, and differentiation. Significant variation in the mechanical properties between different cell types suggests that control of the cell metabolism is feasible through manipulation of the cell mechanical parameters using external physical stimuli. We investigated the electrocoupling mechanisms of cellular biomechanics modulation by an electrical stimulation in two mechanically distinct cell types—human mesenchymal stem cells and osteoblasts. Application of a 2 V/cm direct current electric field resulted in approximately a twofold decrease in the cell elasticity and depleted intracellular ATP. Reduction in the ATP level led to inhibition of the linker proteins that are known to physically couple the cell membrane and cytoskeleton. The membrane separation from the cytoskeleton was confirmed by up to a twofold increase in the membrane tether length that was extracted from the cell membrane after an electrical stimulation. In comparison to human mesenchymal stem cells, the membrane-cytoskeleton attachment in osteoblasts was much stronger but, in response to the same electrical stimulation, the membrane detachment from the cytoskeleton was found to be more pronounced. The observed effects mediated by an electric field are cell type- and serum-dependent and can potentially be used for electrically assisted cell manipulation. An in-depth understanding and control of the mechanisms to regulate cell mechanics by external physical stimulus (e.g., electric field) may have great implications for stem cell-based tissue engineering and regenerative medicine. PMID:19167316

Physical-biological coupling induced aggregation mechanism for the formation of high biomass red tides in low nutrient waters.

PubMed

Lai, Zhigang; Yin, Kedong

2014-01-01

Port Shelter is a semi-enclosed bay in northeast Hong Kong where high biomass red tides are observed to occur frequently in narrow bands along the local bathymetric isobars. Previous study showed that nutrients in the Bay are not high enough to support high biomass red tides. The hypothesis is that physical aggregation and vertical migration of dinoflagellates appear to be the driving mechanism to promote the formation of red tides in this area. To test this hypothesis, we used a high-resolution estuarine circulation model to simulate the near-shore water dynamics based on in situ measured temperature/salinity profiles, winds and tidal constitutes taken from a well-validated regional tidal model. The model results demonstrated that water convergence occurs in a narrow band along the west shore of Port Shelter under a combined effect of stratified tidal current and easterly or northeasterly wind. Using particles as dinoflagellate cells and giving diel vertical migration, the model results showed that the particles aggregate along the convergent zone. By tracking particles in the model predicted current field, we estimated that the physical-biological coupled processes induced aggregation of the particles could cause 20-45 times enhanced cell density in the convergent zone. This indicated that a high cell density red tide under these processes could be initialized without very high nutrients concentrations. This may explain why Port Shelter, a nutrient-poor Bay, is the hot spot for high biomass red tides in Hong Kong in the past 25 years. Our study explains why red tide occurrences are episodic events and shows the importance of taking the physical-biological aggregation mechanism into consideration in the projection of red tides for coastal management. Copyright © 2013 Elsevier B.V. All rights reserved.

Gulf of Maine Harmful Algal Bloom in summer 2005 – Part 2: Coupled Bio-physical Numerical Modeling

PubMed Central

He, Ruoying; McGillicuddy, Dennis J.; Keafer, Bruce A.; Anderson, Donald M.

2017-01-01

A coupled physical/biological modeling system was used to hindcast the 2005 Alexandrium fundyense bloom in the Gulf of Maine and investigate the relative importance of factors governing the bloom’s initiation and development. The coupled system consists of a state-of-the-art, free-surface primitive equation Regional Ocean Modeling System (ROMS) tailored for the Gulf of Maine (GOM) using a multi-nested configuration, and a population dynamics model for A. fundyense. The system was forced by realistic momentum and buoyancy fluxes, tides, river runoff, observed A. fundyense benthic cyst abundance, and climatological nutrient fields. Extensive comparisons were made between simulated (both physical and biological) fields and in-situ observations, revealing that the hindcast model is capable of reproducing the temporal evolution and spatial distribution of the 2005 bloom. Sensitivity experiments were then performed to distinguish the roles of three major factors hypothesized to contribute to the bloom: 1) the high abundance of cysts in western GOM sediments; 2) strong northeaster storms with prevailing downwelling-favorable winds; and 3) a large amount of fresh water input due to abundant rainfall and heavy snowmelt. Results suggested that the high abundance of cysts in western GOM was the primary factor of the 2005 bloom. Wind forcing was an important regulator, as episodic bursts of northeast winds caused onshore advection of offshore populations. These downwelling favorable winds accelerated the alongshore flow, resulting in transport of high cell concentrations into Massachusetts Bay. A large regional bloom would still have happened, however, even with normal or typical winds for that period. Anomalously high river runoff in 2005 resulted in stronger buoyant plumes/currents, which facilitated the transport of cell population to the western GOM. While affecting nearshore cell abundance in Massachusetts Bay, the buoyant plumes were confined near to the coast, and had limited impact on the gulf-wide bloom distribution. PMID:28366964

A mathematical model of the coupled mechanisms of cell adhesion, contraction and spreading

PubMed Central

Vernerey, Franck J.; Farsad, Mehdi

2013-01-01

Recent research has shown that cell spreading is highly dependent on the contractililty of its cytoskeleton and the mechanical properties of the environment it is located in. The dynamics of such process is critical for the development of tissue engineering strategy but is also a key player in wound contraction, tissue maintenance and angiogenesis. To better understand the underlying physics of such phenomena, the paper describes a mathematical formulation of cell spreading and contraction that couples the processes of stress fiber formation, protrusion growth through actin polymerization at the cell edge and dynamics of cross-membrane protein (integrins) enabling cell-substrate attachment. The evolving cell’s cytoskeleton is modeled as a mixture of fluid, proteins and filaments that can exchange mass and generate contraction. In particular, besides self-assembling into stress fibers, actin monomers able to polymerize into an actin meshwork at the cell’s boundary in order to push the membrane forward and generate protrusion. These processes are possible via the development of cell-substrate attachment complexes that arise from the mechano-sensitive equilibrium of membrane proteins, known as integrins. After deriving the governing equation driving the dynamics of cell evolution and spreading, we introduce a numerical solution based on the extended finite element method, combined with a level set formulation. Numerical simulations show that the proposed model is able to capture the dependency of cell spreading and contraction on substrate stiffness and chemistry. The very good agreement between model predictions and experimental observations suggests that mechanics plays a strong role into the coupled mechanisms of contraction, adhesion and spreading of adherent cells. PMID:23463540

Physical confinement alters tumor cell adhesion and migration phenotypes

PubMed Central

Balzer, Eric M.; Tong, Ziqiu; Paul, Colin D.; Hung, Wei-Chien; Stroka, Kimberly M.; Boggs, Amanda E.; Martin, Stuart S.; Konstantopoulos, Konstantinos

2012-01-01

Cell migration on planar surfaces is driven by cycles of actin protrusion, integrin-mediated adhesion, and myosin-mediated contraction; however, this mechanism may not accurately describe movement in 3-dimensional (3D) space. By subjecting cells to restrictive 3D environments, we demonstrate that physical confinement constitutes a biophysical stimulus that alters cell morphology and suppresses mesenchymal motility in human breast carcinoma (MDA-MB-231). Dorsoventral polarity, stress fibers, and focal adhesions are markedly attenuated by confinement. Inhibitors of myosin, Rho/ROCK, or β1-integrins do not impair migration through 3-μm-wide channels (confinement), even though these treatments repress motility in 50-μm-wide channels (unconfined migration) by ≥50%. Strikingly, confined migration persists even when F-actin is disrupted, but depends largely on microtubule (MT) dynamics. Interfering with MT polymerization/depolymerization causes confined cells to undergo frequent directional changes, thereby reducing the average net displacement by ≥80% relative to vehicle controls. Live-cell EB1-GFP imaging reveals that confinement redirects MT polymerization toward the leading edge, where MTs continuously impact during advancement of the cell front. These results demonstrate that physical confinement can induce cytoskeletal alterations that reduce the dependence of migrating cells on adhesion-contraction force coupling. This mechanism may explain why integrins can exhibit reduced or altered function during migration in 3D environments.—Balzer, E. M., Tong, Z., Paul, C. D., Hung, W.-C., Stroka, K. M., Boggs, A. E., Martin, S. S., Konstantopoulos, K. Physical confinement alters tumor cell adhesion and migration phenotypes. PMID:22707566

Effects of coupling between the vibrational modes on CARS signal

NASA Astrophysics Data System (ADS)

Patel, Vishesha; Malinovskaya, Svetlana

2007-06-01

CARS is well suited spectroscopy method for imaging specific molecules, e.g., proteins and live cells, diagnosis of cancerous cells, imaging dueterated compounds, etc. CARS imaging techniques avoid problems associated with photo bleaching and photo induced toxicity. The CARS signal is accompanied by a strong non resonant background which may overshadow the weak signal of interest. Two methods, using femtosecond chriped laser pulses and providing the Rabi oscillation and the adiabatic passage type of control [1], allow one to achieve sensitivity with high resolution and are known to efficiently suppress background. It has been previously shown that coupling between vibrational modes affects the sensitivity of the Raman signal and selective excitation of vibrational modes [2]. In this paper we will discuss simulation results on vibrational coupling between modes and its impact into control mechanisms of the CARS signal. [1] S.A.Malinovskaya, Physical.Rev.A 73, 033416(2006) [2] S.A. Malinovskaya,P.H. Bucksbaum, and P.R. Berman, J. Chem. Phys. 121, 3434 (2004).

Tensegrity: the architectural basis of cellular mechanotransduction

NASA Technical Reports Server (NTRS)

Ingber, D. E.

1997-01-01

Physical forces of gravity, hemodynamic stresses, and movement play a critical role in tissue development. Yet, little is known about how cells convert these mechanical signals into a chemical response. This review attempts to place the potential molecular mediators of mechanotransduction (e.g. stretch-sensitive ion channels, signaling molecules, cytoskeleton, integrins) within the context of the structural complexity of living cells. The model presented relies on recent experimental findings, which suggests that cells use tensegrity architecture for their organization. Tensegrity predicts that cells are hard-wired to respond immediately to mechanical stresses transmitted over cell surface receptors that physically couple the cytoskeleton to extracellular matrix (e.g. integrins) or to other cells (cadherins, selectins, CAMs). Many signal transducing molecules that are activated by cell binding to growth factors and extracellular matrix associate with cytoskeletal scaffolds within focal adhesion complexes. Mechanical signals, therefore, may be integrated with other environmental signals and transduced into a biochemical response through force-dependent changes in scaffold geometry or molecular mechanics. Tensegrity also provides a mechanism to focus mechanical energy on molecular transducers and to orchestrate and tune the cellular response.

Plasmonic Solar Cells: From Rational Design to Mechanism Overview.

PubMed

Jang, Yoon Hee; Jang, Yu Jin; Kim, Seokhyoung; Quan, Li Na; Chung, Kyungwha; Kim, Dong Ha

2016-12-28

Plasmonic effects have been proposed as a solution to overcome the limited light absorption in thin-film photovoltaic devices, and various types of plasmonic solar cells have been developed. This review provides a comprehensive overview of the state-of-the-art progress on the design and fabrication of plasmonic solar cells and their enhancement mechanism. The working principle is first addressed in terms of the combined effects of plasmon decay, scattering, near-field enhancement, and plasmonic energy transfer, including direct hot electron transfer and resonant energy transfer. Then, we summarize recent developments for various types of plasmonic solar cells based on silicon, dye-sensitized, organic photovoltaic, and other types of solar cells, including quantum dot and perovskite variants. We also address several issues regarding the limitations of plasmonic nanostructures, including their electrical, chemical, and physical stability, charge recombination, narrowband absorption, and high cost. Next, we propose a few potentially useful approaches that can improve the performance of plasmonic cells, such as the inclusion of graphene plasmonics, plasmon-upconversion coupling, and coupling between fluorescence resonance energy transfer and plasmon resonance energy transfer. This review is concluded with remarks on future prospects for plasmonic solar cell use.

A coupled diffusion-fluid pressure model to predict cell density distribution for cells encapsulated in a porous hydrogel scaffold under mechanical loading.

PubMed

Zhao, Feihu; Vaughan, Ted J; Mc Garrigle, Myles J; McNamara, Laoise M

2017-10-01

Tissue formation within tissue engineering (TE) scaffolds is preceded by growth of the cells throughout the scaffold volume and attachment of cells to the scaffold substrate. It is known that mechanical stimulation, in the form of fluid perfusion or mechanical strain, enhances cell differentiation and overall tissue formation. However, due to the complex multi-physics environment of cells within TE scaffolds, cell transport under mechanical stimulation is not fully understood. Therefore, in this study, we have developed a coupled multiphysics model to predict cell density distribution in a TE scaffold. In this model, cell transport is modelled as a thermal conduction process, which is driven by the pore fluid pressure under applied loading. As a case study, the model is investigated to predict the cell density patterns of pre-osteoblasts MC3T3-e1 cells under a range of different loading regimes, to obtain an understanding of desirable mechanical stimulation that will enhance cell density distribution within TE scaffolds. The results of this study have demonstrated that fluid perfusion can result in a higher cell density in the scaffold region closed to the outlet, while cell density distribution under mechanical compression was similar with static condition. More importantly, the study provides a novel computational approach to predict cell distribution in TE scaffolds under mechanical loading. Copyright © 2017 Elsevier Ltd. All rights reserved.

Amplification through chaotic synchronization in spatially extended beam-plasma systems

NASA Astrophysics Data System (ADS)

Moskalenko, Olga I.; Frolov, Nikita S.; Koronovskii, Alexey A.; Hramov, Alexander E.

2017-12-01

In this paper, we have studied the relationship between chaotic synchronization and microwave signal amplification in coupled beam-plasma systems. We have considered a 1D particle-in-cell numerical model of unidirectionally coupled beam-plasma oscillatory media being in the regime of electron pattern formation. We have shown the significant gain of microwave oscillation power in coupled beam-plasma media being in the different regimes of generation. The discovered effect has a close connection with the chaotic synchronization phenomenon, so we have observed that amplification appears after the onset of the complete time scale synchronization regime in the analyzed coupled spatially extended systems. We have also provided the numerical study of physical processes in the chain of beam-plasma systems leading to the chaotic synchronization and the amplification of microwave oscillations power, respectively.

Single Cell Spectroscopy: Noninvasive Measures of Small-Scale Structure and Function

PubMed Central

Mousoulis, Charilaos; Xu, Xin; Reiter, David A.; Neu, Corey P.

2013-01-01

The advancement of spectroscopy methods attained through increases in sensitivity, and often with the coupling of complementary techniques, has enabled real-time structure and function measurements of single cells. The purpose of this review is to illustrate, in light of advances, the strengths and the weaknesses of these methods. Included also is an assessment of the impact of the experimental setup and conditions of each method on cellular function and integrity. A particular emphasis is placed on noninvasive and nondestructive techniques for achieving single cell detection, including nuclear magnetic resonance, in addition to physical, optical, and vibrational methods. PMID:23886910

Coupling of Mechanical Behavior of Lithium Ion Cells to Electrochemical-Thermal (ECT) Models for Battery Crush

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

Zhang, Chao; Santhanagopalan, Shriram; Pesaran, Ahmad

Vehicle crashes can lead to crushing of the battery, damaging lithium ion battery cells and causing local shorts, heat generation, and thermal runaway. Simulating all the physics and geometries at the same time is challenging and takes a lot of effort; thus, simplifications are needed. We developed a material model for simultaneously modeling the mechanical-electrochemical-thermal behavior, which predicted the electrical short, voltage drop, and thermal runaway behaviors followed by a mechanical abuse-induced short. The effect of short resistance on the battery cell performance was studied.

Cellular Contraction Can Drive Rapid Epithelial Flows.

PubMed

Vig, Dhruv K; Hamby, Alex E; Wolgemuth, Charles W

2017-10-03

Single, isolated epithelial cells move randomly; however, during wound healing, organism development, cancer metastasis, and many other multicellular phenomena, motile cells group into a collective and migrate persistently in a directed manner. Recent work has examined the physics and biochemistry that coordinates the motions of these groups of cells. Of late, two mechanisms have been touted as being crucial to the physics of these systems: leader cells and jamming. However, the actual importance of these to collective migration remains circumstantial. Fundamentally, collective behavior must arise from the actions of individual cells. Here, we show how biophysical activity of an isolated cell impacts collective dynamics in epithelial layers. Although many reports suggest that wound closure rates depend on isolated cell speed and/or leader cells, we find that these correlations are not universally true, nor do collective dynamics follow the trends suggested by models for jamming. Instead, our experimental data, when coupled with a mathematical model for collective migration, shows that intracellular contractile stress, isolated cell speed, and adhesion all play a substantial role in influencing epithelial dynamics, and that alterations in contraction and/or substrate adhesion can cause confluent epithelial monolayers to exhibit an increase in motility, a feature reminiscent of cancer metastasis. These results directly question the validity of wound-healing assays as a general means for measuring cell migration, and provide further insight into the salient physics of collective migration. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Self-organization of grafted polyelectrolyte layers via the coupling of chemical equilibrium and physical interactions.

PubMed

Tagliazucchi, Mario; de la Cruz, Mónica Olvera; Szleifer, Igal

2010-03-23

The competition between chemical equilibrium, for example protonation, and physical interactions determines the molecular organization and functionality of biological and synthetic systems. Charge regulation by displacement of acid-base equilibrium induced by changes in the local environment provides a feedback mechanism that controls the balance between electrostatic, van der Waals, steric interactions and molecular organization. Which strategies do responsive systems follow to globally optimize chemical equilibrium and physical interactions? We address this question by theoretically studying model layers of end-grafted polyacids. These layers spontaneously form self-assembled aggregates, presenting domains of controlled local pH and whose morphologies can be manipulated by the composition of the solution in contact with the film. Charge regulation stabilizes micellar domains over a wide range of pH by reducing the local charge in the aggregate at the cost of chemical free energy and gaining in hydrophobic interactions. This balance determines the boundaries between different aggregate morphologies. We show that a qualitatively new form of organization arises from the coupling between physical interactions and protonation equilibrium. This optimization strategy presents itself with polyelectrolytes coexisting in two different and well-defined protonation states. Our results underline the need of considering the coupling between chemical equilibrium and physical interactions due to their highly nonadditive behavior. The predictions provide guidelines for the creation of responsive polymer layers presenting self-organized patterns with functional properties and they give insights for the understanding of competing interactions in highly inhomogeneous and constrained environments such as those relevant in nanotechnology and those responsible for biological cells function.

Assessing groundwater policy with coupled economic-groundwater hydrologic modeling

NASA Astrophysics Data System (ADS)

Mulligan, Kevin B.; Brown, Casey; Yang, Yi-Chen E.; Ahlfeld, David P.

2014-03-01

This study explores groundwater management policies and the effect of modeling assumptions on the projected performance of those policies. The study compares an optimal economic allocation for groundwater use subject to streamflow constraints, achieved by a central planner with perfect foresight, with a uniform tax on groundwater use and a uniform quota on groundwater use. The policies are compared with two modeling approaches, the Optimal Control Model (OCM) and the Multi-Agent System Simulation (MASS). The economic decision models are coupled with a physically based representation of the aquifer using a calibrated MODFLOW groundwater model. The results indicate that uniformly applied policies perform poorly when simulated with more realistic, heterogeneous, myopic, and self-interested agents. In particular, the effects of the physical heterogeneity of the basin and the agents undercut the perceived benefits of policy instruments assessed with simple, single-cell groundwater modeling. This study demonstrates the results of coupling realistic hydrogeology and human behavior models to assess groundwater management policies. The Republican River Basin, which overlies a portion of the Ogallala aquifer in the High Plains of the United States, is used as a case study for this analysis.

A gene family for acidic ribosomal proteins in Schizosaccharomyces pombe: two essential and two nonessential genes.

PubMed Central

Beltrame, M; Bianchi, M E

1990-01-01

We have cloned the genes for small acidic ribosomal proteins (A-proteins) of the fission yeast Schizosaccharomyces pombe. S. pombe contains four transcribed genes for small A-proteins per haploid genome, as is the case for Saccharomyces cerevisiae. In contrast, multicellular eucaryotes contain two transcribed genes per haploid genome. The four proteins of S. pombe, besides sharing a high overall similarity, form two couples of nearly identical sequences. Their corresponding genes have a very conserved structure and are transcribed to a similar level. Surprisingly, of each couple of genes coding for nearly identical proteins, one is essential for cell growth, whereas the other is not. We suggest that the unequal importance of the four small A-proteins for cell survival is related to their physical organization in 60S ribosomal subunits. Images PMID:2325655

Propagating gene expression fronts in a one-dimensional coupled system of artificial cells

NASA Astrophysics Data System (ADS)

Tayar, Alexandra M.; Karzbrun, Eyal; Noireaux, Vincent; Bar-Ziv, Roy H.

2015-12-01

Living systems employ front propagation and spatiotemporal patterns encoded in biochemical reactions for communication, self-organization and computation. Emulating such dynamics in minimal systems is important for understanding physical principles in living cells and in vitro. Here, we report a one-dimensional array of DNA compartments in a silicon chip as a coupled system of artificial cells, offering the means to implement reaction-diffusion dynamics by integrated genetic circuits and chip geometry. Using a bistable circuit we programmed a front of protein synthesis propagating in the array as a cascade of signal amplification and short-range diffusion. The front velocity is maximal at a saddle-node bifurcation from a bistable regime with travelling fronts to a monostable regime that is spatially homogeneous. Near the bifurcation the system exhibits large variability between compartments, providing a possible mechanism for population diversity. This demonstrates that on-chip integrated gene circuits are dynamical systems driving spatiotemporal patterns, cellular variability and symmetry breaking.

Biofuel Cell Based on Microscale Nanostructured Electrodes with Inductive Coupling to Rat Brain Neurons

NASA Astrophysics Data System (ADS)

Andoralov, Viktor; Falk, Magnus; Suyatin, Dmitry B.; Granmo, Marcus; Sotres, Javier; Ludwig, Roland; Popov, Vladimir O.; Schouenborg, Jens; Blum, Zoltan; Shleev, Sergey

2013-11-01

Miniature, self-contained biodevices powered by biofuel cells may enable a new generation of implantable, wireless, minimally invasive neural interfaces for neurophysiological in vivo studies and for clinical applications. Here we report on the fabrication of a direct electron transfer based glucose/oxygen enzymatic fuel cell (EFC) from genuinely three-dimensional (3D) nanostructured microscale gold electrodes, modified with suitable biocatalysts. We show that the process underlying the simple fabrication method of 3D nanostructured electrodes is based on an electrochemically driven transformation of physically deposited gold nanoparticles. We experimentally demonstrate that mediator-, cofactor-, and membrane-less EFCs do operate in cerebrospinal fluid and in the brain of a rat, producing amounts of electrical power sufficient to drive a self-contained biodevice, viz. 7 μW cm-2 in vitro and 2 μW cm-2 in vivo at an operating voltage of 0.4 V. Last but not least, we also demonstrate an inductive coupling between 3D nanobioelectrodes and living neurons.

Biofuel cell based on microscale nanostructured electrodes with inductive coupling to rat brain neurons.

PubMed

Andoralov, Viktor; Falk, Magnus; Suyatin, Dmitry B; Granmo, Marcus; Sotres, Javier; Ludwig, Roland; Popov, Vladimir O; Schouenborg, Jens; Blum, Zoltan; Shleev, Sergey

2013-11-20

Miniature, self-contained biodevices powered by biofuel cells may enable a new generation of implantable, wireless, minimally invasive neural interfaces for neurophysiological in vivo studies and for clinical applications. Here we report on the fabrication of a direct electron transfer based glucose/oxygen enzymatic fuel cell (EFC) from genuinely three-dimensional (3D) nanostructured microscale gold electrodes, modified with suitable biocatalysts. We show that the process underlying the simple fabrication method of 3D nanostructured electrodes is based on an electrochemically driven transformation of physically deposited gold nanoparticles. We experimentally demonstrate that mediator-, cofactor-, and membrane-less EFCs do operate in cerebrospinal fluid and in the brain of a rat, producing amounts of electrical power sufficient to drive a self-contained biodevice, viz. 7 μW cm(-2) in vitro and 2 μW cm(-2) in vivo at an operating voltage of 0.4 V. Last but not least, we also demonstrate an inductive coupling between 3D nanobioelectrodes and living neurons.

Exploring the Influence of Topography on Belowground C Processes Using a Coupled Hydrologic-Biogeochemical Model

NASA Astrophysics Data System (ADS)

Shi, Y.; Davis, K. J.; Eissenstat, D. M.; Kaye, J. P.; Duffy, C.; Yu, X.; He, Y.

2014-12-01

Belowground carbon processes are affected by soil moisture and soil temperature, but current biogeochemical models are 1-D and cannot resolve topographically driven hill-slope soil moisture patterns, and cannot simulate the nonlinear effects of soil moisture on carbon processes. Coupling spatially-distributed physically-based hydrologic models with biogeochemical models may yield significant improvements in the representation of topographic influence on belowground C processes. We will couple the Flux-PIHM model to the Biome-BGC (BBGC) model. Flux-PIHM is a coupled physically-based land surface hydrologic model, which incorporates a land-surface scheme into the Penn State Integrated Hydrologic Model (PIHM). The land surface scheme is adapted from the Noah land surface model. Because PIHM is capable of simulating lateral water flow and deep groundwater, Flux-PIHM is able to represent the link between groundwater and the surface energy balance, as well as the land surface heterogeneities caused by topography. The coupled Flux-PIHM-BBGC model will be tested at the Susquehanna/Shale Hills critical zone observatory (SSHCZO). The abundant observations, including eddy covariance fluxes, soil moisture, groundwater level, sap flux, stream discharge, litterfall, leaf area index, above ground carbon stock, and soil carbon efflux, make SSHCZO an ideal test bed for the coupled model. In the coupled model, each Flux-PIHM model grid will couple a BBGC cell. Flux-PIHM will provide BBGC with soil moisture and soil temperature information, while BBGC provides Flux-PIHM with leaf area index. Preliminary results show that when Biome- BGC is driven by PIHM simulated soil moisture pattern, the simulated soil carbon is clearly impacted by topography.

Simultaneous Activation of Induced Heterodimerization between CXCR4 Chemokine Receptor and Cannabinoid Receptor 2 (CB2) Reveals a Mechanism for Regulation of Tumor Progression*

PubMed Central

Coke, Christopher J.; Scarlett, Kisha A.; Chetram, Mahandranauth A.; Jones, Kia J.; Sandifer, Brittney J.; Davis, Ahriea S.; Marcus, Adam I.

2016-01-01

The G-protein-coupled chemokine receptor CXCR4 generates signals that lead to cell migration, cell proliferation, and other survival mechanisms that result in the metastatic spread of primary tumor cells to distal organs. Numerous studies have demonstrated that CXCR4 can form homodimers or can heterodimerize with other G-protein-coupled receptors to form receptor complexes that can amplify or decrease the signaling capacity of each individual receptor. Using biophysical and biochemical approaches, we found that CXCR4 can form an induced heterodimer with cannabinoid receptor 2 (CB2) in human breast and prostate cancer cells. Simultaneous, agonist-dependent activation of CXCR4 and CB2 resulted in reduced CXCR4-mediated expression of phosphorylated ERK1/2 and ultimately reduced cancer cell functions such as calcium mobilization and cellular chemotaxis. Given that treatment with cannabinoids has been shown to reduce invasiveness of cancer cells as well as CXCR4-mediated migration of immune cells, it is plausible that CXCR4 signaling can be silenced through a physical heterodimeric association with CB2, thereby inhibiting subsequent functions of CXCR4. Taken together, the data illustrate a mechanism by which the cannabinoid system can negatively modulate CXCR4 receptor function and perhaps tumor progression. PMID:26841863

Statistical physics of self-replication.

PubMed

England, Jeremy L

2013-09-28

Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self-replication in a system coupled to a thermal bath. We find that the minimum value for the physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self-replicating nucleic acids.

Antiapoptotic activity of argon and xenon

PubMed Central

Spaggiari, Sabrina; Kepp, Oliver; Rello-Varona, Santiago; Chaba, Kariman; Adjemian, Sandy; Pype, Jan; Galluzzi, Lorenzo; Lemaire, Marc; Kroemer, Guido

2013-01-01

Although chemically non-reactive, inert noble gases may influence multiple physiological and pathological processes via hitherto uncharacterized physical effects. Here we report a cell-based detection system for assessing the effects of pre-defined gas mixtures on the induction of apoptotic cell death. In this setting, the conventional atmosphere for cell culture was substituted with gas combinations, including the same amount of oxygen (20%) and carbon dioxide (5%) but 75% helium, neon, argon, krypton, or xenon instead of nitrogen. The replacement of nitrogen with noble gases per se had no effects on the viability of cultured human osteosarcoma cells in vitro. Conversely, argon and xenon (but not helium, neon, and krypton) significantly limited cell loss induced by the broad-spectrum tyrosine kinase inhibitor staurosporine, the DNA-damaging agent mitoxantrone and several mitochondrial toxins. Such cytoprotective effects were coupled to the maintenance of mitochondrial integrity, as demonstrated by means of a mitochondrial transmembrane potential-sensitive dye and by assessing the release of cytochrome c into the cytosol. In line with this notion, argon and xenon inhibited the apoptotic activation of caspase-3, as determined by immunofluorescence microscopy coupled to automated image analysis. The antiapoptotic activity of argon and xenon may explain their clinically relevant cytoprotective effects. PMID:23907115

A framework for quantification and physical modeling of cell mixing applied to oscillator synchronization in vertebrate somitogenesis.

PubMed

Uriu, Koichiro; Bhavna, Rajasekaran; Oates, Andrew C; Morelli, Luis G

2017-08-15

In development and disease, cells move as they exchange signals. One example is found in vertebrate development, during which the timing of segment formation is set by a 'segmentation clock', in which oscillating gene expression is synchronized across a population of cells by Delta-Notch signaling. Delta-Notch signaling requires local cell-cell contact, but in the zebrafish embryonic tailbud, oscillating cells move rapidly, exchanging neighbors. Previous theoretical studies proposed that this relative movement or cell mixing might alter signaling and thereby enhance synchronization. However, it remains unclear whether the mixing timescale in the tissue is in the right range for this effect, because a framework to reliably measure the mixing timescale and compare it with signaling timescale is lacking. Here, we develop such a framework using a quantitative description of cell mixing without the need for an external reference frame and constructing a physical model of cell movement based on the data. Numerical simulations show that mixing with experimentally observed statistics enhances synchronization of coupled phase oscillators, suggesting that mixing in the tailbud is fast enough to affect the coherence of rhythmic gene expression. Our approach will find general application in analyzing the relative movements of communicating cells during development and disease. © 2017. Published by The Company of Biologists Ltd.

A framework for quantification and physical modeling of cell mixing applied to oscillator synchronization in vertebrate somitogenesis

PubMed Central

Bhavna, Rajasekaran; Oates, Andrew C.; Morelli, Luis G.

2017-01-01

ABSTRACT In development and disease, cells move as they exchange signals. One example is found in vertebrate development, during which the timing of segment formation is set by a ‘segmentation clock’, in which oscillating gene expression is synchronized across a population of cells by Delta-Notch signaling. Delta-Notch signaling requires local cell-cell contact, but in the zebrafish embryonic tailbud, oscillating cells move rapidly, exchanging neighbors. Previous theoretical studies proposed that this relative movement or cell mixing might alter signaling and thereby enhance synchronization. However, it remains unclear whether the mixing timescale in the tissue is in the right range for this effect, because a framework to reliably measure the mixing timescale and compare it with signaling timescale is lacking. Here, we develop such a framework using a quantitative description of cell mixing without the need for an external reference frame and constructing a physical model of cell movement based on the data. Numerical simulations show that mixing with experimentally observed statistics enhances synchronization of coupled phase oscillators, suggesting that mixing in the tailbud is fast enough to affect the coherence of rhythmic gene expression. Our approach will find general application in analyzing the relative movements of communicating cells during development and disease. PMID:28652318

Physics of Cellular Movements

NASA Astrophysics Data System (ADS)

Sackmann, Erich; Keber, Felix; Heinrich, Doris

2010-04-01

The survival of cells depends on perpetual active motions, including (a) bending excitations of the soft cell envelopes, (b) the bidirectional transport of materials and organelles between the cell center and the periphery, and (c) the ongoing restructuring of the intracellular macromolecular scaffolds mediating global cell changes associated with cell adhesion locomotion and phagocytosis. Central questions addressed are the following: How can this bustling motion of extremely complex soft structures be characterized and measured? What are the major driving forces? Further topics include (a) the active dynamic control of global shape changes by the interactive coupling of the aster-like soft scaffold of microtubules and the network of actin filaments associated with the cell envelope (the actin cortex) and (b) the generation of propulsion forces by solitary actin gelation waves propagating within the actin cortex.

Development and performance of a new version of the OASIS coupler, OASIS3-MCT_3.0

NASA Astrophysics Data System (ADS)

Craig, Anthony; Valcke, Sophie; Coquart, Laure

2017-09-01

OASIS is coupling software developed primarily for use in the climate community. It provides the ability to couple different models with low implementation and performance overhead. OASIS3-MCT is the latest version of OASIS. It includes several improvements compared to OASIS3, including elimination of a separate hub coupler process, parallelization of the coupling communication and run-time grid interpolation, and the ability to easily reuse mapping weight files. OASIS3-MCT_3.0 is the latest release and includes the ability to couple between components running sequentially on the same set of tasks as well as to couple within a single component between different grids or decompositions such as physics, dynamics, and I/O. OASIS3-MCT has been tested with different configurations on up to 32 000 processes, with components running on high-resolution grids with up to 1.5 million grid cells, and with over 10 000 2-D coupling fields. Several new features will be available in OASIS3-MCT_4.0, and some of those are also described.

A fully coupled 3D transport model in SPH for multi-species reaction-diffusion systems

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

Adami, Stefan; Hu, X. Y.; Adams, N. A.

2011-08-23

Abstract—In this paper we present a fully generalized transport model for multiple species in complex two and threedimensional geometries. Based on previous work [1] we have extended our interfacial reaction-diffusion model to handle arbitrary numbers of species allowing for coupled reaction models. Each species is tracked independently and we consider different physics of a species with respect to the bulk phases in contact. We use our SPH model to simulate the reaction-diffusion problem on a pore-scale level of a solid oxide fuel cell (SOFC) with special emphasize on the effect of surface diffusion.

Physically disconnected non-diffusible cell-to-cell communication between neuroblastoma SH-SY5Y and DRG primary sensory neurons.

PubMed

Chaban, Victor V; Cho, Taehoon; Reid, Christopher B; Norris, Keith C

2013-01-01

Cell-cell communication occurs via a variety of mechanisms, including long distances (hormonal), short distances (paracrine and synaptic) or direct coupling via gap junctions, antigen presentation, or ligand-receptor interactions. We evaluated the possibility of neuro-hormonal independent, non-diffusible, physically disconnected pathways for cell-cell communication using dorsal root ganglion (DRG) neurons. We assessed intracellular calcium ([Ca(2+)]) in primary culture DRG neurons that express ATP-sensitive P2X3, capsaicinsensitive TRPV1 receptors modulated by estradiol. Physically disconnected (dish-in-dish system; inner chamber enclosed) mouse DRG were cultured for 12 hours near: a) media alone (control 1), b) mouse DRG (control 2), c) human neuroblastoma SHSY-5Y cells (cancer intervention), or d) mouse DRG treated with KCl (apoptosis intervention). Chemosensitive receptors [Ca(2+)](i) signaling did not differ between control 1 and 2. ATP (10 μM) and capsaicin (100nM) increased [Ca(2+)](i) transients to 425.86 + 49.5 nM, and 399.21 ± 44.5 nM, respectively. 17β-estradiol (100 nM) exposure reduced ATP (171.17 ± 48.9 nM) and capsaicin (175.01±34.8 nM) [Ca(2+)](i) transients. The presence of cancer cells reduced ATP- and capsaicin-induced [Ca(2+)](i) by >50% (p<0.05) and abolished the 17β-estradiol effect. By contrast, apoptotic DRG cells increased initial ATP-induced [Ca(2+)](i), flux four fold and abolished subsequent [Ca(2+)](i), responses to ATP stimulation (p<0.001). Capsaicin (100nM) induced [Ca(2+)](i) responses were totally abolished. The local presence of apoptotic DRG or human neuroblastoma cells induced differing abnormal ATP and capsaicin-mediated [Ca(2+)](i) fluxes in normal DRG. These findings support physically disconnected, non-diffusible cell-to-cell signaling. Further studies are needed to delineate the mechanism(s) of and model(s) of communication.

Coupled Mechanical-Electrochemical-Thermal Modeling for Accelerated Design of EV Batteries

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

Santhanagopalan, Shriram; Zhang, Chao; Kim, Gi-Heon

2015-05-03

This presentation provides an overview of the mechanical electrochemical-thermal (M-ECT) modeling efforts. The physical phenomena occurring in a battery are many and complex and operate at different scales (particle, electrodes, cell, and pack). A better understanding of the interplay between different physics occurring at different scales through modeling could provide insight to design improved batteries for electric vehicles. Work funded by the U.S. DOE has resulted in development of computer-aided engineering (CAE) tools to accelerate electrochemical and thermal design of batteries; mechanical modeling is under way. Three competitive CAE tools are now commercially available.

Growth-rate-dependent dynamics of a bacterial genetic oscillator

NASA Astrophysics Data System (ADS)

Osella, Matteo; Lagomarsino, Marco Cosentino

2013-01-01

Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available analyses generally neglect the coupling of regulatory circuits with the cellular “chassis” in which the circuits are embedded. For example, the intracellular macromolecular composition of fast-growing bacteria changes with growth rate. As a consequence, important parameters of gene expression, such as ribosome concentration or cell volume, are growth-rate dependent, ultimately coupling the dynamics of genetic circuits with cell physiology. This work addresses the effects of growth rate on the dynamics of a paradigmatic example of genetic oscillator, the repressilator. Making use of empirical growth-rate dependencies of parameters in bacteria, we show that the repressilator dynamics can switch between oscillations and convergence to a fixed point depending on the cellular state of growth, and thus on the nutrients it is fed. The physical support of the circuit (type of plasmid or gene positions on the chromosome) also plays an important role in determining the oscillation stability and the growth-rate dependence of period and amplitude. This analysis has potential application in the field of synthetic biology, and suggests that the coupling between endogenous genetic oscillators and cell physiology can have substantial consequences for their functionality.

Acoustic metamaterials with synergetic coupling

NASA Astrophysics Data System (ADS)

Ma, Fuyin; Huang, Meng; Wu, Jiu Hui

2017-12-01

In this paper, we propose a general design concept for acoustic metamaterials that introduces a ubiquitous synergetic behavior into the design procedure, in which the structure of the design is driven by its functional requirements. Since the physical properties of the widely used, resonant-type metamaterials are mainly determined by the eigenmodes of the structure, we first introduce the design concept through the modal displacement distributions on two typical plate-type structures. Next, by employing broadband sound attenuations that involve both the insulation and absorption as the typical targets, two synergetic coupling behaviors are systematically revealed among the dense resonant modes and multi-cell. Furthermore, through plate-type multiple-cell structures assembled from nine oscillators, the design is shown to realize strong broadband attenuations with either the average sound transmission loss (STL) below 2000 Hz higher than 40 dB or the absorption approximately 0.99 in the range of 400-700 Hz wherein the average absorption below 800 Hz remains higher than 0.8. Finally, two multi-cell plate-type samples are fabricated and then used experimentally to measure the STLs in support of the proposed synergetic coupling design method. Both the computational and experimental results demonstrate that the proposed synergetic design concept could effectively initiate a design for metamaterials that offer a new degree of freedom for broadband sound attenuations.

Investigation of resistance switching in SiO x RRAM cells using a 3D multi-scale kinetic Monte Carlo simulator

NASA Astrophysics Data System (ADS)

Sadi, Toufik; Mehonic, Adnan; Montesi, Luca; Buckwell, Mark; Kenyon, Anthony; Asenov, Asen

2018-02-01

We employ an advanced three-dimensional (3D) electro-thermal simulator to explore the physics and potential of oxide-based resistive random-access memory (RRAM) cells. The physical simulation model has been developed recently, and couples a kinetic Monte Carlo study of electron and ionic transport to the self-heating phenomenon while accounting carefully for the physics of vacancy generation and recombination, and trapping mechanisms. The simulation framework successfully captures resistance switching, including the electroforming, set and reset processes, by modeling the dynamics of conductive filaments in the 3D space. This work focuses on the promising yet less studied RRAM structures based on silicon-rich silica (SiO x ) RRAMs. We explain the intrinsic nature of resistance switching of the SiO x layer, analyze the effect of self-heating on device performance, highlight the role of the initial vacancy distributions acting as precursors for switching, and also stress the importance of using 3D physics-based models to capture accurately the switching processes. The simulation work is backed by experimental studies. The simulator is useful for improving our understanding of the little-known physics of SiO x resistive memory devices, as well as other oxide-based RRAM systems (e.g. transition metal oxide RRAMs), offering design and optimization capabilities with regard to the reliability and variability of memory cells.

Toxic Alexandrium blooms in the western Gulf of Maine: The plume advection hypothesis revisited

USGS Publications Warehouse

Anderson, D.M.; Keafer, B.A.; Geyer, W.R.; Signell, R.P.; Loder, T.C.

2005-01-01

The plume advection hypothesis links blooms of the toxic dinoflagellate Alexandrium fundyense in the western Gulf of Maine (GOM) to a buoyant plume derived from river outflows. This hypothesis was examined with cruise and moored-instrument observations in 1993 when levels of paralytic shellfish poisoning (PSP) toxins were high, and in 1994 when toxicity was low. A coupled physical-biological model simulated hydrography and A. fundyense distributions. Initial A. fundyense populations were restricted to low-salinity nearshore waters near Casco Bay, but also occurred in higher salinity waters along the plume boundary. This suggests two sources of cells - those from shallow-water cyst populations and those transported to shore from offshore blooms in the eastern segment of the Maine coastal current (EMCC). Observations confirm the role of the plume in A. fundyense transport and growth. Downwelling-favorable winds in 1993 transported the plume and its cells rapidly alongshore, enhancing toxicity and propagating PSP to the south. In 1994, sustained upwelling moved the plume offshore, resulting in low toxicity in intertidal shellfish. A. fundyense blooms were likely nutrient limited, leading to low growth rates and moderate cell abundances. These observations and mechanisms were reproduced by coupled physical-biological model simulations. The plume advection hypothesis provides a viable explanation for outbreaks of PSP in the western GOM, but should be refined to include two sources for cells that populate the plume and two major pathways for transport: one within the low-salinity plume and another where A. fundyense cells originating in the EMCC are transported along the outer boundary of the plume front with the western segment of the Maine coastal current.

High-resolution coupled physics solvers for analysing fine-scale nuclear reactor design problems.

PubMed

Mahadevan, Vijay S; Merzari, Elia; Tautges, Timothy; Jain, Rajeev; Obabko, Aleksandr; Smith, Michael; Fischer, Paul

2014-08-06

An integrated multi-physics simulation capability for the design and analysis of current and future nuclear reactor models is being investigated, to tightly couple neutron transport and thermal-hydraulics physics under the SHARP framework. Over several years, high-fidelity, validated mono-physics solvers with proven scalability on petascale architectures have been developed independently. Based on a unified component-based architecture, these existing codes can be coupled with a mesh-data backplane and a flexible coupling-strategy-based driver suite to produce a viable tool for analysts. The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The coupling methodology and software interfaces of the framework are presented, along with verification studies on two representative fast sodium-cooled reactor demonstration problems to prove the usability of the SHARP framework.

High-resolution coupled physics solvers for analysing fine-scale nuclear reactor design problems

PubMed Central

Mahadevan, Vijay S.; Merzari, Elia; Tautges, Timothy; Jain, Rajeev; Obabko, Aleksandr; Smith, Michael; Fischer, Paul

2014-01-01

An integrated multi-physics simulation capability for the design and analysis of current and future nuclear reactor models is being investigated, to tightly couple neutron transport and thermal-hydraulics physics under the SHARP framework. Over several years, high-fidelity, validated mono-physics solvers with proven scalability on petascale architectures have been developed independently. Based on a unified component-based architecture, these existing codes can be coupled with a mesh-data backplane and a flexible coupling-strategy-based driver suite to produce a viable tool for analysts. The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The coupling methodology and software interfaces of the framework are presented, along with verification studies on two representative fast sodium-cooled reactor demonstration problems to prove the usability of the SHARP framework. PMID:24982250

Oscillators that sync and swarm.

PubMed

O'Keeffe, Kevin P; Hong, Hyunsuk; Strogatz, Steven H

2017-11-15

Synchronization occurs in many natural and technological systems, from cardiac pacemaker cells to coupled lasers. In the synchronized state, the individual cells or lasers coordinate the timing of their oscillations, but they do not move through space. A complementary form of self-organization occurs among swarming insects, flocking birds, or schooling fish; now the individuals move through space, but without conspicuously altering their internal states. Here we explore systems in which both synchronization and swarming occur together. Specifically, we consider oscillators whose phase dynamics and spatial dynamics are coupled. We call them swarmalators, to highlight their dual character. A case study of a generalized Kuramoto model predicts five collective states as possible long-term modes of organization. These states may be observable in groups of sperm, Japanese tree frogs, colloidal suspensions of magnetic particles, and other biological and physical systems in which self-assembly and synchronization interact.

A Vertex Model of Drosophila Ventral Furrow Formation

PubMed Central

Spahn, Philipp; Reuter, Rolf

2013-01-01

Ventral furrow formation in Drosophila is an outstanding model system to study the mechanisms involved in large-scale tissue rearrangements. Ventral cells accumulate myosin at their apical sides and, while being tightly coupled to each other via apical adherens junctions, execute actomyosin contractions that lead to reduction of their apical cell surface. Thereby, a band of constricted cells along the ventral epithelium emerges which will form a tissue indentation along the ventral midline (the ventral furrow). Here we adopt a 2D vertex model to simulate ventral furrow formation in a surface view allowing easy comparison with confocal live-recordings. We show that in order to reproduce furrow morphology seen in vivo, a gradient of contractility must be assumed in the ventral epithelium which renders cells more contractile the closer they lie to the ventral midline. The model predicts previous experimental findings, such as the gain of eccentric morphology of constricting cells and an incremental fashion of apical cell area reduction. Analysis of the model suggests that this incremental area reduction is caused by the dynamical interplay of cell elasticity and stochastic contractility as well as by the opposing forces from contracting neighbour cells. We underpin results from the model through in vivo analysis of ventral furrow formation in wildtype and twi mutant embryos. Our results show that ventral furrow formation can be accomplished as a “tug-of-war” between stochastically contracting, mechanically coupled cells and may require less rigorous regulation than previously thought. Summary For the developmental biologist it is a fascinating question how cells can coordinate major tissue movements during embryonic development. The so-called ventral furrow of the Drosophila embryo is a well-studied example of such a process when cells from a ventral band, spanning nearly the entire length of the embryo, undergo dramatic shape change by contracting their tips and then fold inwards into the interior of the embryo. Although numerous genes have been identified that are critical for ventral furrow formation, it is an open question how cells work together to elicit this tissue rearrangement. We use a computational model to mimic the physical properties of cells in the ventral epithelium and simulate the formation of the furrow. We find that the ventral furrow can form through stochastic self-organisation and that previous experimental observations can be readily explained in our model by considering forces that arise when cells execute contractions while being coupled to each other in a mechanically coherent epithelium. The model highlights the importance of a physical perspective when studying tissue morphogenesis and shows that only a minimal genetic regulation may be required to drive complex processes in embryonic development. PMID:24066163

A reliability design method for a lithium-ion battery pack considering the thermal disequilibrium in electric vehicles

NASA Astrophysics Data System (ADS)

Xia, Quan; Wang, Zili; Ren, Yi; Sun, Bo; Yang, Dezhen; Feng, Qiang

2018-05-01

With the rapid development of lithium-ion battery technology in the electric vehicle (EV) industry, the lifetime of the battery cell increases substantially; however, the reliability of the battery pack is still inadequate. Because of the complexity of the battery pack, a reliability design method for a lithium-ion battery pack considering the thermal disequilibrium is proposed in this paper based on cell redundancy. Based on this method, a three-dimensional electric-thermal-flow-coupled model, a stochastic degradation model of cells under field dynamic conditions and a multi-state system reliability model of a battery pack are established. The relationships between the multi-physics coupling model, the degradation model and the system reliability model are first constructed to analyze the reliability of the battery pack and followed by analysis examples with different redundancy strategies. By comparing the reliability of battery packs of different redundant cell numbers and configurations, several conclusions for the redundancy strategy are obtained. More notably, the reliability does not monotonically increase with the number of redundant cells for the thermal disequilibrium effects. In this work, the reliability of a 6 × 5 parallel-series configuration is the optimal system structure. In addition, the effect of the cell arrangement and cooling conditions are investigated.

Dynamic interaction between actin and nesprin2 maintain the cell nucleus in a prestressed state

NASA Astrophysics Data System (ADS)

Kumar, Abhishek; Shivashankar, G. V.

2016-12-01

Mechanical coupling between the nucleus and the cytoskeleton is indispensable for direct force transduction from the extra cellular matrix (ECM) to the chromatin. Although this physical coupling has been shown to be crucial for nuclear positioning and its function, the quantification of nuclear-cytoskeleton interaction has been lacking. In this paper, using various quantitative fluorescence spectroscopy techniques, we investigate the nature of this connection. High-resolution 3D imaging shows that nesprin2G forms short linear structures along actin stress fibers (ASFs) in the apical region of the nucleus. Fluorescence recovery after photobleaching (FRAP) revealed that the alignment of nesprin2G becomes heterogeneous when cell shape is engineered from elongated rectangular shape to square using micropatterned substrates. Further, fluorescence cross-correlation spectroscopy (FCCS) revealed that actin interacts transiently with outer nuclear membrane protein nesprin2G with a time scale of 12 ms. In addition, fluorescence resonance energy transfer (FRET) experiments show that the apical ASFs and nesprin2G are in close physical proximity. This interaction is spatially heterogeneous with high FRET along the ASFs. Lastly, we show that the disruption of actin to nuclear connection by over-expression of Dominant Negative Klarsicht, ANC-1, Syne Homology (DNKASH) leads to an increase in nuclear height. These results not only reveal the characteristics of actin-nesprin2G interaction and its significance in regulating nuclear morphology, but also validate the utility of quantitative fluorescence techniques in deciphering physical connections that are essential for mechanotransduction.

Whole-cell based hybrid materials for green energy production, environmental remediation and smart cell-therapy.

PubMed

Léonard, Alexandre; Dandoy, Philippe; Danloy, Emeric; Leroux, Grégory; Meunier, Christophe F; Rooke, Joanna C; Su, Bao-Lian

2011-02-01

This critical review highlights the advances that have been made over recent years in the domain of whole-cell immobilisation and encapsulation for applications relating to the environment and human health, particularly focusing on examples of photosynthetic plant cells, bacteria and algae as well as animal cells. Evidence that encapsulated photosynthetic cells remain active in terms of CO(2) sequestration and biotransformation (solar driven conversion of CO(2) into biofuels, drugs, fine chemicals etc.), coupled with the most recent advances made in the field of cell therapy, reveals the need to develop novel devices based on the preservation of living cells within abiotic porous frameworks. This review shall corroborate this statement by selecting precise examples that unambiguously demonstrate the necessity and the benefits of such smart materials. As will be described, the handling and exploitation of photosynthetic cells are enhanced by entrapment or encapsulation since the cells are physically separated from the liquid medium, thereby facilitating the recovery of the metabolites produced. In the case of animal cells, their encapsulation within a matrix is essential in order to create a physical barrier that can protect the cells auto-immune defenders upon implantation into a living body. For these two research axes, the key parameters that have to be kept in mind when designing hybrid materials will be identified, concentrating on essential aspects such as biocompatibility, mechanical strength and controlled porosity (264 references).

Culture on electrospun polyurethane scaffolds decreases atrial natriuretic peptide expression by cardiomyocytes in vitro.

PubMed

Rockwood, Danielle N; Akins, Robert E; Parrag, Ian C; Woodhouse, Kimberly A; Rabolt, John F

2008-12-01

The function of the mammalian heart depends on the functional alignment of cardiomyocytes, and controlling cell alignment is an important consideration in biomaterial design for cardiac tissue engineering and research. The physical cues that guide functional cell alignment in vitro and the impact of substrate-imposed alignment on cell phenotype, however, are only partially understood. In this report, primary cardiac ventricular cells were grown on electrospun, biodegradable polyurethane (ES-PU) with either aligned or unaligned microfibers. ES-PU scaffolds supported high-density cultures and cell subpopulations remained intact over two weeks in culture. ES-PU cultures contained electrically-coupled cardiomyocytes with connexin-43 localized to points of cell:cell contact. Multi-cellular organization correlated with microfiber orientation and aligned materials yielded highly oriented cardiomyocyte groupings. Atrial natriuretic peptide, a molecular marker that shows decreasing expression during ventricular cell maturation, was significantly lower in cultures grown on ES-PU scaffolds than in those grown on tissue culture polystyrene. Cells grown on aligned ES-PU had significantly lower steady state levels of ANP and constitutively released less ANP over time indicating that scaffold-imposed cell organization resulted in a shift in cell phenotype to a more mature state. We conclude that the physical organization of microfibers in ES-PU scaffolds impacts both multi-cellular architecture and cardiac cell phenotype in vitro.

Multicoordination Control Strategy Performance in Hybrid Power Systems

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

Pezzini, Paolo; Bryden, Kenneth M.; Tucker, David

This paper evaluates a state-space methodology of a multi-input multi-output (MIMO) control strategy using a 2 × 2 tightly coupled scenario applied to a physical gas turbine fuel cell hybrid power system. A centralized MIMO controller was preferred compared to a decentralized control approach because previous simulation studies showed that the coupling effect identified during the simultaneous control of the turbine speed and cathode airflow was better minimized. The MIMO controller was developed using a state-space dynamic model of the system that was derived using first-order transfer functions empirically obtained through experimental tests. The controller performance was evaluated in termsmore » of disturbance rejection through perturbations in the gas turbine operation, and setpoint tracking maneuver through turbine speed and cathode airflow steps. The experimental results illustrate that a multicoordination control strategy was able to mitigate the coupling of each actuator to each output during the simultaneous control of the system, and improved the overall system performance during transient conditions. On the other hand, the controller showed different performance during validation in simulation environment compared to validation in the physical facility, which will require a better dynamic modeling of the system for the implementation of future multivariable control strategies.« less

Multicoordination Control Strategy Performance in Hybrid Power Systems

DOE PAGES

Pezzini, Paolo; Bryden, Kenneth M.; Tucker, David

2018-04-11

This paper evaluates a state-space methodology of a multi-input multi-output (MIMO) control strategy using a 2 × 2 tightly coupled scenario applied to a physical gas turbine fuel cell hybrid power system. A centralized MIMO controller was preferred compared to a decentralized control approach because previous simulation studies showed that the coupling effect identified during the simultaneous control of the turbine speed and cathode airflow was better minimized. The MIMO controller was developed using a state-space dynamic model of the system that was derived using first-order transfer functions empirically obtained through experimental tests. The controller performance was evaluated in termsmore » of disturbance rejection through perturbations in the gas turbine operation, and setpoint tracking maneuver through turbine speed and cathode airflow steps. The experimental results illustrate that a multicoordination control strategy was able to mitigate the coupling of each actuator to each output during the simultaneous control of the system, and improved the overall system performance during transient conditions. On the other hand, the controller showed different performance during validation in simulation environment compared to validation in the physical facility, which will require a better dynamic modeling of the system for the implementation of future multivariable control strategies.« less

CVD-MPFA full pressure support, coupled unstructured discrete fracture-matrix Darcy-flux approximations

NASA Astrophysics Data System (ADS)

Ahmed, Raheel; Edwards, Michael G.; Lamine, Sadok; Huisman, Bastiaan A. H.; Pal, Mayur

2017-11-01

Two novel control-volume methods are presented for flow in fractured media, and involve coupling the control-volume distributed multi-point flux approximation (CVD-MPFA) constructed with full pressure support (FPS), to two types of discrete fracture-matrix approximation for simulation on unstructured grids; (i) involving hybrid grids and (ii) a lower dimensional fracture model. Flow is governed by Darcy's law together with mass conservation both in the matrix and the fractures, where large discontinuities in permeability tensors can occur. Finite-volume FPS schemes are more robust than the earlier CVD-MPFA triangular pressure support (TPS) schemes for problems involving highly anisotropic homogeneous and heterogeneous full-tensor permeability fields. We use a cell-centred hybrid-grid method, where fractures are modelled by lower-dimensional interfaces between matrix cells in the physical mesh but expanded to equi-dimensional cells in the computational domain. We present a simple procedure to form a consistent hybrid-grid locally for a dual-cell. We also propose a novel hybrid-grid for intersecting fractures, for the FPS method, which reduces the condition number of the global linear system and leads to larger time steps for tracer transport. The transport equation for tracer flow is coupled with the pressure equation and provides flow parameter assessment of the fracture models. Transport results obtained via TPS and FPS hybrid-grid formulations are compared with the corresponding results of fine-scale explicit equi-dimensional formulations. The results show that the hybrid-grid FPS method applies to general full-tensor fields and provides improved robust approximations compared to the hybrid-grid TPS method for fractured domains, for both weakly anisotropic permeability fields and very strong anisotropic full-tensor permeability fields where the TPS scheme exhibits spurious oscillations. The hybrid-grid FPS formulation is extended to compressible flow and the results demonstrate the method is also robust for transient flow. Furthermore, we present FPS coupled with a lower-dimensional fracture model, where fractures are strictly lower-dimensional in the physical mesh as well as in the computational domain. We present a comparison of the hybrid-grid FPS method and the lower-dimensional fracture model for several cases of isotropic and anisotropic fractured media which illustrate the benefits of the respective methods.

Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

NASA Astrophysics Data System (ADS)

Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

2010-12-01

Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs to homogeneous and heterogeneous porous media, respectively. In 1D columns, calcium carbonate mineral precipitation was driven by urea hydrolysis catalyzed by urease enzyme, and in 2D flow cells, calcium carbonate mineral forming reactants were injected sequentially, forming migrating reaction fronts that are typically highly nonuniform. The RAT simulation results for the spatial and temporal distributions of precipitates, reaction rates and major species in the system, and also for changes in porosity and permeability, were compared to both laboratory experimental data and computational results obtained using other reactive transport simulators. The comparisons demonstrate the ability of RAT to simulate complex nonlinear systems and the advantages of fully coupled approaches, over de-coupled methods, for accurate simulation of complex, dynamic processes such as engineered mineral precipitation in subsurface environments.

Responds of Bone Cells to Microgravity: Ground-Based Research

NASA Astrophysics Data System (ADS)

Zhang, Jian; Li, Jingbao; Xu, Huiyun; Yang, Pengfei; Xie, Li; Qian, Airong; Zhao, Yong; Shang, Peng

2015-11-01

Severe loss of bone occurs due to long-duration spaceflight. Mechanical loading stimulates bone formation, while bone degradation happens under mechanical unloading. Bone remodeling is a dynamic process in which bone formation and bone resorption are tightly coupled. Increased bone resorption and decreased bone formation caused by reduced mechanical loading, generally result in disrupted bone remodeling. Bone remodeling is orchestrated by multiple bone cells including osteoblast, osteocyte, osteoclast and mesenchymal stem cell. It is yet not clear that how these bone cells sense altered gravity, translate physical stimulus into biochemical signals, and then regulate themselves structurally and functionally. In this paper, studies elucidating the bioeffects of microgravity on bone cells (osteoblast, osteocyte, osteoclast, mesenchymal stem cell) using various platforms including spaceflight and ground-based simulated microgravity were summarized. Promising gravity-sensitive signaling pathways and protein molecules were proposed.

Direct Simulations of Coupled Transport and Reaction on Nano-Scale X-Ray Computed Tomography Images of Platinum Group Metal-Free Catalyst Cathodes

DOE PAGES

Ogawa, S.; Komini Babu, S.; Chung, H. T.; ...

2016-08-22

The nano/micro-scale geometry of polymer electrolyte fuel cell (PEFC) catalyst layers critically affects cell performance. The small length scales and complex structure of these composite layers make it challenging to analyze cell performance and physics at the particle scale by experiment. We present a computational method to simulate transport and chemical reaction phenomena at the pore/particle-scale and apply it to a PEFC cathode with platinum group metal free (PGM-free) catalyst. Here, we numerically solve the governing equations for the physics with heterogeneous oxygen diffusion coefficient and proton conductivity evaluated using the actual electrode structure and ionomer distribution obtained using nano-scalemore » resolution X-ray computed tomography (nano-CT). Using this approach, the oxygen concentration and electrolyte potential distributions imposed by the oxygen reduction reaction are solved and the impact of the catalyst layer structure on performance is evaluated.« less

Safety modelling and testing of lithium-ion batteries in electrified vehicles

NASA Astrophysics Data System (ADS)

Deng, Jie; Bae, Chulheung; Marcicki, James; Masias, Alvaro; Miller, Theodore

2018-04-01

To optimize the safety of batteries, it is important to understand their behaviours when subjected to abuse conditions. Most early efforts in battery safety modelling focused on either one battery cell or a single field of interest such as mechanical or thermal failure. These efforts may not completely reflect the failure of batteries in automotive applications, where various physical processes can take place in a large number of cells simultaneously. In this Perspective, we review modelling and testing approaches for battery safety under abuse conditions. We then propose a general framework for large-scale multi-physics modelling and experimental work to address safety issues of automotive batteries in real-world applications. In particular, we consider modelling coupled mechanical, electrical, electrochemical and thermal behaviours of batteries, and explore strategies to extend simulations to the battery module and pack level. Moreover, we evaluate safety test approaches for an entire range of automotive hardware sets from cell to pack. We also discuss challenges in building this framework and directions for its future development.

Direct Simulations of Coupled Transport and Reaction on Nano-Scale X-Ray Computed Tomography Images of Platinum Group Metal-Free Catalyst Cathodes

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

Ogawa, S.; Komini Babu, S.; Chung, H. T.

The nano/micro-scale geometry of polymer electrolyte fuel cell (PEFC) catalyst layers critically affects cell performance. The small length scales and complex structure of these composite layers make it challenging to analyze cell performance and physics at the particle scale by experiment. We present a computational method to simulate transport and chemical reaction phenomena at the pore/particle-scale and apply it to a PEFC cathode with platinum group metal free (PGM-free) catalyst. Here, we numerically solve the governing equations for the physics with heterogeneous oxygen diffusion coefficient and proton conductivity evaluated using the actual electrode structure and ionomer distribution obtained using nano-scalemore » resolution X-ray computed tomography (nano-CT). Using this approach, the oxygen concentration and electrolyte potential distributions imposed by the oxygen reduction reaction are solved and the impact of the catalyst layer structure on performance is evaluated.« less

Bursting synchronization dynamics of pancreatic β-cells with electrical and chemical coupling.

PubMed

Meng, Pan; Wang, Qingyun; Lu, Qishao

2013-06-01

Based on bifurcation analysis, the synchronization behaviors of two identical pancreatic β-cells connected by electrical and chemical coupling are investigated, respectively. Various firing patterns are produced in coupled cells when a single cell exhibits tonic spiking or square-wave bursting individually, irrespectively of what the cells are connected by electrical or chemical coupling. On the one hand, cells can burst synchronously for both weak electrical and chemical coupling when an isolated cell exhibits tonic spiking itself. In particular, for electrically coupled cells, under the variation of the coupling strength there exist complex transition processes of synchronous firing patterns such as "fold/limit cycle" type of bursting, then anti-phase continuous spiking, followed by the "fold/torus" type of bursting, and finally in-phase tonic spiking. On the other hand, it is shown that when the individual cell exhibits square-wave bursting, suitable coupling strength can make the electrically coupled system generate "fold/Hopf" bursting via "fold/fold" hysteresis loop; whereas, the chemically coupled cells generate "fold/subHopf" bursting. Especially, chemically coupled bursters can exhibit inverse period-adding bursting sequence. Fast-slow dynamics analysis is applied to explore the generation mechanism of these bursting oscillations. The above analysis of bursting types and the transition may provide us with better insight into understanding the role of coupling in the dynamic behaviors of pancreatic β-cells.

Elongator complex is critical for cell cycle progression and leaf patterning in Arabidopsis.

PubMed

Xu, Deyang; Huang, Weihua; Li, Yang; Wang, Hua; Huang, Hai; Cui, Xiaofeng

2012-03-01

The mitotic cell cycle in higher eukaryotes is of pivotal importance for organ growth and development. Here, we report that Elongator, an evolutionarily conserved histone acetyltransferase complex, acts as an important regulator of mitotic cell cycle to promote leaf patterning in Arabidopsis. Mutations in genes encoding Elongator subunits resulted in aberrant cell cycle progression, and the altered cell division affects leaf polarity formation. The defective cell cycle progression is caused by aberrant DNA replication and increased DNA damage, which activate the DNA replication checkpoint to arrest the cell cycle. Elongator interacts with proliferating cell nuclear antigen (PCNA) and is required for efficient histone 3 (H3) and H4 acetylation coupled with DNA replication. Levels of chromatin-bound H3K56Ac and H4K5Ac known to associate with replicons during DNA replication were reduced in the mutants of both Elongator and chromatin assembly factor 1 (CAF-1), another protein complex that physically interacts with PCNA for DNA replication-coupled chromatin assembly. Disruptions of CAF-1 also led to severe leaf polarity defects, which indicated that Elongator and CAF-1 act, at least partially, in the same pathway to promote cell cycle progression. Collectively, our results demonstrate that Elongator is an important regulator of mitotic cell cycle, and the Elongator pathway plays critical roles in promoting leaf polarity formation. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

GnRH Episodic Secretion Is Altered by Pharmacological Blockade of Gap Junctions: Possible Involvement of Glial Cells.

PubMed

Pinet-Charvet, Caroline; Geller, Sarah; Desroziers, Elodie; Ottogalli, Monique; Lomet, Didier; Georgelin, Christine; Tillet, Yves; Franceschini, Isabelle; Vaudin, Pascal; Duittoz, Anne

2016-01-01

Episodic release of GnRH is essential for reproductive function. In vitro studies have established that this episodic release is an endogenous property of GnRH neurons and that GnRH secretory pulses are associated with synchronization of GnRH neuron activity. The cellular mechanisms by which GnRH neurons synchronize remain largely unknown. There is no clear evidence of physical coupling of GnRH neurons through gap junctions to explain episodic synchronization. However, coupling of glial cells through gap junctions has been shown to regulate neuron activity in their microenvironment. The present study investigated whether glial cell communication through gap junctions plays a role in GnRH neuron activity and secretion in the mouse. Our findings show that Glial Fibrillary Acidic Protein-expressing glial cells located in the median eminence in close vicinity to GnRH fibers expressed Gja1 encoding connexin-43. To study the impact of glial-gap junction coupling on GnRH neuron activity, an in vitro model of primary cultures from mouse embryo nasal placodes was used. In this model, GnRH neurons possess a glial microenvironment and were able to release GnRH in an episodic manner. Our findings show that in vitro glial cells forming the microenvironment of GnRH neurons expressed connexin-43 and displayed functional gap junctions. Pharmacological blockade of the gap junctions with 50 μM 18-α-glycyrrhetinic acid decreased GnRH secretion by reducing pulse frequency and amplitude, suppressed neuronal synchronization and drastically reduced spontaneous electrical activity, all these effects were reversed upon 18-α-glycyrrhetinic acid washout.

How I treat and manage strokes in sickle cell disease

PubMed Central

Kassim, Adetola A.; Galadanci, Najibah A.; Pruthi, Sumit

2015-01-01

Neurologic complications are a major cause of morbidity and mortality in sickle cell disease (SCD). In children with sickle cell anemia, routine use of transcranial Doppler screening, coupled with regular blood transfusion therapy, has decreased the prevalence of overt stroke from ∼11% to 1%. Limited evidence is available to guide acute and chronic management of individuals with SCD and strokes. Current management strategies are based primarily on single arm clinical trials and observational studies, coupled with principles of neurology and hematology. Initial management of a focal neurologic deficit includes evaluation by a multidisciplinary team (a hematologist, neurologist, neuroradiologist, and transfusion medicine specialist); prompt neuro-imaging and an initial blood transfusion (simple followed immediately by an exchange transfusion or only exchange transfusion) is recommended if the hemoglobin is >4 gm/dL and <10 gm/dL. Standard therapy for secondary prevention of strokes and silent cerebral infarcts includes regular blood transfusion therapy and in selected cases, hematopoietic stem cell transplantation. A critical component of the medical care following an infarct is cognitive and physical rehabilitation. We will discuss our strategy of acute and long-term management of strokes in SCD. PMID:25824688

Rab-coupling protein coordinates recycling of alpha5beta1 integrin and EGFR1 to promote cell migration in 3D microenvironments.

PubMed

Caswell, Patrick T; Chan, May; Lindsay, Andrew J; McCaffrey, Mary W; Boettiger, David; Norman, Jim C

2008-10-06

Here we show that blocking the adhesive function of alphavbeta3 integrin with soluble RGD ligands, such as osteopontin or cilengitide, promoted association of Rab-coupling protein (RCP) with alpha5beta1 integrin and drove RCP-dependent recycling of alpha5beta1 to the plasma membrane and its mobilization to dynamic ruffling protrusions at the cell front. These RCP-driven changes in alpha5beta1 trafficking led to acquisition of rapid/random movement on two-dimensional substrates and to a marked increase in fibronectin-dependent migration of tumor cells into three-dimensional matrices. Recycling of alpha5beta1 integrin did not affect its regulation or ability to form adhesive bonds with substrate fibronectin. Instead, alpha5beta1 controlled the association of EGFR1 with RCP to promote the coordinate recycling of these two receptors. This modified signaling downstream of EGFR1 to increase its autophosphorylation and activation of the proinvasive kinase PKB/Akt. We conclude that RCP provides a scaffold that promotes the physical association and coordinate trafficking of alpha5beta1 and EGFR1 and that this drives migration of tumor cells into three-dimensional matrices.

High-resolution coupled physics solvers for analysing fine-scale nuclear reactor design problems

DOE PAGES

Mahadevan, Vijay S.; Merzari, Elia; Tautges, Timothy; ...

2014-06-30

An integrated multi-physics simulation capability for the design and analysis of current and future nuclear reactor models is being investigated, to tightly couple neutron transport and thermal-hydraulics physics under the SHARP framework. Over several years, high-fidelity, validated mono-physics solvers with proven scalability on petascale architectures have been developed independently. Based on a unified component-based architecture, these existing codes can be coupled with a mesh-data backplane and a flexible coupling-strategy-based driver suite to produce a viable tool for analysts. The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in ordermore » to reduce the overall numerical uncertainty while leveraging available computational resources. Finally, the coupling methodology and software interfaces of the framework are presented, along with verification studies on two representative fast sodium-cooled reactor demonstration problems to prove the usability of the SHARP framework.« less

A pressure relaxation closure model for one-dimensional, two-material Lagrangian hydrodynamics based on the Riemann problem

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

Kamm, James R; Shashkov, Mikhail J

2009-01-01

Despite decades of development, Lagrangian hydrodynamics of strengthfree materials presents numerous open issues, even in one dimension. We focus on the problem of closing a system of equations for a two-material cell under the assumption of a single velocity model. There are several existing models and approaches, each possessing different levels of fidelity to the underlying physics and each exhibiting unique features in the computed solutions. We consider the case in which the change in heat in the constituent materials in the mixed cell is assumed equal. An instantaneous pressure equilibration model for a mixed cell can be cast asmore » four equations in four unknowns, comprised of the updated values of the specific internal energy and the specific volume for each of the two materials in the mixed cell. The unique contribution of our approach is a physics-inspired, geometry-based model in which the updated values of the sub-cell, relaxing-toward-equilibrium constituent pressures are related to a local Riemann problem through an optimization principle. This approach couples the modeling problem of assigning sub-cell pressures to the physics associated with the local, dynamic evolution. We package our approach in the framework of a standard predictor-corrector time integration scheme. We evaluate our model using idealized, two material problems using either ideal-gas or stiffened-gas equations of state and compare these results to those computed with the method of Tipton and with corresponding pure-material calculations.« less

Simultaneous Activation of Induced Heterodimerization between CXCR4 Chemokine Receptor and Cannabinoid Receptor 2 (CB2) Reveals a Mechanism for Regulation of Tumor Progression.

PubMed

Coke, Christopher J; Scarlett, Kisha A; Chetram, Mahandranauth A; Jones, Kia J; Sandifer, Brittney J; Davis, Ahriea S; Marcus, Adam I; Hinton, Cimona V

2016-05-06

The G-protein-coupled chemokine receptor CXCR4 generates signals that lead to cell migration, cell proliferation, and other survival mechanisms that result in the metastatic spread of primary tumor cells to distal organs. Numerous studies have demonstrated that CXCR4 can form homodimers or can heterodimerize with other G-protein-coupled receptors to form receptor complexes that can amplify or decrease the signaling capacity of each individual receptor. Using biophysical and biochemical approaches, we found that CXCR4 can form an induced heterodimer with cannabinoid receptor 2 (CB2) in human breast and prostate cancer cells. Simultaneous, agonist-dependent activation of CXCR4 and CB2 resulted in reduced CXCR4-mediated expression of phosphorylated ERK1/2 and ultimately reduced cancer cell functions such as calcium mobilization and cellular chemotaxis. Given that treatment with cannabinoids has been shown to reduce invasiveness of cancer cells as well as CXCR4-mediated migration of immune cells, it is plausible that CXCR4 signaling can be silenced through a physical heterodimeric association with CB2, thereby inhibiting subsequent functions of CXCR4. Taken together, the data illustrate a mechanism by which the cannabinoid system can negatively modulate CXCR4 receptor function and perhaps tumor progression. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

A novel mechanistic modeling framework for analysis of electrode balancing and degradation modes in commercial lithium-ion cells

NASA Astrophysics Data System (ADS)

Schindler, Stefan; Danzer, Michael A.

2017-03-01

Aiming at a long-term stable and safe operation of rechargeable lithium-ion cells, elementary design aspects and degradation phenomena have to be considered depending on the specific application. Among the degrees of freedom in cell design, electrode balancing is of particular interest and has a distinct effect on useable capacity and voltage range. Concerning intrinsic degradation modes, understanding the underlying electrochemical processes and tracing the overall degradation history are the most crucial tasks. In this study, a model-based, minimal parameter framework for combined elucidation of electrode balancing and degradation pathways in commercial lithium-ion cells is introduced. The framework rests upon the simulation of full cell voltage profiles from the superposition of equivalent, artificially degraded half-cell profiles and allows to separate aging contributions from loss of available lithium and active materials in both electrodes. A physically meaningful coupling between thermodynamic and kinetic degradation modes based on the correlation between altered impedance features and loss of available lithium as well as loss of active material is proposed and validated by a low temperature degradation profile examined in one of our recent publications. The coupled framework is able to determine the electrode balancing within an error range of < 1% and the projected cell degradation is qualitatively and quantitatively in line with experimental observations.

A physical multifield model predicts the development of volume and structure in the human brain

NASA Astrophysics Data System (ADS)

Rooij, Rijk de; Kuhl, Ellen

2018-03-01

The prenatal development of the human brain is characterized by a rapid increase in brain volume and a development of a highly folded cortex. At the cellular level, these events are enabled by symmetric and asymmetric cell division in the ventricular regions of the brain followed by an outwards cell migration towards the peripheral regions. The role of mechanics during brain development has been suggested and acknowledged in past decades, but remains insufficiently understood. Here we propose a mechanistic model that couples cell division, cell migration, and brain volume growth to accurately model the developing brain between weeks 10 and 29 of gestation. Our model accurately predicts a 160-fold volume increase from 1.5 cm3 at week 10 to 235 cm3 at week 29 of gestation. In agreement with human brain development, the cortex begins to form around week 22 and accounts for about 30% of the total brain volume at week 29. Our results show that cell division and coupling between cell density and volume growth are essential to accurately model brain volume development, whereas cell migration and diffusion contribute mainly to the development of the cortex. We demonstrate that complex folding patterns, including sinusoidal folds and creases, emerge naturally as the cortex develops, even for low stiffness contrasts between the cortex and subcortex.

Gravity effects on endogenous movements

NASA Astrophysics Data System (ADS)

Johnsson, Anders; Antonsen, Frank

Gravity effects on endogenous movements A. Johnsson * and F. Antonsen *+ * Department of Physics, Norwegian University of Science and Technology,NO-7491, Trond-heim, Norway, E-mail: anders.johnsson@ntnu.no + Present address: Statoil Research Center Trondheim, NO-7005, Trondheim, Norway Circumnutations in stems/shoots exist in many plants and often consists of more or less regular helical movements around the plumb line under Earth conditions. Recent results on circumnu-tations of Arabidopsis in space (Johnsson et al. 2009) showed that minute amplitude oscilla-tions exist in weightlessness, but that centripetal acceleration (mimicking the gravity) amplified and/or created large amplitude oscillations. Fundamental mechanisms underlying these results will be discussed by modeling the plant tissue as a cylinder of cells coupled together. As a starting point we have modeled (Antonsen 1998) standing waves on a ring of biological cells, as first discussed in a classical paper (Turing 1952). If the coupled cells can change their water content, an `extension' wave could move around the ring. We have studied several, stacked rings of cells coupled into a cylinder that together represent a cylindrical plant tissue. Waves of extensions travelling around the cylinder could then represent the observable circumnutations. The coupling between cells can be due to cell-to-cell diffusion, or to transport via channels, and the coupling can be modeled to vary in both longitudinal and transversal direction of the cylinder. The results from ISS experiments indicate that this cylindrical model of coupled cells should be able to 1) show self-sustained oscillations without the impact of gravity (being en-dogenous) and 2) show how an environmental factor like gravity can amplify or generate the oscillatory movements. Gravity has been introduced in the model by a negative, time-delayed feed-back transport across the cylinder. This represents the physiological reactions to acceler-ation stimulations (gravitropism reactions). Such a negative feedback can account for gravity initiated transport, resulting in lateral water transport and overall movements. The simulation results indicate that self-sustained oscillations can occur on such a cylinder of cells. It will also be demonstrated that the introduction of feedback in the model results in longer circum-nutation periods. It will be discussed how this generic modeling approach could be applied to discuss oscillatory plant movements in general and how other environmental factors, as for instance light gradients, could couple to the self-sustained movements. The oscillations require weightlessness for proper investigations. References: Antonsen F.: Biophysical studies of plant growth movements in microgravity and under 1 g conditions. PhD thesis, Norwegian University of Science and Technology 1998. Johnsson A., Solheim BGB, Iversen T.-H.: Gravity amplifies and microgravity decreases cir-cumnutations in Arabidopsis thaliana stems: results from a space experiment.-New Phytologist 182: 621-629. 2009. Turing AM.: The chemical basis for morphogenesis.-Phil Trans. R. Soc. London Ser B237:37 -72. 1952.

Biomedical Platforms Based on Composite Nanomaterials and Cellular Toxicity

NASA Astrophysics Data System (ADS)

Bellucci, Stefano; Bergamaschi, A.; Bottini, M.; Magrini, A.; Mustelin, T.

2007-03-01

Carbon nanotubes possess unique chemical, physical, optical, and magnetic properties, which make them suitable for many uses in industrial products and in the field of nanotechnology, including nanomedicine. We describe fluorescent nanocomposites for use in biosensors or nanoelectronics. Then we describe recent results on the issue of cytotoxicity of carbon nanotubes obtained in our labs. Silica nanoparticles have been widely used for biosensing and catalytic applications due to their large surface area-to-volume ratio, straightforward manufacture, and the compatibility of silica chemistry with covalent coupling of biomolecules. Carbon nanotubes-composite materials, such as those based on Carbon nanotubes bound to nanoparticles, are suitable, in order to tailor Carbon nanotubes properties for specific applications. We present a tunable synthesis of Multi Wall Carbon nanotubes-Silica nanoparticles. The control of the nanotube morphology and the bead size, coupled with the versatility of silica chemistry, makes these structures an excellent platform for the development of biosensors (optical, magnetic and catalytic applications). We describe the construction and characterization of supramolecular nanostructures consisting of ruthenium-complex luminophores, directly grafted onto short oxidized single-walled carbon nanotubes or physically entrapped in silica nanobeads, which had been covalently linked to short oxidized single-walled carbon nanotubes or hydrophobically adsorbed onto full-length multi-walled carbon nanotubes. These structures have been evaluated as potential electron-acceptor complexes for use in the fabrication of photovoltaic devices, and for their properties as fluorescent nanocomposites for use in biosensors or nanoelectronics. Finally, we compare the toxicity of pristine and oxidized Multi Walled Carbon nanotubes on human T cells - which would be among the first exposed cell types upon intravenous administration of Carbon nanotubes in therapeutic and diagnostic nanodevices. Our results suggest that carbon nanotubes indeed can be very toxic and induce massive loss of cell viability through programmed cell death at sufficiently high concentrations (>1ng/cell). The cytotoxicity of Carbon nanotubes does depend on many other factors than concentration, including their physical form, diameter, length, and the nature of attached molecules or nanomaterials: carbon black, for instance, is less toxic than pristine CNTs (what shows the relevance of structure and topology); oxidized CNTs are more toxic than pristine CNTs.

A novel scaling law relating the geometrical dimensions of a photocathode radio frequency gun to its radio frequency properties

NASA Astrophysics Data System (ADS)

Lal, Shankar; Pant, K. K.; Krishnagopal, S.

2011-12-01

Developing a photocathode RF gun with the desired RF properties of the π-mode, such as field balance (eb) ˜1, resonant frequency fπ = 2856 MHz, and waveguide-to-cavity coupling coefficient βπ ˜1, requires precise tuning of the resonant frequencies of the independent full- and half-cells (ff and fh), and of the waveguide-to-full-cell coupling coefficient (βf). While contemporary electromagnetic codes and precision machining capability have made it possible to design and tune independent cells of a photocathode RF gun for desired RF properties, thereby eliminating the need for tuning, access to such computational resources and quality of machining is not very widespread. Therefore, many such structures require tuning after machining by employing conventional tuning techniques that are iterative in nature. Any procedure that improves understanding of the tuning process and consequently reduces the number of iterations and the associated risks in tuning a photocathode gun would, therefore, be useful. In this paper, we discuss a method devised by us to tune a photocathode RF gun for desired RF properties under operating conditions. We develop and employ a simple scaling law that accounts for inter-dependence between frequency of independent cells and waveguide-to-cavity coupling coefficient, and the effect of brazing clearance for joining of the two cells. The method has been employed to successfully develop multiple 1.6 cell BNL/SLAC/UCLA type S-band photocathode RF guns with the desired RF properties, without the need to tune them by a tiresome cut-and-measure process. Our analysis also provides a physical insight into how the geometrical dimensions affect the RF properties of the photo-cathode RF gun.

Physics of Coupled CME and Flare Systems

DTIC Science & Technology

2016-12-21

AFRL-RV-PS- AFRL-RV-PS- TR-2016-0162 TR-2016-0162 PHYSICS OF COUPLED CME AND FLARE SYSTEMS K. S. Balasubramaniam, et al. 21 December 2016 Final...30 Sep 2016 4. TITLE AND SUBTITLE Physics of Coupled CME and Flare Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 61102F...objectives for this task were: (i) derive measureable physical properties and discernible structural circumstances in solar active regions that

Robust impact of coupled stratospheric ozone chemistry on the response of the Austral circulation to increased greenhouse gases

NASA Astrophysics Data System (ADS)

Chiodo, G.; Polvani, L. M.

2016-12-01

Due to computational constraints, interactive stratospheric chemistry is commonly neglected in most GCMs participating in inter-comparison projects. The impact of this simplification on the modeled response to external forcings remains largely unexplored. In this work, we examine the impact of the stratospheric chemistry coupling on the SH circulation response to an abrupt quadrupling of CO2. We accomplish this with a version of the Whole Atmosphere Community Climate (WACCM) model, which allows coupling and de-coupling stratospheric chemistry, without altering any other physical parameterization. We find that the chemistry coupling in WACCM significantly reduces (by about 20%) the response of both eddy-driven mid-latitude jet and the Hadley Cell strength, without altering the surface temperature response. This behavior is linked to the representation of stratospheric ozone, and its effects on the meridional temperature gradient at the extratropical tropopause. Our results imply that neglecting stratospheric ozone chemistry results in a potential overestimation of the circulation response to GHGs. Hence, stratospheric ozone chemistry produces a substantial negative feedback on the response of the atmospheric circulation to increased greenhouse gases.

Underdamped long Josephson junction coupled to overdamped single-flux-quantum circuits

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

Zhang, Y.M.; Borzenets, V.; Kaplunenko, V.K.

1997-09-01

We report a circuit that integrates an underdamped long Josephson junction with overdamped single-flux-quantum (SFQ) circuits. We confirm that the resonant soliton modes in the long junction are not affected by SFQ cells coupled to the junction, and demonstrate that the radiation frequency and linewidth of the soliton resonances can be measured with SFQ T-flip-flops. Our experimental results also show that a 4{pi} quantum mechanical phase leap at the end of the long junction, which is due to the reflection of a soliton, creates two single flux quanta propagating in the overdamped Josephson transmission line. {copyright} {ital 1997 American Institutemore » of Physics.}« less

Photonic light-trapping versus Lambertian limits in thin film silicon solar cells with 1D and 2D periodic patterns.

PubMed

Bozzola, Angelo; Liscidini, Marco; Andreani, Lucio Claudio

2012-03-12

We theoretically investigate the light-trapping properties of one- and two-dimensional periodic patterns etched on the front surface of c-Si and a-Si thin film solar cells with a silver back reflector and an anti-reflection coating. For each active material and configuration, absorbance A and short-circuit current density Jsc are calculated by means of rigorous coupled wave analysis (RCWA), for different active materials thicknesses in the range of interest of thin film solar cells and in a wide range of geometrical parameters. The results are then compared with Lambertian limits to light-trapping for the case of zero absorption and for the general case of finite absorption in the active material. With a proper optimization, patterns can give substantial absorption enhancement, especially for 2D patterns and for thinner cells. The effects of the photonic patterns on light harvesting are investigated from the optical spectra of the optimized configurations. We focus on the main physical effects of patterning, namely a reduction of reflection losses (better impedance matching conditions), diffraction of light in air or inside the cell, and coupling of incident radiation into quasi-guided optical modes of the structure, which is characteristic of photonic light-trapping.

The fundamental role of mechanical properties in the progression of cancer disease and inflammation

NASA Astrophysics Data System (ADS)

Mierke, Claudia Tanja

2014-07-01

The role of mechanical properties in cancer disease and inflammation is still underinvestigated and even ignored in many oncological and immunological reviews. In particular, eight classical hallmarks of cancer have been proposed, but they still ignore the mechanics behind the processes that facilitate cancer progression. To define the malignant transformation of neoplasms and finally reveal the functional pathway that enables cancer cells to promote cancer progression, these classical hallmarks of cancer require the inclusion of specific mechanical properties of cancer cells and their microenvironment such as the extracellular matrix as well as embedded cells such as fibroblasts, macrophages or endothelial cells. Thus, this review will present current cancer research from a biophysical point of view and will therefore focus on novel physical aspects and biophysical methods to investigate the aggressiveness of cancer cells and the process of inflammation. As cancer or immune cells are embedded in a certain microenvironment such as the extracellular matrix, the mechanical properties of this microenvironment cannot be neglected, and alterations of the microenvironment may have an impact on the mechanical properties of the cancer or immune cells. Here, it is highlighted how biophysical approaches, both experimental and theoretical, have an impact on the classical hallmarks of cancer and inflammation. It is even pointed out how these biophysical approaches contribute to the understanding of the regulation of cancer disease and inflammatory responses after tissue injury through physical microenvironmental property sensing mechanisms. The recognized physical signals are transduced into biochemical signaling events that guide cellular responses, such as malignant tumor progression, after the transition of cancer cells from an epithelial to a mesenchymal phenotype or an inflammatory response due to tissue injury. Moreover, cell adaptation to mechanical alterations, in particular the understanding of mechano-coupling and mechano-regulating functions in cell invasion, appears as an important step in cancer progression and inflammatory response to injuries. This may lead to novel insights into cancer disease and inflammatory diseases and will overcome classical views on cancer and inflammation. In addition, this review will discuss how the physics of cancer and inflammation can help to reveal whether cancer cells will invade connective tissue and metastasize or how leukocytes extravasate and migrate through the tissue. In this review, the physical concepts of cancer progression, including the tissue basement membrane a cancer cell is crossing, its invasion and transendothelial migration as well as the basic physical concepts of inflammatory processes and the cellular responses to the mechanical stress of the microenvironment such as external forces and matrix stiffness, are presented and discussed. In conclusion, this review will finally show how physical measurements can improve classical approaches that investigate cancer and inflammatory diseases, and how these physical insights can be integrated into classical tumor biological approaches.

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses

PubMed Central

Dekas, Anne E; Connon, Stephanie A; Chadwick, Grayson L; Trembath-Reichert, Elizabeth; Orphan, Victoria J

2016-01-01

To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5′-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no 15NH4+ assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living' population, and are not dependent on methane or ANME activity. We investigated the possibility of N2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. 15N2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, 15N2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced 15N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations. PMID:26394007

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses

DOE PAGES

Dekas, Anne E.; Connon, Stephanie A.; Chadwick, Grayson L.; ...

2015-09-22

To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteo-bacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5'-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no 15NHmore » $$+\\atop{4}$$ assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living’ population, and are not dependent on methane or ANME activity. We investigated the possibility of N 2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. 15N 2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, 15N 2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced 15N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. In conclusion, with this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations.« less

Multiple-Scale Physics During Magnetic Reconnection

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

Jara-Almonte, Jonathan

Magnetic reconnection is a key fundamental process in magnetized plasmas wherein the global magnetic topology is modified and stored energy is transferred from fields to particles. Reconnection is an inherently local process, and mechanisms to couple global-scale dynamics are not well understood. This dissertation explores two different mechanisms for cross-scale coupling during magnetic reconnection. As one example, we theoretically examine reconnection in a collisionless plasma using particle-in-cell simulations and demonstrate that large scale reconnection physics can couple to and drive microscopic instabilities, even in two-dimensional systems if significant scale separation exists between the Debye length and the electron skin depth.more » The physics underlying these instabilities is explained using simple theoretical models, and their potential connection to existing discrepancies between laboratory experiments and numerical simulations is explored. In three-dimensional systems, these instabilities are shown to generate anomalous resistivity that balances a substantial fraction of the electric field. In contrast, we also use experiments to investigate cross-scale couplings during reconnection in a collisional plasma. A leading candidate for coupling global and local scales is the hierarchical breakdown of elongated, reconnecting current sheets into numerous smaller current sheets -– the plasmoid instability. In the Magnetic Reconnection Experiment (MRX), recent hardware improvements have extended the accessible parameter space allowing for the study of long-lived, elongated current sheets. Moreover, by using Argon, reproducible and collisional plasmas are produced, which allow for a detailed statistical study of collisional reconnection. As a result, we have conclusively measured the onset of sub-ion-scale plasmoids during resistive, anti-parallel reconnection for the first time. The current sheet thickness is intermediate between ion and electron kinetic scales such that the plasma is in the Hall-MHD regime. Surprisingly, plasmoids are observed at Lundquist numbers < 100 well below theoretical predictions (> 10,000). The number of plasmoids scales with both Lundquist number and current sheet aspect ratio. The Hall quadrupolar fields are shown to suppress plasmoids. Finally, plasmoids are shown to couple local and global physics by enhancing the reconnection rate. These results are compared with prior studies of tearing and plasmoid instability, and implications for astrophysical plasmas, laboratory experiments, and theoretical studies of reconnection are discussed.« less

Interaction between G Protein-Coupled Receptor 143 and Tyrosinase: Implications for Understanding Ocular Albinism Type 1.

PubMed

De Filippo, Elisabetta; Schiedel, Anke C; Manga, Prashiela

2017-02-01

Developmental eye defects in X-linked ocular albinism type 1 are caused by G-protein coupled receptor 143 (GPR143) mutations. Mutations result in dysfunctional melanosome biogenesis and macromelanosome formation in pigment cells, including melanocytes and retinal pigment epithelium. GPR143, primarily expressed in pigment cells, localizes exclusively to endolysosomal and melanosomal membranes unlike most G protein-coupled receptors, which localize to the plasma membrane. There is some debate regarding GPR143 function and elucidating the role of this receptor may be instrumental for understanding neurogenesis during eye development and for devising therapies for ocular albinism type I. Many G protein-coupled receptors require association with other proteins to function. These G protein-coupled receptor-interacting proteins also facilitate fine-tuning of receptor activity and tissue specificity. We therefore investigated potential GPR143 interaction partners, with a focus on the melanogenic enzyme tyrosinase. GPR143 coimmunoprecipitated with tyrosinase, while confocal microscopy demonstrated colocalization of the proteins. Furthermore, tyrosinase localized to the plasma membrane when coexpressed with a GPR143 trafficking mutant. The physical interaction between the proteins was confirmed using fluorescence resonance energy transfer. This interaction may be required in order for GPR143 to function as a monitor of melanosome maturation. Identifying tyrosinase as a potential GPR143 binding protein opens new avenues for investigating the mechanisms that regulate pigmentation and neurogenesis. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

An evolving research agenda for human-coastal systems

NASA Astrophysics Data System (ADS)

Lazarus, Eli D.; Ellis, Michael A.; Brad Murray, A.; Hall, Damon M.

2016-03-01

Within the broad discourses of environmental change, sustainability science, and anthropogenic Earth-surface systems, a focused body of work involves the coupled economic and physical dynamics of developed shorelines. Rapid rates of change in coastal environments, from wetlands and deltas to inlets and dune systems, help researchers recognize, observe, and investigate coupling in natural (non-human) morphodynamics and biomorphodynamics. This same intrinsic quality of fast-paced change also makes developed coastal zones exemplars of observable coupling between physical processes and human activities. In many coastal communities, beach erosion is a natural hazard with economic costs that coastal management counters through a variety of mitigation strategies, including beach replenishment, groynes, revetments, and seawalls. As cycles of erosion and mitigation iterate, coastline change and economically driven interventions become mutually linked. Emergent dynamics of two-way economic-physical coupling is a recent research discovery. Having established a strong theoretical basis, research into coupled human-coastal systems has passed its early proof-of-concept phase. This paper frames three major challenges that need resolving in order to advance theoretical and empirical treatments of human-coastal systems: (1) codifying salient individual and social behaviors of decision-making in ways that capture societal actions across a range of scales (thus engaging economics, social science, and policy disciplines); (2) quantifying anthropogenic effects on alongshore and cross-shore sediment pathways and long-term landscape evolution in coastal zones through time, including direct measurement of cumulative changes to sediment cells resulting from coastal development and management practices (e.g., construction of buildings and artificial dunes, bulldozer removal of overwash after major storms); and (3) reciprocal knowledge and data exchange between researchers in coastal morphodynamics and practitioners of coastal management. Future research into human-coastal systems can benefit from decades of interdisciplinary work on the complex dynamics of common-pool resources, from computational efficiency and new techniques in numerical modeling, and from the growing catalog of high-resolution geospatial data for natural and developed coastlines around the world.

Growth of Bacterial Colonies

NASA Astrophysics Data System (ADS)

Warren, Mya; Hwa, Terence

2013-03-01

On hard agar gel, there is insufficient surface hydration for bacteria to swim or swarm. Instead, growth occurs in colonies of close-packed cells, which expand purely due to repulsive interactions: individual bacteria push each other out of the way through the force of their growth. In this way, bacterial colonies represent a new type of ``active'' granular matter. In this study, we investigate the physical, biochemical, and genetic elements that determine the static and dynamic aspects of this mode of bacterial growth for E. coli. We characterize the process of colony expansion empirically, and use discrete and continuum models to examine the extent to which our observations can be explained by the growth characteristics of non-communicating cells, coupled together by physical forces, nutrients, and waste products. Our results challenge the commonly accepted modes of bacterial colony growth and provide insight into sources of growth limitation in crowded bacterial communities.

The Role of RNA in Biological Phase Separations.

PubMed

Fay, Marta M; Anderson, Paul J

2018-05-10

Phase transitions that alter the physical state of ribonucleoprotein particles contribute to the spacial and temporal organization of the densely packed intracellular environment. This allows cells to organize biologically coupled processes as well as respond to environmental stimuli. RNA plays a key role in phase separation events that modulate various aspects of RNA metabolism. Here, we review the role that RNA plays in ribonucleoprotein phase separations. Copyright © 2018 Elsevier Ltd. All rights reserved.

Preparation of hydroxy-PAAm hydrogels for decoupling the effects of mechanotransduction cues.

PubMed

Grevesse, Thomas; Versaevel, Marie; Gabriele, Sylvain

2014-08-28

It is now well established that many cellular functions are regulated by interactions of cells with physicochemical and mechanical cues of their extracellular matrix (ECM) environment. Eukaryotic cells constantly sense their local microenvironment through surface mechanosensors to transduce physical changes of ECM into biochemical signals, and integrate these signals to achieve specific changes in gene expression. Interestingly, physicochemical and mechanical parameters of the ECM can couple with each other to regulate cell fate. Therefore, a key to understanding mechanotransduction is to decouple the relative contribution of ECM cues on cellular functions. Here we present a detailed experimental protocol to rapidly and easily generate biologically relevant hydrogels for the independent tuning of mechanotransduction cues in vitro. We chemically modified polyacrylamide hydrogels (PAAm) to surmount their intrinsically non-adhesive properties by incorporating hydroxyl-functionalized acrylamide monomers during the polymerization. We obtained a novel PAAm hydrogel, called hydroxy-PAAm, which permits immobilization of any desired nature of ECM proteins. The combination of hydroxy-PAAm hydrogels with microcontact printing allows to independently control the morphology of single-cells, the matrix stiffness, the nature and the density of ECM proteins. We provide a simple and rapid method that can be set up in every biology lab to study in vitro cell mechanotransduction processes. We validate this novel two-dimensional platform by conducting experiments on endothelial cells that demonstrate a mechanical coupling between ECM stiffness and the nucleus.

The FAK–Arp2/3 interaction promotes leading edge advance and haptosensing by coupling nascent adhesions to lamellipodia actin

PubMed Central

Swaminathan, Vinay; Fischer, R. S.; Waterman, Clare M.

2016-01-01

Cell migration is initiated in response to biochemical or physical cues in the environment that promote actin-mediated lamellipodial protrusion followed by the formation of nascent integrin adhesions (NAs) within the protrusion to drive leading edge advance. Although FAK is known to be required for cell migration through effects on focal adhesions, its role in NA formation and lamellipodial dynamics is unclear. Live-cell microscopy of FAK−/− cells with expression of phosphorylation deficient or a FERM-domain mutant deficient in Arp2/3 binding revealed a requirement for FAK in promoting the dense formation, transient stabilization, and timely turnover of NA within lamellipodia to couple actin-driven protrusion to adhesion and advance of the leading edge. Phosphorylation on Y397 of FAK promotes dense NA formation but is dispensable for transient NA stabilization and leading edge advance. In contrast, transient NA stabilization and advance of the cell edge requires FAK–Arp2/3 interaction, which promotes Arp2/3 localization to NA and reduces FAK activity. Haptosensing of extracellular matrix (ECM) concentration during migration requires the interaction between FAK and Arp2/3, whereas FAK phosphorylation modulates mechanosensing of ECM stiffness during spreading. Taken together, our results show that mechanistically separable functions of FAK in NA are required for cells to distinguish distinct properties of their environment during migration. PMID:26842895

Coupled thermal, electrical, and fluid flow analyses of AMTEC multitube cell with adiabatic side wall

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

Schock, A.; Or, C.; Noravian, H.

1997-01-01

The paper describes a novel OSC-generated methodology for analyzing the performance of multitube AMTEC (Alkali Metal Thermal-to-Electrical Conversion) cells, which are under development by AMPS (Advanced Modular Power Systems, Inc.) for the Air Force Phillips Laboratory (AFPL) and NASA{close_quote}s Jet Propulsion Laboratory (JPL), for possible application to the Pluto Express and other space missions. The OSC study was supported by the Department of Energy (DOE), and was strongly encouraged by JPL, AFPL, and AMPS. It resulted in an iterative procedure for the coupled solution of the interdependent thermal, electrical, and fluid flow differential and integral equations governing the performance ofmore » AMTEC cells and generators. The paper clarifies the OSC procedure by presenting detailed results of its application to an illustrative example of a converter cell with an adiabatic side wall, including the non-linear axial variation of temperature, pressure, open-circuit voltage, interelectrode voltage, current density, axial current, sodium mass flow, and power density. The next paper in these proceedings describes parametric results obtained by applying the same procedure to variations of the baseline adiabatic converter design, culminating in an OSC-recommended revised cell design. A subsequent paper in these proceedings extends the procedure to analyze a variety of OSC-designed radioisotope-heated generators employing non-adiabatic multitube AMTEC cells. {copyright} {ital 1997 American Institute of Physics.}« less

Preparing CAM-SE for Multi-Tracer Applications: CAM-SE-Cslam

NASA Astrophysics Data System (ADS)

Lauritzen, P. H.; Taylor, M.; Goldhaber, S.

2014-12-01

The NCAR-DOE spectral element (SE) dynamical core comes from the HOMME (High-Order Modeling Environment; Dennis et al., 2012) and it is available in CAM. The CAM-SE dynamical core is designed with intrinsic mimetic properties guaranteeing total energy conservation (to time-truncation errors) and mass-conservation, and has demonstrated excellent scalability on massively parallel compute platforms (Taylor, 2011). For applications involving many tracers such as chemistry and biochemistry modeling, CAM-SE has been found to be significantly more computationally costly than the current "workhorse" model CAM-FV (Finite-Volume; Lin 2004). Hence a multi-tracer efficient scheme, called the CSLAM (Conservative Semi-Lagrangian Multi-tracer; Lauritzen et al., 2011) scheme, has been implemented in the HOMME (Erath et al., 2012). The CSLAM scheme has recently been cast in flux-form in HOMME so that it can be coupled to the SE dynamical core through conventional flux-coupling methods where the SE dynamical core provides background air mass fluxes to CSLAM. Since the CSLAM scheme makes use of a finite-volume gnomonic cubed-sphere grid and hence does not operate on the SE quadrature grid, the capability of running tracer advection, the physical parameterization suite and dynamics on separate grids has been implemented in CAM-SE. The default CAM-SE-CSLAM setup is to run physics on the quasi-equal area CSLAM grid. The capability of running physics on a different grid than the SE dynamical core may provide a more consistent coupling since the physics grid option operates with quasi-equal-area cell average values rather than non-equi-distant grid-point (SE quadrature point) values. Preliminary results on the performance of CAM-SE-CSLAM will be presented.

Integrins, tensegrity, and mechanotransduction.

PubMed

Ingber, D E

1997-06-01

Physical forces, such as those due to gravity, play an important role in tissue development and remodeling. Yet, little is known about how individual cells sense mechanical signals or how they transduce them into a chemical response. Rather than listing the numerous signal pathways that have been found to be sensitive to mechanical stimulation, we need to place potential molecular signaling mechanisms within the context of the entire cell. The model presented is based on the concept that cells use tensegrity architecture to organize their cytoskeleton and stabilize their form. Studies with stick and string tensegrity cell models predict that living cells are hard-wired to respond immediately to external mechanical stresses. This hard-wiring exists in the form of discrete cytoskeletal filament networks that mechanically couple specific cell surface receptors, such as integrins, to nuclear matrix scaffolds and to potential transducing molecules that physically associate with the cytoskeleton. If these signaling molecules do function in a "solid-state", then mechanical stresses may be transduced into biochemical responses through force-dependent changes in cytoskeletal geometry or through local alterations in thermodynamic or kinetic parameters. Changes in cytoskeletal tension (prestress) also may play a role in signal amplification and adaptation. Recent experimental results are described which provide direct support for the tensegrity theory.

Integrins, tensegrity, and mechanotransduction

NASA Technical Reports Server (NTRS)

Ingber, D. E.

1997-01-01

Physical forces, such as those due to gravity, play an important role in tissue development and remodeling. Yet, little is known about how individual cells sense mechanical signals or how they transduce them into a chemical response. Rather than listing the numerous signal pathways that have been found to be sensitive to mechanical stimulation, we need to place potential molecular signaling mechanisms within the context of the entire cell. The model presented is based on the concept that cells use tensegrity architecture to organize their cytoskeleton and stabilize their form. Studies with stick and string tensegrity cell models predict that living cells are hard-wired to respond immediately to external mechanical stresses. This hard-wiring exists in the form of discrete cytoskeletal filament networks that mechanically couple specific cell surface receptors, such as integrins, to nuclear matrix scaffolds and to potential transducing molecules that physically associate with the cytoskeleton. If these signaling molecules do function in a "solid-state", then mechanical stresses may be transduced into biochemical responses through force-dependent changes in cytoskeletal geometry or through local alterations in thermodynamic or kinetic parameters. Changes in cytoskeletal tension (prestress) also may play a role in signal amplification and adaptation. Recent experimental results are described which provide direct support for the tensegrity theory.

Flower Development as an Interplay between Dynamical Physical Fields and Genetic Networks

PubMed Central

Barrio, Rafael Ángel; Hernández-Machado, Aurora; Varea, C.; Romero-Arias, José Roberto; Álvarez-Buylla, Elena

2010-01-01

In this paper we propose a model to describe the mechanisms by which undifferentiated cells attain gene configurations underlying cell fate determination during morphogenesis. Despite the complicated mechanisms that surely intervene in this process, it is clear that the fundamental fact is that cells obtain spatial and temporal information that bias their destiny. Our main hypothesis assumes that there is at least one macroscopic field that breaks the symmetry of space at a given time. This field provides the information required for the process of cell differentiation to occur by being dynamically coupled to a signal transduction mechanism that, in turn, acts directly upon the gene regulatory network (GRN) underlying cell-fate decisions within cells. We illustrate and test our proposal with a GRN model grounded on experimental data for cell fate specification during organ formation in early Arabidopsis thaliana flower development. We show that our model is able to recover the multigene configurations characteristic of sepal, petal, stamen and carpel primordial cells arranged in concentric rings, in a similar pattern to that observed during actual floral organ determination. Such pattern is robust to alterations of the model parameters and simulated failures predict altered spatio-temporal patterns that mimic those described for several mutants. Furthermore, simulated alterations in the physical fields predict a pattern equivalent to that found in Lacandonia schismatica, the only flowering species with central stamens surrounded by carpels. PMID:21048956

Flower development as an interplay between dynamical physical fields and genetic networks.

PubMed

Barrio, Rafael Ángel; Hernández-Machado, Aurora; Varea, C; Romero-Arias, José Roberto; Alvarez-Buylla, Elena

2010-10-27

In this paper we propose a model to describe the mechanisms by which undifferentiated cells attain gene configurations underlying cell fate determination during morphogenesis. Despite the complicated mechanisms that surely intervene in this process, it is clear that the fundamental fact is that cells obtain spatial and temporal information that bias their destiny. Our main hypothesis assumes that there is at least one macroscopic field that breaks the symmetry of space at a given time. This field provides the information required for the process of cell differentiation to occur by being dynamically coupled to a signal transduction mechanism that, in turn, acts directly upon the gene regulatory network (GRN) underlying cell-fate decisions within cells. We illustrate and test our proposal with a GRN model grounded on experimental data for cell fate specification during organ formation in early Arabidopsis thaliana flower development. We show that our model is able to recover the multigene configurations characteristic of sepal, petal, stamen and carpel primordial cells arranged in concentric rings, in a similar pattern to that observed during actual floral organ determination. Such pattern is robust to alterations of the model parameters and simulated failures predict altered spatio-temporal patterns that mimic those described for several mutants. Furthermore, simulated alterations in the physical fields predict a pattern equivalent to that found in Lacandonia schismatica, the only flowering species with central stamens surrounded by carpels.

Synergistic effect of defined artificial extracellular matrices and pulsed electric fields on osteogenic differentiation of human MSCs.

PubMed

Hess, Ricarda; Jaeschke, Anna; Neubert, Holger; Hintze, Vera; Moeller, Stephanie; Schnabelrauch, Matthias; Wiesmann, Hans-Peter; Hart, David A; Scharnweber, Dieter

2012-12-01

In vivo, bone formation is a complex, tightly regulated process, influenced by multiple biochemical and physical factors. To develop a vital bone tissue engineering construct, all of these individual components have to be considered and integrated to gain an in vivo-like stimulation of target cells. The purpose of the present studies was to investigate the synergistic role of defined biochemical and physical microenvironments with respect to osteogenic differentiation of human mesenchymal stem cells (MSCs). Biochemical microenvironments have been designed using artificial extracellular matrices (aECMs), containing collagen I (coll) and glycosaminoglycans (GAGs) like chondroitin sulfate (CS), or a high-sulfated hyaluronan derivative (sHya), formulated as coatings on three-dimensional poly(caprolactone-co-lactide) (PCL) scaffolds. As part of the physical microenvironment, cells were exposed to pulsed electric fields via transformer-like coupling (TC). Results showed that aECM containing sHya enhanced osteogenic differentiation represented by increases in ALP activity and gene-expression (RT-qPCR) of several bone-related proteins (RUNX-2, ALP, OPN). Electric field stimulation alone did not influence cell proliferation, but osteogenic differentiation was enhanced if osteogenic supplements were provided, showing synergistic effects by the combination of sHya and electric fields. These results will improve the understanding of bone regeneration processes and support the development of effective tissue engineered bone constructs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Helping Yourself by Offering Help: Mediators of Expressive Helping in Survivors of Hematopoietic Stem Cell Transplant.

PubMed

Williamson, Timothy J; Stanton, Annette L; Austin, Jane E; Valdimarsdottir, Heiddis B; Wu, Lisa M; Krull, Jennifer L; Rini, Christine M

2017-10-01

A randomized experiment by Rini et al. (Health Psychol. 33(12):1541-1551, 2014) demonstrated that expressive helping, which involves three expressive writing sessions regarding hematopoietic stem cell transplant, followed by one writing session directed toward helping other stem cell transplant recipients, reduced psychological distress and bothersome physical symptoms among stem cell transplant recipients with elevated survivorship problems, relative to a neutral writing control condition. The current study evaluated whether word use reflective of emotional expression, cognitive processing, and change in perspective mediates the effects of expressive helping. The essays of 67 stem cell transplant recipients with high survivorship problems were analyzed with Linguistic Inquiry and Word Count. Multiple mediation modeling was used to test the hypothesized mechanisms of expressive helping on distress and bothersome physical symptoms. Relative to the control condition, expressive helping produced significant reductions in psychological distress and marginal reductions in physical symptom bother in the analyzed subset of participants from the parent study. Results indicated that positive emotion word use significantly mediated effects of expressive helping on reduced distress, but only for participants who used average (compared to above or below average) rates of negative emotion words. Cognitive processing and change in perspective did not significantly mediate benefits of expressive helping. Expressive helping carried its positive effects on distress through participants' higher expression of positive emotions when coupled with moderate rates of negative emotions. Findings highlight the benefit of expressing both positive and negative emotions in stressful situations.

Intact vinculin protein is required for control of cell shape, cell mechanics, and rac-dependent lamellipodia formation

NASA Technical Reports Server (NTRS)

Goldmann, Wolfgang H.; Ingber, Donald E.

2002-01-01

Studies were carried out using vinculin-deficient F9 embryonic carcinoma (gamma229) cells to analyze the relationship between structure and function within the focal adhesion protein vinculin, in the context of control of cell shape, cell mechanics, and movement. Atomic force microscopy studies revealed that transfection of the head (aa 1-821) or tail (aa 811-1066) domain of vinculin, alone or together, was unable to fully reverse the decrease in cell stiffness, spreading, and lamellipodia formation caused by vinculin deficiency. In contrast, replacement with intact vinculin completely restored normal cell mechanics and spreading regardless of whether its tyrosine phosphorylation site was deleted. Constitutively active rac also only induced extension of lamellipodia when microinjected into cells that expressed intact vinculin protein. These data indicate that vinculin's ability to physically couple integrins to the cytoskeleton, to mechanically stabilize cell shape, and to support rac-dependent lamellipodia formation all appear to depend on its intact three-dimensional structure.

Streptavidin mutants

DOEpatents

Sano, Takeshi; Cantor, Charles R.; Vajda, Sandor; Reznik, Gabriel O.; Smith, Cassandra L.; Pandori, Mark W.

2000-01-01

The present invention relates to streptavidin proteins and peptides having a altered physical properties such as an increased stability or increased or decreased affinity for binding biotin. The invention also relates to methods for the detection, identification, separation and isolation of targets using streptavidin proteins or peptides. Streptavidin with increased or reduced affinity allows for the use of the streptavidin-biotin coupling systems for detection and isolation systems wherein it is necessary to remove of one or the other of the binding partners. Such systems are useful for the purification of functional proteins and viable cells. The invention also relates to nucleic acids which encode these streptavidin proteins and peptides and to recombinant cells such as bacteria, yeast and mammalian cells which contain these nucleic acids.

A Simple BODIPY-Based Viscosity Probe for Imaging of Cellular Viscosity in Live Cells

PubMed Central

Su, Dongdong; Teoh, Chai Lean; Gao, Nengyue; Xu, Qing-Hua; Chang, Young-Tae

2016-01-01

Intracellular viscosity is a fundamental physical parameter that indicates the functioning of cells. In this work, we developed a simple boron-dipyrromethene (BODIPY)-based probe, BTV, for cellular mitochondria viscosity imaging by coupling a simple BODIPY rotor with a mitochondria-targeting unit. The BTV exhibited a significant fluorescence intensity enhancement of more than 100-fold as the solvent viscosity increased. Also, the probe showed a direct linear relationship between the fluorescence lifetime and the media viscosity, which makes it possible to trace the change of the medium viscosity. Furthermore, it was demonstrated that BTV could achieve practical applicability in the monitoring of mitochondrial viscosity changes in live cells through fluorescence lifetime imaging microscopy (FLIM). PMID:27589762

A Simple BODIPY-Based Viscosity Probe for Imaging of Cellular Viscosity in Live Cells.

PubMed

Su, Dongdong; Teoh, Chai Lean; Gao, Nengyue; Xu, Qing-Hua; Chang, Young-Tae

2016-08-31

Intracellular viscosity is a fundamental physical parameter that indicates the functioning of cells. In this work, we developed a simple boron-dipyrromethene (BODIPY)-based probe, BTV, for cellular mitochondria viscosity imaging by coupling a simple BODIPY rotor with a mitochondria-targeting unit. The BTV exhibited a significant fluorescence intensity enhancement of more than 100-fold as the solvent viscosity increased. Also, the probe showed a direct linear relationship between the fluorescence lifetime and the media viscosity, which makes it possible to trace the change of the medium viscosity. Furthermore, it was demonstrated that BTV could achieve practical applicability in the monitoring of mitochondrial viscosity changes in live cells through fluorescence lifetime imaging microscopy (FLIM).

Collisional Thermalization in Strongly Coupled Ultracold Neutral Plasmas

DTIC Science & Technology

2017-01-25

Beaumont, TX (4/16). “Studying Strongly Coupled Systems with Ultracold Plasmas," Department of Physics and Astronomy Colloquium, University of South...Alabama, Mobile, AL (11/15). “Collective Modes and Correlations in Strongly Coupled Ultracold Plasmas," Department of Physics and Astronomy

Amplified effect of Brownian motion in bacterial near-surface swimming

PubMed Central

Li, Guanglai; Tam, Lick-Kong; Tang, Jay X.

2008-01-01

Brownian motion influences bacterial swimming by randomizing displacement and direction. Here, we report that the influence of Brownian motion is amplified when it is coupled to hydrodynamic interaction. We examine swimming trajectories of the singly flagellated bacterium Caulobacter crescentus near a glass surface with total internal reflection fluorescence microscopy and observe large fluctuations over time in the distance of the cell from the solid surface caused by Brownian motion. The observation is compared with computer simulation based on analysis of relevant physical factors, including electrostatics, van der Waals force, hydrodynamics, and Brownian motion. The simulation reproduces the experimental findings and reveals contribution from fluctuations of the cell orientation beyond the resolution of present observation. Coupled with hydrodynamic interaction between the bacterium and the boundary surface, the fluctuations in distance and orientation subsequently lead to variation of the swimming speed and local radius of curvature of swimming trajectory. These results shed light on the fundamental roles of Brownian motion in microbial motility, nutrient uptake, and adhesion. PMID:19015518

A finite difference method for a coupled model of wave propagation in poroelastic materials.

PubMed

Zhang, Yang; Song, Limin; Deffenbaugh, Max; Toksöz, M Nafi

2010-05-01

A computational method for time-domain multi-physics simulation of wave propagation in a poroelastic medium is presented. The medium is composed of an elastic matrix saturated with a Newtonian fluid, and the method operates on a digital representation of the medium where a distinct material phase and properties are specified at each volume cell. The dynamic response to an acoustic excitation is modeled mathematically with a coupled system of equations: elastic wave equation in the solid matrix and linearized Navier-Stokes equation in the fluid. Implementation of the solution is simplified by introducing a common numerical form for both solid and fluid cells and using a rotated-staggered-grid which allows stable solutions without explicitly handling the fluid-solid boundary conditions. A stability analysis is presented which can be used to select gridding and time step size as a function of material properties. The numerical results are shown to agree with the analytical solution for an idealized porous medium of periodically alternating solid and fluid layers.

Physical impaction injury effects on bacterial cells during spread plating influenced by cell characteristics of the organisms.

PubMed

Thomas, P; Mujawar, M M; Sekhar, A C; Upreti, R

2014-04-01

To understand the factors that contribute to the variations in colony-forming units (CFU) in different bacteria during spread plating. Employing a mix culture of vegetative cells of ten organisms varying in cell characteristics (Gram reaction, cell shape and cell size), spread plating to the extent of just drying the agar surface (50-60 s) was tested in comparison with the alternate spotting-and-tilt-spreading (SATS) approach where 100 μl inoculum was distributed by mere tilting of plate after spotting as 20-25 microdrops. The former imparted a significant reduction in CFU by 20% over the spreader-independent SATS approach. Extending the testing to single organisms, Gram-negative proteobacteria with relatively larger cells (Escherichia, Enterobacter, Agrobacterium, Ralstonia, Pantoea, Pseudomonas and Sphingomonas spp.) showed significant CFU reduction with spread plating except for slow-growing Methylobacterium sp., while those with small rods (Xenophilus sp.) and cocci (Acinetobacter sp.) were less affected. Among Gram-positive nonspore formers, Staphylococcus epidermidis showed significant CFU reduction while Staphylococcus haemolyticus and actinobacteria (Microbacterium, Cellulosimicrobium and Brachybacterium spp.) with small rods/cocci were unaffected. Vegetative cells of Bacillus pumilus and B. subtilis were generally unaffected while others with larger rods (B. thuringiensis, Brevibacillus, Lysinibacillus and Paenibacillus spp.) were significantly affected. A simulated plating study coupled with live-dead bacterial staining endorsed the chances of cell disruption with spreader impaction in afflicted organisms. Significant reduction in CFU could occur during spread plating due to physical impaction injury to bacterial cells depending on the spreader usage and the variable effects on different organisms are determined by Gram reaction, cell size and cell shape. The inoculum spreader could impart physical disruption of vegetative cells against a hard surface. Possibility of CFU reduction in sensitive organisms and the skewed selection of hardier organisms during spread plating, and the recommendation of SATS as an easier and safer alternative for CFU enumerations. © 2013 The Society for Applied Microbiology.

Tinamit: Making coupled system dynamics models accessible to stakeholders

NASA Astrophysics Data System (ADS)

Malard, Julien; Inam Baig, Azhar; Rojas Díaz, Marcela; Hassanzadeh, Elmira; Adamowski, Jan; Tuy, Héctor; Melgar-Quiñonez, Hugo

2017-04-01

Model coupling is increasingly used as a method of combining the best of two models when representing socio-environmental systems, though barriers to successful model adoption by stakeholders are particularly present with the use of coupled models, due to their high complexity and typically low implementation flexibility. Coupled system dynamics - physically-based modelling is a promising method to improve stakeholder participation in environmental modelling while retaining a high level of complexity for physical process representation, as the system dynamics components are readily understandable and can be built by stakeholders themselves. However, this method is not without limitations in practice, including 1) inflexible and complicated coupling methods, 2) difficult model maintenance after the end of the project, and 3) a wide variety of end-user cultures and languages. We have developed the open-source Python-language software tool Tinamit to overcome some of these limitations to the adoption of stakeholder-based coupled system dynamics - physically-based modelling. The software is unique in 1) its inclusion of both a graphical user interface (GUI) and a library of available commands (API) that allow users with little or no coding abilities to rapidly, effectively, and flexibly couple models, 2) its multilingual support for the GUI, allowing users to couple models in their preferred language (and to add new languages as necessary for their community work), and 3) its modular structure allowing for very easy model coupling and modification without the direct use of code, and to which programming-savvy users can easily add support for new types of physically-based models. We discuss how the use of Tinamit for model coupling can greatly increase the accessibility of coupled models to stakeholders, using an example of a stakeholder-built system dynamics model of soil salinity issues in Pakistan coupled with the physically-based soil salinity and water flow model SAHYSMOD. Different socioeconomic and environmental policies for soil salinity remediation are tested within the coupled model, allowing for the identification of the most efficient actions from an environmental and a farmer economy standpoint while taking into account the complex feedbacks between socioeconomics and the physical environment.

The Effects of Partnered Exercise on Physical Intimacy in Couples Coping with Prostate Cancer

PubMed Central

Lyons, Karen S.; Winters-Stone, Kerri M.; Bennett, Jill A.; Beer, Tomasz M.

2015-01-01

Objective The study examined whether couples coping with prostate cancer participating in a partnered exercise program - Exercising Together (ET) - experienced higher levels of physical intimacy (i.e., affectionate & sexual behavior) than couples in a usual care (UC) control group. Method Men and their wives (n=64 couples) were randomly assigned to either the ET or UC group. Couples in the ET group engaged in partnered strength-training twice weekly for six months. Multilevel modeling was used to explore the effects of ET on husband and wife engagement in both affectionate and sexual behaviors over time. Results Controlling for relationship quality, wives in ET showed significant increases in engagement in affectionate behaviors compared to wives in UC. No intervention effects were found for husbands. Conclusion Couple-based approaches to physical intimacy, after a cancer diagnosis, that facilitate collaborative engagement in non-sexual physical activities for the couple have potential to be effective for wives. More research is needed in this area to determine couples most amenable to such exercise strategies, optimal timing in the cancer trajectory, and the benefits of combining partnered exercise with more traditional relationship-focused strategies. PMID:26462060

Mechanical continuity and reversible chromosome disassembly within intact genomes removed from living cells

NASA Technical Reports Server (NTRS)

Maniotis, A. J.; Bojanowski, K.; Ingber, D. E.

1997-01-01

Chromatin is thought to be structurally discontinuous because it is packaged into morphologically distinct chromosomes that appear physically isolated from one another in metaphase preparations used for cytogenetic studies. However, analysis of chromosome positioning and movement suggest that different chromosomes often behave as if they were physically connected in interphase as well as mitosis. To address this paradox directly, we used a microsurgical technique to physically remove nucleoplasm or chromosomes from living cells under isotonic conditions. Using this approach, we found that pulling a single nucleolus or chromosome out from interphase or mitotic cells resulted in sequential removal of the remaining nucleoli and chromosomes, interconnected by a continuous elastic thread. Enzymatic treatments of interphase nucleoplasm and chromosome chains held under tension revealed that mechanical continuity within the chromatin was mediated by elements sensitive to DNase or micrococcal nuclease, but not RNases, formamide at high temperature, or proteases. In contrast, mechanical coupling between mitotic chromosomes and the surrounding cytoplasm appeared to be mediated by gelsolin-sensitive microfilaments. Furthermore, when ion concentrations were raised and lowered, both the chromosomes and the interconnecting strands underwent multiple rounds of decondensation and recondensation. As a result of these dynamic structural alterations, the mitotic chains also became sensitive to disruption by restriction enzymes. Ion-induced chromosome decondensation could be blocked by treatment with DNA binding dyes, agents that reduce protein disulfide linkages within nuclear matrix, or an antibody directed against histones. Fully decondensed chromatin strands also could be induced to recondense into chromosomes with pre-existing size, shape, number, and position by adding anti-histone antibodies. Conversely, removal of histones by proteolysis or heparin treatment produced chromosome decondensation which could be reversed by addition of histone H1, but not histones H2b or H3. These data suggest that DNA, its associated protein scaffolds, and surrounding cytoskeletal networks function as a structurally-unified system. Mechanical coupling within the nucleoplasm may coordinate dynamic alterations in chromatin structure, guide chromosome movement, and ensure fidelity of mitosis.

Matrix Rigidity Activates Wnt Signaling through Down-regulation of Dickkopf-1 Protein*

PubMed Central

Barbolina, Maria V.; Liu, Yiuying; Gurler, Hilal; Kim, Mijung; Kajdacsy-Balla, Andre A.; Rooper, Lisa; Shepard, Jaclyn; Weiss, Michael; Shea, Lonnie D.; Penzes, Peter; Ravosa, Matthew J.; Stack, M. Sharon

2013-01-01

Cells respond to changes in the physical properties of the extracellular matrix with altered behavior and gene expression, highlighting the important role of the microenvironment in the regulation of cell function. In the current study, culture of epithelial ovarian cancer cells on three-dimensional collagen I gels led to a dramatic down-regulation of the Wnt signaling inhibitor dickkopf-1 with a concomitant increase in nuclear β-catenin and enhanced β-catenin/Tcf/Lef transcriptional activity. Increased three-dimensional collagen gel invasion was accompanied by transcriptional up-regulation of the membrane-tethered collagenase membrane type 1 matrix metalloproteinase, and an inverse relationship between dickkopf-1 and membrane type 1 matrix metalloproteinase was observed in human epithelial ovarian cancer specimens. Similar results were obtained in other tissue-invasive cells such as vascular endothelial cells, suggesting a novel mechanism for functional coupling of matrix adhesion with Wnt signaling. PMID:23152495

Matrix rigidity activates Wnt signaling through down-regulation of Dickkopf-1 protein.

PubMed

Barbolina, Maria V; Liu, Yiuying; Gurler, Hilal; Kim, Mijung; Kajdacsy-Balla, Andre A; Rooper, Lisa; Shepard, Jaclyn; Weiss, Michael; Shea, Lonnie D; Penzes, Peter; Ravosa, Matthew J; Stack, M Sharon

2013-01-04

Cells respond to changes in the physical properties of the extracellular matrix with altered behavior and gene expression, highlighting the important role of the microenvironment in the regulation of cell function. In the current study, culture of epithelial ovarian cancer cells on three-dimensional collagen I gels led to a dramatic down-regulation of the Wnt signaling inhibitor dickkopf-1 with a concomitant increase in nuclear β-catenin and enhanced β-catenin/Tcf/Lef transcriptional activity. Increased three-dimensional collagen gel invasion was accompanied by transcriptional up-regulation of the membrane-tethered collagenase membrane type 1 matrix metalloproteinase, and an inverse relationship between dickkopf-1 and membrane type 1 matrix metalloproteinase was observed in human epithelial ovarian cancer specimens. Similar results were obtained in other tissue-invasive cells such as vascular endothelial cells, suggesting a novel mechanism for functional coupling of matrix adhesion with Wnt signaling.

Comparison of the function of exchange in couples of similar and differing physical attractiveness.

PubMed

Murstein, Bernard I; Reif, Jeffrey A; Syracuse-Siewert, Gia

2002-08-01

Couples (22 young, married, 18 young unmarried) completed the Exchange Orientation Scale, which measures how much individuals believe equality of exchange should characterize their social relationships, as well as the Norman Personality Trait Scale, which gives measures for the self and ideal-self. Couples also rated their sexual satisfaction, their partners' physical attractiveness, their own attractiveness, and had their photographs evaluated for attractiveness by disinterested raters. Subgroups were formed of physically attractive couples, couples in which the members were of disparate attractiveness, and couples in which the individuals perceived themselves as equal to their partners in attractiveness or as inferior. In accordance with exchange theory, the hypotheses were (1) unmarried men would show higher exchange scores than married men, (2) attractive men in disparately attractive couples would show greater exchange scores than attractive men in both-attractive couples, (3) attractive members of disparately attractive couples would possess lower self-acceptance and (4) experience greater sexual satisfaction than attractive members of both-attractive couples. Results supported all hypotheses in varying extents.

Fluorescence recovery after photobleaching reveals regulation and distribution of connexin36 gap junction coupling within mouse islets of Langerhans

PubMed Central

Farnsworth, Nikki L; Hemmati, Alireza; Pozzoli, Marina; Benninger, Richard K P

2014-01-01

The pancreatic islets are central to the maintenance of glucose homeostasis through insulin secretion. Glucose-stimulated insulin secretion is tightly linked to electrical activity in β cells within the islet. Gap junctions, composed of connexin36 (Cx36), form intercellular channels between β cells, synchronizing electrical activity and insulin secretion. Loss of gap junction coupling leads to altered insulin secretion dynamics and disrupted glucose homeostasis. Gap junction coupling is known to be disrupted in mouse models of pre-diabetes. Although approaches to measure gap junction coupling have been devised, they either lack cell specificity, suitable quantification of coupling or spatial resolution, or are invasive. The purpose of this study was to develop fluorescence recovery after photobleaching (FRAP) as a technique to accurately and robustly measure gap junction coupling in the islet. The cationic dye Rhodamine 123 was used with FRAP to quantify dye diffusion between islet β cells as a measure of Cx36 gap junction coupling. Measurements in islets with reduced Cx36 verified the accuracy of this technique in distinguishing between distinct levels of gap junction coupling. Analysis of individual cells revealed that the distribution of coupling across the islet is highly heterogeneous. Analysis of several modulators of gap junction coupling revealed glucose- and cAMP-dependent modulation of gap junction coupling in islets. Finally, FRAP was used to determine cell population specific coupling, where no functional gap junction coupling was observed between α cells and β cells in the islet. The results of this study show FRAP to be a robust technique which provides the cellular resolution to quantify the distribution and regulation of Cx36 gap junction coupling in specific cell populations within the islet. Future studies utilizing this technique may elucidate the role of gap junction coupling in the progression of diabetes and identify mechanisms of gap junction regulation for potential therapies. PMID:25172942

Fluorescence recovery after photobleaching reveals regulation and distribution of connexin36 gap junction coupling within mouse islets of Langerhans.

PubMed

Farnsworth, Nikki L; Hemmati, Alireza; Pozzoli, Marina; Benninger, Richard K P

2014-10-15

The pancreatic islets are central to the maintenance of glucose homeostasis through insulin secretion. Glucose‐stimulated insulin secretion is tightly linked to electrical activity in β cells within the islet. Gap junctions, composed of connexin36 (Cx36), form intercellular channels between β cells, synchronizing electrical activity and insulin secretion. Loss of gap junction coupling leads to altered insulin secretion dynamics and disrupted glucose homeostasis. Gap junction coupling is known to be disrupted in mouse models of pre‐diabetes. Although approaches to measure gap junction coupling have been devised, they either lack cell specificity, suitable quantification of coupling or spatial resolution, or are invasive. The purpose of this study was to develop fluorescence recovery after photobleaching (FRAP) as a technique to accurately and robustly measure gap junction coupling in the islet. The cationic dye Rhodamine 123 was used with FRAP to quantify dye diffusion between islet β cells as a measure of Cx36 gap junction coupling. Measurements in islets with reduced Cx36 verified the accuracy of this technique in distinguishing between distinct levels of gap junction coupling. Analysis of individual cells revealed that the distribution of coupling across the islet is highly heterogeneous. Analysis of several modulators of gap junction coupling revealed glucose‐ and cAMP‐dependent modulation of gap junction coupling in islets. Finally, FRAP was used to determine cell population specific coupling, where no functional gap junction coupling was observed between α cells and β cells in the islet. The results of this study show FRAP to be a robust technique which provides the cellular resolution to quantify the distribution and regulation of Cx36 gap junction coupling in specific cell populations within the islet. Future studies utilizing this technique may elucidate the role of gap junction coupling in the progression of diabetes and identify mechanisms of gap junction regulation for potential therapies.

Electrical coupling between A17 cells enhances reciprocal inhibitory feedback to rod bipolar cells.

PubMed

Elgueta, Claudio; Leroy, Felix; Vielma, Alex H; Schmachtenberg, Oliver; Palacios, Adrian G

2018-02-15

A17 amacrine cells are an important part of the scotopic pathway. Their synaptic varicosities receive glutamatergic inputs from rod bipolar cells (RBC) and release GABA onto the same RBC terminal, forming a reciprocal feedback that shapes RBC depolarization. Here, using patch-clamp recordings, we characterized electrical coupling between A17 cells of the rat retina and report the presence of strongly interconnected and non-coupled A17 cells. In coupled A17 cells, evoked currents preferentially flow out of the cell through GJs and cross-synchronization of presynaptic signals in a pair of A17 cells is correlated to their coupling degree. Moreover, we demonstrate that stimulation of one A17 cell can induce electrical and calcium transients in neighboring A17 cells, thus confirming a functional flow of information through electrical synapses in the A17 coupled network. Finally, blocking GJs caused a strong decrease in the amplitude of the inhibitory feedback onto RBCs. We therefore propose that electrical coupling between A17 cells enhances feedback onto RBCs by synchronizing and facilitating GABA release from inhibitory varicosities surrounding each RBC axon terminal. GJs between A17 cells are therefore critical in shaping the visual flow through the scotopic pathway.

Critical behavior of subcellular density organization during neutrophil activation and migration.

PubMed

Baker-Groberg, Sandra M; Phillips, Kevin G; Healy, Laura D; Itakura, Asako; Porter, Juliana E; Newton, Paul K; Nan, Xiaolin; McCarty, Owen J T

2015-12-01

Physical theories of active matter continue to provide a quantitative understanding of dynamic cellular phenomena, including cell locomotion. Although various investigations of the rheology of cells have identified important viscoelastic and traction force parameters for use in these theoretical approaches, a key variable has remained elusive both in theoretical and experimental approaches: the spatiotemporal behavior of the subcellular density. The evolution of the subcellular density has been qualitatively observed for decades as it provides the source of image contrast in label-free imaging modalities (e.g., differential interference contrast, phase contrast) used to investigate cellular specimens. While these modalities directly visualize cell structure, they do not provide quantitative access to the structures being visualized. We present an established quantitative imaging approach, non-interferometric quantitative phase microscopy, to elucidate the subcellular density dynamics in neutrophils undergoing chemokinesis following uniform bacterial peptide stimulation. Through this approach, we identify a power law dependence of the neutrophil mean density on time with a critical point, suggesting a critical density is required for motility on 2D substrates. Next we elucidate a continuum law relating mean cell density, area, and total mass that is conserved during neutrophil polarization and migration. Together, our approach and quantitative findings will enable investigators to define the physics coupling cytoskeletal dynamics with subcellular density dynamics during cell migration.

Critical behavior of subcellular density organization during neutrophil activation and migration

PubMed Central

Baker-Groberg, Sandra M.; Phillips, Kevin G.; Healy, Laura D.; Itakura, Asako; Porter, Juliana E.; Newton, Paul K.; Nan, Xiaolin; McCarty, Owen J.T.

2015-01-01

Physical theories of active matter continue to provide a quantitative understanding of dynamic cellular phenomena, including cell locomotion. Although various investigations of the rheology of cells have identified important viscoelastic and traction force parameters for use in these theoretical approaches, a key variable has remained elusive both in theoretical and experimental approaches: the spatiotemporal behavior of the subcellular density. The evolution of the subcellular density has been qualitatively observed for decades as it provides the source of image contrast in label-free imaging modalities (e.g., differential interference contrast, phase contrast) used to investigate cellular specimens. While these modalities directly visualize cell structure, they do not provide quantitative access to the structures being visualized. We present an established quantitative imaging approach, non-interferometric quantitative phase microscopy, to elucidate the subcellular density dynamics in neutrophils undergoing chemokinesis following uniform bacterial peptide stimulation. Through this approach, we identify a power law dependence of the neutrophil mean density on time with a critical point, suggesting a critical density is required for motility on 2D substrates. Next we elucidate a continuum law relating mean cell density, area, and total mass that is conserved during neutrophil polarization and migration. Together, our approach and quantitative findings will enable investigators to define the physics coupling cytoskeletal dynamics with subcellular density dynamics during cell migration. PMID:26640599

Emergence of a super-synchronized mobbing state in a large population of coupled chemical oscillators.

PubMed

Ghoshal, Gourab; Muñuzuri, Alberto P; Pérez-Mercader, Juan

2016-01-12

Oscillatory phenomena are ubiquitous in Nature. The ability of a large population of coupled oscillators to synchronize constitutes an important mechanism to express information and establish communication among members. To understand such phenomena, models and experimental realizations of globally coupled oscillators have proven to be invaluable in settings as varied as chemical, biological and physical systems. A variety of rich dynamical behavior has been uncovered, although usually in the context of a single state of synchronization or lack thereof. Through the experimental and numerical study of a large population of discrete chemical oscillators, here we report on the unexpected discovery of a new phenomenon revealing the existence of dynamically distinct synchronized states reflecting different degrees of communication. Specifically, we discover a novel large-amplitude super-synchronized state separated from the conventionally reported synchronized and quiescent states through an unusual sharp jump transition when sampling the strong coupling limit. Our results assume significance for further elucidating globally coherent phenomena, such as in neuropathologies, bacterial cell colonies, social systems and semiconductor lasers.

Emergence of a super-synchronized mobbing state in a large population of coupled chemical oscillators

NASA Astrophysics Data System (ADS)

Ghoshal, Gourab; Muñuzuri, Alberto P.; Pérez-Mercader, Juan

2016-01-01

Oscillatory phenomena are ubiquitous in Nature. The ability of a large population of coupled oscillators to synchronize constitutes an important mechanism to express information and establish communication among members. To understand such phenomena, models and experimental realizations of globally coupled oscillators have proven to be invaluable in settings as varied as chemical, biological and physical systems. A variety of rich dynamical behavior has been uncovered, although usually in the context of a single state of synchronization or lack thereof. Through the experimental and numerical study of a large population of discrete chemical oscillators, here we report on the unexpected discovery of a new phenomenon revealing the existence of dynamically distinct synchronized states reflecting different degrees of communication. Specifically, we discover a novel large-amplitude super-synchronized state separated from the conventionally reported synchronized and quiescent states through an unusual sharp jump transition when sampling the strong coupling limit. Our results assume significance for further elucidating globally coherent phenomena, such as in neuropathologies, bacterial cell colonies, social systems and semiconductor lasers.

Interface- and discontinuity-aware numerical schemes for plasma 3-T radiation diffusion in two and three dimensions

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

Dai, William W., E-mail: dai@lanl.gov; Scannapieco, Anthony J.

2015-11-01

A set of numerical schemes is developed for two- and three-dimensional time-dependent 3-T radiation diffusion equations in systems involving multi-materials. To resolve sub-cell structure, interface reconstruction is implemented within any cell that has more than one material. Therefore, the system of 3-T radiation diffusion equations is solved on two- and three-dimensional polyhedral meshes. The focus of the development is on the fully coupling between radiation and material, the treatment of nonlinearity in the equations, i.e., in the diffusion terms and source terms, treatment of the discontinuity across cell interfaces in material properties, the formulations for both transient and steady states,more » the property for large time steps, and second order accuracy in both space and time. The discontinuity of material properties between different materials is correctly treated based on the governing physics principle for general polyhedral meshes and full nonlinearity. The treatment is exact for arbitrarily strong discontinuity. The scheme is fully nonlinear for the full nonlinearity in the 3-T diffusion equations. Three temperatures are fully coupled and are updated simultaneously. The scheme is general in two and three dimensions on general polyhedral meshes. The features of the scheme are demonstrated through numerical examples for transient problems and steady states. The effects of some simplifications of numerical schemes are also shown through numerical examples, such as linearization, simple average of diffusion coefficient, and approximate treatment for the coupling between radiation and material.« less

A parallel multi-domain solution methodology applied to nonlinear thermal transport problems in nuclear fuel pins

DOE PAGES

Philip, Bobby; Berrill, Mark A.; Allu, Srikanth; ...

2015-01-26

We describe an efficient and nonlinearly consistent parallel solution methodology for solving coupled nonlinear thermal transport problems that occur in nuclear reactor applications over hundreds of individual 3D physical subdomains. Efficiency is obtained by leveraging knowledge of the physical domains, the physics on individual domains, and the couplings between them for preconditioning within a Jacobian Free Newton Krylov method. Details of the computational infrastructure that enabled this work, namely the open source Advanced Multi-Physics (AMP) package developed by the authors are described. The details of verification and validation experiments, and parallel performance analysis in weak and strong scaling studies demonstratingmore » the achieved efficiency of the algorithm are presented. Moreover, numerical experiments demonstrate that the preconditioner developed is independent of the number of fuel subdomains in a fuel rod, which is particularly important when simulating different types of fuel rods. Finally, we demonstrate the power of the coupling methodology by considering problems with couplings between surface and volume physics and coupling of nonlinear thermal transport in fuel rods to an external radiation transport code.« less

Interparticle coupling effect of silver-gold heterodimer to enhance light harvesting in ultrathin perovskite solar cell

NASA Astrophysics Data System (ADS)

Hu, Zhaosheng; Ma, Tingli; Hayase, Shuzi

2018-01-01

Thin perovskite solar cells are under intensive interest since they reduce the amount of absorber layer, especially toxic lead in methylammonium lead iodide (MAPbI3) devices and have wide application in semitransparent and tandem solar cells. However, due to the decrease of the layer thickness, thin perovskite devices with weak light-harvesting have poor performance. Moreover, the performance of plasmonic thin perovskite devices by incorporating noncoupling metal NPs cannot give comparable performance with normal devices. In this perspective, we discuss the implication of employing random silver-gold heterodimers in MAPbI3 solar cells with the aim of establishing some guidelines for the efficient ultrathin perovskite solar cells. This method induces an extraordinarily high light-harvesting for ultrathin perovskite film. And the underlying physical mechanism behind the enhanced absorption is deeply investigated by plasmon hybridization, dipolar-dipolar coupling method and FDTD simulation. We notice that perovskite embedded silver-gold heterodimer overcomes the vanished antibonding plasmon resononse (σ * ) in nonjunction area of gold/silver homodimer. A 150-nm perovskite film with embedded random silver-gold heterodimers with 80 nm size and 25 nm gap distance processes 28.15% absorption enhancement compared to the reference film, which is higher than the reported 10% for gold homodimers. And we also predict a realistic solution-processed, easy, and low-cost fabrication method, which provide a means to realize highly efficient ultrathin perovskite solar cell including other absorber-based photovoltaics.

Bifunctional Carbon-Dot-WS2 Nanorods for Photothermal Therapy and Cell Imaging.

PubMed

Nandi, Sukhendu; Bhunia, Susanta Kumar; Zeiri, Leila; Pour, Maayan; Nachman, Iftach; Raichman, Daniel; Lellouche, Jean-Paul Moshe; Jelinek, Raz

2017-01-18

Multifunctional nanoparticles have attracted significant interest as biomedical vehicles, combining diagnostic, imaging, and therapeutic properties. We describe herein the construction of new nanoparticle conjugates comprising WS 2 nanorods (NRs) coupled to fluorescent carbon dots (C-dots). We show that the WS 2 -C-dot hybrids integrate the unique physical properties of the two species, specifically the photothermal activity of the WS 2 NRs upon irradiation with near-infrared (NIR) light and the excitation-dependent luminescence emission of the C-dots. The WS 2 -C-dot NRs have been shown to be non-cytotoxic and have been successfully employed for multicolour cell imaging and targeted cell killing under NIR irradiation, pointing to their potential utilization as effective therapeutic vehicles. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monopolar fuel cell stack coupled together without use of top or bottom cover plates or tie rods

NASA Technical Reports Server (NTRS)

Narayanan, Sekharipuram R. (Inventor); Valdez, Thomas I. (Inventor)

2009-01-01

A monopolar fuel cell stack comprises a plurality of sealed unit cells coupled together. Each unit cell comprises two outer cathodes adjacent to corresponding membrane electrode assemblies and a center anode plate. An inlet and outlet manifold are coupled to the anode plate and communicate with a channel therein. Fuel flows from the inlet manifold through the channel in contact with the anode plate and flows out through the outlet manifold. The inlet and outlet manifolds are arranged to couple to the inlet and outlet manifolds respectively of an adjacent one of the plurality of unit cells to permit fuel flow in common into all of the inlet manifolds of the plurality of the unit cells when coupled together in a stack and out of all of the outlet manifolds of the plurality of unit cells when coupled together in a stack.

Coupling of lipid membrane elasticity and in-plane dynamics

NASA Astrophysics Data System (ADS)

Tsang, Kuan-Yu; Lai, Yei-Chen; Chiang, Yun-Wei; Chen, Yi-Fan

2017-07-01

Biomembranes exhibit liquid and solid features concomitantly with their in-plane fluidity and elasticity tightly regulated by cells. Here, we present experimental evidence supporting the existence of the dynamics-elasticity correlations for lipid membranes and propose a mechanism involving molecular packing densities to explain them. This paper thereby unifies, at the molecular level, the aspects of the continuum mechanics long used to model the two membrane features. This ultimately may elucidate the universal physical principles governing the cellular phenomena involving biomembranes.

Myo19 ensures symmetric partitioning of mitochondria and coupling of mitochondrial segregation to cell division.

PubMed

Rohn, Jennifer L; Patel, Jigna V; Neumann, Beate; Bulkescher, Jutta; Mchedlishvili, Nunu; McMullan, Rachel C; Quintero, Omar A; Ellenberg, Jan; Baum, Buzz

2014-11-03

During animal cell division, an actin-based ring cleaves the cell into two. Problems with this process can cause chromosome missegregation and defects in cytoplasmic inheritance and the partitioning of organelles, which in turn are associated with human diseases. Although much is known about how chromosome segregation is coupled to cell division, the way organelles coordinate their inheritance during partitioning to daughter cells is less well understood. Here, using a high-content live-imaging small interfering RNA screen, we identify Myosin-XIX (Myo19) as a novel regulator of cell division. Previously, this actin-based motor was shown to control the interphase movement of mitochondria. Our analysis shows that Myo19 is indeed localized to mitochondria and that its silencing leads to defects in the distribution of mitochondria within cells and in mitochondrial partitioning at division. Furthermore, many Myo19 RNAi cells undergo stochastic division failure--a phenotype that can be mimicked using a treatment that blocks mitochondrial fission and rescued by decreasing mitochondrial fusion, implying that mitochondria can physically interfere with cytokinesis. Strikingly, using live imaging we also observe the inappropriate movement of mitochondria to the poles of spindles in cells depleted for Myo19 as they enter anaphase. Since this phenocopies the results of an acute loss of actin filaments in anaphase, these data support a model whereby the Myo19 actin-based motor helps to control mitochondrial movement to ensure their faithful segregation during division. The presence of DNA within mitochondria makes their inheritance an especially important aspect of symmetrical cell division. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Least action and entropy considerations of self-organization in Benard cells

NASA Astrophysics Data System (ADS)

Georgiev, Georgi; Iannacchione, Germano

We study self-organization in complex systems using first principles in physics. Our approach involves the principle of least action and the second law of thermodynamics. In far from equilibrium systems, energy gradients cause internal ordering to facilitate the dissipation of energy in the environment. This internal ordering decreases their internal entropy in order to obey the principle of least action, minimizing the product of time and energy for transport through the system. We are considering the connection between action and entropy decrease inside Benard cells in order to derive some general features of self-organization. We are developing mathematical treatment of this coupling and comparing it to results from experiments and simulations.

Indirect handle on the down-quark Yukawa coupling.

PubMed

Goertz, Florian

2014-12-31

To measure the Yukawa couplings of the up and down quarks, Yu,d, seems to be far beyond the capabilities of current and (near) future experiments in particle physics. By performing a general analysis of the potential misalignment between quark masses and Yukawa couplings, we derive predictions for the magnitude of induced flavor-changing neutral currents (FCNCs), depending on the shift in the physical Yukawa coupling of first-generation quarks. We find that a change of more than 50% in Yd would generically result in ds transitions in conflict with kaon physics. This could already be seen as evidence for a nonvanishing direct coupling of the down quark to the newly discovered Higgs boson. The nonobservation of certain--already well-constrained--processes is thus turned into a powerful indirect measure of otherwise basically unaccessible physical parameters of the effective standard model. Similarly, improvements in limits on FCNCs in the up-type quark sector can lead to valuable information on Yu.

Bacterial Trapping in Porous Media Flows

NASA Astrophysics Data System (ADS)

Dehkharghani, Amin; Waisbord, Nicolas; Dunkel, Jörn; Guasto, Jeffrey

2016-11-01

Swimming bacteria inhabit heterogeneous, microstructured environments that are often characterized by complex, ambient flows. Understanding the physical mechanisms underlying cell transport in these systems is key to controlling important processes such as bioremediation in porous soils and infections in human tissues. We study the transport of swimming bacteria (Bacillus subtilis) in quasi-two-dimensional porous microfluidic channels with a range of periodic microstructures and flow strengths. Measured cell trajectories and the local cell number density reveal the formation of filamentous cell concentration patterns within the porous structures. The local cell densification is maximized at shear rates in the range 1-10 s-1, but widely varies with pore geometry and flow topology. Experimental observations are complemented by Langevin simulations to demonstrate that the filamentous patterns result from a coupling of bacterial motility to the complex flow fields via Jeffery orbits, which effectively 'trap' the bacteria on streamlines. The resulting microscopic heterogeneity observed here suppresses bacterial transport and likely has implications for both mixing and cell nutrient uptake in porous media flows. NSF CBET-1511340.

Investigation of carrier escape and recombination dynamics in GaAsN/GaAs superlattice and resonantly coupled quantum well solar cells

NASA Astrophysics Data System (ADS)

Kharel, Khim; Freundlich, Alexandre

2018-02-01

III-V multijunction devices that incorporate a dilute nitride 1-1.2 eV bottom cell have already demonstrated conversion efficiencies of about 44% under high sunlight concentration (942 Suns). However, the poor minority carrier properties of dilute nitride have, thus far, prevented the full realization of the practical potential for tandem configuration (>40% 1 sun, and >50% at 500X and above). To overcome this shortcoming, our group, over the past years, have focused on dilute nitride-based devices where the degraded minority carrier diffusion length has a minimal impact on the device performance. We have shown that the incorporation of resonantly coupled GaAsN/GaP multi-quantum wells in the intrinsic region of p-i-n GaAs cells allows both a significant sub-GaAs-bandgap photon harvesting while maintaining a high open circuit voltage. Here, in order to gain a better understanding of photo-generated carrier escape and recombination mechanisms in these devices and further optimize the performance, we examine optical and electrical properties of such devices using various characterization techniques such as: photoluminescence (PL), modulated photo-reflectance (PR), photo-current (PC) as well as current-voltage (IV) measurements under dark or illuminated conditions. The temperature dependent analysis enables us to modulate and freezes carrier thermalization phenomena, while simultaneous measurement of photogenerated carrier extraction (SR) and recombination's (PL) as a function of the applied load (bias) enables a close correlation between the evolution of I-V characteristics and the physics at play. Next, typical temperature and bias dependent activation energies reveal interesting details about carrier escape, intra-cells coupling and recombination sequences.

Microfluidics as a functional tool for cell mechanics.

PubMed

Vanapalli, Siva A; Duits, Michel H G; Mugele, Frieder

2009-01-05

Living cells are a fascinating demonstration of nature's most intricate and well-coordinated micromechanical objects. They crawl, spread, contract, and relax-thus performing a multitude of complex mechanical functions. Alternatively, they also respond to physical and chemical cues that lead to remodeling of the cytoskeleton. To understand this intricate coupling between mechanical properties, mechanical function and force-induced biochemical signaling requires tools that are capable of both controlling and manipulating the cell microenvironment and measuring the resulting mechanical response. In this review, the power of microfluidics as a functional tool for research in cell mechanics is highlighted. In particular, current literature is discussed to show that microfluidics powered by soft lithographic techniques offers the following capabilities that are of significance for understanding the mechanical behavior of cells: (i) Microfluidics enables the creation of in vitro models of physiological environments in which cell mechanics can be probed. (ii) Microfluidics is an excellent means to deliver physical cues that affect cell mechanics, such as cell shape, fluid flow, substrate topography, and stiffness. (iii) Microfluidics can also expose cells to chemical cues, such as growth factors and drugs, which alter their mechanical behavior. Moreover, these chemical cues can be delivered either at the whole cell or subcellular level. (iv) Microfluidic devices offer the possibility of measuring the intrinsic mechanical properties of cells in a high throughput fashion. (v) Finally, microfluidic methods provide exquisite control over drop size, generation, and manipulation. As a result, droplets are being increasingly used to control the physicochemical environment of cells and as biomimetic analogs of living cells. These powerful attributes of microfluidics should further stimulate novel means of investigating the link between physicochemical cues and the biomechanical response of cells. Insights from such studies will have implications in areas such as drug delivery, medicine, tissue engineering, and biomedical diagnostics.

Novel instrument for characterizing comprehensive physical properties under multi-mechanical loads and multi-physical field coupling conditions

NASA Astrophysics Data System (ADS)

Liu, Changyi; Zhao, Hongwei; Ma, Zhichao; Qiao, Yuansen; Hong, Kun; Ren, Zhuang; Zhang, Jianhai; Pei, Yongmao; Ren, Luquan

2018-02-01

Functional materials represented by ferromagnetics and ferroelectrics are widely used in advanced sensor and precision actuation due to their special characterization under coupling interactions of complex loads and external physical fields. However, the conventional devices for material characterization can only provide a limited type of loads and physical fields and cannot simulate the actual service conditions of materials. A multi-field coupling instrument for characterization has been designed and implemented to overcome this barrier and measure the comprehensive physical properties under complex service conditions. The testing forms include tension, compression, bending, torsion, and fatigue in mechanical loads, as well as different external physical fields, including electric, magnetic, and thermal fields. In order to offer a variety of information to reveal mechanical damage or deformation forms, a series of measurement methods at the microscale are integrated with the instrument including an indentation unit and in situ microimaging module. Finally, several coupling experiments which cover all the loading and measurement functions of the instrument have been implemented. The results illustrate the functions and characteristics of the instrument and then reveal the variety in mechanical and electromagnetic properties of the piezoelectric transducer ceramic, TbDyFe alloy, and carbon fiber reinforced polymer under coupling conditions.

Coupled Pendulums: A Physical System for Laboratory Investigations at Upper Secondary School

ERIC Educational Resources Information Center

Picciarelli, Vittorio; Stella, Rosa

2010-01-01

The topic of coupled oscillations is rich in physical content which is both interesting and complex. The study of the time evolution of coupled oscillator systems involves a mathematical formalization beyond the level of the upper secondary school student's competence. Here, we present an original approach, suitable even for secondary students, to…

Multidrug efflux transporter activity in sea urchin embryos:Does localization provide a diffusive advantage?

NASA Astrophysics Data System (ADS)

Song, Xianfeng; Setayeshgar, Sima; Cole, Bryan; Hamdoun, Amro; Epel, David

2008-03-01

Experiments have shown upregulation of multidrug efflux transporter activity approximately 30 min after fertilization in the sea urchin embryo [1]. These ATP-hydrolyzing transporter proteins pump moderately hydrophobic molecules out of the cell and represent the cell's first line of defense againstexogenous toxins. It has also been shown that transporters are moved in vesicles along microfilaments and localized to tips of microvilli prior to activation. We have constructed a geometrically realistic model of the embryo, including microvilli, to explore the functional role of this localization in the efficient elimination of toxins from the standpoint of diffusion. We compute diffusion of toxins in extracellular, membrane and intracellular spaces coupled with transporter activity, using experimentally derived values for physical parameters. For transporters uniformly distributed along microvilli and tip-localized transporters we compare regions in parameter space where each distribution provides diffusive advantage, and comment on the physically expected conditions. [1] A. M. Hamdoun, G. N. Cherr, T. A. Roepke and D. Epel, Developmental Biology 276 452 (2004).

Slot-coupled CW standing wave accelerating cavity

DOEpatents

Wang, Shaoheng; Rimmer, Robert; Wang, Haipeng

2017-05-16

A slot-coupled CW standing wave multi-cell accelerating cavity. To achieve high efficiency graded beta acceleration, each cell in the multi-cell cavity may include different cell lengths. Alternatively, to achieve high efficiency with acceleration for particles with beta equal to 1, each cell in the multi-cell cavity may include the same cell design. Coupling between the cells is achieved with a plurality of axially aligned kidney-shaped slots on the wall between cells. The slot-coupling method makes the design very compact. The shape of the cell, including the slots and the cone, are optimized to maximize the power efficiency and minimize the peak power density on the surface. The slots are non-resonant, thereby enabling shorter slots and less power loss.

Myocardial Ca2+ handling and cell-to-cell coupling, key factors in prevention of sudden cardiac death.

PubMed

Tribulova, Narcis; Seki, Shingo; Radosinska, Jana; Kaplan, Peter; Babusikova, Eva; Knezl, Vladimir; Mochizuki, Seibu

2009-12-01

Using whole-heart preparations, we tested our hypothesis that Ca(2+) handling is closely related to cell-to-cell coupling at the gap junctions and that both are critical for the development and particularly the termination of ventricular fibrillation (VF) and hence the prevention of sudden arrhythmic death. Intracellular free calcium concentration ([Ca(2+)](i)), ECG, and left ventricular pressure were continuously monitored in isolated guinea pig hearts before and during development of low K(+)-induced sustained VF and during its conversion into sinus rhythm facilitated by stobadine. We also examined myocardial ultrastructure to detect cell-to-cell coupling alterations. We demonstrated that VF occurrence was preceded by a 55.9% +/- 6.2% increase in diastolic [Ca(2+)](i), which was associated with subcellular alterations indicating Ca(2+) overload of the cardiomyocytes and disorders in coupling among the cells. Moreover, VF itself further increased [Ca(2+)](i) by 58.2% +/- 3.4% and deteriorated subcellular and cell-to-cell coupling abnormalities that were heterogeneously distributed throughout the myocardium. In contrast, termination of VF and its conversion into sinus rhythm was marked by restoration of basal [Ca(2+)](i), resulting in recovery of intercellular coupling linked with synchronous contraction. Furthermore, we have shown that hearts exhibiting lower SERCA2a (sarcoplasmic reticulum Ca(2+)-ATPase) activity and abnormal intercellular coupling (as in older guinea pigs) are more prone to develop Ca(2+) overload associated with cell-to-cell uncoupling than hearts with higher SERCA2a activity (as in young guinea pigs). Consequently, young animals are better able to terminate VF spontaneously. These findings indicate the crucial role of Ca(2+) handling in relation to cell-to-cell coupling in both the occurrence and termination of malignant arrhythmia.

Endocannabinoid Release Modulates Electrical Coupling between CCK Cells Connected via Chemical and Electrical Synapses in CA1

PubMed Central

Iball, Jonathan; Ali, Afia B.

2011-01-01

Electrical coupling between some subclasses of interneurons is thought to promote coordinated firing that generates rhythmic synchronous activity in cortical regions. Synaptic activity of cholecystokinin (CCK) interneurons which co-express cannabinoid type-1 (CB1) receptors are powerful modulators of network activity via the actions of endocannabinoids. We investigated the modulatory actions of endocannabinoids between chemically and electrically connected synapses of CCK cells using paired whole-cell recordings combined with biocytin and double immunofluorescence labeling in acute slices of rat hippocampus at P18–20 days. CA1 stratum radiatum CCK Schaffer collateral-associated cells were coupled electrically with each other as well as CCK basket cells and CCK cells with axonal projections expanding to dentate gyrus. Approximately 50% of electrically coupled cells received facilitating, asynchronously released inhibitory postsynaptic potential (IPSPs) that curtailed the steady-state coupling coefficient by 57%. Tonic CB1 receptor activity which reduces inhibition enhanced electrical coupling between cells that were connected via chemical and electrical synapses. Blocking CB1 receptors with antagonist, AM-251 (5 μM) resulted in the synchronized release of larger IPSPs and this enhanced inhibition further reduced the steady-state coupling coefficient by 85%. Depolarization induced suppression of inhibition (DSI), maintained the asynchronicity of IPSP latency, but reduced IPSP amplitudes by 95% and enhanced the steady-state coupling coefficient by 104% and IPSP duration by 200%. However, DSI did not did not enhance electrical coupling at purely electrical synapses. These data suggest that different morphological subclasses of CCK interneurons are interconnected via gap junctions. The synergy between the chemical and electrical coupling between CCK cells probably plays a role in activity-dependent endocannabinoid modulation of rhythmic synchronization. PMID:22125513

A System for Modelling Cell–Cell Interactions during Plant Morphogenesis

PubMed Central

Dupuy, Lionel; Mackenzie, Jonathan; Rudge, Tim; Haseloff, Jim

2008-01-01

Background and aims During the development of multicellular organisms, cells are capable of interacting with each other through a range of biological and physical mechanisms. A description of these networks of cell–cell interactions is essential for an understanding of how cellular activity is co-ordinated in regionalized functional entities such as tissues or organs. The difficulty of experimenting on living tissues has been a major limitation to describing such systems, and computer modelling appears particularly helpful to characterize the behaviour of multicellular systems. The experimental difficulties inherent to the multitude of parallel interactions that underlie cellular morphogenesis have led to the need for computer models. Methods A new generic model of plant cellular morphogenesis is described that expresses interactions amongst cellular entities explicitly: the plant is described as a multi-scale structure, and interactions between distinct entities is established through a topological neighbourhood. Tissues are represented as 2D biphasic systems where the cell wall responds to turgor pressure through a viscous yielding of the cell wall. Key Results This principle was used in the development of the CellModeller software, a generic tool dedicated to the analysis and modelling of plant morphogenesis. The system was applied to three contrasting study cases illustrating genetic, hormonal and mechanical factors involved in plant morphogenesis. Conclusions Plant morphogenesis is fundamentally a cellular process and the CellModeller software, through its underlying generic model, provides an advanced research tool to analyse coupled physical and biological morphogenetic mechanisms. PMID:17921524

Coupling mechanism in the gate and oscillator model of the SCN

NASA Astrophysics Data System (ADS)

Li, Ying; Liu, Zengrong

2016-09-01

In mammals, the suprachiasmatic nucleus (SCN) of the hypothalamus is considered as the master circadian pacemaker. The SCN is divided into two subgroups of gate and oscillator cells: the ventrolateral (VL) neurons, which receive the periodic light-dark (LD) signal, and the dorsomedial (DM) neurons, which are coupled to the VL cells. The fundamental question is how the individual cellular oscillators, expressing a wide range of periods, interact and assemble to create an integrated pacemaker that can govern behavioral and physiological rhythmicity and be reset by environmental light. The key is that the heterogeneous network formed by the cellular clocks within the SCN must synchronize to maintain timekeeping activity. Based on the structural and functional heterogeneity of the SCN, the authors bring forward a mathematical model including gate cells and oscillator cells with a wide range of periods. The gate neurons offer daily injection to oscillator neurons and the activation of gate is determined by the output of the oscillator neurons. In this model, the authors consider two kinds of coupling: interior coupling among the oscillator cells and exterior coupling from the gate cells to the oscillator cells. The authors mainly analyze the combined effects of these two kinds of coupling on the entrainment of the oscillator cells in the DM part. It is found that the interior coupling is conducive to entrainment, but a stronger coupling is not beneficial to entrainment. The gate mechanism in exterior coupling is more propitious to entrainment than continuous coupling. This study helps to understand collective circadian rhythm in the mammals.

Investigation of marine stratocumulus under coupled and decoupled conditions over the arm Azores site

NASA Astrophysics Data System (ADS)

Schwantes, Adam Christopher

Stratocumuli are a type of low clouds composed of individual convective elements that together form a continuous layer of clouds. Stratocumuli cover large regions of the Earth's surface, which make them important components in the Earth's radiation budget. Stratocumuli strongly reflect solar shortwave radiation, while weakly affecting outgoing longwave radiation. This leads to a strong radiative cooling effect that affects the Earth's radiation budget. Therefore it is important to investigate the mechanisms that affect the longevity of stratocumuli, so that their impact on the Earth's radiation budget can be fully understood. One mechanism that is currently being studied as influencing the lifetime of such cloud layers is boundary layer/surface coupling. It has been shown than in some regions (i.e. the west coast of South America) stratocumuli tend to break up when the boundary layer is decoupled with the surface, because they are cut off from their moisture source. This study will investigate the macro- and micro-physical properties of stratocumuli when boundary layers are either coupled to or decoupled from the surface. This will help advance understanding of the effects these macro- and micro-physical properties have on the lifetime of stratocumuli under different boundary layer conditions. This study used the Department of Energy Atmospheric Radiation Measurement (DOE ARM) mobile measurements facility (AMF) at the Azores site from June 2009 to December 2010. The measurements that were used include temperature profiles from radiosondes, cloud liquid water path (LWP) retrieved from the Microwave radiometer, and cloud base and top heights derived from W-band ARM Cloud Radar and lidar. Satellite images provided by the NASA Langley Research Center were also used to visually decipher cloud types over the region so that only single-layered stratocumuli cases are used in the study. To differentiate between coupled and decoupled cloud layers, two methods are used. The first method compares cloud base height and lifting condensation level (LCL) for surface air parcels. The second method uses potential temperature profiles to indicate whether a boundary layer is coupled or decoupled from the surface. The results from these two methods were then compared using select cases/samples when both methods classified a sample as coupled or decoupled. In this study, a total of seven coupled or decoupled cases (2-3 days long each) have been selected from the 19 month AMF dataset. Characteristics of the coupled and decoupled cases have been studied to identify similarities and differences. Furthermore, comparison results from this study have shown that there are similarities and differences between drizzling/non-drizzling stratocumulus clouds and decoupled/coupled stratocumulus clouds. Drizzling/decoupled stratocumuli tend to have higher LWP, cloud-droplet effective radius (re), cloud-top height, and cloud thickness values while non-drizzling/coupled stratocumuli have higher cloud-droplet number concentration (Nd) and cloud condensation nuclei concentration (NCCN) values. It was also determined that during daytime hours when stratocumuli are decoupled, they tend to be open cells, while coupled stratocumuli tend to be closed cells. Finally, decoupled nighttime stratocumuli were found to have higher LWPs compared to decoupled daytime stratocumuli, which resulted in the significant amount of heavy drizzle events occurring at night.

Electrical Coupling Between Glial Cells in the Rat Retina

PubMed Central

Ceelen, Paul W.; Lockridge, Amber; Newman, Eric A.

2008-01-01

The strength of electrical coupling between retinal glial cells was quantified with simultaneous whole-cell current-clamp recordings from astrocyte–astrocyte, astrocyte–Müller cell, and Müller cell–Müller cell pairs in the acutely isolated rat retina. Experimental results were fit and space constants determined using a resistive model of the glial cell network that assumed a homogeneous two-dimensional glial syncytium. The effective space constant (the distance from the point of stimulation to where the voltage falls to 1/e) equaled 12.9, 6.2, and 3.7 µm, respectively for astrocyte–astrocyte, astrocyte–Müller cell, and Müller cell–Müller cell coupling. The addition of 1 mM Ba2+ had little effect on network space constants, while 0.5 mM octanol shortened the space constants to 4.7, 4.4, and 2.6 µm for the three types of coupling. For a given distance separating cell pairs, the strength of coupling showed considerable variability. This variability in coupling strength was reproduced accurately by a second resistive model of the glial cell network (incorporating discrete astrocytes spaced at varying distances from each other), demonstrating that the variability was an intrinsic property of the glial cell network. Coupling between glial cells in the retina may permit the intercellular spread of ions and small molecules, including messengers mediating Ca2+ wave propagation, but it is too weak to carry significant K+ spatial buffer currents. PMID:11424187

Physics design of APT linac with normal conducting rf cavities

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

Nath, S.; Billen, J.H.; Stovall, J.E.

The accelerator based production of tritium calls for a high-power, cw proton linac. Previous designs for such a linac use a radiofrequency quadrupole (RFQ), followed by a drift-tube linac (DTL) to an intermediate energy and a coupled-cavity linc (CCL) to the final energy. The Los Alamos design uses a high-energy (6.7 MeV) RFQ followed by the newly developed coupled-cavity drift-tube linac (CCDTL) and a CCL. This design accommodates external electromagnetic quadrupole lenses which provide a strong uniform focusing lattice from the end of the RFQ to the end of the CCL. The cell lengths in linacs of traditional design aremore » typically graded as a function of particle velocity. By making groups of cells symmetric in both the CCDTL and CCL, the cavity design as well as mechanical design and fabrication is simplified without compromising the performance. At higher energies, there are some advantages of using superconducting rf cavities. Currently, such schemes are under vigorous study. This paper describes the linac design based on normal conducting cavities and presents simulation results.« less

Numerical heating in Particle-In-Cell simulations with Monte Carlo binary collisions

NASA Astrophysics Data System (ADS)

Alves, E. Paulo; Mori, Warren; Fiuza, Frederico

2017-10-01

The binary Monte Carlo collision (BMCC) algorithm is a robust and popular method to include Coulomb collision effects in Particle-in-Cell (PIC) simulations of plasmas. While a number of works have focused on extending the validity of the model to different physical regimes of temperature and density, little attention has been given to the fundamental coupling between PIC and BMCC algorithms. Here, we show that the coupling between PIC and BMCC algorithms can give rise to (nonphysical) numerical heating of the system, that can be far greater than that observed when these algorithms operate independently. This deleterious numerical heating effect can significantly impact the evolution of the simulated system particularly for long simulation times. In this work, we describe the source of this numerical heating, and derive scaling laws for the numerical heating rates based on the numerical parameters of PIC-BMCC simulations. We compare our theoretical scalings with PIC-BMCC numerical experiments, and discuss strategies to minimize this parasitic effect. This work is supported by DOE FES under FWP 100237 and 100182.

Particle model of a cylindrical inductively coupled ion source

NASA Astrophysics Data System (ADS)

Ippolito, N. D.; Taccogna, F.; Minelli, P.; Cavenago, M.; Veltri, P.

2017-08-01

In spite of the wide use of RF sources, a complete understanding of the mechanisms regulating the RF-coupling of the plasma is still lacking so self-consistent simulations of the involved physics are highly desirable. For this reason we are developing a 2.5D fully kinetic Particle-In-Cell Monte-Carlo-Collision (PIC-MCC) model of a cylindrical ICP-RF source, keeping the time step of the simulation small enough to resolve the plasma frequency scale. The grid cell dimension is now about seven times larger than the average Debye length, because of the large computational demand of the code. It will be scaled down in the next phase of the development of the code. The filling gas is Xenon, in order to minimize the time lost by the MCC collision module in the first stage of development of the code. The results presented here are preliminary, with the code already showing a good robustness. The final goal will be the modeling of the NIO1 (Negative Ion Optimization phase 1) source, operating in Padua at Consorzio RFX.

“Bad Romance”: Links between Psychological and Physical Aggression and Relationship Functioning in Adolescent Couples

PubMed Central

Seiffge-Krenke, Inge; Burk, William J.

2015-01-01

Assortative mating is an important issue in explaining antisocial, aggressive behavior. It is yet unclear, whether the similarity paradigm fully explains frequent displays of aggression in adolescents’ romantic relationships. In a sample of 194 romantic partner dyads, differences between female and male partners’ reports of aggression (psychological and physical) and different measures of relationship functioning (e.g., jealousy, conflicts, and the affiliative and romantic quality of the relationship) were assessed. A hierarchical cluster analysis identified five distinct subgroups of dyads based on male and female reports of psychological and physical aggression: nonaggressive couples, couples with higher perceived aggressiveness (both physical and psychological) by females, couples with higher aggressiveness perceived by males and mutually aggressive couples. A substantial number of non-aggressive dyads emerged. Of note was the high number of females showing one-sided aggression, which was, however, not countered by their partner. The mutually aggressive couples showed the least adaptive relationship functioning, with a lack of supportive, trusting relationship qualities, high conflict rates and high jealousy. The discussion focuses on the different functions of aggression in these early romantic relations, and the aggravating impact of mutual aggression on relationship functioning and its potential antisocial outcomes. PMID:26067515

Coupled Physics Environment (CouPE) library - Design, Implementation, and Release

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

Mahadevan, Vijay S.

Over several years, high fidelity, validated mono-­physics solvers with proven scalability on peta-­scale architectures have been developed independently. Based on a unified component-­based architecture, these existing codes can be coupled with a unified mesh-­data backplane and a flexible coupling-­strategy-­based driver suite to produce a viable tool for analysts. In this report, we present details on the design decisions and developments on CouPE, an acronym that stands for Coupled Physics Environment that orchestrates a coupled physics solver through the interfaces exposed by MOAB array-­based unstructured mesh, both of which are part of SIGMA (Scalable Interfaces for Geometry and Mesh-­Based Applications) toolkit.more » The SIGMA toolkit contains libraries that enable scalable geometry and unstructured mesh creation and handling in a memory and computationally efficient implementation. The CouPE version being prepared for a full open-­source release along with updated documentation will contain several useful examples that will enable users to start developing their applications natively using the native MOAB mesh and couple their models to existing physics applications to analyze and solve real world problems of interest. An integrated multi-­physics simulation capability for the design and analysis of current and future nuclear reactor models is also being investigated as part of the NEAMS RPL, to tightly couple neutron transport, thermal-­hydraulics and structural mechanics physics under the SHARP framework. This report summarizes the efforts that have been invested in CouPE to bring together several existing physics applications namely PROTEUS (neutron transport code), Nek5000 (computational fluid-dynamics code) and Diablo (structural mechanics code). The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The design of CouPE along with motivations that led to implementation choices are also discussed. The first release of the library will be different from the current version of the code that integrates the components in SHARP and explanation on the need for forking the source base will also be provided. Enhancements in the functionality and improved user guides will be available as part of the release. CouPE v0.1 is scheduled for an open-­source release in December 2014 along with SIGMA v1.1 components that provide support for language-agnostic mesh loading, traversal and query interfaces along with scalable solution transfer of fields between different physics codes. The coupling methodology and software interfaces of the library are presented, along with verification studies on two representative fast sodium-­cooled reactor demonstration problems to prove the usability of the CouPE library.« less

Systems Mechanobiology: Tension-Inhibited Protein Turnover Is Sufficient to Physically Control Gene Circuits

PubMed Central

Dingal, P.C. Dave P.; Discher, Dennis E.

2014-01-01

Mechanotransduction pathways convert forces that stress and strain structures within cells into gene expression levels that impact development, homeostasis, and disease. The levels of some key structural proteins in the nucleus, cytoskeleton, or extracellular matrix have been recently reported to scale with tissue- and cell-level forces or mechanical properties such as stiffness, and so the mathematics of mechanotransduction becomes important to understand. Here, we show that if a given structural protein positively regulates its own gene expression, then stresses need only inhibit degradation of that protein to achieve stable, mechanosensitive gene expression. This basic use-it-or-lose-it module is illustrated by application to meshworks of nuclear lamin A, minifilaments of myosin II, and extracellular matrix collagen fibers—all of which possess filamentous coiled-coil/supercoiled structures. Past experiments not only suggest that tension suppresses protein degradation mediated and/or initiated by various enzymes but also that transcript levels vary with protein levels because key transcription factors are regulated by these structural proteins. Coupling between modules occurs within single cells and between cells in tissue, as illustrated during embryonic heart development where cardiac fibroblasts make collagen that cardiomyocytes contract. With few additional assumptions, the basic module has sufficient physics to control key structural genes in both development and disease. PMID:25468352

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

PubMed

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

2015-01-01

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

49 CFR 210.33 - Operation standards (switcher locomotives, load cell test stands, car coupling operations, and...

Code of Federal Regulations, 2010 CFR

2010-10-01

... cell test stands, car coupling operations, and retarders). 210.33 Section 210.33 Transportation Other... (switcher locomotives, load cell test stands, car coupling operations, and retarders). (a) Measurement on receiving property of the noise emission levels from switcher locomotives, load cell test stands, car...

49 CFR 210.33 - Operation standards (switcher locomotives, load cell test stands, car coupling operations, and...

Code of Federal Regulations, 2013 CFR

2013-10-01

... cell test stands, car coupling operations, and retarders). 210.33 Section 210.33 Transportation Other... (switcher locomotives, load cell test stands, car coupling operations, and retarders). (a) Measurement on receiving property of the noise emission levels from switcher locomotives, load cell test stands, car...

49 CFR 210.33 - Operation standards (switcher locomotives, load cell test stands, car coupling operations, and...

Code of Federal Regulations, 2012 CFR

2012-10-01

... cell test stands, car coupling operations, and retarders). 210.33 Section 210.33 Transportation Other... (switcher locomotives, load cell test stands, car coupling operations, and retarders). (a) Measurement on receiving property of the noise emission levels from switcher locomotives, load cell test stands, car...

49 CFR 210.33 - Operation standards (switcher locomotives, load cell test stands, car coupling operations, and...

Code of Federal Regulations, 2014 CFR

2014-10-01

... cell test stands, car coupling operations, and retarders). 210.33 Section 210.33 Transportation Other... (switcher locomotives, load cell test stands, car coupling operations, and retarders). (a) Measurement on receiving property of the noise emission levels from switcher locomotives, load cell test stands, car...

49 CFR 210.33 - Operation standards (switcher locomotives, load cell test stands, car coupling operations, and...

Code of Federal Regulations, 2011 CFR

2011-10-01

... cell test stands, car coupling operations, and retarders). 210.33 Section 210.33 Transportation Other... (switcher locomotives, load cell test stands, car coupling operations, and retarders). (a) Measurement on receiving property of the noise emission levels from switcher locomotives, load cell test stands, car...

Physical and biological evaluations of sintered hydroxyapatite/silicone composite with covalent bonding for a percutaneous implant material.

PubMed

Furuzono, Tsutomu; Wang, Pao-Li; Korematsu, Arata; Miyazaki, Kozo; Oido-Mori, Mari; Kowashi, Yusuke; Ohura, Kiyoshi; Tanaka, Junzo; Kishida, Akio

2003-05-15

A composite (HA/silicone) of hydroxyapatite (HA) microparticles with an average diameter of 2.0 micro m covalently linked to a silicone substrate has been developed, and its physical and biological properties as a percutaneous soft-tissue-compatible material have been evaluated. In tensile property measurement, samples of HA/silicone and the original silicone were similar in tensile strength, ca. 7.8 MPa, and elongation at break, ca. 570%. It was found that chemical surface modification with HA particles presented no mechanical disadvantage. In an adhesive-tape peeling test, scanning electron microscopic (SEM) observation showed that HA particles coupled directly to the substrate were not removed. HA particles may bond strongly with the substrate. In human periodontal ligament fibroblast attachment and proliferation experiments, the number of cells attached to HA/silicone was 14 times greater than that attached to the original silicone after 24 h of incubation. The value on HA/silicone was ca. 80% versus that on a tissue-culture plastic used as a positive control. After 72 h of incubation, the number of cells grown on HA/silicone increased to the level of the positive control. In observation of fluorescence microscopy stained by Hoechst 33342, cells appeared to tightly adhere to HA particles coupled to the silicone sheet due to intact nuclear morphology. Observation of cells by fluorescence dye with rhodamin phalloidin showed an extensive F-actin cytoskeleton on HA/silicone. In a 4-week animal implant test, force required to pull out the HA/silicone sheet was 15 times that of the original silicone. HA-particle coating on silicone with covalent linkage gave the inert surface bioactivity. The HA composite thus effectively prevents germ infection percutaneously. Copyright 2003 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 65B: 217-226, 2003

Spatial distribution of filament elasticity determines the migratory behaviors of a cell

PubMed Central

Harn, Hans I-Chen; Hsu, Chao-Kai; Wang, Yang-Kao; Huang, Yi-Wei; Chiu, Wen-Tai; Lin, Hsi-Hui; Cheng, Chao-Min; Tang, Ming-Jer

2016-01-01

ABSTRACT Any cellular response leading to morphological changes is highly tuned to balance the force generated from structural reorganization, provided by actin cytoskeleton. Actin filaments serve as the backbone of intracellular force, and transduce external mechanical signal via focal adhesion complex into the cell. During migration, cells not only undergo molecular changes but also rapid mechanical modulation. Here we focus on determining, the role of spatial distribution of mechanical changes of actin filaments in epithelial, mesenchymal, fibrotic and cancer cells with non-migration, directional migration, and non-directional migration behaviors using the atomic force microscopy. We found 1) non-migratory cells only generated one type of filament elasticity, 2) cells generating spatially distributed two types of filament elasticity showed directional migration, and 3) pathologic cells that autonomously generated two types of filament elasticity without spatial distribution were actively migrating non-directionally. The demonstration of spatial regulation of filament elasticity of different cell types at the nano-scale highlights the coupling of cytoskeletal function with physical characters at the sub-cellular level, and provides new research directions for migration related disease. PMID:26919488

Sexual values as the key to maintaining satisfying sex after prostate cancer treatment: the physical pleasure-relational intimacy model of sexual motivation.

PubMed

Beck, Andrea M; Robinson, John W; Carlson, Linda E

2013-11-01

Sexual dysfunction is the most significant long lasting effect of prostate cancer (PrCa) treatment. Despite the many medical treatments for erectile dysfunction, many couples report that they are dissatisfied with their sexual relationship and eventually cease sexual relations altogether. We sought to understand what distinguishes successful couples from those who are not successful in adjusting to changes in sexual function subsequent to PrCa treatment. Ten couples who maintained satisfying sexual intimacy after PrCa treatment and seven couples that did not were interviewed conjointly and individually. Interviews were transcribed and analyzed using grounded theory methodology. The theory that resulted suggests that individuals are motivated to engage in sex primarily because of physical pleasure and relational intimacy. The couples who valued sex primarily for relational intimacy were more likely to successfully adjust to changes in sexual function than those who primarily valued sex for physical pleasure. The attributes of acceptance, flexibility, and persistence helped sustain couples through the process of adjustment. Based on these findings, a new theory, the Physical Pleasure-Relational Intimacy Model of Sexual Motivation (PRISM) is presented. The results elucidate the main motives for engaging in sexual activity-physical pleasure and/or relational intimacy-as a determining factor in the successful maintenance of satisfying sexual intimacy after PrCa treatment. The PRISM model predicts that couples who place a greater value on sex for relational intimacy will better adjust to the sexual challenges after PrCa treatment than couples who place a lower value on sex for relational intimacy. Implications of the model for counselling are discussed. This model remains to be tested in future research.

A mathematical model for predicting photo-induced voltage and photostriction of PLZT with coupled multi-physics fields and its application

NASA Astrophysics Data System (ADS)

Huang, J. H.; Wang, X. J.; Wang, J.

2016-02-01

The primary purpose of this paper is to propose a mathematical model of PLZT ceramic with coupled multi-physics fields, e.g. thermal, electric, mechanical and light field. To this end, the coupling relationships of multi-physics fields and the mechanism of some effects resulting in the photostrictive effect are analyzed theoretically, based on which a mathematical model considering coupled multi-physics fields is established. According to the analysis and experimental results, the mathematical model can explain the hysteresis phenomenon and the variation trend of the photo-induced voltage very well and is in agreement with the experimental curves. In addition, the PLZT bimorph is applied as an energy transducer for a photovoltaic-electrostatic hybrid actuated micromirror, and the relation of the rotation angle and the photo-induced voltage is discussed based on the novel photostrictive mathematical model.

Synthesis of adriamycin-coupled polyglutaraldehyde microspheres and evaluation of their cytostatic activity

NASA Technical Reports Server (NTRS)

Tokes, Z. A.; Rogers, K. E.; Rembaum, A.

1982-01-01

Adriamycin was coupled to polyglutaraldehyde microspheres having an average diameter of 4500 A. The coupled microspheres remained stable during incubation with cells. Full cytostatic activity was observed when the coupled adriamycin was tested with murine or human leukemia and murine sarcoma cell lines. A 10-fold increase in sensitivity was obtained with drug-resistant human leukemia cell lines. Repeated use of the coupled microspheres in the cytostatic assays did not decrease their activity, indicating that these complexes can be recycled. The results suggest that coupled adriamycin sufficiently perturbs the plasma membrane to lead to cytostatic activity. It is proposed that this mode of drug delivery provides multiple and repetitious sites for drug-cell interactions. In addition, the drug-polymer complexes may overcome those forms of resistance that are the result of decreased drug binding at the cell surface.

Electron Transport at the Microbe–Mineral Interface: A Synthesis of Current Research Challenges

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

Richardson, David; Fredrickson, Jim K.; Zachara, John M.

2012-12-01

Many bacterial and archaeal species can couple growth to the respiratory reduction or oxidation of insoluble mineral oxides of transition metals. These solid substrates are abundant electron sinks and sources for life on Earth, but, since they are insoluble in water, they cannot enter the bacterial cells. So, to exploit these electron sinks and sources, specific respiratory electron-transfer mechanisms must overcome the physical limitations associated with electron transfer between a microbe and extracellular metal oxides. Recent microbiological, geochemical, biochemical, spectroscopic and structural work is beginning to shed light on the molecular mechanism and impacts of electron transfer at themicrobe–mineral interfacemore » from a nanometre to kilometre scale. The research field is attracting attention in applied quarters from those with interests in nanowires, microbial fuel cells, bioremediation and microbial cell factories.« less

A decay of gap junctions associated with ganglion cell differentiation during retinal regeneration of the adult newt.

PubMed

Oi, Hanako; Chiba, Chikafumi; Saito, Takehiko

2003-12-01

Changes in the gap junctional coupling and maturation of voltage-activated Na(+) currents during regeneration of newt retinas were examined by whole-cell patch-clamping in slice preparations. Progenitor cells in regenerating retinas did not exhibit Na(+) currents but showed prominent electrical and tracer couplings. Cells identified by LY-fills were typically slender. Na(+) currents were detected in premature ganglion cells with round somata in the 'intermediate-II' regenerating retina. No electrical and tracer couplings were observed between these cells. Mature ganglion cells did not exhibit electrical coupling, but showed tracer coupling. On average, the maximum Na(+) current amplitude recorded from premature ganglion cells was roughly 2.5-fold smaller than that of mature ganglion cells. In addition, the activation threshold of the Na(+) current was nearly 11 mV more positive than that of mature cells. We provide morphological and physiological evidence showing that loss of gap junctions between progenitor cells is associated with ganglion cell differentiation during retinal regeneration and that new gap junctions are recreated between mature ganglion cells. Also we provide evidence suggesting that the loss of gap junctions correlates with the appearance of voltage-activated Na(+) currents in ganglion cells.

Peptide mediated intracellular delivery of semiconductor quantum dots

NASA Astrophysics Data System (ADS)

Kapur, Anshika; Safi, Malak; Domitrovic, Tatiana; Medina, Scott; Palui, Goutam; Johnson, John E.; Schneider, Joel; Mattoussi, Hedi

2017-02-01

As control over the growth, stabilization and functionalization of inorganic nanoparticles continue to advance, interest in integrating these materials with biological systems has steadily grown in the past decade. Much attention has been directed towards identifying effective approaches to promote cytosolic internalization of the nanoparticles while avoiding endocytosis. We describe the use of NωV virus derived gamma peptide and a chemically synthesized anticancer peptide, SVS-1 peptide, as vehicles to promote the non-endocytic uptake of luminescent quantum dots (QDs) inside live cells. The gamma peptide is expressed in E. coli as a fusion protein with poly-his tagged MBP (His-MBP-γ) to allow self-assembly onto QDs via metal-histidine conjugation. Conversely, the N-terminal cysteine residue of the SVS-1 peptide is attached to the functionalized QDs via covalent coupling chemistry. Epi-fluorescence microscopy images show that the QD-conjugate staining is distributed throughout the cytoplasm of cell cultures. Additionally, the QD staining does not show co-localization with transferrin-dye-labelled endosomes or DAPI stained nuclei. The QD uptake observed in the presence of physical and pharmacological endocytosis inhibitors further suggest that a physical translocation of QDs through the cell membrane is the driving mechanism for the uptake.

Correlation-based regularization and gradient operators for (joint) inversion on unstructured meshes

NASA Astrophysics Data System (ADS)

Jordi, Claudio; Doetsch, Joseph; Günther, Thomas; Schmelzbach, Cedric; Robertsson, Johan

2017-04-01

When working with unstructured meshes for geophysical inversions, special attention should be paid to the design of the operators that are used for regularizing the inverse problem and coupling of different property models in joint inversions. Regularization constraints for inversions on unstructured meshes are often defined in a rather ad-hoc manner and usually only involve the cell to which the operator is applied and its direct neighbours. Similarly, most structural coupling operators for joint inversion, such as the popular cross-gradients operator, are only defined in the direct neighbourhood of a cell. As a result, the regularization and coupling length scales and strength of these operators depend on the discretization as well as cell sizes and shape. Especially for unstructured meshes, where the cell sizes vary throughout the model domain, the dependency of the operator on the discretization may lead to artefacts. Designing operators that are based on a spatial correlation model allows to define correlation length scales over which an operator acts (called footprint), reducing the dependency on the discretization and the effects of variable cell sizes. Moreover, correlation-based operators can accommodate for expected anisotropy by using different length scales in horizontal and vertical directions. Correlation-based regularization operators also known as stochastic regularization operators have already been successfully applied to inversions on regular grids. Here, we formulate stochastic operators for unstructured meshes and apply them in 2D surface and 3D cross-well electrical resistivity tomography data inversion examples of layered media. Especially for the synthetic cross-well example, improved inversion results are achieved when stochastic regularization is used instead of a classical smoothness constraint. For the case of cross-gradients operators for joint inversion, the correlation model is used to define the footprint of the operator and weigh the contributions of the property values that are used to calculate the cross-gradients. In a first series of synthetic-data tests, we examined the mesh dependency of the cross-gradients operators. Compared to operators that are only defined in the direct neighbourhood of a cell, the dependency on the cell size of the cross-gradients calculation is markedly reduced when using operators with larger footprints. A second test with synthetic models focussed on the effect of small-scale variabilities of the parameter value on the cross-gradients calculation. Small-scale variabilities that are superimposed on a global trend of the property value can potentially degrade the cross-gradients calculation and destabilize joint inversion. We observe that the cross-gradients from operators with footprints larger than the length scale of the variabilities are less affected compared to operators with a small footprint. In joint inversions on unstructured meshes, we thus expect the correlation-based coupling operators to ensure robust coupling on a physically meaningful scale.

CPIC: a curvilinear Particle-In-Cell code for plasma-material interaction studies

NASA Astrophysics Data System (ADS)

Delzanno, G.; Camporeale, E.; Moulton, J. D.; Borovsky, J. E.; MacDonald, E.; Thomsen, M. F.

2012-12-01

We present a recently developed Particle-In-Cell (PIC) code in curvilinear geometry called CPIC (Curvilinear PIC) [1], where the standard PIC algorithm is coupled with a grid generation/adaptation strategy. Through the grid generator, which maps the physical domain to a logical domain where the grid is uniform and Cartesian, the code can simulate domains of arbitrary complexity, including the interaction of complex objects with a plasma. At present the code is electrostatic. Poisson's equation (in logical space) can be solved with either an iterative method based on the Conjugate Gradient (CG) or the Generalized Minimal Residual (GMRES) coupled with a multigrid solver used as a preconditioner, or directly with multigrid. The multigrid strategy is critical for the solver to perform optimally or nearly optimally as the dimension of the problem increases. CPIC also features a hybrid particle mover, where the computational particles are characterized by position in logical space and velocity in physical space. The advantage of a hybrid mover, as opposed to more conventional movers that move particles directly in the physical space, is that the interpolation of the particles in logical space is straightforward and computationally inexpensive, since one does not have to track the position of the particle. We will present our latest progress on the development of the code and document the code performance on standard plasma-physics tests. Then we will present the (preliminary) application of the code to a basic dynamic-charging problem, namely the charging and shielding of a spherical spacecraft in a magnetized plasma for various level of magnetization and including the pulsed emission of an electron beam from the spacecraft. The dynamical evolution of the sheath and the time-dependent current collection will be described. This study is in support of the ConnEx mission concept to use an electron beam from a magnetospheric spacecraft to trace magnetic field lines from the magnetosphere to the ionosphere [2]. [1] G.L. Delzanno, E. Camporeale, "CPIC: a new Particle-in-Cell code for plasma-material interaction studies", in preparation (2012). [2] J.E. Borovsky, D.J. McComas, M.F. Thomsen, J.L. Burch, J. Cravens, C.J. Pollock, T.E. Moore, and S.B. Mende, "Magnetosphere-Ionosphere Observatory (MIO): A multisatellite mission designed to solve the problem of what generates auroral arcs," Eos. Trans. Amer. Geophys. Union 79 (45), F744 (2000).

The skeletal vascular system - Breathing life into bone tissue.

PubMed

Stegen, Steve; Carmeliet, Geert

2017-08-26

During bone development, homeostasis and repair, a dense vascular system provides oxygen and nutrients to highly anabolic skeletal cells. Characteristic for the vascular system in bone is the serial organization of two capillary systems, each typified by specific morphological and physiological features. Especially the arterial capillaries mediate the growth of the bone vascular system, serve as a niche for skeletal and hematopoietic progenitors and couple angiogenesis to osteogenesis. Endothelial cells and osteoprogenitor cells interact not only physically, but also communicate to each other by secretion of growth factors. A vital angiogenic growth factor is vascular endothelial growth factor and its expression in skeletal cells is controlled by osteogenic transcription factors and hypoxia signaling, whereas the secretion of angiocrine factors by endothelial cells is regulated by Notch signaling, blood flow and possibly hypoxia. Bone loss and impaired fracture repair are often associated with reduced and disorganized blood vessel network and therapeutic targeting of the angiogenic response may contribute to enhanced bone regeneration. Copyright © 2017 Elsevier Inc. All rights reserved.

Electrical conditioning of adipose-derived stem cells in a multi-chamber culture platform.

PubMed

Pavesi, A; Soncini, M; Zamperone, A; Pietronave, S; Medico, E; Redaelli, A; Prat, M; Fiore, G B

2014-07-01

In tissue engineering, several factors play key roles in providing adequate stimuli for cells differentiation, in particular biochemical and physical stimuli, which try to mimic the physiological microenvironments. Since electrical stimuli are important in the developing heart, we have developed an easy-to-use, cost-effective cell culture platform, able to provide controlled electrical stimulation aimed at investigating the influence of the electric field in the stem cell differentiation process. This bioreactor consists of an electrical stimulator and 12 independent, petri-like culture chambers and a 3-D computational model was used to characterize the distribution and the intensity of the electric field generated in the cell culture volume. We explored the effects of monophasic and biphasic square wave pulse stimulation on a mouse adipose-derived stem cell line (m17.ASC) comparing cell viability, proliferation, protein, and gene expression. Both monophasic (8 V, 2 ms, 1 Hz) and biphasic (+4 V, 1 ms and -4 V, 1 ms; 1 Hz) stimulation were compatible with cell survival and proliferation. Biphasic stimulation induced the expression of Connexin 43, which was found to localize also at the cell membrane, which is its recognized functional mediating intercellular electrical coupling. Electrically stimulated cells showed an induced transcriptional profile more closely related to that of neonatal cadiomyocytes, particularly for biphasic stimulation. The developed platform thus allowed to set-up precise conditions to drive adult stem cells toward a myocardial phenotype solely by physical stimuli, in the absence of exogenously added expensive bioactive molecules, and can thus represent a valuable tool for translational applications for heart tissue engineering and regeneration. © 2014 Wiley Periodicals, Inc.

Agreement on Reporting of Physical, Psychological, and Sexual Violence among White, Black, and Hispanic Couples in the United States

ERIC Educational Resources Information Center

Caetano, Raul; Field, Craig; Ramisetty-Mikler, Suhasini; Lipsky, Sherry

2009-01-01

This article examines agreement on reports of male-to-female and female-to-male psychological, physical, and sexual violence among White, Black, and Hispanic couples in the United States. Using a probability sample, separate face-to-face interviews were conducted in respondents' homes with both members of 1,025 intact couples living in the 48…

Inverted Ultrathin Organic Solar Cells with a Quasi-Grating Structure for Efficient Carrier Collection and Dip-less Visible Optical Absorption.

PubMed

In, Sungjun; Park, Namkyoo

2016-02-23

We propose a metallic-particle-based two-dimensional quasi-grating structure for application to an organic solar cell. With the use of oblate spheroidal nanoparticles in contact with an anode of inverted, ultrathin organic solar cells (OSCs), the quasi-grating structure offers strong hybridization between localized surface plasmons and plasmonic gap modes leading to broadband (300~800 nm) and uniform (average ~90%) optical absorption spectra. Both strong optical enhancement in extreme confinement within the active layer (90 nm) and improved hole collection are thus realized. A coupled optical-electrical multi-physics optimization shows a large (~33%) enhancement in the optical absorption (corresponding to an absorption efficiency of ~47%, AM1.5G weighted, visible) when compared to a control OSC without the quasi-grating structure. That translates into a significant electrical performance gain of ~22% in short circuit current and ~15% in the power conversion efficiency (PCE), leading to an energy conversion efficiency (~6%) which is comparable to that of optically-thick inverted OSCs (3-7%). Detailed analysis on the influences of mode hybridization to optical field distributions, exciton generation rate, charge carrier collection efficiency and electrical conversion efficiency is provided, to offer an integrated understanding on the coupled optical-electrical optimization of ultrathin OSCs.

Heterogeneity and nearest-neighbor coupling can explain small-worldness and wave properties in pancreatic islets

NASA Astrophysics Data System (ADS)

Cappon, Giacomo; Pedersen, Morten Gram

2016-05-01

Many multicellular systems consist of coupled cells that work as a syncytium. The pancreatic islet of Langerhans is a well-studied example of such a microorgan. The islets are responsible for secretion of glucose-regulating hormones, mainly glucagon and insulin, which are released in distinct pulses. In order to observe pulsatile insulin secretion from the β-cells within the islets, the cellular responses must be synchronized. It is now well established that gap junctions provide the electrical nearest-neighbor coupling that allows excitation waves to spread across islets to synchronize the β-cell population. Surprisingly, functional coupling analysis of calcium responses in β-cells shows small-world properties, i.e., a high degree of local coupling with a few long-range "short-cut" connections that reduce the average path-length greatly. Here, we investigate how such long-range functional coupling can appear as a result of heterogeneity, nearest-neighbor coupling, and wave propagation. Heterogeneity is also able to explain a set of experimentally observed synchronization and wave properties without introducing all-or-none cell coupling and percolation theory. Our theoretical results highlight how local biological coupling can give rise to functional small-world properties via heterogeneity and wave propagation.

Final report on LDRD project : coupling strategies for multi-physics applications.

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

Hopkins, Matthew Morgan; Moffat, Harry K.; Carnes, Brian

Many current and future modeling applications at Sandia including ASC milestones will critically depend on the simultaneous solution of vastly different physical phenomena. Issues due to code coupling are often not addressed, understood, or even recognized. The objectives of the LDRD has been both in theory and in code development. We will show that we have provided a fundamental analysis of coupling, i.e., when strong coupling vs. a successive substitution strategy is needed. We have enabled the implementation of tighter coupling strategies through additions to the NOX and Sierra code suites to make coupling strategies available now. We have leveragedmore » existing functionality to do this. Specifically, we have built into NOX the capability to handle fully coupled simulations from multiple codes, and we have also built into NOX the capability to handle Jacobi Free Newton Krylov simulations that link multiple applications. We show how this capability may be accessed from within the Sierra Framework as well as from outside of Sierra. The critical impact from this LDRD is that we have shown how and have delivered strategies for enabling strong Newton-based coupling while respecting the modularity of existing codes. This will facilitate the use of these codes in a coupled manner to solve multi-physic applications.« less

Optimization methods and silicon solar cell numerical models

NASA Technical Reports Server (NTRS)

Girardini, K.; Jacobsen, S. E.

1986-01-01

An optimization algorithm for use with numerical silicon solar cell models was developed. By coupling an optimization algorithm with a solar cell model, it is possible to simultaneously vary design variables such as impurity concentrations, front junction depth, back junction depth, and cell thickness to maximize the predicted cell efficiency. An optimization algorithm was developed and interfaced with the Solar Cell Analysis Program in 1 Dimension (SCAP1D). SCAP1D uses finite difference methods to solve the differential equations which, along with several relations from the physics of semiconductors, describe mathematically the performance of a solar cell. A major obstacle is that the numerical methods used in SCAP1D require a significant amount of computer time, and during an optimization the model is called iteratively until the design variables converge to the values associated with the maximum efficiency. This problem was alleviated by designing an optimization code specifically for use with numerically intensive simulations, to reduce the number of times the efficiency has to be calculated to achieve convergence to the optimal solution.

TRPV1 Channels Are Functionally Coupled with BK(mSlo1) Channels in Rat Dorsal Root Ganglion (DRG) Neurons

PubMed Central

Yan, Zonghe; Kong, Wenjuan; Liu, Beiying; Li, Xia; Yao, Jing; Zhang, Yuexuan; Qin, Feng; Ding, Jiuping

2013-01-01

The transient receptor potential vanilloid receptor 1 (TRPV1) channel is a nonselective cation channel activated by a variety of exogenous and endogenous physical and chemical stimuli, such as temperature (≥42 °C), capsaicin, a pungent compound in hot chili peppers, and allyl isothiocyanate. Large-conductance calcium- and voltage-activated potassium (BK) channels regulate the electric activities and neurotransmitter releases in excitable cells, responding to changes in membrane potentials and elevation of cytosolic calcium ions (Ca2+). However, it is unknown whether the TRPV1 channels are coupled with the BK channels. Using patch-clamp recording combined with an infrared laser device, we found that BK channels could be activated at 0 mV by a Ca2+ influx through TRPV1 channels not the intracellular calcium stores in submilliseconds. The local calcium concentration around BK is estimated over 10 μM. The crosstalk could be affected by 10 mM BAPTA, whereas 5 mM EGTA was ineffectual. Fluorescence and co-immunoprecipitation experiments also showed that BK and TRPV1 were able to form a TRPV1-BK complex. Furthermore, we demonstrated that the TRPV1-BK coupling also occurs in dosal root ganglion (DRG) cells, which plays a critical physiological role in regulating the “pain” signal transduction pathway in the peripheral nervous system. PMID:24147119

Macroion solutions in the cell model studied by field theory and Monte Carlo simulations.

PubMed

Lue, Leo; Linse, Per

2011-12-14

Aqueous solutions of charged spherical macroions with variable dielectric permittivity and their associated counterions are examined within the cell model using a field theory and Monte Carlo simulations. The field theory is based on separation of fields into short- and long-wavelength terms, which are subjected to different statistical-mechanical treatments. The simulations were performed by using a new, accurate, and fast algorithm for numerical evaluation of the electrostatic polarization interaction. The field theory provides counterion distributions outside a macroion in good agreement with the simulation results over the full range from weak to strong electrostatic coupling. A low-dielectric macroion leads to a displacement of the counterions away from the macroion. © 2011 American Institute of Physics

Fluctuation correlation models for receptor immobilization

NASA Astrophysics Data System (ADS)

Fourcade, B.

2017-12-01

Nanoscale dynamics with cycles of receptor diffusion and immobilization by cell-external-or-internal factors is a key process in living cell adhesion phenomena at the origin of a plethora of signal transduction pathways. Motivated by modern correlation microscopy approaches, the receptor correlation functions in physical models based on diffusion-influenced reaction is studied. Using analytical and stochastic modeling, this paper focuses on the hybrid regime where diffusion and reaction are not truly separable. The time receptor autocorrelation functions are shown to be indexed by different time scales and their asymptotic expansions are given. Stochastic simulations show that this analysis can be extended to situations with a small number of molecules. It is also demonstrated that this analysis applies when receptor immobilization is coupled to environmental noise.

Ocean Surface Temperature Response to Atmosphere-Ocean Interaction of the MJO: A Component of Coupled Air-Wave-Sea Processes in the Subtropics Department Research Initiative

DTIC Science & Technology

2012-09-30

Lamont-Doherty Earth Observatory of Columbia University Ocean and Climate Physics Division 61 Route 9W Palisades , NY 10964 Phone: (845) 365-8547...Route 9W Palisades , NY 10964 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S...convective cells in the region as seen in the S-Pol. The robust large-scale temperature gradient of nearly 1°C is real with window and atmosphere

Can You Be Hit by Your Partner and Be Intensely in Love?

PubMed

Graña, José Luis; Cuenca Montesino, María Luisa; Redondo, Natalia; O'Leary, K Daniel

2016-07-01

This study examines, in a multilevel context, the influence of intensity of love at an individual level on couples' mean reports of psychological and physical aggression in a sample of 2,988 adult couples of both sexes from the Region of Madrid. The percentages of intimate partner aggression considering the highest report of aggression in the couple were around 60% of psychological aggression and 15% of physical aggression. Multilevel models confirm that individuals who were less intensely in love reported a higher level of psychological aggression. Concerning physical aggression, men who declared they were less intensely in love reported a higher level of physical aggression by their partners, but this pattern was not found in the women. Therefore, psychological aggression plays a more relevant role in the intensity of love than physical aggression. © The Author(s) 2015.

Physical mechanisms of active control of sound transmission through rib stiffened double-panel structure

NASA Astrophysics Data System (ADS)

Ma, Xiyue; Chen, Kean; Ding, Shaohu; Yu, Haoxin

2016-06-01

This paper presents an analytical investigation on physical mechanisms of actively controlling sound transmission through a rib stiffened double-panel structure using point source in the cavity. The combined modal expansion and vibro-acoustic coupling methods are applied to establish the theoretical model of such active structure. Under the condition of minimizing radiated power of the radiating ribbed plate, the physical mechanisms are interpreted in detail from the point of view of modal couplings similar as that used in existed literatures. Results obtained demonstrate that the rule of sound energy transmission and the physical mechanisms for the rib stiffened double-panel structure are all changed, and affected by the coupling effects of the rib when compared with the analytical results obtained for unribbed double-panel case. By taking the coupling effects of the rib into considerations, the cavity modal suppression and rearrangement mechanisms obtained in existed investigations are modified and supplemented for the ribbed plate case, which gives a clear interpretation for the physical nature involved in the active rib stiffened double-panel structure.

Evaluation of coupling approaches for thermomechanical simulations

DOE PAGES

Novascone, S. R.; Spencer, B. W.; Hales, J. D.; ...

2015-08-10

Many problems of interest, particularly in the nuclear engineering field, involve coupling between the thermal and mechanical response of an engineered system. The strength of the two-way feedback between the thermal and mechanical solution fields can vary significantly depending on the problem. Contact problems exhibit a particularly high degree of two-way feedback between those fields. This paper describes and demonstrates the application of a flexible simulation environment that permits the solution of coupled physics problems using either a tightly coupled approach or a loosely coupled approach. In the tight coupling approach, Newton iterations include the coupling effects between all physics,more » while in the loosely coupled approach, the individual physics models are solved independently, and fixed-point iterations are performed until the coupled system is converged. These approaches are applied to simple demonstration problems and to realistic nuclear engineering applications. The demonstration problems consist of single and multi-domain thermomechanics with and without thermal and mechanical contact. Simulations of a reactor pressure vessel under pressurized thermal shock conditions and a simulation of light water reactor fuel are also presented. Here, problems that include thermal and mechanical contact, such as the contact between the fuel and cladding in the fuel simulation, exhibit much stronger two-way feedback between the thermal and mechanical solutions, and as a result, are better solved using a tight coupling strategy.« less

Effects of physical and mental health on relationship satisfaction: a dyadic, longitudinal examination of couples facing prostate cancer.

PubMed

Ross, Kaile M; Ranby, Krista W; Wooldridge, Jennalee S; Robertson, Cary; Lipkus, Isaac M

2016-08-01

Prostate cancer may affect quality of life in men diagnosed as well as their spouses. Changes in health may disrupt the couple's relationship functioning which disrupts recovery. This study examined how mental and physical health relates to relationship satisfaction for couples at diagnosis through the year following treatment. Patients with stage I-II prostate cancer and their spouses (N = 159 couples) were recruited from a urology clinic and completed questionnaires at diagnosis, 1 month, 6 months, and 12 months post prostatectomy on demographics, mental and physical health quality of life, and relationship satisfaction. The Actor-Partner Interdependence Model was employed to examine effects of each partners' mental and physical health on their own and their partner's relationship satisfaction. Patients and spouses had declined mental and physical health at 1 month post-surgery. Health improved at 6 and 12 months but did not fully return to pre-surgery levels. Actor effects showed that patient's physical health consistently predicted own relationship satisfaction. Both patient's and spouse's mental health consistently related to their own relationship satisfaction. Partner effects showed that patient's and spouse's physical health had an effect on each other's relationship satisfaction at 1 month. Spouse's mental health predicted patient's relationship satisfaction throughout the year following treatment. The effects of patient and spouse mental and physical health quality of life on their own as well as their partner's relationship satisfaction differed across time which will inform psychosocial interventions for couples with prostate cancer. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Cell-material interactions revealed via material techniques of surface patterning.

PubMed

Yao, Xiang; Peng, Rong; Ding, Jiandong

2013-10-04

Cell-material interactions constitute a key fundamental topic in biomaterials study. Various cell cues and matrix cues as well as soluble factors regulate cell behaviors on materials. These factors are coupled with each other as usual, and thus it is very difficult to unambiguously elucidate the role of each regulator. The recently developed material techniques of surface patterning afford unique ways to reveal the underlying science. This paper reviews the pertinent material techniques to fabricate patterns of microscale and nanoscale resolutions, and corresponding cell studies. Some issues are emphasized, such as cell localization on patterned surfaces of chemical contrast, and effects of cell shape, cell size, cell-cell contact, and seeding density on differentiation of stem cells. Material cues to regulate cell adhesion, cell differentiation and other cell events are further summed up. Effects of some physical properties, such as surface topography and matrix stiffness, on cell behaviors are also discussed; nanoscaled features of substrate surfaces to regulate cell fate are summarized as well. The pertinent work sheds new insight into the cell-material interactions, and is stimulating for biomaterial design in regenerative medicine, tissue engineering, and high-throughput detection, diagnosis, and drug screening. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The FAK-Arp2/3 interaction promotes leading edge advance and haptosensing by coupling nascent adhesions to lamellipodia actin.

PubMed

Swaminathan, Vinay; Fischer, R S; Waterman, Clare M

2016-04-01

Cell migration is initiated in response to biochemical or physical cues in the environment that promote actin-mediated lamellipodial protrusion followed by the formation of nascent integrin adhesions (NAs) within the protrusion to drive leading edge advance. Although FAK is known to be required for cell migration through effects on focal adhesions, its role in NA formation and lamellipodial dynamics is unclear. Live-cell microscopy of FAK(-/-)cells with expression of phosphorylation deficient or a FERM-domain mutant deficient in Arp2/3 binding revealed a requirement for FAK in promoting the dense formation, transient stabilization, and timely turnover of NA within lamellipodia to couple actin-driven protrusion to adhesion and advance of the leading edge. Phosphorylation on Y397 of FAK promotes dense NA formation but is dispensable for transient NA stabilization and leading edge advance. In contrast, transient NA stabilization and advance of the cell edge requires FAK-Arp2/3 interaction, which promotes Arp2/3 localization to NA and reduces FAK activity. Haptosensing of extracellular matrix (ECM) concentration during migration requires the interaction between FAK and Arp2/3, whereas FAK phosphorylation modulates mechanosensing of ECM stiffness during spreading. Taken together, our results show that mechanistically separable functions of FAK in NA are required for cells to distinguish distinct properties of their environment during migration. © 2016 Swaminathan et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Adhesion to the host cell surface is sufficient to mediate Listeria monocytogenes entry into epithelial cells

PubMed Central

Ortega, Fabian E.; Rengarajan, Michelle; Chavez, Natalie; Radhakrishnan, Prathima; Gloerich, Martijn; Bianchini, Julie; Siemers, Kathleen; Luckett, William S.; Lauer, Peter; Nelson, W. James; Theriot, Julie A.

2017-01-01

The intestinal epithelium is the first physiological barrier breached by the Gram-positive facultative pathogen Listeria monocytogenes during an in vivo infection. Listeria monocytogenes binds to the epithelial host cell receptor E-cadherin, which mediates a physical link between the bacterium and filamentous actin (F-actin). However, the importance of anchoring the bacterium to F-actin through E-cadherin for bacterial invasion has not been tested directly in epithelial cells. Here we demonstrate that depleting αE-catenin, which indirectly links E-cadherin to F-actin, did not decrease L. monocytogenes invasion of epithelial cells in tissue culture. Instead, invasion increased due to increased bacterial adhesion to epithelial monolayers with compromised cell–cell junctions. Furthermore, expression of a mutant E-cadherin lacking the intracellular domain was sufficient for efficient L. monocytogenes invasion of epithelial cells. Importantly, direct biotin-mediated binding of bacteria to surface lipids in the plasma membrane of host epithelial cells was sufficient for uptake. Our results indicate that the only requirement for L. monocytogenes invasion of epithelial cells is adhesion to the host cell surface, and that E-cadherin–mediated coupling of the bacterium to F-actin is not required. PMID:28877987

EphA2 cleavage by MT1-MMP triggers single cancer cell invasion via homotypic cell repulsion

PubMed Central

Sugiyama, Nami; Gucciardo, Erika; Tatti, Olga; Varjosalo, Markku; Hyytiäinen, Marko; Gstaiger, Matthias

2013-01-01

Changes in EphA2 signaling can affect cancer cell–cell communication and motility through effects on actomyosin contractility. However, the underlying cell–surface interactions and molecular mechanisms of how EphA2 mediates these effects have remained unclear. We demonstrate here that EphA2 and membrane-anchored membrane type-1 matrix metalloproteinase (MT1-MMP) were selectively up-regulated and coexpressed in invasive breast carcinoma cells, where, upon physical interaction in same cell–surface complexes, MT1-MMP cleaved EphA2 at its Fibronectin type-III domain 1. This cleavage, coupled with EphA2-dependent Src activation, triggered intracellular EphA2 translocation, as well as an increase in RhoA activity and cell junction disassembly, which suggests an overall repulsive effect between cells. Consistent with this, cleavage-prone EphA2-D359I mutant shifted breast carcinoma cell invasion from collective to rounded single-cell invasion within collagen and in vivo. Up-regulated MT1-MMP also codistributed with intracellular EphA2 in invasive cells within human breast carcinomas. These results reveal a new proteolytic regulatory mechanism of cell–cell signaling in cancer invasion. PMID:23629968

Multi-physics transient simulation of monolithic niobium dioxide-tantalum dioxide memristor-selector structures

NASA Astrophysics Data System (ADS)

Sevic, John F.; Kobayashi, Nobuhiko P.

2017-10-01

Self-assembled niobium dioxide (NbO2) thin-film selectors self-aligned to tantalum dioxide (TaO2) memristive memory cells are studied by a multi-physics transient solution of the heat equation coupled to the nonlinear current continuity equation. While a compact model can resolve the quasi-static bulk negative differential resistance (NDR), a self-consistent coupled transport formulation provides a non-equilibrium picture of NbO2-TaO2 selector-memristor operation ab initio. By employing the drift-diffusion transport approximation, a finite element method is used to study the dynamic electrothermal behavior of our experimentally obtained selector-memristor devices, showing that existing conditions are suitable for electroformation of NbO2 selector thin-films. Both transient and steady-state simulations support our theory, suggesting that the phase change due to insulator-metal transition is responsible for NbO2 selector NDR in our as-fabricated selector-memristor devices. Simulation results further suggest that TiN nano-via may play a central role in electroforming, as its dimensions and material properties establish the mutual electrothermal interaction between TiN nano-via and the selector-memristor.

Three-dimensional fuel pin model validation by prediction of hydrogen distribution in cladding and comparison with experiment

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

Aly, A.; Avramova, Maria; Ivanov, Kostadin

To correctly describe and predict this hydrogen distribution there is a need for multi-physics coupling to provide accurate three-dimensional azimuthal, radial, and axial temperature distributions in the cladding. Coupled high-fidelity reactor-physics codes with a sub-channel code as well as with a computational fluid dynamics (CFD) tool have been used to calculate detailed temperature distributions. These high-fidelity coupled neutronics/thermal-hydraulics code systems are coupled further with the fuel-performance BISON code with a kernel (module) for hydrogen. Both hydrogen migration and precipitation/dissolution are included in the model. Results from this multi-physics analysis is validated utilizing calculations of hydrogen distribution using models informed bymore » data from hydrogen experiments and PIE data.« less

Electrical coupling in ensembles of nonexcitable cells: modeling the spatial map of single cell potentials.

PubMed

Cervera, Javier; Manzanares, Jose Antonio; Mafe, Salvador

2015-02-19

We analyze the coupling of model nonexcitable (non-neural) cells assuming that the cell membrane potential is the basic individual property. We obtain this potential on the basis of the inward and outward rectifying voltage-gated channels characteristic of cell membranes. We concentrate on the electrical coupling of a cell ensemble rather than on the biochemical and mechanical characteristics of the individual cells, obtain the map of single cell potentials using simple assumptions, and suggest procedures to collectively modify this spatial map. The response of the cell ensemble to an external perturbation and the consequences of cell isolation, heterogeneity, and ensemble size are also analyzed. The results suggest that simple coupling mechanisms can be significant for the biophysical chemistry of model biomolecular ensembles. In particular, the spatiotemporal map of single cell potentials should be relevant for the uptake and distribution of charged nanoparticles over model cell ensembles and the collective properties of droplet networks incorporating protein ion channels inserted in lipid bilayers.

On coupling fluid plasma and kinetic neutral physics models

DOE PAGES

Joseph, I.; Rensink, M. E.; Stotler, D. P.; ...

2017-03-01

The coupled fluid plasma and kinetic neutral physics equations are analyzed through theory and simulation of benchmark cases. It is shown that coupling methods that do not treat the coupling rates implicitly are restricted to short time steps for stability. Fast charge exchange, ionization and recombination coupling rates exist, even after constraining the solution by requiring that the neutrals are at equilibrium. For explicit coupling, the present implementation of Monte Carlo correlated sampling techniques does not allow for complete convergence in slab geometry. For the benchmark case, residuals decay with particle number and increase with grid size, indicating that theymore » scale in a manner that is similar to the theoretical prediction for nonlinear bias error. Progress is reported on implementation of a fully implicit Jacobian-free Newton–Krylov coupling scheme. The present block Jacobi preconditioning method is still sensitive to time step and methods that better precondition the coupled system are under investigation.« less

Design of Soil Salinity Policies with Tinamit, a Flexible and Rapid Tool to Couple Stakeholder-Built System Dynamics Models with Physically-Based Models

NASA Astrophysics Data System (ADS)

Malard, J. J.; Baig, A. I.; Hassanzadeh, E.; Adamowski, J. F.; Tuy, H.; Melgar-Quiñonez, H.

2016-12-01

Model coupling is a crucial step to constructing many environmental models, as it allows for the integration of independently-built models representing different system sub-components to simulate the entire system. Model coupling has been of particular interest in combining socioeconomic System Dynamics (SD) models, whose visual interface facilitates their direct use by stakeholders, with more complex physically-based models of the environmental system. However, model coupling processes are often cumbersome and inflexible and require extensive programming knowledge, limiting their potential for continued use by stakeholders in policy design and analysis after the end of the project. Here, we present Tinamit, a flexible Python-based model-coupling software tool whose easy-to-use API and graphical user interface make the coupling of stakeholder-built SD models with physically-based models rapid, flexible and simple for users with limited to no coding knowledge. The flexibility of the system allows end users to modify the SD model as well as the linking variables between the two models themselves with no need for recoding. We use Tinamit to couple a stakeholder-built socioeconomic model of soil salinization in Pakistan with the physically-based soil salinity model SAHYSMOD. As climate extremes increase in the region, policies to slow or reverse soil salinity buildup are increasing in urgency and must take both socioeconomic and biophysical spheres into account. We use the Tinamit-coupled model to test the impact of integrated policy options (economic and regulatory incentives to farmers) on soil salinity in the region in the face of future climate change scenarios. Use of the Tinamit model allowed for rapid and flexible coupling of the two models, allowing the end user to continue making model structure and policy changes. In addition, the clear interface (in contrast to most model coupling code) makes the final coupled model easily accessible to stakeholders with limited technical background.

Couple Infertility: From the Perspective of the Close-Relationship Model.

ERIC Educational Resources Information Center

Higgins, Barbara S.

1990-01-01

Presents Close-Relationship Model as comprehensive framework in which to examine interrelated nature of causes and effects of infertility on marital relationship. Includes these factors: physical and psychological characteristics of both partners; joint, couple characteristics; physical and social environment; and relationship itself. Discusses…

The physics of sub-critical lattices in accelerator driven hybrid systems: The MUSE experiments in the MASURCA facility

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

Chauvin, J. P.; Lebrat, J. F.; Soule, R.

Since 1991, the CEA has studied the physics of hybrid systems, involving a sub-critical reactor coupled with an accelerator. These studies have provided information on the potential of hybrid systems to transmute actinides and, long lived fission products. The potential of such a system remains to be proven, specifically in terms of the physical understanding of the different phenomena involved and their modelling, as well as in terms of experimental validation of coupled systems, sub-critical environment/accelerator. This validation must be achieved through mock-up studies of the sub-critical environments coupled to a source of external neutrons. The MUSE-4 mock-up experiment ismore » planed at the MASURCA facility and will use an accelerator coupled to a tritium target. The great step between the generator used in the past and the accelerator will allow to increase the knowledge in hybrid physic and to decrease the experimental biases and the measurement uncertainties.« less

Mexican American adolescent couples' vulnerability for observed negativity and physical violence: Pregnancy and acculturation mismatch.

PubMed

Williams, Lela Rankin; Rueda, Heidi Adams

2016-10-01

Stress and vulnerability for dating violence may be heightened among acculturating Mexican American (MA) adolescents, and MA adolescent parents, because of differing cultural values and norms within romantic relationships. We hypothesized, in a sample of MA heterosexual couples (N = 30, 15-17 years), that: 1) within-couple level acculturation discrepancies, and pregnancy/parenting, would predict physical violence perpetration, and 2) that this association would have an indirect effect through couple-level negativity during an observed dyadic video-taped discussion of conflict. Using a path model we found that pregnant/parenting adolescents (B = .37, SE = .16, p = .002), and couples with greater acculturation mismatch resulted in greater couple negativity (B = .16, SE = .06, p = .01), which was associated with self-reported physical violence perpetration (B = .41, SE = .22, p = .02; indirect effect, B = .15, SE = .07, p = .03). Within-couple acculturation discrepancies and pregnancy/parenting may be a pathway to dating violence through poor communication skills around conflict for MA youth. Support services that strengthen communication skills, particularly for pregnant/parenting couples, are recommended. Copyright © 2016 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa

NASA Astrophysics Data System (ADS)

Deng, Zhaojie; Arsenault, Sam; Caranica, Cristian; Griffith, James; Zhu, Taotao; Al-Omari, Ahmad; Schüttler, Heinz-Bernd; Arnold, Jonathan; Mao, Leidong

2016-10-01

The synchronization of stochastic coupled oscillators is a central problem in physics and an emerging problem in biology, particularly in the context of circadian rhythms. Most measurements on the biological clock are made at the macroscopic level of millions of cells. Here measurements are made on the oscillators in single cells of the model fungal system, Neurospora crassa, with droplet microfluidics and the use of a fluorescent recorder hooked up to a promoter on a clock controlled gene-2 (ccg-2). The oscillators of individual cells are stochastic with a period near 21 hours (h), and using a stochastic clock network ensemble fitted by Markov Chain Monte Carlo implemented on general-purpose graphical processing units (or GPGPUs) we estimated that >94% of the variation in ccg-2 expression was stochastic (as opposed to experimental error). To overcome this stochasticity at the macroscopic level, cells must synchronize their oscillators. Using a classic measure of similarity in cell trajectories within droplets, the intraclass correlation (ICC), the synchronization surface ICC is measured on >25,000 cells as a function of the number of neighboring cells within a droplet and of time. The synchronization surface provides evidence that cells communicate, and synchronization varies with genotype.

Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa

PubMed Central

Deng, Zhaojie; Arsenault, Sam; Caranica, Cristian; Griffith, James; Zhu, Taotao; Al-Omari, Ahmad; Schüttler, Heinz-Bernd; Arnold, Jonathan; Mao, Leidong

2016-01-01

The synchronization of stochastic coupled oscillators is a central problem in physics and an emerging problem in biology, particularly in the context of circadian rhythms. Most measurements on the biological clock are made at the macroscopic level of millions of cells. Here measurements are made on the oscillators in single cells of the model fungal system, Neurospora crassa, with droplet microfluidics and the use of a fluorescent recorder hooked up to a promoter on a clock controlled gene-2 (ccg-2). The oscillators of individual cells are stochastic with a period near 21 hours (h), and using a stochastic clock network ensemble fitted by Markov Chain Monte Carlo implemented on general-purpose graphical processing units (or GPGPUs) we estimated that >94% of the variation in ccg-2 expression was stochastic (as opposed to experimental error). To overcome this stochasticity at the macroscopic level, cells must synchronize their oscillators. Using a classic measure of similarity in cell trajectories within droplets, the intraclass correlation (ICC), the synchronization surface ICC is measured on >25,000 cells as a function of the number of neighboring cells within a droplet and of time. The synchronization surface provides evidence that cells communicate, and synchronization varies with genotype. PMID:27786253

Freedom and imperative: mutual care between older spouses with physical disabilities.

PubMed

Torgé, Cristina Joy

2014-05-01

This article explores mutual caregiving between older spouses aging with physical disabilities. Nine older couples, where both partners had lived long lives with physical disabilities, were interviewed as dyads about mutual caregiving. The couples not only had access to different kinds and degrees of formal support but also provided mutual care to each other in a variety of ways. Interview coding using grounded theory led to two overarching categories from which motivation for mutual caregiving could be understood. These categories were Mutual care as freedom and Mutual care as imperative. The results extend understanding about how older couples with disabilities attached meaning to their mutual caregiving, and why mutual care was sometimes preferable, despite the availability of other sources of help and despite practical difficulties of providing this help. These findings suggest that health care professionals need to be sensitive to the dynamics of the couple relationship and carefully explore the couple's preferences for how formal support can best be provided in ways that honor and sustain the integrity of the couple relationship.

Phototransfection of mouse embryonic stem cells with plasmid DNA using femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Thobakgale, Lebogang; Manoto, Sello Lebohang; Ombinda Lemboumba, Saturnin; Maaza, Malik; Mthunzi-Kufa, Patience

2017-02-01

Cellular manipulation by delivery of molecules into cells has been applied extensively in tissue engineering research for medical applications . The different molecular delivery techniques used range from viral and chemical agents to physical and electrical methods. Although successful in most studies, these techniques have inherent difficulties such as toxicity, unwanted genetic mutations and low reproducibility respectively. Literature recognizes pulsed lasers at femtosecond level to be most efficient in photonic interactions with biological material. As of late, laser pulses have been used for drug and DNA delivery into cells via transient optical perforation of the cellular membrane. Thus in this study, we design and construct an optical system coupled to a femtosecond laser for the purpose of phototransfection or insertion of plasmid DNA (pDNA) into cells using lasers. We used fluorescent green protein (pGFP) to transfect mouse embryonic stem cells as our model. Secondly, we applied fluorescence imaging to view the extent of DNA delivery using this method. We also assessed the biocompatibility of our system by performing molecular assays of the cells post irradiation using adenosine triphosphate (ATP) and lactate dehydrogenase (LDH).

Membrane tension controls adhesion positioning at the leading edge of cells

PubMed Central

Pontes, Bruno; Gole, Laurent; Kosmalska, Anita Joanna; Tam, Zhi Yang; Luo, Weiwei; Kan, Sophie; Viasnoff, Virgile; Roca-Cusachs, Pere; Tucker-Kellogg, Lisa

2017-01-01

Cell migration is dependent on adhesion dynamics and actin cytoskeleton remodeling at the leading edge. These events may be physically constrained by the plasma membrane. Here, we show that the mechanical signal produced by an increase in plasma membrane tension triggers the positioning of new rows of adhesions at the leading edge. During protrusion, as membrane tension increases, velocity slows, and the lamellipodium buckles upward in a myosin II–independent manner. The buckling occurs between the front of the lamellipodium, where nascent adhesions are positioned in rows, and the base of the lamellipodium, where a vinculin-dependent clutch couples actin to previously positioned adhesions. As membrane tension decreases, protrusion resumes and buckling disappears, until the next cycle. We propose that the mechanical signal of membrane tension exerts upstream control in mechanotransduction by periodically compressing and relaxing the lamellipodium, leading to the positioning of adhesions at the leading edge of cells. PMID:28687667

Parametric model of servo-hydraulic actuator coupled with a nonlinear system: Experimental validation

NASA Astrophysics Data System (ADS)

Maghareh, Amin; Silva, Christian E.; Dyke, Shirley J.

2018-05-01

Hydraulic actuators play a key role in experimental structural dynamics. In a previous study, a physics-based model for a servo-hydraulic actuator coupled with a nonlinear physical system was developed. Later, this dynamical model was transformed into controllable canonical form for position tracking control purposes. For this study, a nonlinear device is designed and fabricated to exhibit various nonlinear force-displacement profiles depending on the initial condition and the type of materials used as replaceable coupons. Using this nonlinear system, the controllable canonical dynamical model is experimentally validated for a servo-hydraulic actuator coupled with a nonlinear physical system.

The Role of the Rab Coupling Protein in ErbB2-Driven Mammary Tumorigenesis and Metastasis

DTIC Science & Technology

2014-10-01

Coupling Protein/Rab11FIP1/RCP, Epithelial Mesenchymal Transition , Cell junctions , Cell Proliferation, Senescence. 16. SECURITY CLASSIFICATION OF: 17...Tyrosine Kinase, Her/ErbB2 signaling, Rab Coupling Protein/Rab11FIP1/RCP, Epithelial Mesenchymal Transition , Cell junctions , Cell Proliferation...lines included RCP condition to internalization and detection of E-cadherin, a well-known adherent junction and epithelial mesenchymal transition

Coupled reactors analysis: New needs and advances using Monte Carlo methodology

DOE PAGES

Aufiero, M.; Palmiotti, G.; Salvatores, M.; ...

2016-08-20

Coupled reactors and the coupling features of large or heterogeneous core reactors can be investigated with the Avery theory that allows a physics understanding of the main features of these systems. However, the complex geometries that are often encountered in association with coupled reactors, require a detailed geometry description that can be easily provided by modern Monte Carlo (MC) codes. This implies a MC calculation of the coupling parameters defined by Avery and of the sensitivity coefficients that allow further detailed physics analysis. The results presented in this paper show that the MC code SERPENT has been successfully modifed tomore » meet the required capabilities.« less

Influence of the sign of the coupling on the temperature dependence of optical properties of one-dimensional exciton models

NASA Astrophysics Data System (ADS)

Cruzeiro, L.

2008-10-01

A new physical cause for a temperature-dependent double peak in exciton systems is put forward within a thermal equilibrium approach for the calculation of optical properties of exciton systems. Indeed, it is found that one-dimensional exciton systems with only one molecule per unit cell can have an absorption spectrum characterized by a double peak provided that the coupling between excitations in different molecules is positive. The two peaks, whose relative intensities vary with temperature, are located around the exciton band edges, being separated by an energy of approximately 4V, where V is the average coupling between nearest neighbours. For small amounts of diagonal and off-diagonal disorder, the contributions from the intermediate states in the band are also visible as intermediate structure between the two peaks, this being enhanced for systems with periodic boundary conditions. At a qualitative level, these results correlate well with experimental observations in the molecular aggregates of the thiacarbocyanine dye THIATS and in the organic crystals of acetanilide and N-methylacetamide.

Pressurizing Field-Effect Transistors of Few-Layer MoS 2 in a Diamond Anvil Cell

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

Chen, Yabin; Ke, Feng; Ci, Penghong

Hydrostatic pressure applied using diamond anvil cells (DAC) has been widely explored to modulate physical properties of materials by tuning their lattice degree of freedom. Independently, electrical field is able to tune the electronic degree of freedom of functional materials via, for example, the field-effect transistor (FET) configuration. Combining these two orthogonal approaches would allow discovery of new physical properties and phases going beyond the known phase space. Such experiments are, however, technically challenging and have not been demonstrated. In this paper, we report a feasible strategy to prepare and measure FETs in a DAC by lithographically patterning the nanodevicesmore » onto the diamond culet. Multiple-terminal FETs were fabricated in the DAC using few-layer MoS 2 and BN as the channel semiconductor and dielectric layer, respectively. It is found that the mobility, conductance, carrier concentration, and contact conductance of MoS 2 can all be significantly enhanced with pressure. Finally, we expect that the approach could enable unprecedented ways to explore new phases and properties of materials under coupled mechano-electrostatic modulation.« less

Premarital mental disorders and physical violence in marriage: cross-national study of married couples

PubMed Central

Miller, Elizabeth; Breslau, Joshua; Petukhova, Maria; Fayyad, John; Green, Jennifer Greif; Kola, Lola; Seedat, Soraya; Stein, Dan J.; Tsang, Adley; Viana, Maria Carmen; Andrade, Laura Helena; Demyttenaere, Koen; de Girolamo, Giovanni; Haro, Josep Maria; Hu, Chiyi; Karam, Elie G.; Kovess-Masfety, Viviane; Tomov, Toma; Kessler, Ronald C.

2011-01-01

Background Mental disorders may increase the risk of physical violence among married couples. Aims To estimate associations between premarital mental disorders and marital violence in a cross-national sample of married couples. Method A total of 1821 married couples (3642 individuals) from 11 countries were interviewed as part of the World Health Organization's World Mental Health Survey Initiative. Sixteen mental disorders with onset prior to marriage were examined as predictors of marital violence reported by either spouse. Results Any physical violence was reported by one or both spouses in 20% of couples, and was associated with husbands' externalising disorders (OR = 1.7, 95% CI 1.2-2.3). Overall, the population attributable risk for marital violence related to premarital mental disorders was estimated to be 17.2%. Conclusions Husbands' externalising disorders had a modest but consistent association with marital violence across diverse countries. This finding has implications for the development of targeted interventions to reduce risk of marital violence. PMID:21778172

Interplay between the b →s l l anomalies and dark matter physics

NASA Astrophysics Data System (ADS)

Kawamura, Junichiro; Okawa, Shohei; Omura, Yuji

2017-10-01

Recently, the LHCb Collaboration has reported the excesses in the b →s l l processes. One of the promising candidates for new physics to explain the anomalies is the extended Standard Model (SM) with vectorlike quarks and leptons. In that model, Yukawa couplings between the extra fermions and SM fermions are introduced, adding extra scalars. Then, the box diagrams involving the extra fields achieve the b →s l l anomalies. It has been known that the excesses require the large Yukawa couplings of leptons, so that this kind of model can be tested by studying correlations with other observables. In this paper, we consider the extra scalar to be a dark matter (DM) candidate, and investigate DM physics as well as the flavor physics and the LHC physics. The DM relic density and the direct-detection cross section are also dominantly given by the Yukawa couplings, so that we find some explicit correlations between DM physics and the flavor physics. In particular, we find the predictions of the b →s l l anomalies against the direct detection of DM.

The CAMSAP3-ACF7 Complex Couples Noncentrosomal Microtubules with Actin Filaments to Coordinate Their Dynamics.

PubMed

Ning, Wenxiu; Yu, Yanan; Xu, Honglin; Liu, Xiaofei; Wang, Daiwei; Wang, Jing; Wang, Yingchun; Meng, Wenxiang

2016-10-10

For adaptation to complex cellular functions, dynamic cytoskeletal networks are required. There are two major components of the cytoskeleton, microtubules and actin filaments, which form an intricate network maintaining an exquisite cooperation to build the physical basis for their cellular function. However, little is known about the molecular mechanism underlying their synergism. Here, we show that in Caco2 epithelial cells, noncentrosomal microtubules crosstalk with F-actin through their minus ends and contribute to the regulation of focal adhesion size and cell migration. We demonstrate that ACF7, a member of the spectraplakin family of cytoskeletal crosslinking proteins, interacts with Nezha (also called CAMSAP3) at the minus ends of noncentrosomal microtubules and anchors them to actin filaments. Those noncentrosomal microtubules cooperate with actin filaments through retrograde flow to keep their length and orientation perpendicular to the cell edge as well as regulate focal adhesion size and cell migration. Copyright © 2016 Elsevier Inc. All rights reserved.

A model for Entropy Production, Entropy Decrease and Action Minimization in Self-Organization

NASA Astrophysics Data System (ADS)

Georgiev, Georgi; Chatterjee, Atanu; Vu, Thanh; Iannacchione, Germano

In self-organization energy gradients across complex systems lead to change in the structure of systems, decreasing their internal entropy to ensure the most efficient energy transport and therefore maximum entropy production in the surroundings. This approach stems from fundamental variational principles in physics, such as the principle of least action. It is coupled to the total energy flowing through a system, which leads to increase the action efficiency. We compare energy transport through a fluid cell which has random motion of its molecules, and a cell which can form convection cells. We examine the signs of change of entropy, and the action needed for the motion inside those systems. The system in which convective motion occurs, reduces the time for energy transmission, compared to random motion. For more complex systems, those convection cells form a network of transport channels, for the purpose of obeying the equations of motion in this geometry. Those transport networks are an essential feature of complex systems in biology, ecology, economy and society.

Quantum cellular automata

NASA Astrophysics Data System (ADS)

Porod, Wolfgang; Lent, Craig S.; Bernstein, Gary H.

1994-06-01

The Notre Dame group has developed a new paradigm for ultra-dense and ultra-fast information processing in nanoelectronic systems. These Quantum Cellular Automata (QCA's) are the first concrete proposal for a technology based on arrays of coupled quantum dots. The basic building block of these cellular arrays is the Notre Dame Logic Cell, as it has been called in the literature. The phenomenon of Coulomb exclusion, which is a synergistic interplay of quantum confinement and Coulomb interaction, leads to a bistable behavior of each cell which makes possible their use in large-scale cellular arrays. The physical interaction between neighboring cells has been exploited to implement logic functions. New functionality may be achieved in this fashion, and the Notre Dame group invented a versatile majority logic gate. In a series of papers, the feasibility of QCA wires, wire crossing, inverters, and Boolean logic gates was demonstrated. A major finding is that all logic functions may be integrated in a hierarchial fashion which allows the design of complicated QCA structures. The most complicated system which was simulated to date is a one-bit full adder consisting of some 200 cells. In addition to exploring these new concepts, efforts are under way to physically realize such structures both in semiconductor and metal systems. Extensive modeling work of semiconductor quantum dot structures has helped identify optimum design parameters for QCA experimental implementations.

Benefits of partnered strength training for prostate cancer survivors and spouses: results from a randomized controlled trial of the Exercising Together project.

PubMed

Winters-Stone, Kerri M; Lyons, Karen S; Dobek, Jessica; Dieckmann, Nathan F; Bennett, Jill A; Nail, Lillian; Beer, Tomasz M

2016-08-01

Prostate cancer can negatively impact quality of life of the patient and his spouse caregiver, but interventions rarely target the health of both partners simultaneously. We tested the feasibility and preliminary efficacy of a partnered strength training program on the physical and mental health of prostate cancer survivors (PCS) and spouse caregivers. Sixty-four couples were randomly assigned to 6 months of partnered strength training (Exercising Together, N = 32) or usual care (UC, N = 32). Objective measures included body composition (lean, fat and trunk fat mass (kg), and % body fat) by DXA, upper and lower body muscle strength by 1-repetition maximum, and physical function by the physical performance battery (PPB). Self-reported measures included the physical and mental health summary scales and physical function and fatigue subscales of the SF-36 and physical activity with the CHAMPS questionnaire. Couple retention rates were 100 % for Exercising Together and 84 % for UC. Median attendance of couples to Exercising Together sessions was 75 %. Men in Exercising Together became stronger in the upper body (p < 0.01) and more physically active (p < 0.01) than UC. Women in Exercising Together increased muscle mass (p = 0.05) and improved upper (p < 0.01) and lower body (p < 0.01) strength and PPB scores (p = 0.01) more than UC. Exercising Together is a novel couples-based approach to exercise that was feasible and improved several health outcomes for both PCS and their spouses. A couples-based approach should be considered in cancer survivorship programs so that outcomes can mutually benefit both partners. ClinicalTrials.gov NCT00954044.

Altered Actin Centripetal Retrograde Flow in Physically Restricted Immunological Synapses

PubMed Central

Yu, Cheng-han; Wu, Hung-Jen; Kaizuka, Yoshihisa; Vale, Ronald D.; Groves, Jay T.

2010-01-01

Antigen recognition by T cells involves large scale spatial reorganization of numerous receptor, adhesion, and costimulatory proteins within the T cell-antigen presenting cell (APC) junction. The resulting patterns can be distinctive, and are collectively known as the immunological synapse. Dynamical assembly of cytoskeletal network is believed to play an important role in driving these assembly processes. In one experimental strategy, the APC is replaced with a synthetic supported membrane. An advantage of this configuration is that solid structures patterned onto the underlying substrate can guide immunological synapse assembly into altered patterns. Here, we use mobile anti-CD3ε on the spatial-partitioned supported bilayer to ligate and trigger T cell receptor (TCR) in live Jurkat T cells. Simultaneous tracking of both TCR clusters and GFP-actin speckles reveals their dynamic association and individual flow patterns. Actin retrograde flow directs the inward transport of TCR clusters. Flow-based particle tracking algorithms allow us to investigate the velocity distribution of actin flow field across the whole synapse, and centripetal velocity of actin flow decreases as it moves toward the center of synapse. Localized actin flow analysis reveals that, while there is no influence on actin motion from substrate patterns directly, velocity differences of actin are observed over physically trapped TCR clusters. Actin flow regains its velocity immediately after passing through confined TCR clusters. These observations are consistent with a dynamic and dissipative coupling between TCR clusters and viscoelastic actin network. PMID:20686692

Effects of large vessel on temperature distribution based on photothermal coupling interaction model

NASA Astrophysics Data System (ADS)

Li, Zhifang; Zhang, Xiyang; Li, Zuoran; Li, Hui

2016-10-01

This paper is based on the finite element analysis method for studying effects of large blood vessel on temperature based on photothermal coupling interaction model, and it couples the physical field of optical transmission with the physical field of heat transfer in biological tissue by using COMSOL Multiphysics 4.4 software. The results demonstrate the cooling effect of large blood vessel, which can be potential application for the treatment of liver tumors.

Coupled-cluster computations of atomic nuclei

NASA Astrophysics Data System (ADS)

Hagen, G.; Papenbrock, T.; Hjorth-Jensen, M.; Dean, D. J.

2014-09-01

In the past decade, coupled-cluster theory has seen a renaissance in nuclear physics, with computations of neutron-rich and medium-mass nuclei. The method is efficient for nuclei with product-state references, and it describes many aspects of weakly bound and unbound nuclei. This report reviews the technical and conceptual developments of this method in nuclear physics, and the results of coupled-cluster calculations for nucleonic matter, and for exotic isotopes of helium, oxygen, calcium, and some of their neighbors.

Weak synchronization and large-scale collective oscillation in dense bacterial suspensions

NASA Astrophysics Data System (ADS)

Chen, Chong; Liu, Song; Shi, Xia-Qing; Chaté, Hugues; Wu, Yilin

2017-01-01

Collective oscillatory behaviour is ubiquitous in nature, having a vital role in many biological processes from embryogenesis and organ development to pace-making in neuron networks. Elucidating the mechanisms that give rise to synchronization is essential to the understanding of biological self-organization. Collective oscillations in biological multicellular systems often arise from long-range coupling mediated by diffusive chemicals, by electrochemical mechanisms, or by biomechanical interaction between cells and their physical environment. In these examples, the phase of some oscillatory intracellular degree of freedom is synchronized. Here, in contrast, we report the discovery of a weak synchronization mechanism that does not require long-range coupling or inherent oscillation of individual cells. We find that millions of motile cells in dense bacterial suspensions can self-organize into highly robust collective oscillatory motion, while individual cells move in an erratic manner, without obvious periodic motion but with frequent, abrupt and random directional changes. So erratic are individual trajectories that uncovering the collective oscillations of our micrometre-sized cells requires individual velocities to be averaged over tens or hundreds of micrometres. On such large scales, the oscillations appear to be in phase and the mean position of cells typically describes a regular elliptic trajectory. We found that the phase of the oscillations is organized into a centimetre-scale travelling wave. We present a model of noisy self-propelled particles with strictly local interactions that accounts faithfully for our observations, suggesting that self-organized collective oscillatory motion results from spontaneous chiral and rotational symmetry breaking. These findings reveal a previously unseen type of long-range order in active matter systems (those in which energy is spent locally to produce non-random motion). This mechanism of collective oscillation may inspire new strategies to control the self-organization of active matter and swarming robots.

Weak synchronization and large-scale collective oscillation in dense bacterial suspensions.

PubMed

Chen, Chong; Liu, Song; Shi, Xia-Qing; Chaté, Hugues; Wu, Yilin

2017-02-09

Collective oscillatory behaviour is ubiquitous in nature, having a vital role in many biological processes from embryogenesis and organ development to pace-making in neuron networks. Elucidating the mechanisms that give rise to synchronization is essential to the understanding of biological self-organization. Collective oscillations in biological multicellular systems often arise from long-range coupling mediated by diffusive chemicals, by electrochemical mechanisms, or by biomechanical interaction between cells and their physical environment. In these examples, the phase of some oscillatory intracellular degree of freedom is synchronized. Here, in contrast, we report the discovery of a weak synchronization mechanism that does not require long-range coupling or inherent oscillation of individual cells. We find that millions of motile cells in dense bacterial suspensions can self-organize into highly robust collective oscillatory motion, while individual cells move in an erratic manner, without obvious periodic motion but with frequent, abrupt and random directional changes. So erratic are individual trajectories that uncovering the collective oscillations of our micrometre-sized cells requires individual velocities to be averaged over tens or hundreds of micrometres. On such large scales, the oscillations appear to be in phase and the mean position of cells typically describes a regular elliptic trajectory. We found that the phase of the oscillations is organized into a centimetre-scale travelling wave. We present a model of noisy self-propelled particles with strictly local interactions that accounts faithfully for our observations, suggesting that self-organized collective oscillatory motion results from spontaneous chiral and rotational symmetry breaking. These findings reveal a previously unseen type of long-range order in active matter systems (those in which energy is spent locally to produce non-random motion). This mechanism of collective oscillation may inspire new strategies to control the self-organization of active matter and swarming robots.

HAI: A new TDLAS hygrometer for the HALO research aircraft

NASA Astrophysics Data System (ADS)

Klostermann, Tim; Afchine, Armin; Barthel, Jochen; Höh, Matthias; Wagner, Steven; Witzel, Oliver; Saathoff, Harald; Schiller, Cornelius; Ebert, Volker

2010-05-01

Water vapor is the most important greenhouse gas in the Earth's atmosphere and a key component for several physical and chemical processes. Therefore it is a key parameter to be measured during most research campaigns. The Hygrometer for Atmospheric Investigations (HAI) is especially designed for operations on the research aircraft HALO (High Altitude and LOng range research aircraft). HAI permits both, the in-situ measurement of water vapor with an open-path cell and the measurement of total water with an extractive close-path absorption cell. We are using TDLAS (Tunable Diode Laser Absorption Spectroscopy) in two water absorption bands with different line strength to increase the dynamical range. With this concept it is possible to measure from the middle troposphere up to the stratosphere. The open-path cell outside of the fuselage consists of a robust, aerodynamically designed aluminum structure with a single integrated White-cell for both laser beams. Although the mirror separation is only 15cm the cell allows an open absorption path of 4.8m. The detection of higher H2O concentrations is realized with a fiber coupled 1.4µm DFB diode laser. Inside the UTLS layer were small concentrations in the low ppm range are common, we employ up to 20 times stronger fundamental ro-vibration lines of the water molecule near 2.6µm. To supply this, the fiber coupled 2.6µm laser setup was developed and is a part of the HAI. Both detection wavelengths are introduced in the same open path cell via glass fibers which provide water measurements with a minimum of parasitic absorption. We will present the spectrometer design for high-quality airborne water measurements. Furthermore, first laboratory measurements will be shown.

Coupled electric fields in photorefractive driven liquid crystal hybrid cells - theory and numerical simulation

NASA Astrophysics Data System (ADS)

Moszczyński, P.; Walczak, A.; Marciniak, P.

2016-12-01

In cyclic articles previously published we described and analysed self-organized light fibres inside a liquid crystalline (LC) cell contained photosensitive polymer (PP) layer. Such asymmetric LC cell we call a hybrid LC cell. Light fibre arises along a laser beam path directed in plane of an LC cell. It means that a laser beam is parallel to photosensitive layer. We observed the asymmetric LC cell response on an external driving field polarization. Observation has been done for an AC field first. It is the reason we decided to carry out a detailed research for a DC driving field to obtain an LC cell response step by step. The properly prepared LC cell has been built with an isolating layer and garbage ions deletion. We proved by means of a physical model, as well as a numerical simulation that LC asymmetric response strongly depends on junction barriers between PP and LC layers. New parametric model for a junction barrier on PP/LC boundary has been proposed. Such model is very useful because of lack of proper conductivity and charge carriers of band structure data on LC material.

Computational electronics and electromagnetics

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

Shang, C C

The Computational Electronics and Electromagnetics thrust area serves as the focal point for Engineering R and D activities for developing computer-based design and analysis tools. Representative applications include design of particle accelerator cells and beamline components; design of transmission line components; engineering analysis and design of high-power (optical and microwave) components; photonics and optoelectronics circuit design; electromagnetic susceptibility analysis; and antenna synthesis. The FY-97 effort focuses on development and validation of (1) accelerator design codes; (2) 3-D massively parallel, time-dependent EM codes; (3) material models; (4) coupling and application of engineering tools for analysis and design of high-power components; andmore » (5) development of beam control algorithms coupled to beam transport physics codes. These efforts are in association with technology development in the power conversion, nondestructive evaluation, and microtechnology areas. The efforts complement technology development in Lawrence Livermore National programs.« less

Liquid–liquid phase transition in hydrogen by coupled electron–ion Monte Carlo simulations

DOE PAGES

Pierleoni, Carlo; Morales, Miguel A.; Rillo, Giovanni; ...

2016-04-20

The phase diagram of high-pressure hydrogen is of great interest for fundamental research, planetary physics, and energy applications. A first-order phase transition in the fluid phase between a molecular insulating fluid and a monoatomic metallic fluid has been predicted. The existence and precise location of the transition line is relevant for planetary models. Recent experiments reported contrasting results about the location of the transition. Theoretical results based on density functional theory are also very scattered. We report highly accurate coupled electron-ion Monte Carlo calculations of this transition, finding results that lie between the two experimental predictions, close to that measuredmore » in diamond anvil cell experiments but at 25-30 GPa higher pressure. Here, the transition along an isotherm is signaled by a discontinuity in the specific volume, a sudden dissociation of the molecules, a jump in electrical conductivity, and loss of electron localization.« less

Chemical Modification in the Design of Immobilized Enzyme Biocatalysts: Drawbacks and Opportunities.

PubMed

Rueda, Nazzoly; Dos Santos, Jose C S; Ortiz, Claudia; Torres, Rodrigo; Barbosa, Oveimar; Rodrigues, Rafael C; Berenguer-Murcia, Ángel; Fernandez-Lafuente, Roberto

2016-06-01

Chemical modification of enzymes and immobilization used to be considered as separate ways to improve enzyme properties. This review shows how the coupled use of both tools may greatly improve the final biocatalyst performance. Chemical modification of a previously immobilized enzyme is far simpler and easier to control than the modification of the free enzyme. Moreover, if protein modification is performed to improve its immobilization (enriching the enzyme in reactive groups), the final features of the immobilized enzyme may be greatly improved. Chemical modification may be directed to improve enzyme stability, but also to improve selectivity, specificity, activity, and even cell penetrability. Coupling of immobilization and chemical modification with site-directed mutagenesis is a powerful instrument to obtain fully controlled modification. Some new ideas such as photoreceptive enzyme modifiers that change their physical properties under UV exposition are discussed. © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clinical study and numerical simulation of brain cancer dynamics under radiotherapy

NASA Astrophysics Data System (ADS)

Nawrocki, S.; Zubik-Kowal, B.

2015-05-01

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

Electrical coupling: novel mechanism for sleep-wake control.

PubMed

Garcia-Rill, Edgar; Heister, David S; Ye, Meijun; Charlesworth, Amanda; Hayar, Abdallah

2007-11-01

Recent evidence suggests that certain anesthetic agents decrease electrical coupling, whereas the stimulant modafinil appears to increase electrical coupling. We investigated the potential role of electrical coupling in 2 reticular activating system sites, the subcoeruleus nucleus and in the pedunculopontine nucleus, which has been implicated in the modulation of arousal via ascending cholinergic activation of intralaminar thalamus and descending activation of the subcoeruleus nucleus to generate some of the signs of rapid eye movement sleep. We used 6- to 30-day-old rat pups to obtain brainstem slices to perform whole-cell patch-clamp recordings. Recordings from single cells revealed the presence of spikelets, manifestations of action potentials in coupled cells, and of dye coupling of neurons in the pedunculopontine nucleus. Recordings in pairs of pedunculopontine nucleus and subcoeruleus nucleus neurons revealed that some of these were electrically coupled with coupling coefficients of approximately 2%. After blockade of fast synaptic transmission, the cholinergic agonist carbachol was found to induce rhythmic activity in pedunculopontine nucleus and subcoeruleus nucleus neurons, an effect eliminated by the gap junction blockers carbenoxolone or mefloquine. The stimulant modafinil was found to decrease resistance in neurons in the pedunculopontine nucleus and subcoeruleus nucleus after fast synaptic blockade, indicating that the effect may be due to increased coupling. The finding of electrical coupling in specific reticular activating system cell groups supports the concept that this underlying process behind specific neurotransmitter interactions modulates ensemble activity across cell populations to promote changes in sleep-wake state.

From single cilia to collective waves in human airway ciliated tissues

NASA Astrophysics Data System (ADS)

Cicuta, Pietro; Chioccioli, Maurizio; Feriani, Luigi; Pellicciotta, Nicola; Kotar, Jurij

I will present experimental results on activity of motile cilia on various scales: from waveforms on individual cilia to the synchronised motion in cilia carpets of airway cells. Model synthetic experiments have given us an understanding of how cilia could couple with each other through forces transmitted by the fluid, and thus coordinate to beat into well organized waves (previous work is reviewed in Annu. Rev. Condens. Matter Phys. 7, 1-26 (2016)). Working with live imaging of airway human cells at the different scales, we can now test whether the biological system satisfies the ``simple'' behavior expected of the fluid flow coupling, or if other factors of mechanical forces transmission need to be accounted for. In general being able to link from the scale of molecular biological activity up to the phenomenology of collective dynamics requires to understand the relevant physical mechanism. This understanding then allows informed diagnostics (and perhaps therapeutic) approaches to a variety of diseases where mucociliary clearance in the airways is compromised. We have started exploring particularly cystic fibrosis, where the rheological properties of the mucus are affected and prevent efficient cilia synchronization. ERC Grant HydroSync.

Positive illusions about one's partner's physical attractiveness.

PubMed

Barelds-Dijkstra, Pieternel; Barelds, Dick P H

2008-03-01

This study examined couples' ratings of self and partner physical attractiveness. On the basis of the theory of positive illusions, it was expected that individuals would rate their partners as more attractive than their partners would rate themselves. Both members of 93 heterosexual couples, with a mean relationship length of about 14 years, provided ratings of both their own and their partner's physical attractiveness. Results support the theory that individuals hold positive illusions about their partner's physical attractiveness. Implications of these results in terms of relationship-enhancing biases are discussed.

A novel environmental chamber for neuronal network multisite recordings.

PubMed

Biffi, E; Regalia, G; Ghezzi, D; De Ceglia, R; Menegon, A; Ferrigno, G; Fiore, G B; Pedrocchi, A

2012-10-01

Environmental stability is a critical issue for neuronal networks in vitro. Hence, the ability to control the physical and chemical environment of cell cultures during electrophysiological measurements is an important requirement in the experimental design. In this work, we describe the development and the experimental verification of a closed chamber for multisite electrophysiology and optical monitoring. The chamber provides stable temperature, pH and humidity and guarantees cell viability comparable to standard incubators. Besides, it integrates the electronics for long-term neuronal activity recording. The system is portable and adaptable for multiple network housings, which allows performing parallel experiments in the same environment. Our results show that this device can be a solution for long-term electrophysiology, for dual network experiments and for coupled optical and electrical measurements. Copyright © 2012 Wiley Periodicals, Inc.

Influence of Rb/Cs Cation-Exchange on Inorganic Sn Halide Perovskites: From Chemical Structure to Physical Properties.

PubMed

Jung, Young-Kwang; Lee, Ji-Hwan; Walsh, Aron; Soon, Aloysius

2017-04-11

CsSnI 3 is a potential lead-free inorganic perovskite for solar energy applications due to its nontoxicity and attractive optoelectronic properties. Despite these advantages, photovoltaic cells using CsSnI 3 have not been successful to date, in part due to low stability. We demonstrate how gradual substitution of Rb for Cs influences the structural, thermodynamic, and electronic properties on the basis of first-principles density functional theory calculations. By examining the effect of the Rb:Cs ratio, we reveal a correlation between octahedral distortion and band gap, including spin-orbit coupling. We further highlight the cation-induced variation of the ionization potential (work function) and the importance of surface termination for tin-based halide perovskites for engineering high-performance solar cells.

Electrophysiology of sodium-coupled transport in proximal renal tubules.

PubMed

Lang, F; Messner, G; Rehwald, W

1986-06-01

Effects of sodium-coupled transport on intracellular electrolytes and electrical properties of proximal renal tubule cells are described in this review. Simultaneous with addition of substrate for sodium-coupled transport to luminal perfusates, both cell membranes depolarize. The luminal cell membrane depolarizes due to opening of sodium-cotransport pathways. The depolarization of the peritubular cell membrane during sodium-coupled transport is primarily due to a circular current reentering the lumen via the paracellular pathway. The depolarization leads to a transient decrease of basolateral potassium conductance that in turn amplifies the depolarization. However, within 5-10 min of continued exposure to substrate, potassium conductance increases again, and peritubular cell membrane repolarizes. During depolarization the driving force of peritubular bicarbonate exit is reduced. As a result net alkalinization of the cell prevails despite an increase of intracellular sodium activity, which reduces the driving force for the sodium-hydrogen ion exchanger and would thus have been expected to acidify the cell. No evidence is obtained for regulatory inhibition of sodium-coupled transport by intracellular sodium or calcium. Rather, luminal cotransport is altered by the change of driving forces.

Sequential activities of Dynein, Mud and Asp in centrosome-spindle coupling maintain centrosome number upon mitosis.

PubMed

Bosveld, Floris; Ainslie, Anna; Bellaïche, Yohanns

2017-10-15

Centrosomes nucleate microtubules and are tightly coupled to the bipolar spindle to ensure genome integrity, cell division orientation and centrosome segregation. While the mechanisms of centrosome-dependent microtubule nucleation and bipolar spindle assembly have been the focus of numerous works, less is known about the mechanisms ensuring the centrosome-spindle coupling. The conserved NuMA protein (Mud in Drosophila ) is best known for its role in spindle orientation. Here, we analyzed the role of Mud and two of its interactors, Asp and Dynein, in the regulation of centrosome numbers in Drosophila epithelial cells. We found that Dynein and Mud mainly initiate centrosome-spindle coupling prior to nuclear envelope breakdown (NEB) by promoting correct centrosome positioning or separation, while Asp acts largely independently of Dynein and Mud to maintain centrosome-spindle coupling. Failure in the centrosome-spindle coupling leads to mis-segregation of the two centrosomes into one daughter cell, resulting in cells with supernumerary centrosomes during subsequent divisions. Altogether, we propose that Dynein, Mud and Asp operate sequentially during the cell cycle to ensure efficient centrosome-spindle coupling in mitosis, thereby preventing centrosome mis-segregation to maintain centrosome number. © 2017. Published by The Company of Biologists Ltd.

Towards the virtual artery: a multiscale model for vascular physiology at the physics-chemistry-biology interface.

PubMed

Hoekstra, Alfons G; Alowayyed, Saad; Lorenz, Eric; Melnikova, Natalia; Mountrakis, Lampros; van Rooij, Britt; Svitenkov, Andrew; Závodszky, Gábor; Zun, Pavel

2016-11-13

This discussion paper introduces the concept of the Virtual Artery as a multiscale model for arterial physiology and pathologies at the physics-chemistry-biology (PCB) interface. The cellular level is identified as the mesoscopic level, and we argue that by coupling cell-based models with other relevant models on the macro- and microscale, a versatile model of arterial health and disease can be composed. We review the necessary ingredients, both models of arteries at many different scales, as well as generic methods to compose multiscale models. Next, we discuss how this can be combined into the virtual artery. Finally, we argue that the concept of models at the PCB interface could or perhaps should become a powerful paradigm, not only as in our case for studying physiology, but also for many other systems that have such PCB interfaces.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Authors.

Physical Methods for Intracellular Delivery: Practical Aspects from Laboratory Use to Industrial-Scale Processing

PubMed Central

Meacham, J. Mark; Durvasula, Kiranmai; Degertekin, F. Levent; Fedorov, Andrei G.

2015-01-01

Effective intracellular delivery is a significant impediment to research and therapeutic applications at all processing scales. Physical delivery methods have long demonstrated the ability to deliver cargo molecules directly to the cytoplasm or nucleus, and the mechanisms underlying the most common approaches (microinjection, electroporation, and sonoporation) have been extensively investigated. In this review, we discuss established approaches, as well as emerging techniques (magnetofection, optoinjection, and combined modalities). In addition to operating principles and implementation strategies, we address applicability and limitations of various in vitro, ex vivo, and in vivo platforms. Importantly, we perform critical assessments regarding (1) treatment efficacy with diverse cell types and delivered cargo molecules, (2) suitability to different processing scales (from single cell to large populations), (3) suitability for automation/integration with existing workflows, and (4) multiplexing potential and flexibility/adaptability to enable rapid changeover between treatments of varied cell types. Existing techniques typically fall short in one or more of these criteria; however, introduction of micro-/nanotechnology concepts, as well as synergistic coupling of complementary method(s), can improve performance and applicability of a particular approach, overcoming barriers to practical implementation. For this reason, we emphasize these strategies in examining recent advances in development of delivery systems. PMID:23813915

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

PubMed Central

Jost, Daniel; Carrivain, Pascal; Cavalli, Giacomo; Vaillant, Cédric

2014-01-01

Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states. These domains are stably inherited across many cell generations and can be remodeled in response to developmental and external cues, hence contributing to the robustness and plasticity of expression patterns and cell phenotypes. Remarkably, recent studies indicate that these 1D epigenomic domains tend to fold into 3D topologically associated domains forming specialized nuclear chromatin compartments. However, the general mechanisms behind such compartmentalization including the contribution of epigenetic regulation remain unclear. Here, we address the question of the coupling between chromatin folding and epigenome. Using polymer physics, we analyze the properties of a block copolymer model that accounts for local epigenomic information. Considering copolymers build from the epigenomic landscape of Drosophila, we observe a very good agreement with the folding patterns observed in chromosome conformation capture experiments. Moreover, this model provides a physical basis for the existence of multistability in epigenome folding at sub-chromosomal scale. We show how experiments are fully consistent with multistable conformations where topologically associated domains of the same epigenomic state interact dynamically with each other. Our approach provides a general framework to improve our understanding of chromatin folding during cell cycle and differentiation and its relation to epigenetics. PMID:25092923

Virus-Bacterium Coupling Driven by both Turbidity and Hydrodynamics in an Amazonian Floodplain Lake ▿ † ‡

PubMed Central

Barros, Nathan; Farjalla, Vinicius F.; Soares, Maria C.; Melo, Rossana C. N.; Roland, Fábio

2010-01-01

The importance of viruses in aquatic ecosystem functioning has been widely described. However, few studies have examined tropical aquatic ecosystems. Here, we evaluated for the first time viruses and their relationship with other planktonic communities in an Amazonian freshwater ecosystem. Coupling between viruses and bacteria was studied, focusing both on hydrologic dynamics and anthropogenic forced turbidity in the system (Lake Batata). Samples were taken during four hydrologic seasons at both natural and impacted sites to count virus-like particles (VLP) and bacteria. In parallel, virus-infected bacteria were identified and quantified by transmission electron microscopy (TEM). Viral abundance ranged from 0.5 × 107 ± 0.2 × 107 VLP ml−1 (high-water season, impacted site) to 1.7 × 107 ± 0.4 × 107 VLP ml−1 (low-water season, natural site). These data were strongly correlated with the bacterial abundance (r2 = 0.84; P < 0.05), which ranged from 1.0 × 106 ± 0.5 × 106 cells ml−1 (high water, impacted site) to 3.4 × 106 ± 0.7 × 106 cells ml−1 (low water, natural site). Moreover, the viral abundance was weakly correlated with chlorophyll a, suggesting that most viruses were bacteriophages. TEM quantitative analyses revealed that the frequency of visibly infected cells was 20%, with 10 ± 3 phages per cell section. In general, we found a low virus-bacterium ratio (<7). Both the close coupling between the viral and bacterial abundances and the low virus-bacterium ratio suggest that viral abundance tends to be driven by the reduction of hosts for viral infection. Our results demonstrate that viruses are controlled by biological substrates, whereas in addition to grazing, bacteria are regulated by physical processes caused by turbidity, which affect underwater light distribution and dissolved organic carbon availability. PMID:20833790

Virus-bacterium coupling driven by both turbidity and hydrodynamics in an Amazonian floodplain lake.

PubMed

Barros, Nathan; Farjalla, Vinicius F; Soares, Maria C; Melo, Rossana C N; Roland, Fábio

2010-11-01

The importance of viruses in aquatic ecosystem functioning has been widely described. However, few studies have examined tropical aquatic ecosystems. Here, we evaluated for the first time viruses and their relationship with other planktonic communities in an Amazonian freshwater ecosystem. Coupling between viruses and bacteria was studied, focusing both on hydrologic dynamics and anthropogenic forced turbidity in the system (Lake Batata). Samples were taken during four hydrologic seasons at both natural and impacted sites to count virus-like particles (VLP) and bacteria. In parallel, virus-infected bacteria were identified and quantified by transmission electron microscopy (TEM). Viral abundance ranged from 0.5 × 10⁷ ± 0.2 × 10⁷ VLP ml⁻¹ (high-water season, impacted site) to 1.7 × 10⁷ ± 0.4 × 10⁷ VLP ml⁻¹ (low-water season, natural site). These data were strongly correlated with the bacterial abundance (r² = 0.84; P < 0.05), which ranged from 1.0 × 10⁶ ± 0.5 × 10⁶ cells ml⁻¹ (high water, impacted site) to 3.4 × 10⁶ ± 0.7 × 10⁶ cells ml⁻¹ (low water, natural site). Moreover, the viral abundance was weakly correlated with chlorophyll a, suggesting that most viruses were bacteriophages. TEM quantitative analyses revealed that the frequency of visibly infected cells was 20%, with 10 ± 3 phages per cell section. In general, we found a low virus-bacterium ratio (<7). Both the close coupling between the viral and bacterial abundances and the low virus-bacterium ratio suggest that viral abundance tends to be driven by the reduction of hosts for viral infection. Our results demonstrate that viruses are controlled by biological substrates, whereas in addition to grazing, bacteria are regulated by physical processes caused by turbidity, which affect underwater light distribution and dissolved organic carbon availability.

Bone cell communication factors and Semaphorins

PubMed Central

Negishi-Koga, Takako; Takayanagi, Hiroshi

2012-01-01

Bone tissue is continuously renewed throughout adult life by a process called 'remodeling', which involves a dynamic interplay among bone cells including osteoclasts, osteoblasts and osteocytes. For example, a tight coupling between bone resorption and formation is essential for the homeostasis of the skeletal system. Studies on the coupling mechanism in physiological and pathological settings have revealed that osteoclasts or osteoclastic bone resorption promote bone formation through the production of diverse coupling factors. The classical coupling factors are the molecules that promote bone formation after resorption, but there may be distinct mechanisms at work in various phases of bone remodeling. A recent study revealed that the Semaphorin 4D expressed by osteoclasts inhibits bone formation, which represents a mechanism by which coupling is dissociated. Furthermore, it has been demonstrated that osteoblastic expression of Semaphorin 3A exerts an osteoprotective effect by both suppressing bone resorption and increasing bone formation. Thus, recent advances have made it increasingly clear that bone remodeling is regulated by not only classical coupling factors, but also molecules that mediate cell–cell communication among bone cells. We propose that such factors be called bone cell communication factors, which control the delicate balance of the interaction of bone cells so as to maintain bone homeostasis. PMID:24171101

Coherence and frequency in the reticular activating system (RAS)

PubMed Central

Garcia-Rill, Edgar; Kezunovic, Nebojsa; Hyde, James; Simon, Christen; Beck, Paige; Urbano, Francisco J.

2012-01-01

SUMMARY This review considers recent evidence showing that cells in the reticular activating system (RAS) exhibit 1) electrical coupling mainly in GABAergic cells, and 2) gamma band activity in virtually all of the cells. Specifically, cells in the mesopontine pedunculopontine nucleus (PPN), intralaminar parafascicular nucleus (Pf), and pontine dorsal subcoeruleus nucleus dorsalis (SubCD) 1) show electrical coupling, and 2) all fire in the beta/gamma band range when maximally activated, but no higher. The mechanism behind electrical coupling is important because the stimulant modafinil was shown to increase electrical coupling. We also provide recent findings demonstrating that all cells in the PPN and Pf have high threshold, voltage-dependent P/Q-type calcium channels that are essential to gamma band activity. On the other hand, all SubCD, and some PPN, cells manifested sodium-dependent subthreshold oscillations. A novel mechanism for sleep-wake control based on transmitter interactions, electrical coupling, and gamma band activity is described. We speculate that continuous sensory input will modulate coupling and induce gamma band activity in the RAS that could participate in the processes of preconscious awareness, and provide the essential stream of information for the formulation of many of our actions. PMID:23044219

Coherence and frequency in the reticular activating system (RAS).

PubMed

Garcia-Rill, Edgar; Kezunovic, Nebojsa; Hyde, James; Simon, Christen; Beck, Paige; Urbano, Francisco J

2013-06-01

This review considers recent evidence showing that cells in the reticular activating system (RAS) exhibit (1) electrical coupling mainly in GABAergic cells, and (2) gamma band activity in virtually all of the cells. Specifically, cells in the mesopontine pedunculopontine nucleus (PPN), intralaminar parafascicular nucleus (Pf), and pontine dorsal subcoeruleus nucleus dorsalis (SubCD) (1) show electrical coupling, and (2) all fire in the beta/gamma band range when maximally activated, but no higher. The mechanism behind electrical coupling is important because the stimulant modafinil was shown to increase electrical coupling. We also provide recent findings demonstrating that all cells in the PPN and Pf have high threshold, voltage-dependent P/Q-type calcium channels that are essential to gamma band activity. On the other hand, all SubCD, and some PPN, cells manifested sodium-dependent subthreshold oscillations. A novel mechanism for sleep-wake control based on transmitter interactions, electrical coupling, and gamma band activity is described. We speculate that continuous sensory input will modulate coupling and induce gamma band activity in the RAS that could participate in the processes of preconscious awareness, and provide the essential stream of information for the formulation of many of our actions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Weak synchronization and large-scale collective oscillation in dense bacterial suspensions

NASA Astrophysics Data System (ADS)

Wu, Yilin

Collective oscillatory behavior is ubiquitous in nature and it plays a vital role in many biological processes. Collective oscillations in biological multicellular systems often arise from coupling mediated by diffusive chemicals, by electrochemical mechanisms, or by biomechanical interaction between cells and their physical environment. In these examples, the phase of some oscillatory intracellular degree of freedom is synchronized. Here, in contrast, we discovered a unique 'weak synchronization' mechanism that does not require long-range coupling, nor even inherent oscillation of individual cells: We found that millions of motile cells in dense bacterial suspensions can self-organize into highly robust collective oscillatory motion, while individuals move in an erratic manner. Over large spatial scales we found that the phase of the oscillations is in fact organized into a centimeter scale traveling wave. We present a model of noisy self-propelled particles with strictly local interactions that accounts faithfully for our observations. These findings expand our knowledge of biological self-organization and reveal a new type of long-range order in active matter systems. The mechanism of collective oscillation uncovered here may inspire new strategies to control the self-organization of active matter and swarming robots. This work is supported by funding from CUHK Direct research Grants (4053019, 4053079, 4053130), the Research Grants Council of HKSAR (RGC Ref. No. CUHK 409713), and from the National Natural Science Foundation of China (NSFC 21473152).

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

Hu, Yi, E-mail: yihooyi@gmail.com; Ericsson, Ida, E-mail: ida.ericsson@ntnu.no; Doseth, Berit, E-mail: berit.doseth@ntnu.no

Activation-induced cytidine deaminase (AID) is the mutator enzyme in adaptive immunity. AID initiates the antibody diversification processes in activated B cells by deaminating cytosine to uracil in immunoglobulin genes. To some extent other genes are also targeted, which may lead to genome instability and B cell malignancy. Thus, it is crucial to understand its targeting and regulation mechanisms. AID is regulated at several levels including subcellular compartmentalization. However, the complex nuclear distribution and trafficking of AID has not been studied in detail previously. In this work, we examined the subnuclear localization of AID and its interaction partner CTNNBL1 and foundmore » that they associate with spliceosome-associated structures including Cajal bodies and nuclear speckles. Moreover, protein kinase A (PKA), which activates AID by phosphorylation at Ser38, is present together with AID in nuclear speckles. Importantly, we demonstrate that AID physically associates with the major spliceosome subunits (small nuclear ribonucleoproteins, snRNPs), as well as other essential splicing components, in addition to the transcription machinery. Based on our findings and the literature, we suggest a transcription-coupled splicing-associated model for AID targeting and activation. - Highlights: • AID and its interaction partner CTNNBL1 localize to Cajal bodies and nuclear speckles. • AID associates with its activating kinase PKA in nuclear speckles. • AID is linked to the splicing machinery in switching B-cells. • Our findings suggest a transcription-coupled splicing associated mechanism for AID targeting and activation.« less

Cladribine treatment of multiple sclerosis is associated with depletion of memory B cells.

PubMed

Ceronie, Bryan; Jacobs, Benjamin M; Baker, David; Dubuisson, Nicolas; Mao, Zhifeng; Ammoscato, Francesca; Lock, Helen; Longhurst, Hilary J; Giovannoni, Gavin; Schmierer, Klaus

2018-05-01

The mechanism of action of oral cladribine, recently licensed for relapsing multiple sclerosis, is unknown. To determine whether cladribine depletes memory B cells consistent with our recent hypothesis that effective, disease-modifying treatments act by physical/functional depletion of memory B cells. A cross-sectional study examined 40 people with multiple sclerosis at the end of the first cycle of alemtuzumab or injectable cladribine. The relative proportions and absolute numbers of peripheral blood B lymphocyte subsets were measured using flow cytometry. Cell-subtype expression of genes involved in cladribine metabolism was examined from data in public repositories. Cladribine markedly depleted class-switched and unswitched memory B cells to levels comparable with alemtuzumab, but without the associated initial lymphopenia. CD3 + T cell depletion was modest. The mRNA expression of metabolism genes varied between lymphocyte subsets. A high ratio of deoxycytidine kinase to group I cytosolic 5' nucleotidase expression was present in B cells and was particularly high in mature, memory and notably germinal centre B cells, but not plasma cells. Selective B cell cytotoxicity coupled with slow repopulation kinetics results in long-term, memory B cell depletion by cladribine. These may offer a new target, possibly with potential biomarker activity, for future drug development.

Optically Driven Spin Based Quantum Dots for Quantum Computing - Research Area 6 Physics 6.3.2

DTIC Science & Technology

2015-12-15

quantum dots (SAQD) in Schottky diodes . Based on spins in these dots, a scalable architecture has been proposed [Adv. in Physics, 59, 703 (2010)] by us...housed in two coupled quantum dots with tunneling between them, as described above, may not be scalable but can serve as a node in a quantum network. The... tunneling -coupled two-electron spin ground states in the vertically coupled quantum dots for “universal computation” two spin qubits within the universe of

Cell-cell bioelectrical interactions and local heterogeneities in genetic networks: a model for the stabilization of single-cell states and multicellular oscillations.

PubMed

Cervera, Javier; Manzanares, José A; Mafe, Salvador

2018-04-04

Genetic networks operate in the presence of local heterogeneities in single-cell transcription and translation rates. Bioelectrical networks and spatio-temporal maps of cell electric potentials can influence multicellular ensembles. Could cell-cell bioelectrical interactions mediated by intercellular gap junctions contribute to the stabilization of multicellular states against local genetic heterogeneities? We theoretically analyze this question on the basis of two well-established experimental facts: (i) the membrane potential is a reliable read-out of the single-cell electrical state and (ii) when the cells are coupled together, their individual cell potentials can be influenced by ensemble-averaged electrical potentials. We propose a minimal biophysical model for the coupling between genetic and bioelectrical networks that associates the local changes occurring in the transcription and translation rates of an ion channel protein with abnormally low (depolarized) cell potentials. We then analyze the conditions under which the depolarization of a small region (patch) in a multicellular ensemble can be reverted by its bioelectrical coupling with the (normally polarized) neighboring cells. We show also that the coupling between genetic and bioelectric networks of non-excitable cells, modulated by average electric potentials at the multicellular ensemble level, can produce oscillatory phenomena. The simulations show the importance of single-cell potentials characteristic of polarized and depolarized states, the relative sizes of the abnormally polarized patch and the rest of the normally polarized ensemble, and intercellular coupling.

Physics of Intracellular Organization in Bacteria.

PubMed

Wingreen, Ned S; Huang, Kerwyn Casey

2015-01-01

With the realization that bacteria achieve exquisite levels of spatiotemporal organization has come the challenge of discovering the underlying mechanisms. In this review, we describe three classes of such mechanisms, each of which has physical origins: the use of landmarks, the creation of higher-order structures that enable geometric sensing, and the emergence of length scales from systems of chemical reactions coupled to diffusion. We then examine the diversity of geometric cues that exist even in cells with relatively simple geometries, and end by discussing both new technologies that could drive further discovery and the implications of our current knowledge for the behavior, fitness, and evolution of bacteria. The organizational strategies described here are employed in a wide variety of systems and in species across all kingdoms of life; in many ways they provide a general blueprint for organizing the building blocks of life.

Experimental approach to interaction physics challenges of the shock ignition scheme using short pulse lasers.

PubMed

Goyon, C; Depierreux, S; Yahia, V; Loisel, G; Baccou, C; Courvoisier, C; Borisenko, N G; Orekhov, A; Rosmej, O; Labaune, C

2013-12-06

An experimental program was designed to study the most important issues of laser-plasma interaction physics in the context of the shock ignition scheme. In the new experiments presented in this Letter, a combination of kilojoule and short laser pulses was used to study the laser-plasma coupling at high laser intensities for a large range of electron densities and plasma profiles. We find that the backscatter is dominated by stimulated Brillouin scattering with stimulated Raman scattering staying at a limited level. This is in agreement with past experiments using long pulses but laser intensities limited to 2×10(15)  W/cm2, or short pulses with intensities up to 5×10(16)  W/cm2 as well as with 2D particle-in-cell simulations.

A physics-based crystallographic modeling framework for describing the thermal creep behavior of Fe-Cr alloys

DOE PAGES

Wen, Wei; Capolungo, Laurent; Patra, Anirban; ...

2017-02-23

In this work, a physics-based thermal creep model is developed based on the understanding of the microstructure in Fe-Cr alloys. This model is associated with a transition state theory based framework that considers the distribution of internal stresses at sub-material point level. The thermally activated dislocation glide and climb mechanisms are coupled in the obstacle-bypass processes for both dislocation and precipitate-type barriers. A kinetic law is proposed to track the dislocation densities evolution in the subgrain interior and in the cell wall. The predicted results show that this model, embedded in the visco-plastic self-consistent (VPSC) framework, captures well the creepmore » behaviors for primary and steady-state stages under various loading conditions. We also discuss the roles of the mechanisms involved.« less

Lattice dynamics and electron-phonon coupling calculations using nondiagonal supercells

NASA Astrophysics Data System (ADS)

Lloyd-Williams, Jonathan; Monserrat, Bartomeu

Quantities derived from electron-phonon coupling matrix elements require a fine sampling of the vibrational Brillouin zone. Converged results are typically not obtainable using the direct method, in which a perturbation is frozen into the system and the total energy derivatives are calculated using a finite difference approach, because the size of simulation cell needed is prohibitively large. We show that it is possible to determine the response of a periodic system to a perturbation characterized by a wave vector with reduced fractional coordinates (m1 /n1 ,m2 /n2 ,m3 /n3) using a supercell containing a number of primitive cells equal to the least common multiple of n1, n2, and n3. This is accomplished by utilizing supercell matrices containing nonzero off-diagonal elements. We present the results of electron-phonon coupling calculations using the direct method to sample the vibrational Brillouin zone with grids of unprecedented size for a range of systems, including the canonical example of diamond. We also demonstrate that the use of nondiagonal supercells reduces by over an order of magnitude the computational cost of obtaining converged vibrational densities of states and phonon dispersion curves. J.L.-W. is supported by the Engineering and Physical Sciences Research Council (EPSRC). B.M. is supported by Robinson College, Cambridge, and the Cambridge Philosophical Society. This work was supported by EPSRC Grants EP/J017639/1 and EP/K013564/1.

Tunable Plasmonic Nanoprobes for Theranostics of Prostate Cancer

PubMed Central

Lukianova-Hleb, Ekaterina Y.; Oginsky, Alexander O.; Samaniego, Adam P.; Shenefelt, Derek L.; Wagner, Daniel S.; Hafner, Jason H.; Farach-Carson, Mary C.; Lapotko, Dmitri O.

2011-01-01

Theranostic applications require coupling of diagnosis and therapy, a high degree of specificity and adaptability to delivery methods compatible with clinical practice. The tunable physical and biological effects of selective targeting and activation of plasmonic nanobubbles (PNB) were studied in a heterogeneous biological microenvironment of prostate cancer and stromal cells. All cells were targeted with conjugates of gold nanoparticles (NPs) through an antibody-receptor-endocytosis-nanocluster mechanism that produced NP clusters. The simultaneous pulsed optical activation of intracellular NP clusters at several wavelengths resulted in higher optical contrast and therapeutic selectivity of PNBs compared with those of gold NPs alone. The developed mechanism was termed “rainbow plasmonic nanobubbles.” The cellular effect of rainbow PNBs was tuned in situ in target cells, thus supporting a theranostic algorithm of prostate cancer cell detection and follow-up guided destruction without damage to collateral cells. The specificity and tunability of PNBs is promising for theranostic applications and we discuss a fiber optic platform that will capitalize on these features to bring theranostic tools to the clinic. PMID:21547151

A novel integration system of magnetically immobilized cells and a pair of graphite plate-stainless iron mesh electrodes for the bioremediation of coking wastewater.

PubMed

Jiang, Bei; Tan, Liang; Ning, Shuxiang; Shi, Shengnan

2016-09-01

Magnetically immobilized cells of Comamonas sp. JB coupling with electrode reaction was developed to enhance the treatment efficiency of coking wastewater containing phenol, carbazole (CA), dibenzofuran (DBF), and dibenzothiophene (DBT). The pair of graphite plate-stainless iron mesh electrodes was chosen as the most suitable electrodes. Magnetically immobilized cells coupling with graphite plate-stainless iron mesh electrodes (coupling system) exhibited high degradation activity for all the compounds, which were significantly higher than the sum by single magnetically immobilized cells and electrode reaction at the optimal voltage. Recycling experiments demonstrated that the degradation activity of coupling system increased gradually during eight recycles, indicating that there was a coupling effect between the biodegradation and electrode reaction. Phenol hydroxylase and qPCR assays confirmed that appropriate electrical stimulation could improve phenol hydroxylase activity and promote cells growth. Toxicity assessment suggested the treatment of the coking wastewater by coupling system led to less toxicity than untreated wastewater. Copyright © 2016 Elsevier Ltd. All rights reserved.

DURIP: Electrokinetic Injection and Separation System for Analysis of Protein and Peptide Transport, Adsorption and Kinetics Instrumentation Proposal

DTIC Science & Technology

2015-03-18

both the electric double layer that forms at a solid-liquid interface as well as the biomolecules themselves, we can harness the coupled physics of...the biomolecules themselves, we can harness the coupled physics of complex biological fluids in nanofluidic channels towards unique, efficient

Child Maltreatment History among Newlywed Couples: A Longitudinal Study of Marital Outcomes and Mediating Pathways

ERIC Educational Resources Information Center

DiLillo, David; Peugh, James; Walsh, Kate; Panuzio, Jillian; Trask, Emily; Evans, Sarah

2009-01-01

Participants included 202 newlywed couples who reported retrospectively about child maltreatment experiences (sexual abuse, physical abuse, psychological abuse, and neglect) and whose marital functioning was assessed 3 times over a 2-year period. Decreased marital satisfaction at T1 was predicted by childhood physical abuse, psychological abuse,…

VERA 3.6 Release Notes

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

Williamson, Richard L.; Kochunas, Brendan; Adams, Brian M.

The Virtual Environment for Reactor Applications components included in this distribution include selected computational tools and supporting infrastructure that solve neutronics, thermal-hydraulics, fuel performance, and coupled neutronics-thermal hydraulics problems. The infrastructure components provide a simplified common user input capability and provide for the physics integration with data transfer and coupled-physics iterative solution algorithms.

Shadow poles in coupled-channel problems calculated with the Berggren basis

NASA Astrophysics Data System (ADS)

Id Betan, R. M.; Kruppa, A. T.; Vertse, T.

2018-02-01

Background: In coupled-channels models the poles of the scattering S matrix are located on different Riemann sheets. Physical observables are affected mainly by poles closest to the physical region but sometimes shadow poles have considerable effect too. Purpose: The purpose of this paper is to show that in coupled-channels problems all poles of the S matrix can be located by an expansion in terms of a properly constructed complex-energy basis. Method: The Berggren basis is used for expanding the coupled-channels solutions. Results: The locations of the poles of the S matrix for the Cox potential, constructed for coupled-channels problems, were numerically calculated and compared with the exact ones. In a nuclear physics application the Jπ=3 /2+ resonant poles of 5He were calculated in a phenomenological two-channel model. The properties of both the normal and shadow resonances agree with previous findings. Conclusions: We have shown that, with an appropriately chosen Berggren basis, all poles of the S matrix including the shadow poles can be determined. We have found that the shadow pole of 5He migrates between Riemann sheets if the coupling strength is varied.

Biophysical assays to probe the mechanical properties of the interphase cell nucleus: substrate strain application and microneedle manipulation.

PubMed

Lombardi, Maria L; Zwerger, Monika; Lammerding, Jan

2011-09-14

In most eukaryotic cells, the nucleus is the largest organelle and is typically 2 to 10 times stiffer than the surrounding cytoskeleton; consequently, the physical properties of the nucleus contribute significantly to the overall biomechanical behavior of cells under physiological and pathological conditions. For example, in migrating neutrophils and invading cancer cells, nuclear stiffness can pose a major obstacle during extravasation or passage through narrow spaces within tissues.(1) On the other hand, the nucleus of cells in mechanically active tissue such as muscle requires sufficient structural support to withstand repetitive mechanical stress. Importantly, the nucleus is tightly integrated into the cellular architecture; it is physically connected to the surrounding cytoskeleton, which is a critical requirement for the intracellular movement and positioning of the nucleus, for example, in polarized cells, synaptic nuclei at neuromuscular junctions, or in migrating cells.(2) Not surprisingly, mutations in nuclear envelope proteins such as lamins and nesprins, which play a critical role in determining nuclear stiffness and nucleo-cytoskeletal coupling, have been shown recently to result in a number of human diseases, including Emery-Dreifuss muscular dystrophy, limb-girdle muscular dystrophy, and dilated cardiomyopathy.(3) To investigate the biophysical function of diverse nuclear envelope proteins and the effect of specific mutations, we have developed experimental methods to study the physical properties of the nucleus in single, living cells subjected to global or localized mechanical perturbation. Measuring induced nuclear deformations in response to precisely applied substrate strain application yields important information on the deformability of the nucleus and allows quantitative comparison between different mutations or cell lines deficient for specific nuclear envelope proteins. Localized cytoskeletal strain application with a microneedle is used to complement this assay and can yield additional information on intracellular force transmission between the nucleus and the cytoskeleton. Studying nuclear mechanics in intact living cells preserves the normal intracellular architecture and avoids potential artifacts that can arise when working with isolated nuclei. Furthermore, substrate strain application presents a good model for the physiological stress experienced by cells in muscle or other tissues (e.g., vascular smooth muscle cells exposed to vessel strain). Lastly, while these tools have been developed primarily to study nuclear mechanics, they can also be applied to investigate the function of cytoskeletal proteins and mechanotransduction signaling.

Inheritance of Cell-Cycle Duration in the Presence of Periodic Forcing

NASA Astrophysics Data System (ADS)

Mosheiff, Noga; Martins, Bruno M. C.; Pearl-Mizrahi, Sivan; Grünberger, Alexander; Helfrich, Stefan; Mihalcescu, Irina; Kohlheyer, Dietrich; Locke, James C. W.; Glass, Leon; Balaban, Nathalie Q.

2018-04-01

Periodic forcing of nonlinear oscillators leads to a large number of dynamic behaviors. The coupling of the cell cycle to the circadian clock provides a biological realization of such forcing. A previous model of forcing leads to nontrivial relations between correlations along cell lineages. Here, we present a simplified two-dimensional nonlinear map for the periodic forcing of the cell cycle. Using high-throughput single-cell microscopy, we have studied the correlations between cell-cycle duration in discrete lineages of several different organisms, including those with known coupling to a circadian clock and those without known coupling to a circadian clock. The model reproduces the paradoxical correlations and predicts new features that can be compared with the experimental data. By fitting the model to the data, we extract the important parameters that govern the dynamics. Interestingly, the model reproduces bimodal distributions for cell-cycle duration, as well as the gating of cell division by the phase of the clock, without having been explicitly fed into the model. In addition, the model predicts that circadian coupling may increase cell-to-cell variability in a clonal population of cells. In agreement with this prediction, deletion of the circadian clock reduces variability. Our results show that simple correlations can identify systems under periodic forcing and that studies of nonlinear coupling of biological oscillators provide insight into basic cellular processes of growth.

On understanding the very different science premises meaningful to CAM versus orthodox medicine: Part II--applications of Part I fundamentals to five different space-time examples.

PubMed

Tiller, William A

2010-04-01

In Part I of this pair of articles, the fundamental experimental observations and theoretical perspectives were provided for one to understand the key differences between our normal, uncoupled state of physical reality and the human consciousness-induced coupled state of physical reality. Here in Part II, the thermodynamics of complementary and alternative medicine, which deals with the partially coupled state of physical reality, is explored via the use of five different foci of relevance to today's science and medicine: (1) homeopathy; (2) the placebo effect; (3) long-range, room temperature, macroscopic size-scale, information entanglement; (4) an explanation for dark matter/energy plus human levitation possibility; and (5) electrodermal diagnostic devices. The purpose of this pair of articles is to clearly differentiate the use and limitations of uncoupled state physics in both nature and today's orthodox medicine from coupled state physics in tomorrow's complementary and alternative medicine.

Manipulation of Suspended Single Cells by Microfluidics and Optical Tweezers

PubMed Central

Nève, Nathalie; Kohles, Sean S.; Winn, Shelley R.; Tretheway, Derek C.

2010-01-01

Chondrocytes and osteoblasts experience multiple stresses in vivo. The optimum mechanical conditions for cell health are not fully understood. This paper describes the optical and microfluidic mechanical manipulation of single suspended cells enabled by the μPIVOT, an integrated micron resolution particle image velocimeter (μPIV) and dual optical tweezers instrument (OT). In this study, we examine the viability and trap stiffness of cartilage cells, identify the maximum fluid-induced stresses possible in uniform and extensional flows, and compare the deformation characteristics of bone and muscle cells. These results indicate cell photodamage of chondrocytes is negligible for at least 20 min for laser powers below 30 mW, a dead cell presents less resistance to internal organelle rearrangement and deforms globally more than a viable cell, the maximum fluid-induced shear stresses are limited to ~15 mPa for uniform flows but may exceed 1 Pa for extensional flows, and osteoblasts show no deformation for shear stresses up to 250 mPa while myoblasts are more easily deformed and exhibit a modulated response to increasing stress. This suggests that global and/or local stresses can be applied to single cells without physical contact. Coupled with microfluidic sensors, these manipulations may provide unique methods to explore single cell biomechanics. PMID:20824110

Microfluidic cardiac cell culture model (μCCCM).

PubMed

Giridharan, Guruprasad A; Nguyen, Mai-Dung; Estrada, Rosendo; Parichehreh, Vahidreza; Hamid, Tariq; Ismahil, Mohamed Ameen; Prabhu, Sumanth D; Sethu, Palaniappan

2010-09-15

Physiological heart development and cardiac function rely on the response of cardiac cells to mechanical stress during hemodynamic loading and unloading. These stresses, especially if sustained, can induce changes in cell structure, contractile function, and gene expression. Current cell culture techniques commonly fail to adequately replicate physical loading observed in the native heart. Therefore, there is a need for physiologically relevant in vitro models that recreate mechanical loading conditions seen in both normal and pathological conditions. To fulfill this need, we have developed a microfluidic cardiac cell culture model (μCCCM) that for the first time allows in vitro hemodynamic stimulation of cardiomyocytes by directly coupling cell structure and function with fluid induced loading. Cells are cultured in a small (1 cm diameter) cell culture chamber on a thin flexible silicone membrane. Integrating the cell culture chamber with a pump, collapsible pulsatile valve and an adjustable resistance element (hemostatic valve) in series allow replication of various loading conditions experienced in the heart. This paper details the design, modeling, fabrication and characterization of fluid flow, pressure and stretch generated at various frequencies to mimic hemodynamic conditions associated with the normal and failing heart. Proof-of-concept studies demonstrate successful culture of an embryonic cardiomyoblast line (H9c2 cells) and establishment of an in vivo like phenotype within this system.

Electrical Coupling: Novel Mechanism for Sleep-Wake Control

PubMed Central

Garcia-Rill, Edgar; Heister, David S.; Ye, Meijun; Charlesworth, Amanda; Hayar, Abdallah

2007-01-01

Study Objectives: Recent evidence suggests that certain anesthetic agents decrease electrical coupling, whereas the stimulant modafinil appears to increase electrical coupling. We investigated the potential role of electrical coupling in 2 reticular activating system sites, the subcoeruleus nucleus and in the pedunculopontine nucleus, which has been implicated in the modulation of arousal via ascending cholinergic activation of intralaminar thalamus and descending activation of the subcoeruleus nucleus to generate some of the signs of rapid eye movement sleep. Design: We used 6- to 30-day-old rat pups to obtain brainstem slices to perform whole-cell patch-clamp recordings. Measurements and Results: Recordings from single cells revealed the presence of spikelets, manifestations of action potentials in coupled cells, and of dye coupling of neurons in the pedunculopontine nucleus. Recordings in pairs of pedunculopontine nucleus and subcoeruleus nucleus neurons revealed that some of these were electrically coupled with coupling coefficients of approximately 2%. After blockade of fast synaptic transmission, the cholinergic agonist carbachol was found to induce rhythmic activity in pedunculopontine nucleus and subcoeruleus nucleus neurons, an effect eliminated by the gap junction blockers carbenoxolone or mefloquine. The stimulant modafinil was found to decrease resistance in neurons in the pedunculopontine nucleus and subcoeruleus nucleus after fast synaptic blockade, indicating that the effect may be due to increased coupling. Conclusions: The finding of electrical coupling in specific reticular activating system cell groups supports the concept that this underlying process behind specific neurotransmitter interactions modulates ensemble activity across cell populations to promote changes in sleep-wake state. Citation: Garcia-Rill E; Heister DS; Ye M; Charlesworth A; Hayar A. Electrical coupling: novel mechanism for sleep-wake control. SLEEP 2007;30(11):1405-1414. PMID:18041475

Review of inductively coupled plasmas: Nano-applications and bistable hysteresis physics

NASA Astrophysics Data System (ADS)

Lee, Hyo-Chang

2018-03-01

Many different gas discharges and plasmas exhibit bistable states under a given set of conditions, and the history-dependent hysteresis that is manifested by intensive quantities of the system upon variation of an external parameter has been observed in inductively coupled plasmas (ICPs). When the external parameters (such as discharge powers) increase, the plasma density increases suddenly from a low- to high-density mode, whereas decreasing the power maintains the plasma in a relatively high-density mode, resulting in significant hysteresis. To date, a comprehensive description of plasma hysteresis and a physical understanding of the main mechanism underlying their bistability remain elusive, despite many experimental observations of plasma bistability conducted under radio-frequency ICP excitation. This fundamental understanding of mode transitions and hysteresis is essential and highly important in various applied fields owing to the widespread use of ICPs, such as semiconductor/display/solar-cell processing (etching, deposition, and ashing), wireless light lamp, nanostructure fabrication, nuclear-fusion operation, spacecraft propulsion, gas reformation, and the removal of hazardous gases and materials. If, in such applications, plasma undergoes a mode transition and hysteresis occurs in response to external perturbations, the process result will be strongly affected. Due to these reasons, this paper comprehensively reviews both the current knowledge in the context of the various applied fields and the global understanding of the bistability and hysteresis physics in the ICPs. At first, the basic understanding of the ICP is given. After that, applications of ICPs to various applied fields of nano/environmental/energy-science are introduced. Finally, the mode transition and hysteresis in ICPs are studied in detail. This study will show the fundamental understanding of hysteresis physics in plasmas and give open possibilities for applications to various applied fields to find novel control knob and optimizing processing conditions.

Coupling functions: Universal insights into dynamical interaction mechanisms

NASA Astrophysics Data System (ADS)

Stankovski, Tomislav; Pereira, Tiago; McClintock, Peter V. E.; Stefanovska, Aneta

2017-10-01

The dynamical systems found in nature are rarely isolated. Instead they interact and influence each other. The coupling functions that connect them contain detailed information about the functional mechanisms underlying the interactions and prescribe the physical rule specifying how an interaction occurs. A coherent and comprehensive review is presented encompassing the rapid progress made recently in the analysis, understanding, and applications of coupling functions. The basic concepts and characteristics of coupling functions are presented through demonstrative examples of different domains, revealing the mechanisms and emphasizing their multivariate nature. The theory of coupling functions is discussed through gradually increasing complexity from strong and weak interactions to globally coupled systems and networks. A variety of methods that have been developed for the detection and reconstruction of coupling functions from measured data is described. These methods are based on different statistical techniques for dynamical inference. Stemming from physics, such methods are being applied in diverse areas of science and technology, including chemistry, biology, physiology, neuroscience, social sciences, mechanics, and secure communications. This breadth of application illustrates the universality of coupling functions for studying the interaction mechanisms of coupled dynamical systems.

Traveling wave linear accelerator with RF power flow outside of accelerating cavities

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

Dolgashev, Valery A.

A high power RF traveling wave accelerator structure includes a symmetric RF feed, an input matching cell coupled to the symmetric RF feed, a sequence of regular accelerating cavities coupled to the input matching cell at an input beam pipe end of the sequence, one or more waveguides parallel to and coupled to the sequence of regular accelerating cavities, an output matching cell coupled to the sequence of regular accelerating cavities at an output beam pipe end of the sequence, and output waveguide circuit or RF loads coupled to the output matching cell. Each of the regular accelerating cavities hasmore » a nose cone that cuts off field propagating into the beam pipe and therefore all power flows in a traveling wave along the structure in the waveguide.« less

Gap junctional coupling in the vertebrate retina: variations on one theme?

PubMed

Völgyi, Béla; Kovács-Oller, Tamás; Atlasz, Tamás; Wilhelm, Márta; Gábriel, Róbert

2013-05-01

Gap junctions connect cells in the bodies of all multicellular organisms, forming either homologous or heterologous (i.e. established between identical or different cell types, respectively) cell-to-cell contacts by utilizing identical (homotypic) or different (heterotypic) connexin protein subunits. Gap junctions in the nervous system serve electrical signaling between neurons, thus they are also called electrical synapses. Such electrical synapses are particularly abundant in the vertebrate retina where they are specialized to form links between neurons as well as glial cells. In this article, we summarize recent findings on retinal cell-to-cell coupling in different vertebrates and identify general features in the light of the evergrowing body of data. In particular, we describe and discuss tracer coupling patterns, connexin proteins, junctional conductances and modulatory processes. This multispecies comparison serves to point out that most features are remarkably conserved across the vertebrate classes, including (i) the cell types connected via electrical synapses; (ii) the connexin makeup and the conductance of each cell-to-cell contact; (iii) the probable function of each gap junction in retinal circuitry; (iv) the fact that gap junctions underlie both electrical and/or tracer coupling between glial cells. These pan-vertebrate features thus demonstrate that retinal gap junctions have changed little during the over 500 million years of vertebrate evolution. Therefore, the fundamental architecture of electrically coupled retinal circuits seems as old as the retina itself, indicating that gap junctions deeply incorporated in retinal wiring from the very beginning of the eye formation of vertebrates. In addition to hard wiring provided by fast synaptic transmitter-releasing neurons and soft wiring contributed by peptidergic, aminergic and purinergic systems, electrical coupling may serve as the 'skeleton' of lateral processing, enabling important functions such as signal averaging and synchronization. 2013 Elsevier Ltd. All rights reserved.

Optimization of coupled multiphysics methodology for safety analysis of pebble bed modular reactor

NASA Astrophysics Data System (ADS)

Mkhabela, Peter Tshepo

The research conducted within the framework of this PhD thesis is devoted to the high-fidelity multi-physics (based on neutronics/thermal-hydraulics coupling) analysis of Pebble Bed Modular Reactor (PBMR), which is a High Temperature Reactor (HTR). The Next Generation Nuclear Plant (NGNP) will be a HTR design. The core design and safety analysis methods are considerably less developed and mature for HTR analysis than those currently used for Light Water Reactors (LWRs). Compared to LWRs, the HTR transient analysis is more demanding since it requires proper treatment of both slower and much longer transients (of time scale in hours and days) and fast and short transients (of time scale in minutes and seconds). There is limited operation and experimental data available for HTRs for validation of coupled multi-physics methodologies. This PhD work developed and verified reliable high fidelity coupled multi-physics models subsequently implemented in robust, efficient, and accurate computational tools to analyse the neutronics and thermal-hydraulic behaviour for design optimization and safety evaluation of PBMR concept The study provided a contribution to a greater accuracy of neutronics calculations by including the feedback from thermal hydraulics driven temperature calculation and various multi-physics effects that can influence it. Consideration of the feedback due to the influence of leakage was taken into account by development and implementation of improved buckling feedback models. Modifications were made in the calculation procedure to ensure that the xenon depletion models were accurate for proper interpolation from cross section tables. To achieve this, the NEM/THERMIX coupled code system was developed to create the system that is efficient and stable over the duration of transient calculations that last over several tens of hours. Another achievement of the PhD thesis was development and demonstration of full-physics, three-dimensional safety analysis methodology for the PBMR to provide reference solutions. Investigation of different aspects of the coupled methodology and development of efficient kinetics treatment for the PBMR were carried out, which accounts for all feedback phenomena in an efficient manner. The OECD/NEA PBMR-400 coupled code benchmark was used as a test matrix for the proposed investigations. The integrated thermal-hydraulics and neutronics (multi-physics) methods were extended to enable modeling of a wider range of transients pertinent to the PBMR. First, the effect of the spatial mapping schemes (spatial coupling) was studied and quantified for different types of transients, which resulted in implementation of improved mapping methodology based on user defined criteria. The second aspect that was studied and optimized is the temporal coupling and meshing schemes between the neutronics and thermal-hydraulics time step selection algorithms. The coupled code convergence was achieved supplemented by application of methods to accelerate it. Finally, the modeling of all feedback phenomena in PBMRs was investigated and a novel treatment of cross-section dependencies was introduced for improving the representation of cross-section variations. The added benefit was that in the process of studying and improving the coupled multi-physics methodology more insight was gained into the physics and dynamics of PBMR, which will help also to optimize the PBMR design and improve its safety. One unique contribution of the PhD research is the investigation of the importance of the correct representation of the three-dimensional (3-D) effects in the PBMR analysis. The performed studies demonstrated that explicit 3-D modeling of control rod movement is superior and removes the errors associated with the grey curtain (2-D homogenized) approximation.

Couple Conflict and Rope-a-Dope.

ERIC Educational Resources Information Center

Downing, Jerry; Harrison, Tom

1993-01-01

Draws analogy between Muhammad Ali's boxing technique of "rope-a-dope" and behavioral patterns frequently occurring in couple conflicts. Presents basics of Ali's technique as similar to fighting patterns of many couples. Suggests that this behavior may lead to physical violence. Describes use of analogy in working with couples. Presents strategies…

What's love got to do with it: Relationship functioning and mental and physical quality of life among pregnant adolescent couples.

PubMed

Kershaw, Trace; Murphy, Alexandrea; Divney, Anna; Magriples, Urania; Niccolai, Linda; Gordon, Derrick

2013-12-01

The study objective was to describe relationship adjustment and its association with mental and physical quality of life for young couples expecting a baby. 296 young pregnant couples recruited from urban obstetric clinics reported on relationship strengths (e.g., equity, romantic love, and attractiveness), relationship risks (e.g., attachment, intimate partner violence), external family support, relationship adjustment, and mental and physical quality of life. Using the Actor Partner Interdependence Model we assessed both actor and partner effects of relationship variables on relationship adjustment and quality of life. Sixty-one percent of couples had at least one member with moderate or severe relationship distress. Lower attachment avoidance, lower attachment anxiety, higher relationship equity, lack of intimate partner violence, feelings of love, perceived partner attractiveness, and family support of the relationship related to better relationship adjustment. Associations were fairly consistent across gender. Better relationship adjustment related to more positive mental and physical quality of life for both young women and men. Our results highlight the potential importance of strong relationships on the well-being of expecting parents. Our results suggest that secure attachments, equitable relationships, feelings of love, and a lack of violence may be particularly important in having strong relationships and improved mental and physical health during pregnancy.

What’s Love Got to Do with It: Relationship Functioning and Mental and Physical Quality of Life Among Pregnant Adolescent Couples

PubMed Central

Murphy, Alexandrea; Divney, Anna; Magriples, Urania; Niccolai, Linda; Gordon, Derrick

2014-01-01

The study objective was to describe relationship adjustment and its association with mental and physical quality of life for young couples expecting a baby. 296 young pregnant couples recruited from urban obstetric clinics reported on relationship strengths (e.g., equity, romantic love, and attractiveness), relationship risks (e.g., attachment, intimate partner violence), external family support, relationship adjustment, and mental and physical quality of life. Using the Actor Partner Interdependence Model we assessed both actor and partner effects of relationship variables on relationship adjustment and quality of life. Sixty-one percent of couples had at least one member with moderate or severe relationship distress. Lower attachment avoidance, lower attachment anxiety, higher relationship equity, lack of intimate partner violence, feelings of love, perceived partner attractiveness, and family support of the relationship related to better relationship adjustment. Associations were fairly consistent across gender. Better relationship adjustment related to more positive mental and physical quality of life for both young women and men. Our results highlight the potential importance of strong relationships on the well-being of expecting parents. Our results suggest that secure attachments, equitable relationships, feelings of love, and a lack of violence may be particularly important in having strong relationships and improved mental and physical health during pregnancy. PMID:24091562

A dual role of extrinsic noise in coupled synthetic clock cells due to a two-steps synchronization mechanism

NASA Astrophysics Data System (ADS)

Liu, Quan; Yu, FengZhen; Li, ZhiHong; Xiong, Juan; Chen, JianJun; Yi, Ming

2018-07-01

Based on the model describing two coupled synthetic clock cells, the synchronization dynamics under stochastic noise are explored. As extrinsic noise from signal is the predominant form of noise for all gene promoters, we investigate the effects of extrinsic noise original from signal molecule by evaluating the order parameters. It is found that strong noise is beneficial for the synchronization of loose-coupling system, while it destroys the synchronization of tight-coupling system. The underlying mechanisms of these two opposite effects are clarified numerically and theoretically. Our research illustrates that (i) when the coupling strength is small, the noise mainly adjusts the period difference of two cells and the system becomes regular. Theoretical study reveals that the mean effect of noise is like to be influx while signal flow is efflux under such a situation. (ii) With the increment of coupling strength, the cells have the same frequency. It is obvious that the noise mainly changes the phase difference between the two cells and destroys the synchronization of the system. (iii) We also demonstrate that, under certain moderate noise intensities, the noise can induce the synchronization order to be the worst. This nonlinear behavior only can be observed in a very narrow region of coupling strength.

Teaching the Physics of a String-Coupled Pendulum Oscillator: Not Just for Seniors Anymore

ERIC Educational Resources Information Center

Cho, Young-Ki

2012-01-01

Coupled oscillators are an example of resonant energy exchange that is an interesting topic for many students in various majors, such as physics, chemistry, and electrical and mechanical engineering. However, this subject matter is considered too advanced for freshmen and sophomores, usually because of the level of mathematics involved.…

Connecting Self-Efficacy and Views about the Nature of Science in Undergraduate Research Experiences

ERIC Educational Resources Information Center

Quan, Gina M.; Elby, Andrew

2016-01-01

Undergraduate research can support students' more central participation in physics. We analyze markers of two coupled shifts in participation: changes in students' views about the nature of science coupled to shifts in self-efficacy toward physics research. Students in the study worked with faculty and graduate student mentors on research projects…

Spiral-wave dynamics in a mathematical model of human ventricular tissue with myocytes and Purkinje fibers.

PubMed

Nayak, Alok Ranjan; Panfilov, A V; Pandit, Rahul

2017-02-01

We present systematic numerical studies of the possible effects of the coupling of human endocardial and Purkinje cells at cellular and two-dimensional tissue levels. We find that the autorhythmic-activity frequency of the Purkinje cell in a composite decreases with an increase in the coupling strength; this can even eliminate the autorhythmicity. We observe a delay between the beginning of the action potentials of endocardial and Purkinje cells in a composite; such a delay increases as we decrease the diffusive coupling, and eventually a failure of transmission occurs. An increase in the diffusive coupling decreases the slope of the action-potential-duration-restitution curve of an endocardial cell in a composite. By using a minimal model for the Purkinje network, in which we have a two-dimensional, bilayer tissue, with a layer of Purkinje cells on top of a layer of endocardial cells, we can stabilize spiral-wave turbulence; however, for a sparse distribution of Purkinje-ventricular junctions, at which these two layers are coupled, we can also obtain additional focal activity and many complex transient regimes. We also present additional effects resulting from the coupling of Purkinje and endocardial layers and discuss the relation of our results to the studies performed in anatomically accurate models of the Purkinje network.

Spiral-wave dynamics in a mathematical model of human ventricular tissue with myocytes and Purkinje fibers

NASA Astrophysics Data System (ADS)

Nayak, Alok Ranjan; Panfilov, A. V.; Pandit, Rahul

2017-02-01

We present systematic numerical studies of the possible effects of the coupling of human endocardial and Purkinje cells at cellular and two-dimensional tissue levels. We find that the autorhythmic-activity frequency of the Purkinje cell in a composite decreases with an increase in the coupling strength; this can even eliminate the autorhythmicity. We observe a delay between the beginning of the action potentials of endocardial and Purkinje cells in a composite; such a delay increases as we decrease the diffusive coupling, and eventually a failure of transmission occurs. An increase in the diffusive coupling decreases the slope of the action-potential-duration-restitution curve of an endocardial cell in a composite. By using a minimal model for the Purkinje network, in which we have a two-dimensional, bilayer tissue, with a layer of Purkinje cells on top of a layer of endocardial cells, we can stabilize spiral-wave turbulence; however, for a sparse distribution of Purkinje-ventricular junctions, at which these two layers are coupled, we can also obtain additional focal activity and many complex transient regimes. We also present additional effects resulting from the coupling of Purkinje and endocardial layers and discuss the relation of our results to the studies performed in anatomically accurate models of the Purkinje network.

Design of a Modular Monolithic Implicit Solver for Multi-Physics Applications

NASA Technical Reports Server (NTRS)

Carton De Wiart, Corentin; Diosady, Laslo T.; Garai, Anirban; Burgess, Nicholas; Blonigan, Patrick; Ekelschot, Dirk; Murman, Scott M.

2018-01-01

The design of a modular multi-physics high-order space-time finite-element framework is presented together with its extension to allow monolithic coupling of different physics. One of the main objectives of the framework is to perform efficient high- fidelity simulations of capsule/parachute systems. This problem requires simulating multiple physics including, but not limited to, the compressible Navier-Stokes equations, the dynamics of a moving body with mesh deformations and adaptation, the linear shell equations, non-re effective boundary conditions and wall modeling. The solver is based on high-order space-time - finite element methods. Continuous, discontinuous and C1-discontinuous Galerkin methods are implemented, allowing one to discretize various physical models. Tangent and adjoint sensitivity analysis are also targeted in order to conduct gradient-based optimization, error estimation, mesh adaptation, and flow control, adding another layer of complexity to the framework. The decisions made to tackle these challenges are presented. The discussion focuses first on the "single-physics" solver and later on its extension to the monolithic coupling of different physics. The implementation of different physics modules, relevant to the capsule/parachute system, are also presented. Finally, examples of coupled computations are presented, paving the way to the simulation of the full capsule/parachute system.

Solid oxide fuel cell simulation and design optimization with numerical adjoint techniques

NASA Astrophysics Data System (ADS)

Elliott, Louie C.

This dissertation reports on the application of numerical optimization techniques as applied to fuel cell simulation and design. Due to the "multi-physics" inherent in a fuel cell, which results in a highly coupled and non-linear behavior, an experimental program to analyze and improve the performance of fuel cells is extremely difficult. This program applies new optimization techniques with computational methods from the field of aerospace engineering to the fuel cell design problem. After an overview of fuel cell history, importance, and classification, a mathematical model of solid oxide fuel cells (SOFC) is presented. The governing equations are discretized and solved with computational fluid dynamics (CFD) techniques including unstructured meshes, non-linear solution methods, numerical derivatives with complex variables, and sensitivity analysis with adjoint methods. Following the validation of the fuel cell model in 2-D and 3-D, the results of the sensitivity analysis are presented. The sensitivity derivative for a cost function with respect to a design variable is found with three increasingly sophisticated techniques: finite difference, direct differentiation, and adjoint. A design cycle is performed using a simple optimization method to improve the value of the implemented cost function. The results from this program could improve fuel cell performance and lessen the world's dependence on fossil fuels.

SU-E-T-565: RAdiation Resistance of Cancer CElls Using GEANT4 DNA: RACE

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

Perrot, Y; Payno, H; Delage, E

2014-06-01

Purpose: The objective of the RACE project is to develop a comparison between Monte Carlo simulation using the Geant4-DNA toolkit and measurements of radiation damage on 3D melanoma and chondrosarcoma culture cells coupled with gadolinium nanoparticles. We currently expose the status of the developments regarding simulations. Methods: Monte Carlo studies are driven using the Geant4 toolkit and the Geant4-DNA extension. In order to model the geometry of a cell population, the opensource CPOP++ program is being developed for the geometrical representation of 3D cell populations including a specific cell mesh coupled with a multi-agent system. Each cell includes cytoplasm andmore » nucleus. The correct modeling of the cell population has been validated with confocal microscopy images of spheroids. The Geant4 Livermore physics models are used to simulate the interactions of a 250 keV X-ray beam and the production of secondaries from gadolinium nanoparticles supposed to be fixed on the cell membranes. Geant4-DNA processes are used to simulate the interactions of charged particles with the cells. An atomistic description of the DNA molecule, from PDB (Protein Data Bank) files, is provided by the so-called PDB4DNA Geant4 user application we developed to score energy depositions in DNA base pairs and sugar-phosphate groups. Results: At the microscopic level, our simulations enable assessing microscopic energy distribution in each cell compartment of a realistic 3D cell population. Dose enhancement factors due to the presence of gadolinium nanoparticles can be estimated. At the nanometer scale, direct damages on nuclear DNA are also estimated. Conclusion: We successfully simulated the impact of direct radiations on a realistic 3D cell population model compatible with microdosimetry calculations using the Geant4-DNA toolkit. Upcoming validation and the future integration of the radiochemistry module of Geant4-DNA will propose to correlate clusters of ionizations with in vitro experiments. All those developments will be released publicly. This work was supported by grants from Plan Cancer 2009-2013 French national initiative managed by INSERM (Institut National de la Sante et de la Recherche Medicale)« less

Gap-junction coupling and ATP-sensitive potassium channels in human β -cell clusters: Effects on emergent dynamics

NASA Astrophysics Data System (ADS)

Loppini, A.; Pedersen, M. G.; Braun, M.; Filippi, S.

2017-09-01

The importance of gap-junction coupling between β cells in pancreatic islets is well established in mouse. Such ultrastructural connections synchronize cellular activity, confine biological heterogeneity, and enhance insulin pulsatility. Dysfunction of coupling has been associated with diabetes and altered β -cell function. However, the role of gap junctions between human β cells is still largely unexplored. By using patch-clamp recordings of β cells from human donors, we previously estimated electrical properties of these channels by mathematical modeling of pairs of human β cells. In this work we revise our estimate by modeling triplet configurations and larger heterogeneous clusters. We find that a coupling conductance in the range 0.005 -0.020 nS/pF can reproduce experiments in almost all the simulated arrangements. We finally explore the consequence of gap-junction coupling of this magnitude between β cells with mutant variants of the ATP-sensitive potassium channels involved in some metabolic disorders and diabetic conditions, translating studies performed on rodents to the human case. Our results are finally discussed from the perspective of therapeutic strategies. In summary, modeling of more realistic clusters with more than two β cells slightly lowers our previous estimate of gap-junction conductance and gives rise to patterns that more closely resemble experimental traces.

Electrotonic coupling of excitable and nonexcitable cells in the heart revealed by optogenetics

PubMed Central

Quinn, T. Alexander; Camelliti, Patrizia; Rog-Zielinska, Eva A.; Siedlecka, Urszula; Poggioli, Tommaso; O'Toole, Eileen T.; Knöpfel, Thomas; Kohl, Peter

2016-01-01

Electrophysiological studies of excitable organs usually focus on action potential (AP)-generating cells, whereas nonexcitable cells are generally considered as barriers to electrical conduction. Whether nonexcitable cells may modulate excitable cell function or even contribute to AP conduction via direct electrotonic coupling to AP-generating cells is unresolved in the heart: such coupling is present in vitro, but conclusive evidence in situ is lacking. We used genetically encoded voltage-sensitive fluorescent protein 2.3 (VSFP2.3) to monitor transmembrane potential in either myocytes or nonmyocytes of murine hearts. We confirm that VSFP2.3 allows measurement of cell type-specific electrical activity. We show that VSFP2.3, expressed solely in nonmyocytes, can report cardiomyocyte AP-like signals at the border of healed cryoinjuries. Using EM-based tomographic reconstruction, we further discovered tunneling nanotube connections between myocytes and nonmyocytes in cardiac scar border tissue. Our results provide direct electrophysiological evidence of heterocellular electrotonic coupling in native myocardium and identify tunneling nanotubes as a possible substrate for electrical cell coupling that may be in addition to previously discovered connexins at sites of myocyte–nonmyocyte contact in the heart. These findings call for reevaluation of cardiac nonmyocyte roles in electrical connectivity of the heterocellular heart. PMID:27930302

A Dyadic Analysis of Relationships and Health: Does Couple-Level Context Condition Partner Effects?

PubMed Central

Barr, Ashley B.; Simons, Ronald L.

2014-01-01

Adding to the growing literature explicating the links between romantic relationships and health, this study examined how both couple-level characteristics, particularly union type (e.g. dating, cohabiting, or marriage) and interracial pairing, and interpersonal characteristics (e.g. partner strain and support) predicted young adults’ physical and mental health. Using dyadic data from a sample of 249 young, primarily African American couples, we hypothesized and found support for the importance of couple-level context, partner behavior, and their interaction in predicting health. Interracial couples (all Black/non-Black pairings) reported worse health than monoracial Black couples. Union type, however, did not directly predict health but was a significant moderator of partner strain. That is, the negative association between partner strain and self-reported health was stronger for cohabiting and married couples versus their dating counterparts, suggesting that coresidence more so than marital status may be important for understanding partner effects on physical health. For psychological distress, however, partner support proved equally beneficial across union types. PMID:25090254

A dyadic analysis of relationships and health: does couple-level context condition partner effects?

PubMed

Barr, Ashley B; Simons, Ronald L

2014-08-01

Adding to the growing literature explicating the links between romantic relationships and health, this study examined how both couple-level characteristics, particularly union type (e.g., dating, cohabiting, or marriage) and interracial pairing, and interpersonal characteristics (e.g., partner strain and support), predicted young adults' physical and mental health. Using dyadic data from a sample of 249 young, primarily Black couples, we hypothesized and found support for the importance of couple-level context, partner behavior, and their interaction in predicting health. Interracial couples (all Black/non-Black pairings) reported worse health than monoracial Black couples. Union type, however, did not directly predict health but was a significant moderator of partner strain. That is, the negative association between partner strain and self-reported health was stronger for cohabiting and married couples versus their dating counterparts, suggesting that coresidence, more so than marital status, may be important for understanding partner effects on physical health. For psychological distress, however, partner support proved equally beneficial across union types.

Stress spillover, African Americans' couple and health outcomes, and the stress-buffering effect of family-centered prevention.

PubMed

Barton, Allen W; Beach, Steven R H; Bryant, Chalandra M; Lavner, Justin A; Brody, Gene H

2018-03-01

This study investigated (a) the stress spillover pathways linking contextual stressors, changes in couple relationship functioning and depressive symptoms, and changes in individuals' physical health, and (b) the stress-buffering effect of participation in an efficacious, family centered prevention program designed to protect couples from the deleterious effects of stressors. The sample consisted of 346 rural African American couples (63% married) who participated in a randomized controlled trial of the Protecting Strong African American Families (ProSAAF) program. Participants were assessed at three time points across 17 months. Results examining stress spillover within the control group indicated that elevated current, but not prior, financial hardship was associated with decreased effective communication, relationship satisfaction, and relationship confidence as well as increased depressive symptoms; current levels of racial discrimination also predicted greater depressive symptoms. Relationship confidence and relationship satisfaction, but not communication or depressive symptoms, in turn predicted declines in self-reported physical health. Results examining stress-buffering effects suggested that participation in ProSAAF protected individuals' relationship confidence from declines associated with elevated financial hardship. In addition, the indirect effect linking financial hardship to declines in physical health through relationship confidence that emerged among participants in the control group was no longer evident for ProSAAF couples. Results highlight the effect of contextual stressors on African Americans' couple and individual well-being and the potential for the ProSAAF program to provide a constructed resilience resource, protecting couple's confidence in their relationship from the negative effects of financial hardship and, consequently, promoting physical health. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Scheme Variations of the QCD Coupling and Hadronic τ Decays

NASA Astrophysics Data System (ADS)

Boito, Diogo; Jamin, Matthias; Miravitllas, Ramon

2016-10-01

The quantum chromodynamics (QCD) coupling αs is not a physical observable of the theory, since it depends on conventions related to the renormalization procedure. We introduce a definition of the QCD coupling, denoted by α^s, whose running is explicitly renormalization scheme invariant. The scheme dependence of the new coupling α^s is parametrized by a single parameter C , related to transformations of the QCD scale Λ . It is demonstrated that appropriate choices of C can lead to substantial improvements in the perturbative prediction of physical observables. As phenomenological applications, we study e+e- scattering and decays of the τ lepton into hadrons, both being governed by the QCD Adler function.

Tissue-specific activities of the Fat1 cadherin cooperate to control neuromuscular morphogenesis

PubMed Central

2018-01-01

Muscle morphogenesis is tightly coupled with that of motor neurons (MNs). Both MNs and muscle progenitors simultaneously explore the surrounding tissues while exchanging reciprocal signals to tune their behaviors. We previously identified the Fat1 cadherin as a regulator of muscle morphogenesis and showed that it is required in the myogenic lineage to control the polarity of progenitor migration. To expand our knowledge on how Fat1 exerts its tissue-morphogenesis regulator activity, we dissected its functions by tissue-specific genetic ablation. An emblematic example of muscle under such morphogenetic control is the cutaneous maximus (CM) muscle, a flat subcutaneous muscle in which progenitor migration is physically separated from the process of myogenic differentiation but tightly associated with elongating axons of its partner MNs. Here, we show that constitutive Fat1 disruption interferes with expansion and differentiation of the CM muscle, with its motor innervation and with specification of its associated MN pool. Fat1 is expressed in muscle progenitors, in associated mesenchymal cells, and in MN subsets, including the CM-innervating pool. We identify mesenchyme-derived connective tissue (CT) as a cell type in which Fat1 activity is required for the non–cell-autonomous control of CM muscle progenitor spreading, myogenic differentiation, motor innervation, and for motor pool specification. In parallel, Fat1 is required in MNs to promote their axonal growth and specification, indirectly influencing muscle progenitor progression. These results illustrate how Fat1 coordinates the coupling of muscular and neuronal morphogenesis by playing distinct but complementary actions in several cell types. PMID:29768404

A multi scale multi-dimensional thermo electrochemical modelling of high capacity lithium-ion cells

NASA Astrophysics Data System (ADS)

Tourani, Abbas; White, Peter; Ivey, Paul

2014-06-01

Lithium iron phosphate (LFP) and lithium manganese oxide (LMO) are competitive and complementary to each other as cathode materials for lithium-ion batteries, especially for use in electric vehicles. A multi scale multi-dimensional physic-based model is proposed in this paper to study the thermal behaviour of the two lithium-ion chemistries. The model consists of two sub models, a one dimensional (1D) electrochemical sub model and a two dimensional (2D) thermo-electric sub model, which are coupled and solved concurrently. The 1D model predicts the heat generation rate (Qh) and voltage (V) of the battery cell through different load cycles. The 2D model of the battery cell accounts for temperature distribution and current distribution across the surface of the battery cell. The two cells are examined experimentally through 90 h load cycles including high/low charge/discharge rates. The experimental results are compared with the model results and they are in good agreement. The presented results in this paper verify the cells temperature behaviour at different operating conditions which will lead to the design of a cost effective thermal management system for the battery pack.

New advances in probing cell–extracellular matrix interactions

PubMed Central

2017-01-01

The extracellular matrix (ECM) provides structural and biochemical support to cells within tissues. An emerging body of evidence has established that the ECM plays a key role in cell mechanotransduction – the study of coupling between mechanical inputs and cellular phenotype – through either mediating transmission of forces to the cells, or presenting mechanical cues that guide cellular behaviors. Recent progress in cell mechanotransduction research has been facilitated by advances of experimental tools, particularly microtechnologies, engineered biomaterials, and imaging and analytical methods. Microtechnologies have enabled the design and fabrication of controlled physical microenvironments for the study and measurement of cell–ECM interactions. Advances in engineered biomaterials have allowed researchers to develop synthetic ECMs that mimic tissue microenvironments and investigate the impact of altered physicochemical properties on various cellular processes. Finally, advanced imaging and spectroscopy techniques have facilitated the visualization of the complex interaction between cells and ECM in vitro and in living tissues. This review will highlight the application of recent innovations in these areas to probing cell–ECM interactions. We believe cross-disciplinary approaches, combining aspects of the different technologies reviewed here, will inspire innovative ideas to further elucidate the secrets of ECM-mediated cell control. PMID:28352896

G Protein-Coupled Receptor Signaling in Stem Cells and Cancer.

PubMed

Lynch, Jennifer R; Wang, Jenny Yingzi

2016-05-11

G protein-coupled receptors (GPCRs) are a large superfamily of cell-surface signaling proteins that bind extracellular ligands and transduce signals into cells via heterotrimeric G proteins. GPCRs are highly tractable drug targets. Aberrant expression of GPCRs and G proteins has been observed in various cancers and their importance in cancer stem cells has begun to be appreciated. We have recently reported essential roles for G protein-coupled receptor 84 (GPR84) and G protein subunit Gαq in the maintenance of cancer stem cells in acute myeloid leukemia. This review will discuss how GPCRs and G proteins regulate stem cells with a focus on cancer stem cells, as well as their implications for the development of novel targeted cancer therapies.

G Protein-Coupled Receptor Signaling in Stem Cells and Cancer

PubMed Central

Lynch, Jennifer R.; Wang, Jenny Yingzi

2016-01-01

G protein-coupled receptors (GPCRs) are a large superfamily of cell-surface signaling proteins that bind extracellular ligands and transduce signals into cells via heterotrimeric G proteins. GPCRs are highly tractable drug targets. Aberrant expression of GPCRs and G proteins has been observed in various cancers and their importance in cancer stem cells has begun to be appreciated. We have recently reported essential roles for G protein-coupled receptor 84 (GPR84) and G protein subunit Gαq in the maintenance of cancer stem cells in acute myeloid leukemia. This review will discuss how GPCRs and G proteins regulate stem cells with a focus on cancer stem cells, as well as their implications for the development of novel targeted cancer therapies. PMID:27187360

Multistage Force Amplification of Piezoelectric Stacks

NASA Technical Reports Server (NTRS)

Xu, Tian-Bing (Inventor); Siochi, Emilie J. (Inventor); Zuo, Lei (Inventor); Jiang, Xiaoning (Inventor); Kang, Jin Ho (Inventor)

2015-01-01

Embodiments of the disclosure include an apparatus and methods for using a piezoelectric device, that includes an outer flextensional casing, a first cell and a last cell serially coupled to each other and coupled to the outer flextensional casing such that each cell having a flextensional cell structure and each cell receives an input force and provides an output force that is amplified based on the input force. The apparatus further includes a piezoelectric stack coupled to each cell such that the piezoelectric stack of each cell provides piezoelectric energy based on the output force for each cell. Further, the last cell receives an input force that is the output force from the first cell and the last cell provides an output apparatus force In addition, the piezoelectric energy harvested is based on the output apparatus force. Moreover, the apparatus provides displacement based on the output apparatus force.

Regulation of Replication Fork Advance and Stability by Nucleosome Assembly

PubMed Central

Prado, Felix; Maya, Douglas

2017-01-01

The advance of replication forks to duplicate chromosomes in dividing cells requires the disassembly of nucleosomes ahead of the fork and the rapid assembly of parental and de novo histones at the newly synthesized strands behind the fork. Replication-coupled chromatin assembly provides a unique opportunity to regulate fork advance and stability. Through post-translational histone modifications and tightly regulated physical and genetic interactions between chromatin assembly factors and replisome components, chromatin assembly: (1) controls the rate of DNA synthesis and adjusts it to histone availability; (2) provides a mechanism to protect the integrity of the advancing fork; and (3) regulates the mechanisms of DNA damage tolerance in response to replication-blocking lesions. Uncoupling DNA synthesis from nucleosome assembly has deleterious effects on genome integrity and cell cycle progression and is linked to genetic diseases, cancer, and aging. PMID:28125036

The Dark Matter of Biology.

PubMed

Ross, Jennifer L

2016-09-06

The inside of the cell is full of important, yet invisible species of molecules and proteins that interact weakly but couple together to have huge and important effects in many biological processes. Such "dark matter" inside cells remains mostly hidden, because our tools were developed to investigate strongly interacting species and folded proteins. Example dark-matter species include intrinsically disordered proteins, posttranslational states, ion species, and rare, transient, and weak interactions undetectable by biochemical assays. The dark matter of biology is likely to have multiple, vital roles to regulate signaling, rates of reactions, water structure and viscosity, crowding, and other cellular activities. We need to create new tools to image, detect, and understand these dark-matter species if we are to truly understand fundamental physical principles of biology. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Multidecadal simulation of coastal fog with a regional climate model

NASA Astrophysics Data System (ADS)

O'Brien, Travis A.; Sloan, Lisa C.; Chuang, Patrick Y.; Faloona, Ian C.; Johnstone, James A.

2013-06-01

In order to model stratocumulus clouds and coastal fog, we have coupled the University of Washington boundary layer model to the regional climate model, RegCM (RegCM-UW). By comparing fog occurrences observed at various coastal airports in the western United States, we show that RegCM-UW has success at modeling the spatial and temporal (diurnal, seasonal, and interannual) climatology of northern California coastal fog. The quality of the modeled fog estimate depends on whether coast-adjacent ocean or land grid cells are used; for the model runs shown here, the oceanic grid cells seem to be most appropriate. The interannual variability of oceanic northern California summertime fog, from a multi-decadal simulation, has a high and statistically significant correlation with the observed interannual variability ( r = 0.72), which indicates that RegCM-UW is capable of investigating the response of fog to long-term climatological forcing. While RegCM-UW has a number of aspects that would benefit from further investigation and development, RegCM-UW is a new tool for investigating the climatology of coastal fog and the physical processes that govern it. We expect that with appropriate physical parameterizations and moderate horizontal resolution, other climate models should be capable of simulating coastal fog. The source code for RegCM-UW is publicly available, under the GNU license, through the International Centre for Theoretical Physics.

Coupling System Dynamics and Physically-based Models for Participatory Water Management - A Methodological Framework, with Two Case Studies: Water Quality in Quebec, and Soil Salinity in Pakistan

NASA Astrophysics Data System (ADS)

Boisvert-Chouinard, J.; Halbe, J.; Baig, A. I.; Adamowski, J. F.

2014-12-01

The principles of Integrated Water Resource Management outline the importance of stakeholder participation in water management processes, but in practice, there is a lack of meaningful engagement in water planning and implementation, and participation is often limited to public consultation and education. When models are used to support water planning, stakeholders are usually not involved in their development and use, and the models commonly fail to represent important feedbacks between socio-economic and physical processes. This paper presents the development of holistic models of the Du Chêne basin in Quebec, and the Rechna Doab basin in Pakistan, that simulate socio-economic and physical processes related to, respectively, water quality management, and soil salinity management. The models each consists of two sub-components: a System Dynamics (SD) model, and a physically based model. The SD component was developed in collaboration with key stakeholders in the basins. The Du Chêne SD model was coupled with a Soil and Water Assessment Tool (SWAT) model, while the Rechna Doab SD model was coupled with SahysMod, a soil salinity model. The coupled models were used to assess the environmental and socio-economic impacts of different management scenarios proposed by stakeholders. Results indicate that coupled SD - physically-based models can be used as effective tools for participatory water planning and implementation. The participatory modeling process provides a structure for meaningful stakeholder engagement, and the models themselves can be used to transparently and coherently assess and compare different management options.

Gender Inequality in the Couple Relationship and Leisure-Based Physical Exercise.

PubMed

Annandale, Ellen; Hammarström, Anne

2015-01-01

To analyse whether gender inequality in the couple relationship was related to leisure-based physical activity, after controlling for earlier physical activity and confounders. Data drawn from the Northern Swedish Cohort of all pupils in their final year of compulsory schooling in a town in the North of Sweden. The sample consisted of 772 respondents (n = 381 men, n = 391 women) in the 26-year follow-up (in 2007, aged 42) who were either married or cohabiting. Ordinal regression, for men and women separately, was used to assess the association between gender inequality (measured as self-perceived equality in the couple relationship using dummy variables) and a measure of exercise frequency, controlling for prior exercise frequency, socioeconomic status, the presence of children in the home, and longer than usual hours in paid work. The perception of greater gender equality in the couple relationship was associated with higher levels of physical activity for both men and women. This remained significant when the other variables were controlled for. Amongst men the confidence intervals were high. The results point to the potential of perceived gender equality in the couple relationship to counteract the general time poverty and household burden that often arises from the combination of paid work and responsibility for children and the home, especially for women. The high confidence intervals among men indicate the need for more research within the field with larger samples.

Suicidal Behavior among Low-Income, African American Female Victims of Intimate Terrorism and Situational Couple Violence

ERIC Educational Resources Information Center

Leone, Janel M.

2011-01-01

This study examined risk of suicidal behavior among low-income, African American women (N = 369) in three types of male intimate relationships--intimate terrorism (IT) (i.e., physical violence used within a general pattern of coercive control), situational couple violence (SCV; i.e., episodic physical violence that is not part of a general pattern…

Superfluid helium quantum interference devices: physics and applications.

PubMed

Sato, Y; Packard, R E

2012-01-01

We present an overview of recent developments related to superfluid helium quantum interference devices (SHeQUIDs). We discuss the physics of two reservoirs of superfluid helium coupled together and describe the quantum oscillations that result from varying the coupling strength. We explain the principles behind SHeQUIDs that can be built based on these oscillations and review some techniques and applications.

The Calcium-Sensing Receptor Couples to Gαs and Regulates PTHrP and ACTH Secretion in Pituitary Cells

PubMed Central

Mamillapalli, Ramanaiah; Wysolmerski, John

2013-01-01

The calcium-sensing receptor (CaR) is a G-protein-coupled receptor (GPCR) that binds and signals in response to extracellular calcium and other polycations. It is highly expressed on parathyroid and kidney cells, where it participates in the regulation of systemic calcium homeostasis. It is also expressed on many other cell types and is involved in a wide array of biological functions such as cell growth and differentiation, ion transport and hormone secretion. It has been described to couple to several different G-proteins including Gαi/0, Gαq/11 and Gα12/13. Recently, it has also been shown to stimulate cAMP production by coupling to Gαs in immortalized or malignant breast cells. The CaR is expressed on cells in the anterior pituitary and had previously been described to stimulate cAMP production in these cells. In this report, we examined signaling from the CaR in murine pituitary corticotroph-derived, AtT-20 cells. We found that CaR activation led to the stimulation of cAMP production, and PTHrP and ACTH secretion from these cells. Furthermore, manipulation of cAMP levels was able to modulate PTHrP and ACTH secretion independent of changes in extracellular calcium. Finally, we demonstrated that the CaR couples to Gαs in AtT-20 cells. Therefore, in pituitary corticotroph-like cells, as in breast cancer cells, the CaR utilizes Gαs and activates cAMP production to stimulate hormone secretion. PMID:20032198

Ca2+ homeostasis in microvascular endothelial cells from an insulin-dependent diabetic model: role of endosomes/lysosomes

NASA Astrophysics Data System (ADS)

Sanka, Shankar C.; Bennett, David C.; Rojas, Jose D.; Tasby, Geraldine B.; Meininger, Cynthia J.; Wu, Guoyao; Wesson, Donald E.; Pfarr, Curtis M.; Martinez-Zaguilan, Raul

2000-04-01

Cytosolic Ca2+ ([Ca2+]cyt) regulates several cellular functions, e.g. cell growth, contraction, secretion, etc. In many cell types, ion homeostasis appears to be coupled with glucose metabolism. In certain cell types, a strict coupling between glycolysis and the activity of Sarcoplasmic/Endoplasmic Reticulum Ca2+-ATPases (SERCA) has been suggested. Glucose metabolism is altered in diabetes. We hypothesize that: (1) Ca2+ homeostasis is altered in microvascular endothelial cells from diabetic animals due to the dysfunction of glycolysis coupling the activity of SERCA; (2) endosomal/lysosomal compartments expressing SERCA are involved in the dysfunction associated with diabetes.

Higgs physics at the CLIC electron-positron linear collider.

PubMed

Abramowicz, H; Abusleme, A; Afanaciev, K; Alipour Tehrani, N; Balázs, C; Benhammou, Y; Benoit, M; Bilki, B; Blaising, J-J; Boland, M J; Boronat, M; Borysov, O; Božović-Jelisavčić, I; Buckland, M; Bugiel, S; Burrows, P N; Charles, T K; Daniluk, W; Dannheim, D; Dasgupta, R; Demarteau, M; Díaz Gutierrez, M A; Eigen, G; Elsener, K; Felzmann, U; Firlej, M; Firu, E; Fiutowski, T; Fuster, J; Gabriel, M; Gaede, F; García, I; Ghenescu, V; Goldstein, J; Green, S; Grefe, C; Hauschild, M; Hawkes, C; Hynds, D; Idzik, M; Kačarević, G; Kalinowski, J; Kananov, S; Klempt, W; Kopec, M; Krawczyk, M; Krupa, B; Kucharczyk, M; Kulis, S; Laštovička, T; Lesiak, T; Levy, A; Levy, I; Linssen, L; Lukić, S; Maier, A A; Makarenko, V; Marshall, J S; Martin, V J; Mei, K; Milutinović-Dumbelović, G; Moroń, J; Moszczyński, A; Moya, D; Münker, R M; Münnich, A; Neagu, A T; Nikiforou, N; Nikolopoulos, K; Nürnberg, A; Pandurović, M; Pawlik, B; Perez Codina, E; Peric, I; Petric, M; Pitters, F; Poss, S G; Preda, T; Protopopescu, D; Rassool, R; Redford, S; Repond, J; Robson, A; Roloff, P; Ros, E; Rosenblat, O; Ruiz-Jimeno, A; Sailer, A; Schlatter, D; Schulte, D; Shumeiko, N; Sicking, E; Simon, F; Simoniello, R; Sopicki, P; Stapnes, S; Ström, R; Strube, J; Świentek, K P; Szalay, M; Tesař, M; Thomson, M A; Trenado, J; Uggerhøj, U I; van der Kolk, N; van der Kraaij, E; Vicente Barreto Pinto, M; Vila, I; Vogel Gonzalez, M; Vos, M; Vossebeld, J; Watson, M; Watson, N; Weber, M A; Weerts, H; Wells, J D; Weuste, L; Winter, A; Wojtoń, T; Xia, L; Xu, B; Żarnecki, A F; Zawiejski, L; Zgura, I-S

2017-01-01

The Compact Linear Collider (CLIC) is an option for a future [Formula: see text] collider operating at centre-of-mass energies up to [Formula: see text], providing sensitivity to a wide range of new physics phenomena and precision physics measurements at the energy frontier. This paper is the first comprehensive presentation of the Higgs physics reach of CLIC operating at three energy stages: [Formula: see text], 1.4 and [Formula: see text]. The initial stage of operation allows the study of Higgs boson production in Higgsstrahlung ([Formula: see text]) and [Formula: see text]-fusion ([Formula: see text]), resulting in precise measurements of the production cross sections, the Higgs total decay width [Formula: see text], and model-independent determinations of the Higgs couplings. Operation at [Formula: see text] provides high-statistics samples of Higgs bosons produced through [Formula: see text]-fusion, enabling tight constraints on the Higgs boson couplings. Studies of the rarer processes [Formula: see text] and [Formula: see text] allow measurements of the top Yukawa coupling and the Higgs boson self-coupling. This paper presents detailed studies of the precision achievable with Higgs measurements at CLIC and describes the interpretation of these measurements in a global fit.

Quantum metabolism explains the allometric scaling of metabolic rates.

PubMed

Demetrius, Lloyd; Tuszynski, J A

2010-03-06

A general model explaining the origin of allometric laws of physiology is proposed based on coupled energy-transducing oscillator networks embedded in a physical d-dimensional space (d = 1, 2, 3). This approach integrates Mitchell's theory of chemi-osmosis with the Debye model of the thermal properties of solids. We derive a scaling rule that relates the energy generated by redox reactions in cells, the dimensionality of the physical space and the mean cycle time. Two major regimes are found corresponding to classical and quantum behaviour. The classical behaviour leads to allometric isometry while the quantum regime leads to scaling laws relating metabolic rate and body size that cover a broad range of exponents that depend on dimensionality and specific parameter values. The regimes are consistent with a range of behaviours encountered in micelles, plants and animals and provide a conceptual framework for a theory of the metabolic function of living systems.

Effects of curcumin and ursolic acid on the mitochondrial coupling efficiency and hydrogen peroxide emission of intact skeletal myoblasts.

PubMed

Tueller, Daniel J; Harley, Jackson S; Hancock, Chad R

2017-10-21

Curcumin may improve blood glucose management, but the mechanism is not fully established. We demonstrated that curcumin (40 μM) reduced the mitochondrial coupling efficiency (percentage of oxygen consumption coupled to ATP synthesis) of intact skeletal muscle cells. A 30-minute pretreatment with curcumin reduced mitochondrial coupling efficiency by 17.0 ± 0.4% relative to vehicle (p < 0.008). Curcumin pretreatment also decreased the rate of hydrogen peroxide emission by 43 ± 13% compared to vehicle (p < 0.05). Analysis of cell respiration in the presence of curcumin revealed a 40 ± 4% increase in the rate of oxygen consumption upon curcumin administration (p < 0.05 compared to vehicle). No difference in mitochondrial coupling efficiency was observed between vehicle- and curcumin-pretreated cells after permeabilization of cell membranes (p > 0.7). The interaction between curcumin and ursolic acid, another natural compound that may improve blood glucose management, was also examined. Pretreatment with ursolic acid (0.12 μM) increased the mitochondrial coupling efficiency of intact cells by 4.1 ± 1.1% relative to vehicle (p < 0.008) and attenuated the effect of curcumin when the two compounds were used in combination. The observed changes to mitochondrial coupling efficiency and hydrogen peroxide emission were consistent with the established effects of curcumin on blood glucose control. Our findings also show that changes to mitochondrial coupling efficiency after curcumin pretreatment may go undetected unless cells are assessed in the intact condition. Copyright © 2017 Elsevier Inc. All rights reserved.

Kinetics of microbial reduction of Solid phase U(VI).

PubMed

Liu, Chongxuan; Jeon, Byong-Hun; Zachara, John M; Wang, Zheming; Dohnalkova, Alice; Fredrickson, James K

2006-10-15

Sodium boltwoodite (NaUO2SiO3OH x 1.5 H2O) was used to assess the kinetics of microbial reduction of solid-phase U(VI) by a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1. The bioreduction kinetics was studied with Na-boltwoodite in suspension or within alginate beads in a nongrowth medium with lactate as electron donor at pH 6.8 buffered with PIPES. Concentrations of U(VI)tot and cell number were varied to evaluate the coupling of U(VI) dissolution, diffusion, and microbial activity. Microscopic and spectroscopic analyses with transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), and laser-induced fluorescence spectroscopy (LIFS) collectively indicated that solid-phase U(VI) was first dissolved and diffused out of grain interiors before it was reduced on bacterial surfaces and/or within the periplasm. The kinetics of solid-phase U(VI) bioreduction was well described by a coupled model of bicarbonate-promoted dissolution of Na-boltwoodite, intragrain uranyl diffusion, and Monod type bioreduction kinetics with respect to dissolved U(VI) concentration. The results demonstrated that microbial reduction of solid-phase U(VI) is controlled by coupled biological, chemical, and physical processes.

Emergence of Critical Behavior in β-Cell Network

NASA Astrophysics Data System (ADS)

Westacott, Matthew; Hraha, Thomas; McClatchey, Mason; Pozzoli, Marina; Benninger, Richard

2014-03-01

The β-cell is a cell type located in the Islet of Langerhans, a micro-organ of the pancreas which maintains glucose homeostasis through secretion of insulin. An electrophysiological process governing insulin release occurs through initial uptake of blood glucose and generation of ATP which inhibits the ATP sensitive potassium channel (K-ATP) causing membrane depolarization (activation). Neighboring β-cells are electrically coupled through gap junctions which allow passage of cationic molecules, creating a network of coupled electrical oscillators. Cells exhibiting hyperpolzarized (inactive) membrane potential affect behavior of neighboring cells by electrically suppressing their depolarization. Here we observe critical behavior between global active-inactive states by increasing the number of inactive elements with the K-ATP inhibitor Diazoxide and a tunable ATP insensitive transgenic mouse model. We show this behavior occurs due to from cell-cell coupling as mice lacking β-cell gap junctions show no critical behavior. Also, a computational β-cell model was expanded to construct a coupled β-cell network and we show this model replicates the critical behavior seen in-vitro.While electrical activity of single β-cells is well studied these data highlight a newly defined characteristic of their emergent multicellular behavior within the Islet of Langerhans and may elucidate pathophysiology of Diabetes due to mutations in the K-ATP channel.

Assessment of the simulation of Indian Ocean Dipole in the CESM—Impacts of atmospheric physics and model resolution

NASA Astrophysics Data System (ADS)

Yao, Zhixiong; Tang, Youmin; Chen, Dake; Zhou, Lei; Li, Xiaojing; Lian, Tao; Ul Islam, Siraj

2016-12-01

This study examines the possible impacts of coupling processes on simulations of the Indian Ocean Dipole (IOD). Emphasis is placed on the atmospheric model resolution and physics. Five experiments were conducted for this purpose, including one control run of the ocean-only model, four coupled experiments using two different versions of the Community Atmosphere Model (CAM4 and CAM5) and two different resolutions. The results show that the control run could effectively simulate various features of the IOD. The coupled experiments run at the higher resolution yielded more realistic IOD period and intensity than their counterparts at the low resolution. The coupled experiments using CAM5 generally showed a better simulation skill in the tropical Indian SST climatology and phase-locking than those using CAM4, but the wind anomalies were stronger and the IOD period were longer in the former experiments than in the latter. In all coupled experiments, the IOD intensity was much stronger than the observed intensity, which is attributable to wind-thermocline depth feedback and thermocline depth-subsurface temperature feedback. The CAM5 physics seems beneficial for the simulation of summer rainfall over the eastern equatorial Indian Ocean and the CAM4 physics tends to produce less biases over the western equatorial Indian Ocean, whereas the higher resolution tends to generate unrealistically strong meridional winds. The IOD-ENSO relationship was captured reasonably well in coupled experiments, with improvements in CAM5 relative to CAM4. However, the teleconnection of the IOD-Indian summer monsoon and ENSO-Indian summer monsoon was not realistically simulated in all experiments.

Warthog: Coupling Status Update

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

Hart, Shane W. D.; Reardon, Bradley T.

The Warthog code was developed to couple codes that are developed in both the Multi-Physics Object-Oriented Simulation Environment (MOOSE) from Idaho National Laboratory (INL) and SHARP from Argonne National Laboratory (ANL). The initial phase of this work, focused on coupling the neutronics code PROTEUS with the fuel performance code BISON. The main technical challenge involves mapping the power density solution determined by PROTEUS to the fuel in BISON. This presents a challenge since PROTEUS uses the MOAB mesh format, but BISON, like all other MOOSE codes, uses the libMesh format. When coupling the different codes, one must consider that Warthogmore » is a light-weight MOOSE-based program that uses the Data Transfer Kit (DTK) to transfer data between the various mesh types. Users set up inputs for the codes they want to run, and then Warthog transfers the data between them. Currently Warthog supports XSProc from SCALE or the Sub-Group Application Programming Interface (SGAPI) in PROTEUS for generating cross sections. It supports arbitrary geometries using PROTEUS and BISON. DTK will transfer power densities and temperatures between the codes where the domains overlap. In the past fiscal year (FY), much work has gone into demonstrating two-way coupling for simple pin cells of various materials. XSProc was used to calculate the cross sections, which were then passed to PROTEUS in an external file. PROTEUS calculates the fission/power density, and Warthog uses DTK to pass this information to BISON, where it is used as the heat source. BISON then calculates the temperature profile of the pin cell and sends it back to XSProc to obtain the temperature corrected cross sections. This process is repeated until the convergence criteria (tolerance on BISON solve, or number of time steps) is reached. Models have been constructed and run for both uranium oxide and uranium silicide fuels. These models demonstrate a clear difference in power shape that is not accounted for in a stand-alone BISON run. Future work involves improving the user interface (UI), likely through integration with the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench. Furthermore, automating the input creation would ease the user experience. The next priority is to continue coupling the work with other codes in the SHARP package. Efforts on other projects include work to couple the Nek5000 thermo-hydraulics code to MOOSE, but this is in the preliminary stages.« less

Implicit time-integration method for simultaneous solution of a coupled non-linear system

NASA Astrophysics Data System (ADS)

Watson, Justin Kyle

Historically large physical problems have been divided into smaller problems based on the physics involved. This is no different in reactor safety analysis. The problem of analyzing a nuclear reactor for design basis accidents is performed by a handful of computer codes each solving a portion of the problem. The reactor thermal hydraulic response to an event is determined using a system code like TRAC RELAP Advanced Computational Engine (TRACE). The core power response to the same accident scenario is determined using a core physics code like Purdue Advanced Core Simulator (PARCS). Containment response to the reactor depressurization in a Loss Of Coolant Accident (LOCA) type event is calculated by a separate code. Sub-channel analysis is performed with yet another computer code. This is just a sample of the computer codes used to solve the overall problems of nuclear reactor design basis accidents. Traditionally each of these codes operates independently from each other using only the global results from one calculation as boundary conditions to another. Industry's drive to uprate power for reactors has motivated analysts to move from a conservative approach to design basis accident towards a best estimate method. To achieve a best estimate calculation efforts have been aimed at coupling the individual physics models to improve the accuracy of the analysis and reduce margins. The current coupling techniques are sequential in nature. During a calculation time-step data is passed between the two codes. The individual codes solve their portion of the calculation and converge to a solution before the calculation is allowed to proceed to the next time-step. This thesis presents a fully implicit method of simultaneous solving the neutron balance equations, heat conduction equations and the constitutive fluid dynamics equations. It discusses the problems involved in coupling different physics phenomena within multi-physics codes and presents a solution to these problems. The thesis also outlines the basic concepts behind the nodal balance equations, heat transfer equations and the thermal hydraulic equations, which will be coupled to form a fully implicit nonlinear system of equations. The coupling of separate physics models to solve a larger problem and improve accuracy and efficiency of a calculation is not a new idea, however implementing them in an implicit manner and solving the system simultaneously is. Also the application to reactor safety codes is new and has not be done with thermal hydraulics and neutronics codes on realistic applications in the past. The coupling technique described in this thesis is applicable to other similar coupled thermal hydraulic and core physics reactor safety codes. This technique is demonstrated using coupled input decks to show that the system is solved correctly and then verified by using two derivative test problems based on international benchmark problems the OECD/NRC Three mile Island (TMI) Main Steam Line Break (MSLB) problem (representative of pressurized water reactor analysis) and the OECD/NRC Peach Bottom (PB) Turbine Trip (TT) benchmark (representative of boiling water reactor analysis).

Local 3D matrix microenvironment regulates cell migration through spatiotemporal dynamics of contractility-dependent adhesions

NASA Astrophysics Data System (ADS)

Doyle, Andrew D.; Carvajal, Nicole; Jin, Albert; Matsumoto, Kazue; Yamada, Kenneth M.

2015-11-01

The physical properties of two-dimensional (2D) extracellular matrices (ECMs) modulate cell adhesion dynamics and motility, but little is known about the roles of local microenvironmental differences in three-dimensional (3D) ECMs. Here we generate 3D collagen gels of varying matrix microarchitectures to characterize their regulation of 3D adhesion dynamics and cell migration. ECMs containing bundled fibrils demonstrate enhanced local adhesion-scale stiffness and increased adhesion stability through balanced ECM/adhesion coupling, whereas highly pliable reticular matrices promote adhesion retraction. 3D adhesion dynamics are locally regulated by ECM rigidity together with integrin/ECM association and myosin II contractility. Unlike 2D migration, abrogating contractility stalls 3D migration regardless of ECM pore size. We find force is not required for clustering of activated integrins on 3D native collagen fibrils. We propose that efficient 3D migration requires local balancing of contractility with ECM stiffness to stabilize adhesions, which facilitates the detachment of activated integrins from ECM fibrils.

Ultrafast decoherence dynamics govern photocarrier generation efficiencies in polymer solar cells

PubMed Central

Vella, Eleonora; Li, Hao; Grégoire, Pascal; Tuladhar, Sachetan M.; Vezie, Michelle S.; Few, Sheridan; Bazán, Claudia M.; Nelson, Jenny; Silva-Acuña, Carlos; Bittner, Eric R.

2016-01-01

All-organic-based photovoltaic solar cells have attracted considerable attention because of their low-cost processing and short energy payback time. In such systems the primary dissociation of an optical excitation into a pair of photocarriers has been recently shown to be extremely rapid and efficient, but the physical reason for this remains unclear. Here, two-dimensional photocurrent excitation spectroscopy, a novel non-linear optical spectroscopy, is used to probe the ultrafast coherent decay of photoexcitations into charge-producing states in a polymer:fullerene based solar cell. The two-dimensional photocurrent spectra are interpreted by introducing a theoretical model for the description of the coupling of the electronic states of the system to an external environment and to the applied laser fields. The experimental data show no cross-peaks in the twodimensional photocurrent spectra, as predicted by the model for coherence times between the exciton and the photocurrent producing states of 20 fs or less. PMID:27412119

Sarcoplasmic reticulum-mitochondria communication in cardiovascular pathophysiology.

PubMed

Lopez-Crisosto, Camila; Pennanen, Christian; Vasquez-Trincado, Cesar; Morales, Pablo E; Bravo-Sagua, Roberto; Quest, Andrew F G; Chiong, Mario; Lavandero, Sergio

2017-06-01

Repetitive, calcium-mediated contractile activity renders cardiomyocytes critically dependent on a sustained energy supply and adequate calcium buffering, both of which are provided by mitochondria. Moreover, in vascular smooth muscle cells, mitochondrial metabolism modulates cell growth and proliferation, whereas cytosolic calcium levels regulate the arterial vascular tone. Physical and functional communication between mitochondria and sarco/endoplasmic reticulum and balanced mitochondrial dynamics seem to have a critical role for optimal calcium transfer to mitochondria, which is crucial in calcium homeostasis and mitochondrial metabolism in both types of muscle cells. Moreover, mitochondrial dysfunction has been associated with myocardial damage and dysregulation of vascular smooth muscle proliferation. Therefore, sarco/endoplasmic reticulum-mitochondria coupling and mitochondrial dynamics are now viewed as relevant factors in the pathogenesis of cardiac and vascular diseases, including coronary artery disease, heart failure, and pulmonary arterial hypertension. In this Review, we summarize the evidence related to the role of sarco/endoplasmic reticulum-mitochondria communication in cardiac and vascular muscle physiology, with a focus on how perturbations contribute to the pathogenesis of cardiovascular disorders.

Constraints on new physics from K → π ν {\\bar{ν }}

NASA Astrophysics Data System (ADS)

He, Xiao-Gang; Valencia, German; Wong, Keith

2018-06-01

We study generic effects of new physics on the rare decay modes K_L → π ^0 ν {\\bar{ν }} and K^+ → π ^+ ν {\\bar{ν }}. We discuss several cases: left-handed neutrino couplings; right handed neutrino couplings; neutrino lepton flavour violating (LFV) interactions; and Δ I =3/2 interactions. The first of these cases has been studied before as it covers many new physics extensions of the standard model; the second one requires the existence of a new light (sterile) right-handed neutrino and its contribution to both branching ratios is always additive to the SM. The case of neutrino LFV couplings introduces a CP conserving contribution to K_L → π ^0 ν {\\bar{ν }} which affects the rates in a similar manner as a right handed neutrino as neither one of these interferes with the standard model amplitudes. Finally, we consider new physics with Δ I =3/2 interactions to go beyond the Grossman-Nir bound. We find that the rare kaon rates are only sensitive to new physics scales up to a few GeV for this scenario.

Collective Cellular Decision-Making Gives Developmental Plasticity: A Model of Signaling in Branching Roots

NASA Astrophysics Data System (ADS)

McCleery, W. Tyler; Mohd-Radzman, Nadiatul A.; Grieneisen, Veronica A.

Cells within tissues can be regarded as autonomous entities that respond to their local environment and signaling from neighbors. Cell coordination is particularly important in plants, where root architecture must strategically invest resources for growth to optimize nutrient acquisition. Thus, root cells are constantly adapting to environmental cues and neighbor communication in a non-linear manner. To explain such plasticity, we view the root as a swarm of coupled multi-cellular structures, ''metamers'', rather than as a continuum of identical cells. These metamers are individually programmed to achieve a local objective - developing a lateral root primordia, which aids in local foraging of nutrients. Collectively, such individual attempts may be halted, structuring root architecture as an emergent behavior. Each metamer's decision to branch is coordinated locally and globally through hormone signaling, including processes of controlled diffusion, active polar transport, and dynamic feedback. We present a physical model of the signaling mechanism that coordinates branching decisions in response to the environment. This work was funded by the European Commission 7th Framework Program, Project No. 601062, SWARM-ORGAN.

Measurement of Bacterial Bioluminescence Intensity and Spectrum: Current Physical Techniques and Principles.

PubMed

Jia, Kun; Ionescu, Rodica Elena

2016-01-01

: Bioluminescence is light production by living organisms, which can be observed in numerous marine creatures and some terrestrial invertebrates. More specifically, bacterial bioluminescence is the "cold light" produced and emitted by bacterial cells, including both wild-type luminescent and genetically engineered bacteria. Because of the lively interplay of synthetic biology, microbiology, toxicology, and biophysics, different configurations of whole-cell biosensors based on bacterial bioluminescence have been designed and are widely used in different fields, such as ecotoxicology, food toxicity, and environmental pollution. This chapter first discusses the background of the bioluminescence phenomenon in terms of optical spectrum. Platforms for bacterial bioluminescence detection using various techniques are then introduced, such as a photomultiplier tube, charge-coupled device (CCD) camera, micro-electro-mechanical systems (MEMS), and complementary metal-oxide-semiconductor (CMOS) based integrated circuit. Furthermore, some typical biochemical methods to optimize the analytical performances of bacterial bioluminescent biosensors/assays are reviewed, followed by a presentation of author's recent work concerning the improved sensitivity of a bioluminescent assay for pesticides. Finally, bacterial bioluminescence as implemented in eukaryotic cells, bioluminescent imaging, and cancer cell therapies is discussed.

Self-organization: the fundament of cell biology

PubMed Central

Betz, Timo

2018-01-01

Self-organization refers to the emergence of an overall order in time and space of a given system that results from the collective interactions of its individual components. This concept has been widely recognized as a core principle in pattern formation for multi-component systems of the physical, chemical and biological world. It can be distinguished from self-assembly by the constant input of energy required to maintain order—and self-organization therefore typically occurs in non-equilibrium or dissipative systems. Cells, with their constant energy consumption and myriads of local interactions between distinct proteins, lipids, carbohydrates and nucleic acids, represent the perfect playground for self-organization. It therefore comes as no surprise that many properties and features of self-organized systems, such as spontaneous formation of patterns, nonlinear coupling of reactions, bi-stable switches, waves and oscillations, are found in all aspects of modern cell biology. Ultimately, self-organization lies at the heart of the robustness and adaptability found in cellular and organismal organization, and hence constitutes a fundamental basis for natural selection and evolution. This article is part of the theme issue ‘Self-organization in cell biology’. PMID:29632257

On the nature of a supposed water model

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

Heckmann, Lotta, E-mail: lotta@fkp.tu-darmstadt.de; Drossel, Barbara

2014-08-15

A cell model that has been proposed by Stanley and Franzese in 2002 for modeling water is based on Potts variables that represent the possible orientations of bonds between water molecules. We show that in the liquid phase, where all cells are occupied by a molecule, the Hamiltonian of the cell model can be rewritten as a Hamiltonian of a conventional Potts model, albeit with two types of coupling constants. We argue that such a model, while having a first-order phase transition, cannot display the critical end point that is postulated for the phase transition between a high- and low-densitymore » liquid. A closer look at the mean-field calculations that claim to find such an end point in the cell model reveals that the mean-field theory is constructed such that the symmetry constraints on the order parameter are violated. This is equivalent to introducing an external field. The introduction of such a field can be given a physical justification due to the fact that water does not have the type of long-range order occurring in the Potts model.« less

Criteria for robustness of heteroclinic cycles in neural microcircuits

PubMed Central

2011-01-01

We introduce a test for robustness of heteroclinic cycles that appear in neural microcircuits modeled as coupled dynamical cells. Robust heteroclinic cycles (RHCs) can appear as robust attractors in Lotka-Volterra-type winnerless competition (WLC) models as well as in more general coupled and/or symmetric systems. It has been previously suggested that RHCs may be relevant to a range of neural activities, from encoding and binding to spatio-temporal sequence generation. The robustness or otherwise of such cycles depends both on the coupling structure and the internal structure of the neurons. We verify that robust heteroclinic cycles can appear in systems of three identical cells, but only if we require perturbations to preserve some invariant subspaces for the individual cells. On the other hand, heteroclinic attractors can appear robustly in systems of four or more identical cells for some symmetric coupling patterns, without restriction on the internal dynamics of the cells. PMID:22656192

Gauge coupling beta functions in the standard model to three loops.

PubMed

Mihaila, Luminita N; Salomon, Jens; Steinhauser, Matthias

2012-04-13

In this Letter, we compute the three-loop corrections to the beta functions of the three gauge couplings in the standard model of particle physics using the minimal subtraction scheme and taking into account Yukawa and Higgs self-couplings.

Attraction and repulsion of spiral waves by inhomogeneity of conduction anisotropy--a model of spiral wave interaction with electrical remodeling of heart tissue.

PubMed

Kuklik, Pawel; Sanders, Prashanthan; Szumowski, Lukasz; Żebrowski, Jan J

2013-01-01

Various forms of heart disease are associated with remodeling of the heart muscle, which results in a perturbation of cell-to-cell electrical coupling. These perturbations may alter the trajectory of spiral wave drift in the heart muscle. We investigate the effect of spatially extended inhomogeneity of transverse cell coupling on the spiral wave trajectory using a simple active media model. The spiral wave was either attracted or repelled from the center of inhomogeneity as a function of cell excitability and gradient of the cell coupling. High levels of excitability resulted in an attraction of the wave to the center of inhomogeneity, whereas low levels resulted in an escape and termination of the spiral wave. The spiral wave drift velocity was related to the gradient of the coupling and the initial position of the wave. In a diseased heart, a region of altered transverse coupling corresponds with local gap junction remodeling that may be responsible for stabilization-destabilization of spiral waves and hence reflect potentially important targets in the treatment of heart arrhythmias.

Targeting to cells of fluorescent liposomes covalently coupled with monoclonal antibody or protein A

NASA Astrophysics Data System (ADS)

Leserman, Lee D.; Barbet, Jacques; Kourilsky, François; Weinstein, John N.

1980-12-01

Many applications envisioned for liposomes in cell biology and chemotherapy require their direction to specific cellular targets1-3. The ability to use antibody as a means of conferring specificity to liposomes would markedly increase their usefulness. We report here a method for covalently coupling soluble proteins, including monoclonal antibody and Staphylococcus aureus protein A (ref. 4), to small sonicated liposomes, by using the heterobifunctional cross-linking reagent N-hydroxysuccinimidyl 3-(2-pyridyldithio)propionate (SPDP, Pharmacia). Liposomes bearing covalently coupled mouse monoclonal antibody against human β2-microglobulin [antibody B1.1G6 (IgG2a, κ) (B. Malissen et al., in preparation)] bound specifically to human, but not to mouse cells. Liposomes bearing protein A became bound to human cells previously incubated with the B1.1G6 antibody, but not to cells incubated without antibody. The coupling method results in efficient binding of protein to the liposomes without aggregation and without denaturation of the coupled ligand; at least 60% of liposomes bound functional protein. Further, liposomes did not leak encapsulated carboxyfluorescein (CF) as a consequence of the reaction.

Physically coupling two objects in a bimanual task alters kinematics but not end-state comfort.

PubMed

Hughes, Charmayne M L; Haddad, Jeffrey M; Franz, Elizabeth A; Zelaznik, Howard N; Ryu, Joong Hyun

2011-06-01

People often grasp objects with an awkward grip to ensure a comfortable hand posture at the end of the movement. This end-state comfort effect is a predominant constraint during unimanual movements. However, during bimanual movements the tendency for both hands to satisfy end-state comfort is affected by factors such as end-orientation congruency and task context. Although bimanual end-state comfort has been examined when the hands manipulate two independent objects, no research has examined end-state comfort when the hands are required to manipulate two physically-coupled objects. In the present experiment, kinematics and grasp behavior during a unimanual and bimanual reaching and placing tasks were examined, when the hands manipulate two physically-connected objects. Forty-five participants were assigned to one of three groups; unimanual, bimanual no-spring (the objects were not physically connected), and bimanual spring (the objects were connected by a spring), and instructed to grasp and place objects in various end-orientations, depending on condition. Physically connecting the objects did not affect end-state comfort prevalence. However, it resulted in decreased interlimb coupling. This finding supports the notion of a flexible constraint hierarchy, in which action goals guide the selection of lower level action features (i.e., hand grip used for grasping), and the particular movements used to accomplish that goal (i.e., interlimb coupling) are controlled throughout the movement.

Dynamic Properties of Electrotonic Coupling between Cells of Early Xenopus Embryos

PubMed Central

DiCaprio, R. A.; French, A. S.; Sanders, E. J.

1974-01-01

Frequency response functions were measured between the cells of Xenopus laevis embryos during the first two cleavage stages. Linear systems theory was then used to produce electronic models which account for the electrical behavior of the systems. Coupling between the cells may be explained by models which have simple resistive elements joining each cell to its neighbors. The vitelline, or fertilization, membrane which surrounds the embryos has no detectable resistance to the passage of electric current. The electrical properties of the four-cell embryo can only be explained by the existence of individual junctions linking each pair of cells. This arrangement suggests that electrotonic coupling is important in the development of the embryos, at least until the four-cell stage. ImagesFIGURE 5FIGURE 14FIGURE 15 PMID:19431351

Nonlinear Chemical Dynamics and Synchronization

NASA Astrophysics Data System (ADS)

Li, Ning

Alan Turing's work on morphogenesis, more than half a century ago, continues to motivate and inspire theoretical and experimental biologists even today. That said, there are very few experimental systems for which Turing's theory is applicable. In this thesis we present an experimental reaction-diffusion system ideally suited for testing Turing's ideas in synthetic "cells" consisting of microfluidically produced surfactant-stabilized emulsions in which droplets containing the Belousov-Zhabotinsky (BZ) oscillatory chemical reactants are dispersed in oil. The BZ reaction has become the prototype of nonlinear dynamics in chemistry and a preferred system for exploring the behavior of coupled nonlinear oscillators. Our system consists of a surfactant stabilized monodisperse emulsion of drops of aqueous BZ solution dispersed in a continuous phase of oil. In contrast to biology, here the chemistry is understood, rate constants are measured and interdrop coupling is purely diffusive. We explore a large set of parameters through control of rate constants, drop size, spacing, and spatial arrangement of the drops in lines and rings in one-dimension (1D) and hexagonal arrays in two-dimensions (2D). The Turing model is regarded as a metaphor for morphogenesis in biology but not for prediction. Here, we develop a quantitative and falsifiable reaction-diffusion model that we experimentally test with synthetic cells. We quantitatively establish the extent to which the Turing model in 1D describes both stationary pattern formation and temporal synchronization of chemical oscillators via reaction-diffusion and in 2D demonstrate that chemical morphogenesis drives physical differentiation in synthetic cells.

SIERRA Multimechanics Module: Aria User Manual Version 4.44

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

Sierra Thermal /Fluid Team

2017-04-01

Aria is a Galerkin fnite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process fows via the incompressible Navier-Stokes equations specialized to a low Reynolds number ( %3C 1 ) regime. Enhanced modeling support of manufacturing processing is made possible through use of eithermore » arbitrary Lagrangian- Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton's method with analytic or numerical sensitivities, fully-coupled Newton- Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic h -adaptivity and dynamic load balancing are some of Aria's more advanced capabilities. Aria is based upon the Sierra Framework.« less

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

Sierra Thermal/Fluid Team

Aria is a Galerkin fnite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process fows via the incompressible Navier-Stokes equations specialized to a low Reynolds number ( %3C 1 ) regime. Enhanced modeling support of manufacturing processing is made possible through use of eithermore » arbitrary Lagrangian- Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton's method with analytic or numerical sensitivities, fully-coupled Newton- Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic h -adaptivity and dynamic load balancing are some of Aria's more advanced capabilities. Aria is based upon the Sierra Framework.« less

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

Sierra Thermal /Fluid Team

Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes thermal energy transport, species transport, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for manufacturing process flows via the incompressible Navier-Stokes equations specialized to a low Reynolds number (Re %3C 1) regime. Enhanced modeling support of manufacturing processing is made possible through use of either arbitrarymore » Lagrangian- Eulerian (ALE) and level set based free and moving boundary tracking in conjunction with quasi-static nonlinear elastic solid mechanics for mesh control. Coupled physics problems are solved in several ways including fully-coupled Newton's method with analytic or numerical sensitivities, fully-coupled Newton- Krylov methods and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic h-adaptivity and dynamic load balancing are some of Aria's more advanced capabilities. Aria is based upon the Sierra Framework.« less

Macroscopic Magnetic Coupling Effect: The Physical Origination of a High-Temperature Superconducting Flux Pump

NASA Astrophysics Data System (ADS)

Wang, Wei; Coombs, Tim

2018-04-01

We have uncovered at the macroscopic scale a magnetic coupling phenomenon in a superconducting YBa2Cu3O7 -δ (YBCO) film, which physically explains the mechanism of the high-temperature superconducting flux pump. The coupling occurs between the applied magnetic poles and clusters of vortices induced in the YBCO film, with each cluster containing millions of vortices. The coupling energy is verified to originate from the inhomogeneous field of the magnetic poles, which reshapes the vortex distribution, aggregates millions of vortices into a single cluster, and accordingly moves with the poles. A contrast study is designed to verify that, to provide the effective coupling energy, the applied wavelength must be short while the field amplitude must be strong, i.e., local-field inhomogeneity is the crucial factor. This finding broadens our understanding of the collective vortex behavior in an applied magnetic field with strong local inhomogeneity. Moreover, this phenomenon largely increases the controlled vortex flow rate by several orders of magnitude compared with existing methods, providing motivation for and physical support to a new branch of wireless superconducting dc power sources, i.e., the high-temperature superconducting flux pump.

Adenosine receptors regulate gap junction coupling of the human cerebral microvascular endothelial cells hCMEC/D3 by Ca2+ influx through cyclic nucleotide-gated channels.

PubMed

Bader, Almke; Bintig, Willem; Begandt, Daniela; Klett, Anne; Siller, Ina G; Gregor, Carola; Schaarschmidt, Frank; Weksler, Babette; Romero, Ignacio; Couraud, Pierre-Olivier; Hell, Stefan W; Ngezahayo, Anaclet

2017-04-15

Gap junction channels are essential for the formation and regulation of physiological units in tissues by allowing the lateral cell-to-cell diffusion of ions, metabolites and second messengers. Stimulation of the adenosine receptor subtype A 2B increases the gap junction coupling in the human blood-brain barrier endothelial cell line hCMEC/D3. Although the increased gap junction coupling is cAMP-dependent, neither the protein kinase A nor the exchange protein directly activated by cAMP were involved in this increase. We found that cAMP activates cyclic nucleotide-gated (CNG) channels and thereby induces a Ca 2+ influx, which leads to the increase in gap junction coupling. The report identifies CNG channels as a possible physiological link between adenosine receptors and the regulation of gap junction channels in endothelial cells of the blood-brain barrier. The human cerebral microvascular endothelial cell line hCMEC/D3 was used to characterize the physiological link between adenosine receptors and the gap junction coupling in endothelial cells of the blood-brain barrier. Expressed adenosine receptor subtypes and connexin (Cx) isoforms were identified by RT-PCR. Scrape loading/dye transfer was used to evaluate the impact of the A 2A and A 2B adenosine receptor subtype agonist 2-phenylaminoadenosine (2-PAA) on the gap junction coupling. We found that 2-PAA stimulated cAMP synthesis and enhanced gap junction coupling in a concentration-dependent manner. This enhancement was accompanied by an increase in gap junction plaques formed by Cx43. Inhibition of protein kinase A did not affect the 2-PAA-related enhancement of gap junction coupling. In contrast, the cyclic nucleotide-gated (CNG) channel inhibitor l-cis-diltiazem, as well as the chelation of intracellular Ca 2+ with BAPTA, or the absence of external Ca 2+ , suppressed the 2-PAA-related enhancement of gap junction coupling. Moreover, we observed a 2-PAA-dependent activation of CNG channels by a combination of electrophysiology and pharmacology. In conclusion, the stimulation of adenosine receptors in hCMEC/D3 cells induces a Ca 2+ influx by opening CNG channels in a cAMP-dependent manner. Ca 2+ in turn induces the formation of new gap junction plaques and a consecutive sustained enhancement of gap junction coupling. The report identifies CNG channels as a physiological link that integrates gap junction coupling into the adenosine receptor-dependent signalling of endothelial cells of the blood-brain barrier. © 2017 The Authors. The Journal of Physiology © 2017 The Physiological Society.

Coherent manipulation of spontaneous emission spectra in coupled semiconductor quantum well structures.

PubMed

Chen, Aixi

2014-11-03

In triple coupled semiconductor quantum well structures (SQWs) interacting with a coherent driving filed, a coherent coupling field and a weak probe field, spontaneous emission spectra are investigated. Our studies show emission spectra can easily be manipulated through changing the intensity of the driving and coupling field, detuning of the driving field. Some interesting physical phenomena such as spectral-line enhancement/suppression, spectral-line narrowing and spontaneous emission quenching may be obtained in our system. The theoretical studies of spontaneous emission spectra in SQWS have potential application in high-precision spectroscopy. Our studies are based on the real physical system [Appl. Phys. Lett.86(20), 201112 (2005)], and this scheme might be realizable with presently available techniques.

Scheme variations of the QCD coupling

NASA Astrophysics Data System (ADS)

Boito, Diogo; Jamin, Matthias; Miravitllas, Ramon

2017-03-01

The Quantum Chromodynamics (QCD) coupling αs is a central parameter in the Standard Model of particle physics. However, it depends on theoretical conventions related to renormalisation and hence is not an observable quantity. In order to capture this dependence in a transparent way, a novel definition of the QCD coupling, denoted by â, is introduced, whose running is explicitly renormalisation scheme invariant. The remaining renormalisation scheme dependence is related to transformations of the QCD scale Λ, and can be parametrised by a single parameter C. Hence, we call â the C-scheme coupling. The dependence on C can be exploited to study and improve perturbative predictions of physical observables. This is demonstrated for the QCD Adler function and hadronic decays of the τ lepton.

Electrical conductivity in Li2O2 and its role in determining capacity limitations in non-aqueous Li-O2 batteries.

PubMed

Viswanathan, V; Thygesen, K S; Hummelshøj, J S; Nørskov, J K; Girishkumar, G; McCloskey, B D; Luntz, A C

2011-12-07

Non-aqueous Li-air or Li-O(2) cells show considerable promise as a very high energy density battery couple. Such cells, however, show sudden death at capacities far below their theoretical capacity and this, among other problems, limits their practicality. In this paper, we show that this sudden death arises from limited charge transport through the growing Li(2)O(2) film to the Li(2)O(2)-electrolyte interface, and this limitation defines a critical film thickness, above which it is not possible to support electrochemistry at the Li(2)O(2)-electrolyte interface. We report both electrochemical experiments using a reversible internal redox couple and a first principles metal-insulator-metal charge transport model to probe the electrical conductivity through Li(2)O(2) films produced during Li-O(2) discharge. Both experiment and theory show a "sudden death" in charge transport when film thickness is ~5 to 10 nm. The theoretical model shows that this occurs when the tunneling current through the film can no longer support the electrochemical current. Thus, engineering charge transport through Li(2)O(2) is a serious challenge if Li-O(2) batteries are ever to reach their potential. © 2011 American Institute of Physics

Development and evaluation of a local grid refinement method for block-centered finite-difference groundwater models using shared nodes

USGS Publications Warehouse

Mehl, S.; Hill, M.C.

2002-01-01

A new method of local grid refinement for two-dimensional block-centered finite-difference meshes is presented in the context of steady-state groundwater-flow modeling. The method uses an iteration-based feedback with shared nodes to couple two separate grids. The new method is evaluated by comparison with results using a uniform fine mesh, a variably spaced mesh, and a traditional method of local grid refinement without a feedback. Results indicate: (1) The new method exhibits quadratic convergence for homogeneous systems and convergence equivalent to uniform-grid refinement for heterogeneous systems. (2) Coupling the coarse grid with the refined grid in a numerically rigorous way allowed for improvement in the coarse-grid results. (3) For heterogeneous systems, commonly used linear interpolation of heads from the large model onto the boundary of the refined model produced heads that are inconsistent with the physics of the flow field. (4) The traditional method works well in situations where the better resolution of the locally refined grid has little influence on the overall flow-system dynamics, but if this is not true, lack of a feedback mechanism produced errors in head up to 3.6% and errors in cell-to-cell flows up to 25%. ?? 2002 Elsevier Science Ltd. All rights reserved.

In Vivo Quantification of Cell Coupling in Plants with Different Phloem-Loading Strategies[W][OA

PubMed Central

Liesche, Johannes; Schulz, Alexander

2012-01-01

Uptake of photoassimilates into the leaf phloem is the key step in carbon partitioning and phloem transport. Symplasmic and apoplasmic loading strategies have been defined in different plant taxa based on the abundance of plasmodesmata between mesophyll and phloem. For apoplasmic loading to occur, an absence of plasmodesmata is a sufficient but not a necessary criterion, as passage of molecules through plasmodesmata might well be blocked or restricted. Here, we present a noninvasive, whole-plant approach to test symplasmic coupling and quantify the intercellular flux of small molecules using photoactivation microscopy. Quantification of coupling between all cells along the prephloem pathways of the apoplasmic loader Vicia faba and Nicotiana tabacum showed, to our knowledge for the first time in vivo, that small solutes like sucrose can diffuse through plasmodesmata up to the phloem sieve element companion cell complex (SECCC). As expected, the SECCC was found to be symplasmically isolated for small solutes. In contrast, the prephloem pathway of the symplasmic loader Cucurbita maxima was found to be well coupled with the SECCC. Phloem loading in gymnosperms is not well understood, due to a profoundly different leaf anatomy and a scarcity of molecular data compared with angiosperms. A cell-coupling analysis for Pinus sylvestris showed high symplasmic coupling along the entire prephloem pathway, comprising at least seven cell border interfaces between mesophyll and sieve elements. Cell coupling together with measurements of leaf sap osmolality indicate a passive symplasmic loading type. Similarities and differences of this loading type with that of angiosperm trees are discussed. PMID:22422939

A geometrical multi-scale numerical method for coupled hygro-thermo-mechanical problems in photovoltaic laminates.

PubMed

Lenarda, P; Paggi, M

A comprehensive computational framework based on the finite element method for the simulation of coupled hygro-thermo-mechanical problems in photovoltaic laminates is herein proposed. While the thermo-mechanical problem takes place in the three-dimensional space of the laminate, moisture diffusion occurs in a two-dimensional domain represented by the polymeric layers and by the vertical channel cracks in the solar cells. Therefore, a geometrical multi-scale solution strategy is pursued by solving the partial differential equations governing heat transfer and thermo-elasticity in the three-dimensional space, and the partial differential equation for moisture diffusion in the two dimensional domains. By exploiting a staggered scheme, the thermo-mechanical problem is solved first via a fully implicit solution scheme in space and time, with a specific treatment of the polymeric layers as zero-thickness interfaces whose constitutive response is governed by a novel thermo-visco-elastic cohesive zone model based on fractional calculus. Temperature and relative displacements along the domains where moisture diffusion takes place are then projected to the finite element model of diffusion, coupled with the thermo-mechanical problem by the temperature and crack opening dependent diffusion coefficient. The application of the proposed method to photovoltaic modules pinpoints two important physical aspects: (i) moisture diffusion in humidity freeze tests with a temperature dependent diffusivity is a much slower process than in the case of a constant diffusion coefficient; (ii) channel cracks through Silicon solar cells significantly enhance moisture diffusion and electric degradation, as confirmed by experimental tests.

Specification of the near-Earth space environment with SHIELDS

DOE PAGES

Jordanova, Vania Koleva; Delzanno, Gian Luca; Henderson, Michael Gerard; ...

2017-11-26

Here, predicting variations in the near-Earth space environment that can lead to spacecraft damage and failure is one example of “space weather” and a big space physics challenge. A project recently funded through the Los Alamos National Laboratory (LANL) Directed Research and Development (LDRD) program aims at developing a new capability to understand, model, and predict Space Hazards Induced near Earth by Large Dynamic Storms, the SHIELDS framework. The project goals are to understand the dynamics of the surface charging environment (SCE), the hot (keV) electrons representing the source and seed populations for the radiation belts, on both macro- andmore » micro-scale. Important physics questions related to particle injection and acceleration associated with magnetospheric storms and substorms, as well as plasma waves, are investigated. These challenging problems are addressed using a team of world-class experts in the fields of space science and computational plasma physics, and state-of-the-art models and computational facilities. A full two-way coupling of physics-based models across multiple scales, including a global MHD (BATS-R-US) embedding a particle-in-cell (iPIC3D) and an inner magnetosphere (RAM-SCB) codes, is achieved. New data assimilation techniques employing in situ satellite data are developed; these provide an order of magnitude improvement in the accuracy in the simulation of the SCE. SHIELDS also includes a post-processing tool designed to calculate the surface charging for specific spacecraft geometry using the Curvilinear Particle-In-Cell (CPIC) code that can be used for reanalysis of satellite failures or for satellite design.« less

Specification of the near-Earth space environment with SHIELDS

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

Jordanova, Vania Koleva; Delzanno, Gian Luca; Henderson, Michael Gerard

Here, predicting variations in the near-Earth space environment that can lead to spacecraft damage and failure is one example of “space weather” and a big space physics challenge. A project recently funded through the Los Alamos National Laboratory (LANL) Directed Research and Development (LDRD) program aims at developing a new capability to understand, model, and predict Space Hazards Induced near Earth by Large Dynamic Storms, the SHIELDS framework. The project goals are to understand the dynamics of the surface charging environment (SCE), the hot (keV) electrons representing the source and seed populations for the radiation belts, on both macro- andmore » micro-scale. Important physics questions related to particle injection and acceleration associated with magnetospheric storms and substorms, as well as plasma waves, are investigated. These challenging problems are addressed using a team of world-class experts in the fields of space science and computational plasma physics, and state-of-the-art models and computational facilities. A full two-way coupling of physics-based models across multiple scales, including a global MHD (BATS-R-US) embedding a particle-in-cell (iPIC3D) and an inner magnetosphere (RAM-SCB) codes, is achieved. New data assimilation techniques employing in situ satellite data are developed; these provide an order of magnitude improvement in the accuracy in the simulation of the SCE. SHIELDS also includes a post-processing tool designed to calculate the surface charging for specific spacecraft geometry using the Curvilinear Particle-In-Cell (CPIC) code that can be used for reanalysis of satellite failures or for satellite design.« less

Coupling of Processes and Data in PennState Integrated Hydrologic Modeling (PIHM) System

NASA Astrophysics Data System (ADS)

Kumar, M.; Duffy, C.

2007-12-01

Full physical coupling, "natural" numerical coupling and parsimonious but accurate data coupling is needed to comprehensively and accurately capture the interaction between different components of a hydrologic continuum. Here we present a physically based, spatially distributed hydrologic model that incorporates all the three coupling strategies. Physical coupling of interception, snow melt, transpiration, overland flow, subsurface flow, river flow, macropore based infiltration and stormflow, flow through and over hydraulic structures likes weirs and dams, and evaporation from interception, ground and overland flow is performed. All the physically coupled components are numerically coupled through semi-discrete form of ordinary differential equations, that define each hydrologic process, using Finite-Volume based approach. The fully implicit solution methodology using CVODE solver solves for all the state variables simultaneously at each adaptive time steps thus providing robustness, stability and accuracy. The accurate data coupling is aided by use of constrained unstructured meshes, flexible data model and use of PIHMgis. The spatial adaptivity of decomposed domain and temporal adaptivity of the numerical solver facilitates capture of varied spatio-temporal scales that are inherent in hydrologic process interactions. The implementation of the model has been performed on a meso-scale Little-Juniata Watershed. Model results are validated by comparison of streamflow at multiple locations. We discuss some of the interesting hydrologic interactions between surface, subsurface and atmosphere witnessed during the year long simulation such as a) inverse relationship between evaporation from interception storage and transpiration b) relative influence of forcing (precipitation, temperature and radiation) and source (soil moisture and overland flow) on evaporation c) influence of local topography on gaining, loosing or "flow-through" behavior of river-aquifer interactions d) role of macropores on base flow during wetting and drying conditions. In addition to its use as a potential predictive and exploratory science tool, we present a test case for the application of model in water management by mapping of water table decline index for the whole watershed. Also discussed will be the efficient parallelization strategy of the model for high spatio-temporal resolution simulations.

Distributed coupling high efficiency linear accelerator

DOEpatents

Tantawi, Sami G.; Neilson, Jeffrey

2016-07-19

A microwave circuit for a linear accelerator includes multiple monolithic metallic cell plates stacked upon each other so that the beam axis passes vertically through a central acceleration cavity of each plate. Each plate has a directional coupler with coupling arms. A first coupling slot couples the directional coupler to an adjacent directional coupler of an adjacent cell plate, and a second coupling slot couples the directional coupler to the central acceleration cavity. Each directional coupler also has an iris protrusion spaced from corners joining the arms, a convex rounded corner at a first corner joining the arms, and a corner protrusion at a second corner joining the arms.

Conflict in Maritally Distressed Military Couples.

ERIC Educational Resources Information Center

Griffin, William A.; Morgan, Allison R.

1988-01-01

Investigated whether 30 maritally distressed military couples differed from 30 distressed civilian couples using marital satisfaction questionnaires. Found same-sex differences across groups, and cross-sex differences within groups. Found military wives were more likely to be physically abused than were civilian wives, and more often requested…

Inverse size scaling of the nucleolus by a concentration-dependent phase transition.

PubMed

Weber, Stephanie C; Brangwynne, Clifford P

2015-03-02

Just as organ size typically increases with body size, the size of intracellular structures changes as cells grow and divide. Indeed, many organelles, such as the nucleus [1, 2], mitochondria [3], mitotic spindle [4, 5], and centrosome [6], exhibit size scaling, a phenomenon in which organelle size depends linearly on cell size. However, the mechanisms of organelle size scaling remain unclear. Here, we show that the size of the nucleolus, a membraneless organelle important for cell-size homeostasis [7], is coupled to cell size by an intracellular phase transition. We find that nucleolar size directly scales with cell size in early C. elegans embryos. Surprisingly, however, when embryo size is altered, we observe inverse scaling: nucleolar size increases in small cells and decreases in large cells. We demonstrate that this seemingly contradictory result arises from maternal loading of a fixed number rather than a fixed concentration of nucleolar components, which condense into nucleoli only above a threshold concentration. Our results suggest that the physics of phase transitions can dictate whether an organelle assembles, and, if so, its size, providing a mechanistic link between organelle assembly and cell size. Since the nucleolus is known to play a key role in cell growth, this biophysical readout of cell size could provide a novel feedback mechanism for growth control. Copyright © 2015 Elsevier Ltd. All rights reserved.

Butyl benzyl phthalate suppresses the ATP-induced cell proliferation in human osteosarcoma HOS cells

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

Liu, P.-S., E-mail: pslediting@mail.scu.edu.t; Chen, C.-Y.

2010-05-01

Butyl benzyl phthalate (BBP), an endocrine disruptor present in the environment, exerts its genomic effects via intracellular steroid receptors and elicits non-genomic effects by interfering with membrane ion-channel receptors. We previously found that BBP blocks the calcium signaling coupled with P2X receptors in PC12 cells (Liu and Chen, 2006). Osteoblast P2X receptors were recently reported to play a role in cell proliferation and bone remodeling. In this present study, the effects of BBP on ATP-induced responses were investigated in human osteosarcoma HOS cells. These receptors mRNA had been detected, named P2X4, P2X7, P2Y2, P2Y4, P2Y5, P2Y9, and P2Y11, in humanmore » osteosarcoma HOS cells by RT-PCR. The enhancement of cell proliferation and the decrease of cytoviability had both been shown to be coupled to stimulation via different concentrations of ATP. BBP suppressed the ATP-induced calcium influx (mainly coupled with P2X) and cell proliferation but not the ATP-induced intracellular calcium release (mainly coupled with P2Y) and cytotoxicity in human osteosarcoma HOS cells. Suramin, a common P2 receptor's antagonist, blocked the ATP-induced calcium signaling, cell proliferation, and cytotoxicity. We suggest that P2X is mainly responsible for cell proliferation, and P2Y might be partially responsible for the observed cytotoxicity. BBP suppressed the calcium signaling coupled with P2X, suppressing cell proliferation. Since the importance of P2X receptors during bone metastasis has recently become apparent, the possible toxic risk of environmental BBP during bone remodeling is a public problem of concern.« less

Atrial natriuretic peptide receptor heterogeneity and effects on cyclic GMP accumulation

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

Leitman, D.C.

1988-01-01

The effects of atrial natriuretic peptide (ANP), oxytocin (OT) and vasopressin (AVP) on guanylate cyclase activity and cyclic GMP accumulation were examined, since these hormones appear to be intimately associated with blood pressure and intravascular volume homeostasis. ANP was found to increase cyclic GMP accumulation in ten cell culture systems, which were derived from blood vessels, adrenal cortex, kidney, lung, testes and mammary gland. ANP receptors were characterized in intact cultured cells using {sup 125}I-ANP{sub 8-33}. Specific {sup 125}I-ANP binding was saturable and of high affinity. Scratchard analysis of the binding data for all cell types exhibited a straight line,more » indicating that these cells possessed a single class of binding sites. Despite the presence of linear Scatchard plots, these studies demonstrated that cultured cells possess two functionally and physically distinct ANP-binding sites. Most of the ANP-binding sites in cultured cells have a molecular size of 66,000 daltons under reducing conditions. The identification of cultured cell types in which hormones (ANP and oxytocin) regulate guanylate cyclase activity and increase cyclic GMP synthesis will provide valuable systems to determine the mechanisms of hormone-receptor coupling to guanylate cyclase and the cellular processes regulated by cyclic GMP.« less

Visualization of channels connecting cells in filamentous nitrogen-fixing cyanobacteria.

PubMed

Omairi-Nasser, Amin; Haselkorn, Robert; Austin, Jotham

2014-07-01

Cyanobacteria, formerly called blue-green algae, are abundant bacteria that carry out green plant photosynthesis, fixing CO2 and generating O2. Many species can also fix N2 when reduced nitrogen sources are scarce. Many studies imply the existence of intracellular communicating channels in filamentous cyanobacteria, in particular, the nitrogen-fixing species. In a species such as Anabaena, growth in nitrogen-depleted medium, in which ∼10% of the cells differentiate into anaerobic factories for nitrogen fixation (heterocysts), requires the transport of amino acids from heterocysts to vegetative cells, and reciprocally, the transport of sugar from vegetative cells to heterocysts. Convincing physical evidence for such channels has been slim. Using improved preservation of structure by high-pressure rapid freezing of samples for electron microscopy, coupled with high-resolution 3D tomography, it has been possible to visualize and measure the dimensions of channels that breach the peptidoglycan between vegetative cells and between heterocysts and vegetative cells. The channels appear to be straight tubes, 21 nm long and 14 nm in diameter for the latter and 12 nm long and 12 nm in diameter for the former.-Omairi-Nasser, A., Haselkorn, R., Austin, J. II. Visualization of channels connecting cells in filamentous nitrogen-fixing cyanobacteria. © FASEB.

Modeling, analysis and control of fuel cell hybrid power systems

NASA Astrophysics Data System (ADS)

Suh, Kyung Won

Transient performance is a key characteristic of fuel cells, that is sometimes more critical than efficiency, due to the importance of accepting unpredictable electric loads. To fulfill the transient requirement in vehicle propulsion and portable fuel cell applications, a fuel cell stack is typically coupled with a battery through a DC/DC converter to form a hybrid power system. Although many power management strategies already exist, they all rely on low level controllers that realize the power split. In this dissertation we design controllers that realize various power split strategies by directly manipulating physical actuators (low level commands). We maintain the causality of the electric dynamics (voltage and current) and investigate how the electric architecture affects the hybridization level and the power management. We first establish the performance limitations associated with a stand-alone and power-autonomous fuel cell system that is not supplemented by an additional energy storage and powers all its auxiliary components by itself. Specifically, we examine the transient performance in fuel cell power delivery as it is limited by the air supplied by a compressor driven by the fuel cell itself. The performance limitations arise from the intrinsic coupling in the fluid and electrical domain between the compressor and the fuel cell stack. Feedforward and feedback control strategies are used to demonstrate these limitations analytically and with simulations. Experimental tests on a small commercial fuel cell auxiliary power unit (APU) confirm the dynamics and the identified limitations. The dynamics associated with the integration of a fuel cell system and a DC/DC converter is then investigated. Decentralized and fully centralized (using linear quadratic techniques) controllers are designed to regulate the power system voltage and to prevent fuel cell oxygen starvation. Regulating these two performance variables is a difficult task and requires a compromise due to the conflicting objectives. The compromise can be mitigated by augmenting the fuel cell power system with an energy buffer such as a battery. We consider two different and popular ways of connecting the battery and the fuel cell to the load and we refer to them as electric architectures. Various controller gains are used to span the fuel cell operation from load-following to load-leveling, and hence, to determine adequate fuel cell-battery sizing (hybridization level) and the associated trends in the system efficiency.

mTor Regulates Lysosomal ATP-sensitive Two-Pore Na+ Channel to Adapt to Metabolic State

PubMed Central

Navarro, Betsy; Seo, Young-jun; Aranda, Kimberly; Shi, Lucy; Battaglia-Hsu, Shyuefang; Nissim, Itzhak; Clapham, David E.; Ren, Dejian

2014-01-01

SUMMARY Survival in the wild requires organismal adaptations to the availability of nutrients. Endosomes and lysosomes are key intracellular organelles that couple nutrition and metabolic status to cellular responses, but how they detect cytosolic ATP levels is not well understood. Here we identify an endolysosomal ATP-sensitive Na+ channel (lysoNaATP). The channel is a complex formed by Two-Pore Channels (TPC1 and TPC2), ion channels previously thought to be gated by nicotinic acid adenine dinucleotide phosphate (NAADP), and the mammalian target of rapamycin (mTOR). The channel complex detects nutrient status, becomes constitutively open upon nutrient removal and mTOR translocation off the lysosomal membrane, and controls the lysosome's membrane potential, pH stability, and the amino acid homeostasis. Mutant mice lacking lysoNaATP have much reduced exercise endurance after fasting. Thus, TPCs are a new ion channel family that couple the cell's metabolic state to endolysosomal function and are crucial for physical endurance during food restriction. PMID:23394946

Mathematical and computational model for the analysis of micro hybrid rocket motor

NASA Astrophysics Data System (ADS)

Stoia-Djeska, Marius; Mingireanu, Florin

2012-11-01

The hybrid rockets use a two-phase propellant system. In the present work we first develop a simplified model of the coupling of the hybrid combustion process with the complete unsteady flow, starting from the combustion port and ending with the nozzle. The physical and mathematical model are adapted to the simulations of micro hybrid rocket motors. The flow model is based on the one-dimensional Euler equations with source terms. The flow equations and the fuel regression rate law are solved in a coupled manner. The platform of the numerical simulations is an implicit fourth-order Runge-Kutta second order cell-centred finite volume method. The numerical results obtained with this model show a good agreement with published experimental and numerical results. The computational model developed in this work is simple, computationally efficient and offers the advantage of taking into account a large number of functional and constructive parameters that are used by the engineers.

Improvements in continuum modeling for biomolecular systems

NASA Astrophysics Data System (ADS)

Yu, Qiao; Ben-Zhuo, Lu

2016-01-01

Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson- Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress. Project supported by the National Natural Science Foundation of China (Grant No. 91230106) and the Chinese Academy of Sciences Program for Cross & Cooperative Team of the Science & Technology Innovation.

Transforming the legacies of childhood trauma in couple and family therapy.

PubMed

Basham, Kathryn

2004-01-01

A multi-theoretical couple/family therapy clinical social work practice model synthesizes various social, family, trauma, and psychodynamic theories to inform a biopsychosocial assessment that guides clinical interventions. The client population involves adult partners who have negotiated the impact of childhood trauma, i.e., physical, sexual, and emotional abuses, including culturally sanctioned trauma. Couples may also be dealing with the aftermath of acute trauma related to interpersonal violence, political conflict, and/or the dislocations related to refugee or new immigrant status. Clinical examples demonstrate the usefulness of the model as well as contraindications when active physical violence is present. The construct of resilience remains a central focus in assessment and treatment. Specific attention to cultural and racial diversity enriches both assessment and treatment interventions with these high-risk couples and families. This practice model will be explicated in depth in an upcoming publication from Columbia University Press titled Transforming the Legacies of Trauma in Couple Therapy.

End-Directedness and Context in Nonliving Dissipative Systems

NASA Astrophysics Data System (ADS)

Dixon, James A.; Kay, Bruce A.; Davis, Tehran J.; Kondepudi, Dilip

Biological organisms are distinguished from non-living systems, in part, by their ability to choose and strive towards particular ends. This end-directed behavior is seen across all five biological kingdoms, from single-celled organisms to the most advanced primates. The ubiquitous nature of end-directedness, across such a wide variety of biological entities, suggests that a deeper principle may be at work. We propose that end-directedness, rather than being a special ability of living systems, is actually a fundamental property of a larger class of physical systems, called dissipative structures, which are formed and maintained by the flow of energy and matter. Our work shows that dissipative structures "behave so as to persist", seeking states that increase their rate of entropy production, and thus facilitate their own persistence. In addition, we suggest that biological entities create their exquisite sensitivity to context by interweaving this fundamental end-directedness with the contextual and physical constraints of their environments. The result is a repertoire of complex behavior. We provide an example of such complex behavior emerging from contextual and physical constraints coupled with end-directedness.

Microdomains in the membrane landscape shape antigen-presenting cell function.

PubMed

Zuidscherwoude, Malou; de Winde, Charlotte M; Cambi, Alessandra; van Spriel, Annemiek B

2014-02-01

The plasma membrane of immune cells is a highly organized cell structure that is key to the initiation and regulation of innate and adaptive immune responses. It is well-established that immunoreceptors embedded in the plasma membrane have a nonrandom spatial distribution that is important for coupling to components of intracellular signaling cascades. In the last two decades, specialized membrane microdomains, including lipid rafts and TEMs, have been identified. These domains are preformed structures ("physical entities") that compartmentalize proteins, lipids, and signaling molecules into multimolecular assemblies. In APCs, different microdomains containing immunoreceptors (MHC proteins, PRRs, integrins, among others) have been reported that are imperative for efficient pathogen recognition, the formation of the immunological synapse, and subsequent T cell activation. In addition, recent work has demonstrated that tetraspanin microdomains and lipid rafts are involved in BCR signaling and B cell activation. Research into the molecular mechanisms underlying membrane domain formation is fundamental to a comprehensive understanding of membrane-proximal signaling and APC function. This review will also discuss the advances in the microscopy field for the visualization of the plasma membrane, as well as the recent progress in targeting microdomains as novel, therapeutic approach for infectious and malignant diseases.

A dual-electrochemical cell to study the biocorrosion of stainless steel.

PubMed

Lopes, F A; Perrin, S; Féron, D

2007-01-01

The presence of microorganisms on metal surfaces can alter the local physical/chemical conditions and lead to microbiologically influenced corrosion (MIC). The goal of the present work was to study the effect of a mixed aerobic-anaerobic biofilm on the behaviour of stainless steel (316 L) in underground conditions. Rather than testing different bacteria or consortia, investigations were based on the mechanisms of MIC. Mixed biofilms were simulated by the addition of glucose oxidase to reproduce the aerobic conditions and by sulphide or sulphate-reducing bacteria (SRB) for the anaerobic conditions. A double thermostated electrochemical cell has been developed to study the coupling between aerobic and anaerobic conditions. Results suggested a transfer of electrons from the stainless steel sample of the anaerobic cell to the stainless steel sample of the aerobic one. Inorganic sulphide was replaced by SRB in the anaerobic cell revealing an increase of the galvanic current which may be explained by an effect of lactate and/or acetate on the anodic reaction or by a high sulphide concentration in the biofilm. The results of this study underline that the dual-electrochemical cell system is representative of phenomena present in natural environments and should be considered as an option when studying MIC.

Efficient and Stable Photovoltaic Characteristics of Quasi-Solid State DSSC using Polymer Gel Electrolyte Based on Ionic Liquid in Organosiloxane Polymer Gels

NASA Astrophysics Data System (ADS)

Pujiarti, H.; Arsyad, W. S.; Shobih; Muliani, L.; Hidayat, R.

2018-04-01

Dye-Sensitized Solar Cell (DSSC) is still one of the promising solar cell types among the third generation of solar cells because of easiness of fabrication and variety of available materials. In this type of solar cell, the electrolyte is one of the important components for regenerating excited dyes and transporting electric charge carriers to the counter electrode. Indeed, the power conversion efficiency of DSSC can be then significantly affected by the chemical and physical properties of the electrolyte. The simplest electrolyte system of an I-/I3 - redox couple in an organic solvent, however, has some drawbacks due to corrosive properties, volatile and leakage problem. Use of solid phase or gel phase electrolyte may overcome those problems, but it is often considered to suppress the efficiency due to low ion diffusion. Here, we report the photovoltaic characteristics of DSSC using polymer gel electrolyte (PGE), which is composed of ionic liquid and an organosiloxane polymer gel. The better cell performance with power conversion efficiency of about 6% has been obtained by optimizing the mesoporous size of the TiO2 layer and the PGE viscosity.

Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells.

PubMed

Bieler, Jonathan; Cannavo, Rosamaria; Gustafson, Kyle; Gobet, Cedric; Gatfield, David; Naef, Felix

2014-07-15

Circadian cycles and cell cycles are two fundamental periodic processes with a period in the range of 1 day. Consequently, coupling between such cycles can lead to synchronization. Here, we estimated the mutual interactions between the two oscillators by time-lapse imaging of single mammalian NIH3T3 fibroblasts during several days. The analysis of thousands of circadian cycles in dividing cells clearly indicated that both oscillators tick in a 1:1 mode-locked state, with cell divisions occurring tightly 5 h before the peak in circadian Rev-Erbα-YFP reporter expression. In principle, such synchrony may be caused by either unidirectional or bidirectional coupling. While gating of cell division by the circadian cycle has been most studied, our data combined with stochastic modeling unambiguously show that the reverse coupling is predominant in NIH3T3 cells. Moreover, temperature, genetic, and pharmacological perturbations showed that the two interacting cellular oscillators adopt a synchronized state that is highly robust over a wide range of parameters. These findings have implications for circadian function in proliferative tissues, including epidermis, immune cells, and cancer. © 2014 The Authors. Published under the terms of the CC BY 4.0 license.

Macroscopic Modeling of a One-Dimensional Electrochemical Cell using the Poisson-Nernst-Planck Equations

NASA Astrophysics Data System (ADS)

Yan, David

This thesis presents the one-dimensional equations, numerical method and simulations of a model to characterize the dynamical operation of an electrochemical cell. This model extends the current state-of-the art in that it accounts, in a primitive way, for the physics of the electrolyte/electrode interface and incorporates diffuse-charge dynamics, temperature coupling, surface coverage, and polarization phenomena. The one-dimensional equations account for a system with one or two mobile ions of opposite charge, and the electrode reaction we consider (when one is needed) is a one-electron electrodeposition reaction. Though the modeled system is far from representing a realistic electrochemical device, our results show a range of dynamics and behaviors which have not been observed previously, and explore the numerical challenges required when adding more complexity to a model. Furthermore, the basic transport equations (which are developed in three spatial dimensions) can in future accomodate the inclusion of additional physics, and coupling to more complex boundary conditions that incorporate two-dimensional surface phenomena and multi-rate reactions. In the model, the Poisson-Nernst-Planck equations are used to model diffusion and electromigration in an electrolyte, and the generalized Frumkin-Butler-Volmer equation is used to model reaction kinetics at electrodes. An energy balance equation is derived and coupled to the diffusion-migration equation. The model also includes dielectric polarization effects by introducing different values of the dielectric permittivity in different regions of the bulk, as well as accounting for surface coverage effects due to adsorption, and finite size "crowding", or steric effects. Advection effects are not modeled but could in future be incorporated. In order to solve the coupled PDE's, we use a variable step size second order scheme in time and finite differencing in space. Numerical tests are performed on a simplified system and the scheme's stability and convergence properties are discussed. While evaluating different methods for discretizing the coupled flux boundary condition, we discover a thresholding behaviour in the adaptive time stepper, and perform additional tests to investigate it. Finally, a method based on ghost points is chosen for its favorable numerical properties compared to the alternatives. With this method, we are able to run simulations with a large range of parameters, including any value of the nondimensionalized Debye length epsilon. The numerical code is first used to run simulations to explore the effects of polarization, surface coverage, and temperature. The code is also used to perform frequency sweeps of input signals in order to mimic impedance spectroscopy experiments. Finally, in Chapter 5, we use our model to apply ramped voltages to electrochemical systems, and show theoretical and simulated current-voltage curves for liquid and solid thin films, cells with blocking (polarized) electrodes, and electrolytes with background charge. Linear sweep and cyclic voltammetry techniques are important tools for electrochemists and have a variety of applications in engineering. Voltammetry has classically been treated with the Randles-Sevcik equation, which assumes an electroneutral supported electrolyte. No general theory of linear-sweep voltammetry is available, however, for unsupported electrolytes and for other situations where diffuse charge effects play a role. We show theoretical and simulated current-voltage curves for liquid and solid thin films, cells with blocking electrodes, and membranes with fixed background charge. The analysis focuses on the coupling of Faradaic reactions and diffuse charge dynamics, but capacitive charging of the double layers is also studied, for early time transients at reactive electrodes and for non-reactive blocking electrodes. The final chapter highlights the role of diffuse charge in the context of voltammetry, and illustrates which regimes can be approximated using simple analytical expressions and which require more careful consideration.

Evaluation of a physical activity intervention for new parents: protocol paper for a randomized trial.

PubMed

Quinlan, Alison; Rhodes, Ryan E; Beauchamp, Mark R; Symons Downs, Danielle; Warburton, Darren E R; Blanchard, Chris M

2017-11-09

Identifying critical life transitions in people's physical activity behaviors may illuminate the most opportune intervention apertures for chronic disease prevention. A substantive evidence base now indicates that parenthood is one of these critical transition points for physical activity decline. This study will examine whether a brief theory-based intervention can prevent a decline in physical activity among new parents over 6 months following intervention. This study protocol represents the first dyad-based physical activity initiative in the parenthood literature involving both mothers and fathers; prior research has focused on only mothers or only fathers (albeit limited), and has shown only short-term changes in physical activity. This study will be investigating whether a theory-based physical activity intervention can maintain or improve moderate to vigorous intensity physical activity measured via accelerometry of new parents over a 6 month period following intervention compared to a control group. This study is a 6-month longitudinal randomized controlled trial. Parents are measured at baseline (2 months postpartum) with two assessment points at 6 weeks (3.5 months postpartum) and 3 months (5 months postpartum) and a final follow-up assessment at 6 months (8 months postpartum). The content of the theory-based intervention was derived from the results of our prior longitudinal trial of new parents using an adapted theory of planned behavior framework to predict changes in physical activity. A total of 152 couples have been recruited to date. Sixteen couples dropped out after baseline and a total of 88 couples have completed their 6-month measures. If the intervention proves successful, couple-based physical activity promotion efforts among parents could be a promising avenue to pursue to help mitigate the declines of physical activity levels during parenthood. These findings could inform public health materials and practitioners. This trial has been registered with the Clinical Trials Registry maintained by the National Library of Medicine at the National Institutes of Health on April 19, 2014. The registration ID is NCT02290808 .

High-performance coupled poro-hydro-mechanical models to resolve fluid escape pipes

NASA Astrophysics Data System (ADS)

Räss, Ludovic; Makhnenko, Roman; Podladchikov, Yury

2017-04-01

Field observations and laboratory experiments exhibit inelastic deformation features arising in many coupled settings relevant to geo-applications. These irreversible deformations and their specific patterns suggest a rather ductile or brittle mechanism, such as viscous creep or micro cracks, taking place on both geological (long) and human (short) timescales. In order to understand the underlying mechanisms responsible for these deformation features, there is a current need to accurately resolve the non-linearities inherent to strongly coupled physical processes. Among the large variety of modelling tools and softwares available nowadays in the community, very few are capable to efficiently solve coupled systems with high accuracy in both space and time and run efficiently on modern hardware. Here, we propose a robust framework to solve coupled multi-physics hydro-mechanical processes on very high spatial and temporal resolution in both two and three dimensions. Our software relies on the Finite-Difference Method and a pseudo-transient scheme is used to converge to the implicit solution of the system of poro-visco-elasto-plastic equations at each physical time step. The rheology including viscosity estimates for major reservoir rock types is inferred from novel lab experiments and confirms the ease of flow of sedimentary rocks. Our results propose a physical mechanism responsible for the generation of high permeability pathways in fluid saturated porous media and predict their propagation in rates observable on operational timescales. Finally, our software scales linearly on more than 5000 GPUs.

Gender Inequality in the Couple Relationship and Leisure-Based Physical Exercise

PubMed Central

Annandale, Ellen; Hammarström, Anne

2015-01-01

Aims To analyse whether gender inequality in the couple relationship was related to leisure-based physical activity, after controlling for earlier physical activity and confounders. Methods Data drawn from the Northern Swedish Cohort of all pupils in their final year of compulsory schooling in a town in the North of Sweden. The sample consisted of 772 respondents (n = 381 men, n = 391 women) in the 26-year follow-up (in 2007, aged 42) who were either married or cohabiting. Ordinal regression, for men and women separately, was used to assess the association between gender inequality (measured as self-perceived equality in the couple relationship using dummy variables) and a measure of exercise frequency, controlling for prior exercise frequency, socioeconomic status, the presence of children in the home, and longer than usual hours in paid work. Results The perception of greater gender equality in the couple relationship was associated with higher levels of physical activity for both men and women. This remained significant when the other variables were controlled for. Amongst men the confidence intervals were high. Conclusions The results point to the potential of perceived gender equality in the couple relationship to counteract the general time poverty and household burden that often arises from the combination of paid work and responsibility for children and the home, especially for women. The high confidence intervals among men indicate the need for more research within the field with larger samples. PMID:26196280

Estrogen anti-inflammatory activity on human monocytes is mediated through cross-talk between estrogen receptor ERα36 and GPR30/GPER1.

PubMed

Pelekanou, Vasiliki; Kampa, Marilena; Kiagiadaki, Foteini; Deli, Alexandra; Theodoropoulos, Panayiotis; Agrogiannis, George; Patsouris, Efstratios; Tsapis, Andreas; Castanas, Elias; Notas, George

2016-02-01

Estrogens are known modulators of monocyte/macrophage functions; however, the underlying mechanism has not been clearly defined. Recently, a number of estrogen receptor molecules and splice variants were identified that exert different and sometimes opposing actions. We assessed the expression of estrogen receptors and explored their role in mediating estrogenic anti-inflammatory effects on human primary monocytes. We report that the only estrogen receptors expressed are estrogen receptor-α 36-kDa splice variant and G-protein coupled receptor 30/G-protein estrogen receptor 1, in a sex-independent manner. 17-β-Estradiol inhibits the LPS-induced IL-6 inflammatory response, resulting in inhibition of NF-κB transcriptional activity. This is achieved via a direct physical interaction of ligand-activated estrogen receptor-α 36-kDa splice variant with the p65 component of NF-κB in the nucleus. G-protein coupled receptor 30/G-protein estrogen receptor 1, which also physically interacts with estrogen receptor-α 36-kDa splice variant, acts a coregulator in this process, because its inhibition blocks the effect of estrogens on IL-6 expression. However, its activation does not mimic the effect of estrogens, on neither IL-6 nor NF-κB activity. Finally, we show that the estrogen receptor profile observed in monocytes is not modified during their differentiation to macrophages or dendritic cells in vitro and is shared in vivo by macrophages present in atherosclerotic plaques. These results position estrogen receptor-α 36-kDa splice variant and G-protein coupled receptor 30 as important players and potential therapeutic targets in monocyte/macrophage-dependent inflammatory processes. © Society for Leukocyte Biology.

Dynamical coupling between magnetic equilibrium and transport in tokamak scenario modelling, with application to current ramps

NASA Astrophysics Data System (ADS)

Fable, E.; Angioni, C.; Ivanov, A. A.; Lackner, K.; Maj, O.; Medvedev, S. Yu; Pautasso, G.; Pereverzev, G. V.; Treutterer, W.; the ASDEX Upgrade Team

2013-07-01

The modelling of tokamak scenarios requires the simultaneous solution of both the time evolution of the plasma kinetic profiles and of the magnetic equilibrium. Their dynamical coupling involves additional complications, which are not present when the two physical problems are solved separately. Difficulties arise in maintaining consistency in the time evolution among quantities which appear in both the transport and the Grad-Shafranov equations, specifically the poloidal and toroidal magnetic fluxes as a function of each other and of the geometry. The required consistency can be obtained by means of iteration cycles, which are performed outside the equilibrium code and which can have different convergence properties depending on the chosen numerical scheme. When these external iterations are performed, the stability of the coupled system becomes a concern. In contrast, if these iterations are not performed, the coupled system is numerically stable, but can become physically inconsistent. By employing a novel scheme (Fable E et al 2012 Nucl. Fusion submitted), which ensures stability and physical consistency among the same quantities that appear in both the transport and magnetic equilibrium equations, a newly developed version of the ASTRA transport code (Pereverzev G V et al 1991 IPP Report 5/42), which is coupled to the SPIDER equilibrium code (Ivanov A A et al 2005 32nd EPS Conf. on Plasma Physics (Tarragona, 27 June-1 July) vol 29C (ECA) P-5.063), in both prescribed- and free-boundary modes is presented here for the first time. The ASTRA-SPIDER coupled system is then applied to the specific study of the modelling of controlled current ramp-up in ASDEX Upgrade discharges.

Systematic study of electron-phonon coupling to oxygen modes across the cuprates

NASA Astrophysics Data System (ADS)

Johnston, S.; Vernay, F.; Moritz, B.; Shen, Z.-X.; Nagaosa, N.; Zaanen, J.; Devereaux, T. P.

2010-08-01

The large variations in Tc across the cuprate families is one of the major unsolved puzzles in condensed matter physics and is poorly understood. Although there appears to be a great deal of universality in the cuprates, several orders of magnitude changes in Tc can be achieved through changes in the chemical composition and structure of the unit cell. In this paper we formulate a systematic examination of the variations in electron-phonon coupling to oxygen phonons in the cuprates, incorporating a number of effects arising from several aspects of chemical composition and doping across cuprate families. It is argued that the electron-phonon coupling is a very sensitive probe of the material-dependent variations in chemical structure, affecting the orbital character of the band crossing the Fermi level, the strength of local electric fields arising from structural-induced symmetry breaking, doping-dependent changes in the underlying band structure, and ionicity of the crystal governing the ability of the material to screen c -axis perturbations. Using electrostatic Ewald calculations and known experimental structural data, we establish a connection between the material’s maximal Tc at optimal doping and the strength of coupling to c -axis modes. We demonstrate that materials with the largest coupling to the out-of-phase bond-buckling (B1g) oxygen phonon branch also have the largest Tc ’s. In light of this observation we present model Tc calculations using a two-well model where phonons work in conjunction with a dominant pairing interaction, presumably due to spin fluctuations, indicating how phonons can generate sizeable enhancements to Tc despite the relatively small coupling strengths. Combined, these results can provide a natural framework for understanding the doping and material dependence of Tc across the cuprates.

High-resolution coupled ice sheet-ocean modeling using the POPSICLES model

NASA Astrophysics Data System (ADS)

Ng, E. G.; Martin, D. F.; Asay-Davis, X.; Price, S. F.; Collins, W.

2014-12-01

It is expected that a primary driver of future change of the Antarctic ice sheet will be changes in submarine melting driven by incursions of warm ocean water into sub-ice shelf cavities. Correctly modeling this response on a continental scale will require high-resolution modeling of the coupled ice-ocean system. We describe the computational and modeling challenges in our simulations of the full Southern Ocean coupled to a continental-scale Antarctic ice sheet model at unprecedented spatial resolutions (0.1 degree for the ocean model and adaptive mesh refinement down to 500m in the ice sheet model). The POPSICLES model couples the POP2x ocean model, a modified version of the Parallel Ocean Program (Smith and Gent, 2002), with the BISICLES ice-sheet model (Cornford et al., 2012) using a synchronous offline-coupling scheme. Part of the PISCEES SciDAC project and built on the Chombo framework, BISICLES makes use of adaptive mesh refinement to fully resolve dynamically-important regions like grounding lines and employs a momentum balance similar to the vertically-integrated formulation of Schoof and Hindmarsh (2009). Results of BISICLES simulations have compared favorably to comparable simulations with a Stokes momentum balance in both idealized tests like MISMIP3D (Pattyn et al., 2013) and realistic configurations (Favier et al. 2014). POP2x includes sub-ice-shelf circulation using partial top cells (Losch, 2008) and boundary layer physics following Holland and Jenkins (1999), Jenkins (2001), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008) and other continental-scale simulations and melt-rate observations (Kimura et al., 2013; Rignot et al., 2013). For the POPSICLES Antarctic-Southern Ocean simulations, ice sheet and ocean models communicate at one-month coupling intervals.

Use of arginine-glycine-aspartic acid adhesion peptides coupled with a new collagen scaffold to engineer a myocardium-like tissue graft.

PubMed

Schussler, O; Coirault, C; Louis-Tisserand, M; Al-Chare, W; Oliviero, P; Menard, C; Michelot, R; Bochet, P; Salomon, D R; Chachques, J C; Carpentier, A; Lecarpentier, Y

2009-03-01

Cardiac tissue engineering might be useful in treatment of diseased myocardium or cardiac malformations. The creation of functional, biocompatible contractile tissues, however, remains challenging. We hypothesized that coupling of arginine-glycine-aspartic acid-serine (RGD+) adhesion peptides would improve cardiomyocyte viability and differentiation and contractile performance of collagen-cell scaffolds. Clinically approved collagen scaffolds were functionalized with RGD+ cells and seeded with cardiomyocytes. Contractile performance, cardiomyocyte viability and differentiation were analyzed at days 1 and 8 and/or after culture for 1 month. The method used for the RGD+ cell-collagen scaffold coupling enabled the following features: high coupling yields and complete washout of excess reagent and by-products with no need for chromatography; spectroscopic quantification of RGD+ coupling; a spacer arm of 36 A, a length reported as optimal for RGD+-peptide presentation and favorable for integrin-receptor clustering and subsequent activation. Isotonic and isometric mechanical parameters, either spontaneous or electrostimulated, exhibited good performance in RGD+ constructs. Cell number and viability was increased in RGD+ scaffolds, and we saw good organization of cell contractile apparatus with occurrence of cross-striation. We report a novel method of engineering a highly effective collagen-cell scaffold based on RGD+ peptides cross-linked to a clinically approved collagen matrix. The main advantages were cell contractile performance, cardiomyocyte viability and differentiation.

Thiolate/disulfide organic redox couples for efficient organic dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Li, Wen-Yan; Zheng, Hai-Kuo; Wang, Jian-Wen; Zhang, Le-Le; Han, Hui-Min; Wu, Ming-Xing

2017-08-01

A series of organic thiolate/disulfide redox couples based on benz-imidazole/othiazole/oxazole have been synthesized and applied to dye-sensitized solar cells (DSCs). Platinum (Pt) and carbon material are introduced as counter electrode (CE) catalysts towards this kind of organic redox couples regeneration and the photovoltaic performance of the DSCs using this organic redox couples has been investigated. The carbon CE shows high catalytic activity than Pt for the organic redox couples and the DSCs using carbon CE exhibit much higher efficiencies than those of the Pt CE-based devices.

The fabrication of a double-layer atom chip with through silicon vias for an ultra-high-vacuum cell

NASA Astrophysics Data System (ADS)

Chuang, Ho-Chiao; Lin, Yun-Siang; Lin, Yu-Hsin; Huang, Chi-Sheng

2014-04-01

This study presents a double-layer atom chip that provides users with increased diversity in the design of the wire patterns and flexibility in the design of the magnetic field. It is more convenient for use in atomic physics experiments. A negative photoresist, SU-8, was used as the insulating layer between the upper and bottom copper wires. The electrical measurement results show that the upper and bottom wires with a width of 100 µm can sustain a 6 A current without burnout. Another focus of this study is the double-layer atom chips integrated with the through silicon via (TSV) technique, and anodically bonded to a Pyrex glass cell, which makes it a desired vacuum chamber for atomic physics experiments. Thus, the bonded glass cell not only significantly reduces the overall size of the ultra-high-vacuum (UHV) chamber but also conducts the high current from the backside to the front side of the atom chip via the TSV under UHV (9.5 × 10-10 Torr). The TSVs with a diameter of 70 µm were etched through by the inductively coupled plasma ion etching and filled by the bottom-up copper electroplating method. During the anodic bonding process, the electroplated copper wires and TSVs on atom chips also need to pass the examination of the required bonding temperature of 250 °C, under an applied voltage of 1000 V. Finally, the UHV test of the double-layer atom chips with TSVs at room temperature can be reached at 9.5 × 10-10 Torr, thus satisfying the requirements of atomic physics experiments under an UHV environment.

Spin-Orbit Coupled Bose-Einstein Condensates

DTIC Science & Technology

2016-11-03

generalized the new concepts to interacting spin-1/2 bosons in optical lattices and described a superfluid-to-Mott insulator transition in spin-orbit...and quantum phase transitions in topological insulators , Physical Review B, (09 2010): 0. doi: 10.1103/PhysRevB.82.115125 Christopher Varney, Kai...109.235308 J. Radi?, A. Di Ciolo, K. Sun, V. Galitski. Exotic Quantum Spin Models in Spin-Orbit-Coupled Mott Insulators , Physical Review Letters

One-sided and mutually aggressive couples: Differences in attachment, conflict prevalence, and coping.

PubMed

Burk, William J; Seiffge-Krenke, Inge

2015-12-01

This study investigated concurrent links between adolescent romantic couples' reports of aggression (relational and physical) and relationship functioning (e.g., attachment security, conflict prevalence, coping strategies, jealousy, and affiliative and romantic relationship quality) using a pattern-oriented approach. The sample included 194 romantic partner dyads (Mage=16.99 years for females and Mage=18.41 years for males). A hierarchical cluster analysis identified five distinct subgroups of dyads based on male and female reports of relational and physical aggression, ranging from nonaggressive couples (42%), to those characterized by aggressive females (18%), aggressive males (14%), physically aggressive females (20%), and mutually aggressive females and males (6%). Clusters in which one partner was perceived as either relationally or physically aggressive were characterized by higher rates of conflict, less adaptive coping, and more jealousy (particularly in males). The mutually aggressive couples showed the least adaptive relationship functioning, with high rates of conflict, a deficit in reflection and emotion regulation in conflict situations, and a lack of affiliative relationship qualities. The discussion focuses on the formative character of aggression in these early romantic relations, the aggravating impact of mutual aggression on relationship functioning, and the gender-specific functions of aggression in relationships characterized by unilateral aggression. Copyright © 2015 Elsevier Ltd. All rights reserved.

Extended Analytic Device Optimization Employing Asymptotic Expansion

NASA Technical Reports Server (NTRS)

Mackey, Jonathan; Sehirlioglu, Alp; Dynsys, Fred

2013-01-01

Analytic optimization of a thermoelectric junction often introduces several simplifying assumptionsincluding constant material properties, fixed known hot and cold shoe temperatures, and thermallyinsulated leg sides. In fact all of these simplifications will have an effect on device performance,ranging from negligible to significant depending on conditions. Numerical methods, such as FiniteElement Analysis or iterative techniques, are often used to perform more detailed analysis andaccount for these simplifications. While numerical methods may stand as a suitable solution scheme,they are weak in gaining physical understanding and only serve to optimize through iterativesearching techniques. Analytic and asymptotic expansion techniques can be used to solve thegoverning system of thermoelectric differential equations with fewer or less severe assumptionsthan the classic case. Analytic methods can provide meaningful closed form solutions and generatebetter physical understanding of the conditions for when simplifying assumptions may be valid.In obtaining the analytic solutions a set of dimensionless parameters, which characterize allthermoelectric couples, is formulated and provide the limiting cases for validating assumptions.Presentation includes optimization of both classic rectangular couples as well as practically andtheoretically interesting cylindrical couples using optimization parameters physically meaningful toa cylindrical couple. Solutions incorporate the physical behavior for i) thermal resistance of hot andcold shoes, ii) variable material properties with temperature, and iii) lateral heat transfer through legsides.

Do Substance Use, Psychosocial Adjustment, and Sexual Experiences Vary for Dating Violence Victims Based on Type of Violent Relationships?

PubMed

Zweig, Janine M; Yahner, Jennifer; Dank, Meredith; Lachman, Pamela

2016-12-01

We examined whether substance use, psychosocial adjustment, and sexual experiences vary for teen dating violence victims by the type of violence in their relationships. We compared dating youth who reported no victimization in their relationships to those who reported being victims of intimate terrorism (dating violence involving one physically violent and controlling perpetrator) and those who reported experiencing situational couple violence (physical dating violence absent the dynamics of power and control). This was a cross-sectional survey of 3745 dating youth from 10 middle and high schools in the northeastern United States, one third of whom reported physical dating violence. In general, teens experiencing no dating violence reported less frequent substance use, higher psychosocial adjustment, and less sexual activity than victims of either intimate terrorism or situational couple violence. In addition, victims of intimate terrorism reported higher levels of depression, anxiety, and anger/hostility compared to situational couple violence victims; they also were more likely to report having sex, and earlier sexual initiation. Youth who experienced physical violence in their dating relationships, coupled with controlling behaviors from their partner/perpetrator, reported the most psychosocial adjustment issues and the earliest sexual activity. © 2016, American School Health Association.

Flagellar dynamics reveal the distribution of chemotactic signaling molecule CheY-P in E. coli

NASA Astrophysics Data System (ADS)

Bano, Roshni; Mears, Patrick; Chemla, Yann; Golding, Ido

E. colicells swim in a random walk consisting of ''runs'' - during which the flagella that propel the cell rotate counter-clockwise (CCW) - and ''tumbles''- during which one or more flagella rotate clockwise (CW). The tumbling frequency is modulated by the phosphorylation state of the signaling molecule CheY, which depends on the cell's environment. Phosphorylated CheY (CheY-P) binds to a flagellar motor and engenders a change in rotation state from CCW to CW. Despite advances in methods used to observe chemotactic signaling, it remains a challenge to measure the CheY-P level in cells directly. Here, we used an optical trap assay coupled with fluorescence microscopy to observe the dynamics of fluorescently labelled flagella in individual cells. By measuring the distribution of flagellar states in multi-flagellated cells and using our recent finding that each flagellar motor independently measures the cellular CheY-P concentration, we are able to extract the probability distribution of the CheY-P level in the cell. This analysis reveals the magnitude of fluctuations in chemotactic signaling in the live cell. We further investigate how this CheY-P distribution changes when cells encounter chemical gradients and perform chemotaxis. This work was supported by the National Science Foundation (NSF) through the Centre for Physics of Living Cells (CPLC).

Large enhancement of superconducting transition temperature in single-element superconducting rhenium by shear strain

PubMed Central

Mito, Masaki; Matsui, Hideaki; Tsuruta, Kazuki; Yamaguchi, Tomiko; Nakamura, Kazuma; Deguchi, Hiroyuki; Shirakawa, Naoki; Adachi, Hiroki; Yamasaki, Tohru; Iwaoka, Hideaki; Ikoma, Yoshifumi; Horita, Zenji

2016-01-01

Finding a physical approach for increasing the superconducting transition temperature (Tc) is a challenge in the field of material science. Shear strain effects on the superconductivity of rhenium were investigated using magnetic measurements, X-ray diffraction, transmission electron microscopy, and first-principles calculations. A large shear strain reduces the grain size and simultaneously expands the unit cells, resulting in an increase in Tc. Here we show that this shear strain approach is a new method for enhancing Tc and differs from that using hydrostatic strain. The enhancement of Tc is explained by an increase in net electron–electron coupling rather than a change in the density of states near the Fermi level. The shear strain effect in rhenium could be a successful example of manipulating Bardeen–Cooper–Schrieffer-type Cooper pairing, in which the unit cell volumes are indeed a key parameter. PMID:27811983

Modeling Joule Heating Effect on Lunar O2 Generation via Electrolytic Reduction.

NASA Technical Reports Server (NTRS)

Dominquez, Jesus; Poizeau, Sophie; Sibille, Laurent

2009-01-01

Kennedy Space Center is leading research work on lunar O2 generation via electrolytic reduction of regolith; the metal oxide present in the regolith is dissociated in oxygen anions and metal cations leading to the generation of gaseous oxygen at the anode and liquid metal at the cathode. Electrical resistance of molten regolith is high, leading to heating of the melt when electrical current is applied between the electrodes (Joule heating). The authors have developed a 3D model using a rigorous approach for two coupled physics (thermal and electrical potential) to not only study the effect of Joule heating on temperature distribution throughout the molten regolith but also to evaluate and optimize the design of the electrolytic cells. This paper presents the results of the thermal analysis performed on the model and used to validate the design of the electrolytic cell.

Inter-Cellular Forces Orchestrate Contact Inhibition of Locomotion

PubMed Central

Davis, John R.; Luchici, Andrei; Mosis, Fuad; Thackery, James; Salazar, Jesus A.; Mao, Yanlan; Dunn, Graham A.; Betz, Timo; Miodownik, Mark; Stramer, Brian M.

2015-01-01

Summary Contact inhibition of locomotion (CIL) is a multifaceted process that causes many cell types to repel each other upon collision. During development, this seemingly uncoordinated reaction is a critical driver of cellular dispersion within embryonic tissues. Here, we show that Drosophila hemocytes require a precisely orchestrated CIL response for their developmental dispersal. Hemocyte collision and subsequent repulsion involves a stereotyped sequence of kinematic stages that are modulated by global changes in cytoskeletal dynamics. Tracking actin retrograde flow within hemocytes in vivo reveals synchronous reorganization of colliding actin networks through engagement of an inter-cellular adhesion. This inter-cellular actin-clutch leads to a subsequent build-up in lamellar tension, triggering the development of a transient stress fiber, which orchestrates cellular repulsion. Our findings reveal that the physical coupling of the flowing actin networks during CIL acts as a mechanotransducer, allowing cells to haptically sense each other and coordinate their behaviors. PMID:25799385

Nuclear Proximity of Mtr4 with RNA exosome restricts DNA mutational asymmetry

PubMed Central

Lim, Junghyun; Giri, Pankaj Kumar; Kazadi, David; Laffleur, Brice; Zhang, Wanwei; Grinstein, Veronika; Pefanis, Evangelos; Brown, Lewis M.; Ladewig, Erik; Martin, Ophélie; Chen, Yuling; Rabadan, Raul; Boyer, François; Rothschild, Gerson; Cogné, Michel; Pinaud, Eric; Deng, Haiteng; Basu, Uttiya

2017-01-01

SUMMARY The distribution of sense and antisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and neural systems along with the progression of cancer. Because developmentally matured B cells undergo biologically programmed strand-specific DNA mutagenesis at focal DNA/RNA hybrid structures, they make a convenient system to investigate strand-specific mutagenesis mechanisms. We demonstrate that the sense and antisense strand DNA mutagenesis at the immunoglobulin heavy chain locus and some other regions of the B cell genome depends upon localized RNA processing protein complex formation in the nucleus. Both the physical proximity and coupled activities of RNA helicase Mtr4 (and Senataxin) with the noncoding RNA processing function of RNA exosome determine the strand specific distribution of DNA mutations. Our study suggests that strand-specific DNA mutagenesis-associated mechanisms will play major roles in other undiscovered aspects of organismic development. PMID:28431250

Bacterial cells enhance laser driven ion acceleration

PubMed Central

Dalui, Malay; Kundu, M.; Trivikram, T. Madhu; Rajeev, R.; Ray, Krishanu; Krishnamurthy, M.

2014-01-01

Intense laser produced plasmas generate hot electrons which in turn leads to ion acceleration. Ability to generate faster ions or hotter electrons using the same laser parameters is one of the main outstanding paradigms in the intense laser-plasma physics. Here, we present a simple, albeit, unconventional target that succeeds in generating 700 keV carbon ions where conventional targets for the same laser parameters generate at most 40 keV. A few layers of micron sized bacteria coating on a polished surface increases the laser energy coupling and generates a hotter plasma which is more effective for the ion acceleration compared to the conventional polished targets. Particle-in-cell simulations show that micro-particle coated target are much more effective in ion acceleration as seen in the experiment. We envisage that the accelerated, high-energy carbon ions can be used as a source for multiple applications. PMID:25102948

Polyarene mediators for mediated redox flow battery

DOEpatents

Delnick, Frank M.; Ingersoll, David; Liang, Chengdu

2018-01-02

The fundamental charge storage mechanisms in a number of currently studied high energy redox couples are based on intercalation, conversion, or displacement reactions. With exception to certain metal-air chemistries, most often the active redox materials are stored physically in the electrochemical cell stack thereby lowering the practical gravimetric and volumetric energy density as a tradeoff to achieve reasonable power density. In a general embodiment, a mediated redox flow battery includes a series of secondary organic molecules that form highly reduced anionic radicals as reaction mediator pairs for the reduction and oxidation of primary high capacity redox species ex situ from the electrochemical cell stack. Arenes are reduced to stable anionic radicals that in turn reduce a primary anode to the charged state. The primary anode is then discharged using a second lower potential (more positive) arene. Compatible separators and solvents are also disclosed herein.

Quantification of Cell-Penetrating Peptide Associated with Polymeric Nanoparticles Using Isobaric-Tagging and MALDI-TOF MS/MS

NASA Astrophysics Data System (ADS)

Chiu, Jasper Z. S.; Tucker, Ian G.; McDowell, Arlene

2016-11-01

High sensitivity quantification of the putative cell-penetrating peptide di-arginine-histidine (RRH) associated with poly (ethyl-cyanoacrylate) (PECA) nanoparticles was achieved without analyte separation, using a novel application of isobaric-tagging and high matrix-assisted laser desorption/ionization coupled to time-of-flight (MALDI-TOF) mass spectrometry. Isobaric-tagging reaction equilibrium was reached after 5 min, with 90% or greater RRH peptide successfully isobaric-tagged after 60 min. The accuracy was greater than 90%, which indicates good reliability of using isobaric-tagged RRH as an internal standard for RRH quantification. The sample intra- and inter-spot coefficients of variations were less than 11%, which indicate good repeatability. The majority of RRH peptides in the nanoparticle formulation were physically associated with the nanoparticles (46.6%), whereas only a small fraction remained unassociated (13.7%). The unrecovered RRH peptide (~40%) was assumed to be covalently associated with PECA nanoparticles.

Adenosine receptors regulate gap junction coupling of the human cerebral microvascular endothelial cells hCMEC/D3 by Ca2+ influx through cyclic nucleotide‐gated channels

PubMed Central

Bader, Almke; Bintig, Willem; Begandt, Daniela; Klett, Anne; Siller, Ina G.; Gregor, Carola; Schaarschmidt, Frank; Weksler, Babette; Romero, Ignacio; Couraud, Pierre‐Olivier; Hell, Stefan W.

2017-01-01

Key points Gap junction channels are essential for the formation and regulation of physiological units in tissues by allowing the lateral cell‐to‐cell diffusion of ions, metabolites and second messengers.Stimulation of the adenosine receptor subtype A2B increases the gap junction coupling in the human blood–brain barrier endothelial cell line hCMEC/D3.Although the increased gap junction coupling is cAMP‐dependent, neither the protein kinase A nor the exchange protein directly activated by cAMP were involved in this increase.We found that cAMP activates cyclic nucleotide‐gated (CNG) channels and thereby induces a Ca2+ influx, which leads to the increase in gap junction coupling.The report identifies CNG channels as a possible physiological link between adenosine receptors and the regulation of gap junction channels in endothelial cells of the blood–brain barrier. Abstract The human cerebral microvascular endothelial cell line hCMEC/D3 was used to characterize the physiological link between adenosine receptors and the gap junction coupling in endothelial cells of the blood–brain barrier. Expressed adenosine receptor subtypes and connexin (Cx) isoforms were identified by RT‐PCR. Scrape loading/dye transfer was used to evaluate the impact of the A2A and A2B adenosine receptor subtype agonist 2‐phenylaminoadenosine (2‐PAA) on the gap junction coupling. We found that 2‐PAA stimulated cAMP synthesis and enhanced gap junction coupling in a concentration‐dependent manner. This enhancement was accompanied by an increase in gap junction plaques formed by Cx43. Inhibition of protein kinase A did not affect the 2‐PAA‐related enhancement of gap junction coupling. In contrast, the cyclic nucleotide‐gated (CNG) channel inhibitor l‐cis‐diltiazem, as well as the chelation of intracellular Ca2+ with BAPTA, or the absence of external Ca2+, suppressed the 2‐PAA‐related enhancement of gap junction coupling. Moreover, we observed a 2‐PAA‐dependent activation of CNG channels by a combination of electrophysiology and pharmacology. In conclusion, the stimulation of adenosine receptors in hCMEC/D3 cells induces a Ca2+ influx by opening CNG channels in a cAMP‐dependent manner. Ca2+ in turn induces the formation of new gap junction plaques and a consecutive sustained enhancement of gap junction coupling. The report identifies CNG channels as a physiological link that integrates gap junction coupling into the adenosine receptor‐dependent signalling of endothelial cells of the blood–brain barrier. PMID:28075020

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

Smith, Curtis L.; Prescott, Steven; Coleman, Justin

This report describes the current progress and status related to the Industry Application #2 focusing on External Hazards. For this industry application within the Light Water Reactor Sustainability (LWRS) Program Risk-Informed Safety Margin Characterization (RISMC) R&D Pathway, we will create the Risk-Informed Margin Management (RIMM) approach to represent meaningful (i.e., realistic facility representation) event scenarios and consequences by using an advanced 3D facility representation that will evaluate external hazards such as flooding and earthquakes in order to identify, model and analyze the appropriate physics that needs to be included to determine plant vulnerabilities related to external events; manage the communicationmore » and interactions between different physics modeling and analysis technologies; and develop the computational infrastructure through tools related to plant representation, scenario depiction, and physics prediction. One of the unique aspects of the RISMC approach is how it couples probabilistic approaches (the scenario) with mechanistic phenomena representation (the physics) through simulation. This simulation-based modeling allows decision makers to focus on a variety of safety, performance, or economic metrics. In this report, we describe the evaluation of various physics toolkits related to flooding representation. Ultimately, we will be coupling the flooding representation with other events such as earthquakes in order to provide coupled physics analysis for scenarios where interactions exist.« less

Biophysical mechanisms complementing "classical" cell biology.

PubMed

Funk, Richard H W

2018-01-01

This overview addresses phenomena in cell- and molecular biology which are puzzling by their fast and highly coordinated way of organization. Generally, it appears that informative processes probably involved are more on the biophysical than on the classical biochemical side. The coordination problem is explained within the first part of the review by the topic of endogenous electrical phenomena. These are found e.g. in fast tissue organization and reorganization processes like development, wound healing and regeneration. Here, coupling into classical biochemical signaling and reactions can be shown by modern microscopy, electronics and bioinformatics. Further, one can follow the triggered reactions seamlessly via molecular biology till into genetics. Direct observation of intracellular electric processes is very difficult because of e.g. shielding through the cell membrane and damping by other structures. Therefore, we have to rely on photonic and photon - phonon coupling phenomena like molecular vibrations, which are addressed within the second part. Molecules normally possess different charge moieties and thus small electromagnetic (EMF) patterns arise during molecular vibration. These patterns can now be measured best within the optical part of the spectrum - much less in the lower terahertz till kHz and lower Hz part (third part of this review). Finally, EMFs facilitate quantum informative processes in coherent domains of molecular, charge and electron spin motion. This helps to coordinate such manifold and intertwined processes going on within cells, tissues and organs (part 4). Because the phenomena described in part 3 and 4 of the review still await really hard proofs we need concerted efforts and a combination of biophysics, molecular biology and informatics to unravel the described mysteries in "physics of life".

Correspondence of physical activity and fruit/vegetable consumption among prostate cancer survivors and their spouses.

PubMed

Myers Virtue, S; Manne, S L; Kashy, D; Heckman, C J; Zaider, T; Kissane, D W; Kim, I; Lee, D; Olekson, G

2015-11-01

A healthy diet and physical activity are recommended for prostate cancer survivors. Interdependence theory suggests that the spousal relationship influences those health behaviours and the degree of correspondence may be an indicator of this influence. This study evaluated the correspondence between prostate cancer survivors and spouses regarding physical activity and fruit/vegetable consumption. Baseline data from an ongoing randomised control trial were utilised. Men who had been treated for prostate cancer within the past year and their partners (N = 132 couples) completed self-report measures of physical activity, fruit/vegetable consumption, relationship satisfaction and support for partner's healthy diet and physical activity. Couples reported similar fruit/vegetable consumption and physical activity as indicated by high levels of correspondence. Greater fruit/vegetable correspondence was related to higher relationship satisfaction (F = 4.14, P = 0.018) and greater patient (F = 13.29, P < 0.001) and spouse-rated support (F = 7.2, P < 0.001). Greater physical activity correspondence was related to greater patient (F = 3.57, P = 0.028) and spouse-rated support (F = 4.59, P = 0.031). Prostate cancer survivors and spouses may influence each other's diet and exercise behaviours. Couple-based interventions may promote healthy behaviours among this population. © 2015 John Wiley & Sons Ltd.

Single Cell Fluorescence Imaging Using Metal Plasmon-Coupled Probe

PubMed Central

Zhang, Jian; Fu, Yi; Lakowicz, Joseph R.

2009-01-01

This work constitutes the first fluorescent imaging of cells using metal plasmon-coupled probes (PCPs) at single cell resolution. N-(2-Mercapto-propionyl)glycine-coated silver nanoparticles were synthesized by reduction of silver nitrate using sodium borohyride and then succinimidylated via ligand exchange. Alexa Fluor 647-labeled concanavalin A (con A) was chemically bound to the silver particles to make the fluorescent metal plasmon-coupled probes. The fluorescence images were collected using a scanning confocal microscopy. The fluorescence intensity was observed to enhance 7-fold when binding the labeled con A on a single silver particle. PCPs were conjugated on HEK 293 A cells. Imaging results demonstrate that cells labeled by PCPs were 20-fold brighter than those by free labeled con A. PMID:17375898

Constraints on the phase gamma and new physics from B --> kpi decays

PubMed

He; Hsueh; Shi

2000-01-03

Recent results from CLEO on B-->Kpi indicate that the phase gamma may be substantially different from that obtained from other fit to the KM matrix elements in the standard model. We show that gamma extracted using B-->Kpi,pipi is sensitive to new physics occurring at loop level. It provides a powerful method to probe new physics in electroweak penguin interactions. Using effects due to anomalous gauge couplings as an example, we show that within the allowed ranges for these couplings information about gamma obtained from B-->Kpi,pipi can be very different from the standard model prediction.

Gap Junction Coupling and Calcium Waves in the Pancreatic Islet

PubMed Central

Benninger, Richard K. P.; Zhang, Min; Head, W. Steven; Satin, Leslie S.; Piston, David W.

2008-01-01

The pancreatic islet is a highly coupled, multicellular system that exhibits complex spatiotemporal electrical activity in response to elevated glucose levels. The emergent properties of islets, which differ from those arising in isolated islet cells, are believed to arise in part by gap junctional coupling, but the mechanisms through which this coupling occurs are poorly understood. To uncover these mechanisms, we have used both high-speed imaging and theoretical modeling of the electrical activity in pancreatic islets under a reduction in the gap junction mediated electrical coupling. Utilizing islets from a gap junction protein connexin 36 knockout mouse model together with chemical inhibitors, we can modulate the electrical coupling in the islet in a precise manner and quantify this modulation by electrophysiology measurements. We find that after a reduction in electrical coupling, calcium waves are slowed as well as disrupted, and the number of cells showing synchronous calcium oscillations is reduced. This behavior can be reproduced by computational modeling of a heterogeneous population of β-cells with heterogeneous levels of electrical coupling. The resulting quantitative agreement between the data and analytical models of islet connectivity, using only a single free parameter, reveals the mechanistic underpinnings of the multicellular behavior of the islet. PMID:18805925

The Exercising Together Project: Design and recruitment for a randomized, controlled trial to determine the benefits of partnered strength training for couples coping with prostate cancer

PubMed Central

Winters-Stone, Kerri M.; Lyons, Karen S.; Nail, Lillian M.; Beer, Tomasz M.

2011-01-01

Prostate cancer can threaten quality of life for the patient and his spouse and the quality of his marital relationship. The purpose of our study is to evaluate the effects of “Exercising Together” – a partnered strength training program for married couples coping with prostate cancer – on the physical and emotional health of prostate cancer survivors (PCS) and their spouses and on marital quality. We are conducting a 6-month randomized controlled trial with two groups: 1) Exercising Together - a progressive, supervised strength training program and 2) a usual care control condition. The primary aims of this exploratory study are to: 1) Determine the effect of partnered strength training on physical and emotional health (muscle strength, physical function, body composition and self-report physical and mental health) in PCS, 2) Determine the effect of partnered strength training on physical and emotional health in spouses and 3) Explore the effect of partnered strength training on marital quality (incongruence, communication, relationship quality, intimacy) of the PCS and spouse. Target accrual has been met in this study with 64 couples enrolled and randomized to exercise (n=32) or usual care (n=32) groups. This study is the first to examine the feasibility of this exercise format in both the chronically ill patient and spouse and explore benefits at the individual and couple level. PMID:22101224

The Exercising Together project: design and recruitment for a randomized, controlled trial to determine the benefits of partnered strength training for couples coping with prostate cancer.

PubMed

Winters-Stone, Kerri M; Lyons, Karen S; Nail, Lillian M; Beer, Tomasz M

2012-03-01

Prostate cancer can threaten quality of life for the patient and his spouse and the quality of his marital relationship. The purpose of our study is to evaluate the effects of "Exercising Together" - a partnered strength training program for married couples coping with prostate cancer - on the physical and emotional health of prostate cancer survivors (PCS) and their spouses and on marital quality. We are conducting a 6-month randomized controlled trial with two groups: 1) Exercising Together - a progressive, supervised strength training program and 2) a usual care control condition. The primary aims of this exploratory study are to: 1) Determine the effect of partnered strength training on physical and emotional health (muscle strength, physical function, body composition and self-report physical and mental health) in PCS, 2) Determine the effect of partnered strength training on physical and emotional health in spouses and 3) Explore the effect of partnered strength training on marital quality (incongruence, communication, relationship quality, intimacy) of the PCS and spouse. Target accrual has been met in this study with 64 couples enrolled and randomized to exercise (n=32) or usual care (n=32) groups. This study is the first to examine the feasibility of this exercise format in both the chronically ill patient and spouse and explore benefits at the individual and couple level. Copyright © 2011 Elsevier Inc. All rights reserved.

Evaluation and optimization of mass transport of redox species in silicon microwire-array photoelectrodes

PubMed Central

Xiang, Chengxiang; Meng, Andrew C.; Lewis, Nathan S.

2012-01-01

Physical integration of a Ag electrical contact internally into a metal/substrate/microstructured Si wire array/oxide/Ag/electrolyte photoelectrochemical solar cell has produced structures that display relatively low ohmic resistance losses, as well as highly efficient mass transport of redox species in the absence of forced convection. Even with front-side illumination, such wire-array based photoelectrochemical solar cells do not require a transparent conducting oxide top contact. In contact with a test electrolyte that contained 50 mM/5.0 mM of the cobaltocenium+/0 redox species in CH3CN–1.0 M LiClO4, when the counterelectrode was placed in the solution and separated from the photoelectrode, mass transport restrictions of redox species in the internal volume of the Si wire array photoelectrode produced low fill factors and limited the obtainable current densities to 17.6 mA cm-2 even under high illumination. In contrast, when the physically integrated internal Ag film served as the counter electrode, the redox couple species were regenerated inside the internal volume of the photoelectrode, especially in regions where depletion of the redox species due to mass transport limitations would have otherwise occurred. This behavior allowed the integrated assembly to operate as a two-terminal, stand-alone, photoelectrochemical solar cell. The current density vs. voltage behavior of the integrated photoelectrochemical solar cell produced short-circuit current densities in excess of 80 mA cm-2 at high light intensities, and resulted in relatively low losses due to concentration overpotentials at 1 Sun illumination. The integrated wire array-based device architecture also provides design guidance for tandem photoelectrochemical cells for solar-driven water splitting. PMID:22904185

Fluorescent-Magnetic-Biotargeting Multifunctional Nanobioprobes for Detecting and Isolating Multiple Types of Tumor Cells

PubMed Central

Song, Er-Qun; Hu, Jun; Wen, Cong-Ying; Tian, Zhi-Quan; Yu, Xu; Zhang, Zhi-Ling; Shi, Yun-Bo; Pang, Dai-Wen

2011-01-01

Fluorescent-magnetic-biotargeting multifunctional nanobioprobes (FMBMNs) have attracted great attention in recent years due to their increasing, important applications in biomedical research, clinical diagnosis, and biomedicine. We have previously developed such nanobioprobes for the detection and isolation of a single kind of tumor cells. Detection and isolation of multiple tumor markers or tumor cells from complex samples sensitively and with high efficiency is critical for the early diagnosis of tumors, especially malignant tumors or cancers, which will improve clinical diagnosis outcomes and help to select effective treatment approaches. Here, we expanded the application of the monoclonal antibody (mAb)-coupled FMBMNs for multiplexed assays. Multiple types of cancer cells, such as leukemia cells and prostate cancer cells, were detected and collected from mixed samples within 25 minutes by using a magnet and an ordinary fluorescence microscope. The capture efficiencies of mAb-coupled FMBMNs for the above mentioned two types of cells were 96% and 97% respectively. Furthermore, by using the mAb-coupled FMBMNs, specific and sensitive detection and rapid separation of a small number of spiked leukemia cells and prostate cancer cells in a large population of cultured normal cells (about 0.01% were tumor cells) were achieved simply and inexpensively without any sample pretreatment before cell analysis. Therefore, mAb-coupled multicolour FMBMNs may be used for very sensitive detection and rapid isolation of multiple cancer cells in biomedical research and medical diagnostics. PMID:21250650

Gap junction-mediated calcium waves define communication networks among murine postnatal neural progenitor cells.

PubMed

Lacar, Benjamin; Young, Stephanie Z; Platel, Jean-Claude; Bordey, Angélique

2011-12-01

In the postnatal neurogenic niche, two populations of astrocyte-like cells (B cells) persist, one acting as neural progenitor cells (NPCs, B1 cells) and one forming a structural boundary between the neurogenic niche and the striatum (B2 cells, niche astrocytes). Despite being viewed as two distinct entities, we found that B1 and B2 cells express the gap junction protein connexin 43 and display functional coupling involving 50-60 cells. Using neonatal electroporation to label slowly cycling radial glia-derived B1 cells, which send a basal process onto blood vessels, we further confirmed dye coupling between NPCs. To assess the functionality of the coupling, we used calcium imaging in a preparation preserving the three-dimensional architecture of the subventricular zone. Intercellular calcium waves were observed among B cells. These waves travelled bidirectionally between B1 and B2 cells and propagated on blood vessels. Inter-B-cell calcium waves were absent in the presence of a gap junction blocker but persisted with purinergic receptor blockers. These findings show that privileged microdomains of communication networks exist among NPCs and niche astrocytes. Such functional coupling between these two cell types suggests that niche astrocytes do not merely have a structural role, but may play an active role in shaping the behavior of NPCs. © 2011 The Authors. European Journal of Neuroscience © 2011 Federation of European Neuroscience Societies and Blackwell Publishing Ltd.

Micro- to macroscale perspectives on space plasmas

NASA Technical Reports Server (NTRS)

Eastman, Timothy E.

1993-01-01

The Earth's magnetosphere is the most accessible of natural collisionless plasma environments; an astrophysical plasma 'laboratory'. Magnetospheric physics has been in an exploration phase since its origin 35 years ago but new coordinated, multipoint observations, theory, modeling, and simulations are moving this highly interdisciplinary field of plasma science into a new phase of synthesis and understanding. Plasma systems are ones in which binary collisions are relatively negligible and collective behavior beyond the microscale emerges. Most readily accessible natural plasma systems are collisional and nearest-neighbor classical interactions compete with longer-range plasma effects. Except for stars, most space plasmas are collisionless, however, and the effects of electrodynamic coupling dominate. Basic physical processes in such collisionless plasmas occur at micro-, meso-, and macroscales that are not merely reducible to each other in certain crucial ways as illustrated for the global coupling of the Earth's magnetosphere and for the nonlinear dynamics of charged particle motion in the magnetotail. Such global coupling and coherence makes the geospace environment, the domain of solar-terrestrial science, the most highly coupled of all physical geospheres.

Efficient treatment of phenolic wastewater with high salinity using a novel integrated system of magnetically immobilized cells coupling with electrodes.

PubMed

Jiang, Bei; Shi, Shengnan; Song, Lun; Tan, Liang; Li, Meidi; Liu, Jiaxin; Xue, Lanlan

2016-10-01

A novel integrated system in which magnetically immobilized cells coupled with a pair of stainless iron meshes-graphite plate electrodes has been designed and operated to enhance the treatment performance of phenolic wastewater under high salinity. With NaCl concentration increased, phenol, o-cresol, m-cresol, p-cresol and COD removal rates by integrated system increased significantly, which were obviously higher than the sum of removal rates by single magnetically immobilized cells and electrode reaction. This integrated system exhibited higher removal rates for all the compounds than that by single magnetically immobilized cells during six cycles for reuse, and it still performed better, even when the voltage was cut off. These results indicated that there was a coupling effect between biodegradation and electrode reaction. The investigation of phenol hydroxylase activity and cells concentration confirmed that electrode reaction played an important role in this coupling effect. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of inhibitory constituents of NO production from Catalpa ovata using LC-MS coupled with a cell-based assay.

PubMed

Park, Sangmin; Shin, Hyeji; Park, Yeeun; Choi, Ilgyu; Park, Byoungduck; Lee, Ki Yong

2018-05-25

An effective screening method for inhibitors of NO production in natural products using LC-QTOF MS/MS coupled with a cell-based assay was proposed. The ethyl acetate fraction of Catalpa ovata exhibited a strong inhibitory effect on NO production in lipopolysaccharide-induced BV2 microglia cells. We attempted to identify the active constituents of C. ovata by using LC-QTOF MS/MS coupled with a cell-based assay. Peaks at approximately 14-15 min on the MS chromatogram were estimated to be the bioactive constituents. A new iridoid compound, 6-O-trans-feruloyl-3β-hydroxy-7-deoxyrehamaglutin A (4), and nine known compounds (1-3, 5-10) were isolated from the ethyl acetate fraction of C. ovata by repeated column chromatography. Compounds 3, 4, 5, 7, and 8 significantly attenuated lipopolysaccharide-stimulated NO production in BV2 cells. Our results indicate that LC-QTOF MS/MS coupled with a cell-based NO production inhibitory assay successfully predicted active compounds without a time-consuming isolation process. Copyright © 2018 Elsevier Inc. All rights reserved.

G protein-coupled receptor kinase 2 positively regulates epithelial cell migration

PubMed Central

Penela, Petronila; Ribas, Catalina; Aymerich, Ivette; Eijkelkamp, Niels; Barreiro, Olga; Heijnen, Cobi J; Kavelaars, Annemieke; Sánchez-Madrid, Francisco; Mayor, Federico

2008-01-01

Cell migration requires integration of signals arising from both the extracellular matrix and messengers acting through G protein-coupled receptors (GPCRs). We find that increased levels of G protein-coupled receptor kinase 2 (GRK2), a key player in GPCR regulation, potentiate migration of epithelial cells towards fibronectin, whereas such process is decreased in embryonic fibroblasts from hemizygous GRK2 mice or upon knockdown of GRK2 expression. Interestingly, the GRK2 effect on fibronectin-mediated cell migration involves the paracrine/autocrine activation of a sphingosine-1-phosphate (S1P) Gi-coupled GPCR. GRK2 positively modulates the activity of the Rac/PAK/MEK/ERK pathway in response to adhesion and S1P by a mechanism involving the phosphorylation-dependent, dynamic interaction of GRK2 with GIT1, a key scaffolding protein in cell migration processes. Furthermore, decreased GRK2 levels in hemizygous mice result in delayed wound healing rate in vivo, consistent with a physiological role of GRK2 as a regulator of coordinated integrin and GPCR-directed epithelial cell migration. PMID:18369319

Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple).

PubMed

Batiste, Laurent; Unzue, Andrea; Dolbois, Aymeric; Hassler, Fabrice; Wang, Xuan; Deerain, Nicholas; Zhu, Jian; Spiliotopoulos, Dimitrios; Nevado, Cristina; Caflisch, Amedeo

2018-02-28

Expanding the chemical space and simultaneously ensuring synthetic accessibility is of upmost importance, not only for the discovery of effective binders for novel protein classes but, more importantly, for the development of compounds against hard-to-drug proteins. Here, we present AutoCouple, a de novo approach to computational ligand design focused on the diversity-oriented generation of chemical entities via virtual couplings. In a benchmark application, chemically diverse compounds with low-nanomolar potency for the CBP bromodomain and high selectivity against the BRD4(1) bromodomain were achieved by the synthesis of about 50 derivatives of the original fragment. The binding mode was confirmed by X-ray crystallography, target engagement in cells was demonstrated, and antiproliferative activity was showcased in three cancer cell lines. These results reveal AutoCouple as a useful in silico coupling method to expand the chemical space in hit optimization campaigns resulting in potent, selective, and cell permeable bromodomain ligands.

Linear beam dynamics and ampere class superconducting RF cavities at RHIC

NASA Astrophysics Data System (ADS)

Calaga, Rama R.

The Relativistic Heavy Ion Collider (RHIC) is a hadron collider designed to collide a range of ions from protons to gold. RHIC operations began in 2000 and has successfully completed five physics runs with several species including gold, deuteron, copper, and polarized protons. Linear optics and coupling are fundamental issues affecting the collider performance. Measurement and correction of optics and coupling are important to maximize the luminosity and sustain stable operation. A numerical approach, first developed at SLAC, was implemented to measure linear optics from coherent betatron oscillations generated by ac dipoles and recorded at multiple beam position monitors (BPMs) distributed around the collider. The approach is extended to a fully coupled 2D case and equivalence relationships between Hamiltonian and matrix formalisms are derived. Detailed measurements of the transverse coupling terms are carried out at RHIC and correction strategies are applied to compensate coupling both locally and globally. A statistical approach to determine BPM reliability and performance over the past three runs and future improvements also discussed. Aiming at a ten-fold increase in the average heavy-ion luminosity, electron cooling is the enabling technology for the next luminosity upgrade (RHIC II). Cooling gold ion beams at 100 GeV/nucleon requires an electron beam of approximately 54 MeV and a high average current in the range of 50-200 mA. All existing e-Coolers are based on low energy DC accelerators. The only viable option to generate high current, high energy, low emittance CW electron beam is through a superconducting energy-recovery linac (SC-ERL). In this option, an electron beam from a superconducting injector gun is accelerated using a high gradient (˜ 20 MV/m) superconducting RF (SRF) cavity. The electrons are returned back to the cavity with a 180° phase shift to recover the energy back into the cavity before being dumped. A design and development of a half-cell electron gun and a five-cell SRF linac cavity are presented. Several RF and beam dynamics issues ultimately resulting in an optimum cavity design are discussed in detail.

Data-driven modeling reveals cell behaviors controlling self-organization during Myxococcus xanthus development

PubMed Central

Cotter, Christopher R.; Schüttler, Heinz-Bernd; Igoshin, Oleg A.; Shimkets, Lawrence J.

2017-01-01

Collective cell movement is critical to the emergent properties of many multicellular systems, including microbial self-organization in biofilms, embryogenesis, wound healing, and cancer metastasis. However, even the best-studied systems lack a complete picture of how diverse physical and chemical cues act upon individual cells to ensure coordinated multicellular behavior. Known for its social developmental cycle, the bacterium Myxococcus xanthus uses coordinated movement to generate three-dimensional aggregates called fruiting bodies. Despite extensive progress in identifying genes controlling fruiting body development, cell behaviors and cell–cell communication mechanisms that mediate aggregation are largely unknown. We developed an approach to examine emergent behaviors that couples fluorescent cell tracking with data-driven models. A unique feature of this approach is the ability to identify cell behaviors affecting the observed aggregation dynamics without full knowledge of the underlying biological mechanisms. The fluorescent cell tracking revealed large deviations in the behavior of individual cells. Our modeling method indicated that decreased cell motility inside the aggregates, a biased walk toward aggregate centroids, and alignment among neighboring cells in a radial direction to the nearest aggregate are behaviors that enhance aggregation dynamics. Our modeling method also revealed that aggregation is generally robust to perturbations in these behaviors and identified possible compensatory mechanisms. The resulting approach of directly combining behavior quantification with data-driven simulations can be applied to more complex systems of collective cell movement without prior knowledge of the cellular machinery and behavioral cues. PMID:28533367

Magnetically actuated tissue engineered scaffold: insights into mechanism of physical stimulation

NASA Astrophysics Data System (ADS)

Sapir-Lekhovitser, Yulia; Rotenberg, Menahem Y.; Jopp, Juergen; Friedman, Gary; Polyak, Boris; Cohen, Smadar

2016-02-01

Providing the right stimulatory conditions resulting in efficient tissue promoting microenvironment in vitro and in vivo is one of the ultimate goals in tissue development for regenerative medicine. It has been shown that in addition to molecular signals (e.g. growth factors) physical cues are also required for generation of functional cell constructs. These cues are particularly relevant to engineering of biological tissues, within which mechanical stress activates mechano-sensitive receptors, initiating biochemical pathways which lead to the production of functionally mature tissue. Uniform magnetic fields coupled with magnetizable nanoparticles embedded within three dimensional (3D) scaffold structures remotely create transient physical forces that can be transferrable to cells present in close proximity to the nanoparticles. This study investigated the hypothesis that magnetically responsive alginate scaffold can undergo reversible shape deformation due to alignment of scaffold's walls in a uniform magnetic field. Using custom made Helmholtz coil setup adapted to an Atomic Force Microscope we monitored changes in matrix dimensions in situ as a function of applied magnetic field, concentration of magnetic particles within the scaffold wall structure and rigidity of the matrix. Our results show that magnetically responsive scaffolds exposed to an externally applied time-varying uniform magnetic field undergo a reversible shape deformation. This indicates on possibility of generating bending/stretching forces that may exert a mechanical effect on cells due to alternating pattern of scaffold wall alignment and relaxation. We suggest that the matrix structure deformation is produced by immobilized magnetic nanoparticles within the matrix walls resulting in a collective alignment of scaffold walls upon magnetization. The estimated mechanical force that can be imparted on cells grown on the scaffold wall at experimental conditions is in the order of 1 pN, which correlates well with reported threshold to induce mechanotransduction effects on cellular level. This work is our next step in understanding of how to accurately create proper stimulatory microenvironment for promotion of cellular organization to form mature tissue engineered constructs.

Magnetically actuated tissue engineered scaffold: insights into mechanism of physical stimulation

PubMed Central

Sapir-Lekhovitser, Yulia; Rotenberg, Menahem Y.; Jopp, Juergen; Friedman, Gary; Polyak, Boris; Cohen, Smadar

2016-01-01

Providing the right stimulatory conditions resulting in efficient tissue promoting microenvironment in vitro and in vivo is one of the ultimate goals in tissue development for regenerative medicine. It has been shown that in addition to molecular signals (e.g. growth factors) physical cues are also required for generation of functional cell constructs. These cues are particularly relevant to engineering of biological tissues, within which mechanical stress activates mechano-sensitive receptors, initiating biochemical pathways which lead to the production of functionally mature tissue. Uniform magnetic fields coupled with magnetizable nanoparticles embedded within three dimensional (3D) scaffold structures remotely create transient physical forces that can be transferrable to cells present in close proximity to the nanoparticles. This study investigated the hypothesis that magnetically responsive alginate scaffold can undergo reversible shape deformation due to alignment of scaffold’s walls in a uniform magnetic field. Using custom made Helmholtz coil setup adapted to an Atomic Force Microscope we monitored changes in matrix dimensions in situ as a function of applied magnetic field, concentration of magnetic particles within the scaffold wall structure and rigidity of the matrix. Our results show that magnetically responsive scaffolds exposed to an externally applied time-varying uniform magnetic field undergo a reversible shape deformation. This indicates on possibility of generating bending/stretching forces that may exert a mechanical effect on cells due to alternating pattern of scaffold wall alignment and relaxation. We suggest that the matrix structure deformation is produced by immobilized magnetic nanoparticles within the matrix walls resulting in a collective alignment of scaffold walls upon magnetization. The estimated mechanical force that can be imparted on cells grown on the scaffold wall at experimental conditions is in the order of 1 pN, which correlates well with reported threshold to induce mechanotransduction effects on cellular level. This work is our next step in understanding of how to accurately create proper stimulatory microenvironment for promotion of cellular organization to form mature tissue engineered constructs. PMID:26790538

Four simple rules that are sufficient to generate the mammalian blastocyst

PubMed Central

Nissen, Silas Boye; Perera, Marta; Gonzalez, Javier Martin; Morgani, Sophie M.; Jensen, Mogens H.; Sneppen, Kim; Brickman, Joshua M.

2017-01-01

Early mammalian development is both highly regulative and self-organizing. It involves the interplay of cell position, predetermined gene regulatory networks, and environmental interactions to generate the physical arrangement of the blastocyst with precise timing. However, this process occurs in the absence of maternal information and in the presence of transcriptional stochasticity. How does the preimplantation embryo ensure robust, reproducible development in this context? It utilizes a versatile toolbox that includes complex intracellular networks coupled to cell—cell communication, segregation by differential adhesion, and apoptosis. Here, we ask whether a minimal set of developmental rules based on this toolbox is sufficient for successful blastocyst development, and to what extent these rules can explain mutant and experimental phenotypes. We implemented experimentally reported mechanisms for polarity, cell—cell signaling, adhesion, and apoptosis as a set of developmental rules in an agent-based in silico model of physically interacting cells. We find that this model quantitatively reproduces specific mutant phenotypes and provides an explanation for the emergence of heterogeneity without requiring any initial transcriptional variation. It also suggests that a fixed time point for the cells’ competence of fibroblast growth factor (FGF)/extracellular signal—regulated kinase (ERK) sets an embryonic clock that enables certain scaling phenomena, a concept that we evaluate quantitatively by manipulating embryos in vitro. Based on these observations, we conclude that the minimal set of rules enables the embryo to experiment with stochastic gene expression and could provide the robustness necessary for the evolutionary diversification of the preimplantation gene regulatory network. PMID:28700688

A novel planar flow cell for studies of biofilm heterogeneity and flow-biofilm interactions

PubMed Central

Zhang, Wei; Sileika, Tadas S.; Chen, Cheng; Liu, Yang; Lee, Jisun; Packman, Aaron I.

2012-01-01

Biofilms are microbial communities growing on surfaces, and are ubiquitous in nature, in bioreactors, and in human infection. Coupling between physical, chemical, and biological processes is known to regulate the development of biofilms; however, current experimental systems do not provide sufficient control of environmental conditions to enable detailed investigations of these complex interactions. We developed a novel planar flow cell that supports biofilm growth under complex two-dimensional fluid flow conditions. This device provides precise control of flow conditions and can be used to create well-defined physical and chemical gradients that significantly affect biofilm heterogeneity. Moreover, the top and bottom of the flow chamber are transparent, so biofilm growth and flow conditions are fully observable using non-invasive confocal microscopy and high-resolution video imaging. To demonstrate the capability of the device, we observed the growth of Pseudomonas aeruginosa biofilms under imposed flow gradients. We found a positive relationship between patterns of fluid velocity and biofilm biomass because of faster microbial growth under conditions of greater local nutrient influx, but this relationship eventually reversed because high hydrodynamic shear leads to the detachment of cells from the surface. These results reveal that flow gradients play a critical role in the development of biofilm communities. By providing new capability for observing biofilm growth, solute and particle transport, and net chemical transformations under user-specified environmental gradients, this new planar flow cell system has broad utility for studies of environmental biotechnology and basic biofilm microbiology, as well as applications in bioreactor design, environmental engineering, biogeochemistry, geomicrobiology, and biomedical research. PMID:21656713

Short-term depression of gap junctional coupling in reticular thalamic neurons of absence epileptic rats.

PubMed

Kohmann, Denise; Lüttjohann, Annika; Seidenbecher, Thomas; Coulon, Philippe; Pape, Hans-Christian

2016-10-01

Gap junctional electrical coupling between neurons of the reticular thalamic nucleus (RTN) is critical for hypersynchrony in the thalamo-cortical network. This study investigates the role of electrical coupling in pathological rhythmogenesis in RTN neurons in a rat model of absence epilepsy. Rhythmic activation resulted in a Ca(2+) -dependent short-term depression (STD) of electrical coupling between pairs of RTN neurons in epileptic rats, but not in RTN of a non-epileptic control strain. Pharmacological blockade of gap junctions in RTN in vivo induced a depression of seizure activity. The STD of electrical coupling represents a mechanism of Ca(2+) homeostasis in RTN aimed to counteract excessive synchronization. Neurons in the reticular thalamic nucleus (RTN) are coupled by electrical synapses, which play a major role in regulating synchronous activity. This study investigates electrical coupling in RTN neurons from a rat model of childhood absence epilepsy, genetic absence epilepsy rats from Strasbourg (GAERS), compared with a non-epileptic control (NEC) strain, to assess the impact on pathophysiological rhythmogenesis. Whole-cell recordings were obtained from pairs of RTN neurons of GAERS and NEC in vitro. Coupling was determined by injection of hyperpolarizing current steps in one cell and monitoring evoked voltage responses in both activated and coupled cell. The coupling coefficient (cc) was compared under resting condition, during pharmacological interventions and repeated activation using a series of current injections. The effect of gap junctional coupling on seizure expression was investigated by application of gap junctional blockers into RTN of GAERS in vivo. At resting conditions, cc did not differ between GAERS and NEC. During repeated activation, cc declined in GAERS but not in NEC. This depression in cc was restored within 25 s and was prevented by intracellular presence of BAPTA in the activated but not in the coupled cell. Local application of gap junctional blockers into RTN of GAERS in vivo resulted in a decrease of spike wave discharge (SWD) activity. Repeated activation results in a short-term depression (STD) of gap junctional coupling in RTN neurons of GAERS, depending on intracellular Ca(2+) mechanisms in the activated cell. As blockage of gap junctions in vivo results in a decrease of SWD activity, the STD observed in GAERS is considered a compensatory mechanism, aimed to dampen SWD activity. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

Entrainment of the Mammalian Cell Cycle by the Circadian Clock: Modeling Two Coupled Cellular Rhythms

PubMed Central

Gérard, Claude; Goldbeter, Albert

2012-01-01

The cell division cycle and the circadian clock represent two major cellular rhythms. These two periodic processes are coupled in multiple ways, given that several molecular components of the cell cycle network are controlled in a circadian manner. For example, in the network of cyclin-dependent kinases (Cdks) that governs progression along the successive phases of the cell cycle, the synthesis of the kinase Wee1, which inhibits the G2/M transition, is enhanced by the complex CLOCK-BMAL1 that plays a central role in the circadian clock network. Another component of the latter network, REV-ERBα, inhibits the synthesis of the Cdk inhibitor p21. Moreover, the synthesis of the oncogene c-Myc, which promotes G1 cyclin synthesis, is repressed by CLOCK-BMAL1. Using detailed computational models for the two networks we investigate the conditions in which the mammalian cell cycle can be entrained by the circadian clock. We show that the cell cycle can be brought to oscillate at a period of 24 h or 48 h when its autonomous period prior to coupling is in an appropriate range. The model indicates that the combination of multiple modes of coupling does not necessarily facilitate entrainment of the cell cycle by the circadian clock. Entrainment can also occur as a result of circadian variations in the level of a growth factor controlling entry into G1. Outside the range of entrainment, the coupling to the circadian clock may lead to disconnected oscillations in the cell cycle and the circadian system, or to complex oscillatory dynamics of the cell cycle in the form of endoreplication, complex periodic oscillations or chaos. The model predicts that the transition from entrainment to 24 h or 48 h might occur when the strength of coupling to the circadian clock or the level of growth factor decrease below critical values. PMID:22693436

Dynamics of a spherically symmetric inhomogeneous coupled dark energy model with coupling term proportional to non relatvistic matter

NASA Astrophysics Data System (ADS)

Izquierdo, Germán; Blanquet-Jaramillo, Roberto C.; Sussman, Roberto A.

2018-01-01

The quasi-local scalar variables approach is applied to a spherically symmetric inhomogeneous Lemaître-Tolman-Bondi metric containing a mixture of non-relativistic cold dark matter and coupled dark energy with constant equation of state. The quasi-local coupling term considered is proportional to the quasi-local cold dark matter energy density and a quasi-local Hubble factor-like scalar via a coupling constant α . The autonomous numerical system obtained from the evolution equations is classified for different choices of the free parameters: the adiabatic constant of the dark energy w and α . The presence of a past attractor in a non-physical region of the energy densities phase-space of the system makes the coupling term non physical when the energy flows from the matter to the dark energy in order to avoid negative values of the dark energy density in the past. On the other hand, if the energy flux goes from dark energy to dark matter, the past attractor lies in a physical region. The system is also numerically solved for some interesting initial profiles leading to different configurations: an ever expanding mixture, a scenario where the dark energy is completely consumed by the non-relativistic matter by means of the coupling term, a scenario where the dark energy disappears in the inner layers while the outer layers expand as a mixture of both sources, and, finally, a structure formation toy model scenario, where the inner shells containing the mixture collapse while the outer shells expand.

Synaptopodin couples epithelial contractility to α-actinin-4–dependent junction maturation

PubMed Central

Kannan, Nivetha

2015-01-01

The epithelial junction experiences mechanical force exerted by endogenous actomyosin activities and from interactions with neighboring cells. We hypothesize that tension generated at cell–cell adhesive contacts contributes to the maturation and assembly of the junctional complex. To test our hypothesis, we used a hydraulic apparatus that can apply mechanical force to intercellular junction in a confluent monolayer of cells. We found that mechanical force induces α-actinin-4 and actin accumulation at the cell junction in a time- and tension-dependent manner during junction development. Intercellular tension also induces α-actinin-4–dependent recruitment of vinculin to the cell junction. In addition, we have identified a tension-sensitive upstream regulator of α-actinin-4 as synaptopodin. Synaptopodin forms a complex containing α-actinin-4 and β-catenin and interacts with myosin II, indicating that it can physically link adhesion molecules to the cellular contractile apparatus. Synaptopodin depletion prevents junctional accumulation of α-actinin-4, vinculin, and actin. Knockdown of synaptopodin and α-actinin-4 decreases the strength of cell–cell adhesion, reduces the monolayer permeability barrier, and compromises cellular contractility. Our findings underscore the complexity of junction development and implicate a control process via tension-induced sequential incorporation of junctional components. PMID:26504173

Polytypism and unexpected strong interlayer coupling in two-dimensional layered ReS2

NASA Astrophysics Data System (ADS)

Qiao, Xiao-Fen; Wu, Jiang-Bin; Zhou, Linwei; Qiao, Jingsi; Shi, Wei; Chen, Tao; Zhang, Xin; Zhang, Jun; Ji, Wei; Tan, Ping-Heng

2016-04-01

Anisotropic two-dimensional (2D) van der Waals (vdW) layered materials, with both scientific interest and application potential, offer one more dimension than isotropic 2D materials to tune their physical properties. Various physical properties of 2D multi-layer materials are modulated by varying their stacking orders owing to significant interlayer vdW coupling. Multilayer rhenium disulfide (ReS2), a representative anisotropic 2D material, was expected to be randomly stacked and lack interlayer coupling. Here, we demonstrate two stable stacking orders, namely isotropic-like (IS) and anisotropic-like (AI) N layer (NL, N > 1) ReS2 are revealed by ultralow- and high-frequency Raman spectroscopy, photoluminescence and first-principles density functional theory calculation. Two interlayer shear modes are observed in AI-NL-ReS2 while only one shear mode appears in IS-NL-ReS2, suggesting anisotropic- and isotropic-like stacking orders in IS- and AI-NL-ReS2, respectively. This explicit difference in the observed frequencies identifies an unexpected strong interlayer coupling in IS- and AI-NL-ReS2. Quantitatively, the force constants of them are found to be around 55-90% of those of multilayer MoS2. The revealed strong interlayer coupling and polytypism in multi-layer ReS2 may stimulate future studies on engineering physical properties of other anisotropic 2D materials by stacking orders.Anisotropic two-dimensional (2D) van der Waals (vdW) layered materials, with both scientific interest and application potential, offer one more dimension than isotropic 2D materials to tune their physical properties. Various physical properties of 2D multi-layer materials are modulated by varying their stacking orders owing to significant interlayer vdW coupling. Multilayer rhenium disulfide (ReS2), a representative anisotropic 2D material, was expected to be randomly stacked and lack interlayer coupling. Here, we demonstrate two stable stacking orders, namely isotropic-like (IS) and anisotropic-like (AI) N layer (NL, N > 1) ReS2 are revealed by ultralow- and high-frequency Raman spectroscopy, photoluminescence and first-principles density functional theory calculation. Two interlayer shear modes are observed in AI-NL-ReS2 while only one shear mode appears in IS-NL-ReS2, suggesting anisotropic- and isotropic-like stacking orders in IS- and AI-NL-ReS2, respectively. This explicit difference in the observed frequencies identifies an unexpected strong interlayer coupling in IS- and AI-NL-ReS2. Quantitatively, the force constants of them are found to be around 55-90% of those of multilayer MoS2. The revealed strong interlayer coupling and polytypism in multi-layer ReS2 may stimulate future studies on engineering physical properties of other anisotropic 2D materials by stacking orders. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01569g

Microwave-Assisted Synthesis of a MK2 Inhibitor by Suzuki-Miyaura Coupling for Study in Werner Syndrome Cells.

PubMed

Bagley, Mark C; Baashen, Mohammed; Chuckowree, Irina; Dwyer, Jessica E; Kipling, David; Davis, Terence

2015-06-03

Microwave-assisted Suzuki-Miyaura cross-coupling reactions have been employed towards the synthesis of three different MAPKAPK2 (MK2) inhibitors to study accelerated aging in Werner syndrome (WS) cells, including the cross-coupling of a 2-chloroquinoline with a 3-pyridinylboronic acid, the coupling of an aryl bromide with an indolylboronic acid and the reaction of a 3-amino-4-bromopyrazole with 4-carbamoylphenylboronic acid. In all of these processes, the Suzuki-Miyaura reaction was fast and relatively efficient using a palladium catalyst under microwave irradiation. The process was incorporated into a rapid 3-step microwave-assisted method for the synthesis of a MK2 inhibitor involving 3-aminopyrazole formation, pyrazole C-4 bromination using N-bromosuccinimide (NBS), and Suzuki-Miyaura cross-coupling of the pyrazolyl bromide with 4-carbamoylphenylboronic acid to give the target 4-arylpyrazole in 35% overall yield, suitable for study in WS cells.

Coupling strategies for coherent operation of quantum cascade ring laser arrays

NASA Astrophysics Data System (ADS)

Schwarzer, Clemens; Yao, Y.; Mujagić, E.; Ahn, S.; Schrenk, W.; Chen, J.; Gmachl, C.; Strasser, G.

2011-12-01

We report the design, fabrication and operation of coherently coupled ring cavity surface emitting quantum cascade lasers, emitting at wavelength around 8 μm. Special emphasis is placed on the evaluation of optimal coupling approaches and corresponding parameters. Evanescent field coupling as well as direct coupling where both devices are physically connected is presented. Furthermore, exploiting the Vernier-effect was used to obtain enhanced mode selectivity and robust coherent coupling of two ring-type quantum cascade lasers. Investigations were performed at pulsed room-temperature operation.

QCD and strongly coupled gauge theories: Challenges and perspectives

DOE PAGES

Brambilla, N.; Eidelman, S.; Foka, P.; ...

2014-10-21

We highlight the progress, current status, and open challenges of QCD-driven physics, in theory and in experiment. We discuss how the strong interaction is intimately connected to a broad sweep of physical problems, in settings ranging from astrophysics and cosmology to stongly-coupled, complex systems in particle and condensed-matter physics, as well as to searches for physics beyond the Standard Model. We also discuss how success in describing the strong interaction impacts other fields, and, in turn, how such subjects can impact studies of the strong interaction. In the course of the work we offer a perspective on the many researchmore » streams which flow into and out of QCD, as well as a vision for future developments.« less

QCD and strongly coupled gauge theories: challenges and perspectives.

PubMed

Brambilla, N; Eidelman, S; Foka, P; Gardner, S; Kronfeld, A S; Alford, M G; Alkofer, R; Butenschoen, M; Cohen, T D; Erdmenger, J; Fabbietti, L; Faber, M; Goity, J L; Ketzer, B; Lin, H W; Llanes-Estrada, F J; Meyer, H B; Pakhlov, P; Pallante, E; Polikarpov, M I; Sazdjian, H; Schmitt, A; Snow, W M; Vairo, A; Vogt, R; Vuorinen, A; Wittig, H; Arnold, P; Christakoglou, P; Di Nezza, P; Fodor, Z; Garcia I Tormo, X; Höllwieser, R; Janik, M A; Kalweit, A; Keane, D; Kiritsis, E; Mischke, A; Mizuk, R; Odyniec, G; Papadodimas, K; Pich, A; Pittau, R; Qiu, J-W; Ricciardi, G; Salgado, C A; Schwenzer, K; Stefanis, N G; von Hippel, G M; Zakharov, V I

We highlight the progress, current status, and open challenges of QCD-driven physics, in theory and in experiment. We discuss how the strong interaction is intimately connected to a broad sweep of physical problems, in settings ranging from astrophysics and cosmology to strongly coupled, complex systems in particle and condensed-matter physics, as well as to searches for physics beyond the Standard Model. We also discuss how success in describing the strong interaction impacts other fields, and, in turn, how such subjects can impact studies of the strong interaction. In the course of the work we offer a perspective on the many research streams which flow into and out of QCD, as well as a vision for future developments.

Two-way coupling of magnetohydrodynamic simulations with embedded particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Makwana, K. D.; Keppens, R.; Lapenta, G.

2017-12-01

We describe a method for coupling an embedded domain in a magnetohydrodynamic (MHD) simulation with a particle-in-cell (PIC) method. In this two-way coupling we follow the work of Daldorff et al. (2014) [19] in which the PIC domain receives its initial and boundary conditions from MHD variables (MHD to PIC coupling) while the MHD simulation is updated based on the PIC variables (PIC to MHD coupling). This method can be useful for simulating large plasma systems, where kinetic effects captured by particle-in-cell simulations are localized but affect global dynamics. We describe the numerical implementation of this coupling, its time-stepping algorithm, and its parallelization strategy, emphasizing the novel aspects of it. We test the stability and energy/momentum conservation of this method by simulating a steady-state plasma. We test the dynamics of this coupling by propagating plasma waves through the embedded PIC domain. Coupling with MHD shows satisfactory results for the fast magnetosonic wave, but significant distortion for the circularly polarized Alfvén wave. Coupling with Hall-MHD shows excellent coupling for the whistler wave. We also apply this methodology to simulate a Geospace Environmental Modeling (GEM) challenge type of reconnection with the diffusion region simulated by PIC coupled to larger scales with MHD and Hall-MHD. In both these cases we see the expected signatures of kinetic reconnection in the PIC domain, implying that this method can be used for reconnection studies.

Myxococcus xanthus Gliding Motors Are Elastically Coupled to the Substrate as Predicted by the Focal Adhesion Model of Gliding Motility

PubMed Central

Balagam, Rajesh; Litwin, Douglas B.; Czerwinski, Fabian; Sun, Mingzhai; Kaplan, Heidi B.; Shaevitz, Joshua W.; Igoshin, Oleg A.

2014-01-01

Myxococcus xanthus is a model organism for studying bacterial social behaviors due to its ability to form complex multi-cellular structures. Knowledge of M. xanthus surface gliding motility and the mechanisms that coordinated it are critically important to our understanding of collective cell behaviors. Although the mechanism of gliding motility is still under investigation, recent experiments suggest that there are two possible mechanisms underlying force production for cell motility: the focal adhesion mechanism and the helical rotor mechanism, which differ in the biophysics of the cell–substrate interactions. Whereas the focal adhesion model predicts an elastic coupling, the helical rotor model predicts a viscous coupling. Using a combination of computational modeling, imaging, and force microscopy, we find evidence for elastic coupling in support of the focal adhesion model. Using a biophysical model of the M. xanthus cell, we investigated how the mechanical interactions between cells are affected by interactions with the substrate. Comparison of modeling results with experimental data for cell-cell collision events pointed to a strong, elastic attachment between the cell and substrate. These results are robust to variations in the mechanical and geometrical parameters of the model. We then directly measured the motor-substrate coupling by monitoring the motion of optically trapped beads and find that motor velocity decreases exponentially with opposing load. At high loads, motor velocity approaches zero velocity asymptotically and motors remain bound to beads indicating a strong, elastic attachment. PMID:24810164

Unifying Concepts in Stimulus-Secretion Coupling in Endocrine Cells and Some Implications for Therapeutics

ERIC Educational Resources Information Center

Misler, Stanley

2009-01-01

Stimulus-secretion coupling (SSC) in endocrine cells remains underappreciated as a subject for the study/teaching of general physiology. In the present article, we review key new electrophysiological, electrochemical, and fluorescence optical techniques for the study of exocytosis in single cells that have made this a fertile area for recent…

Degenerate quantum gases with spin-orbit coupling: a review.

PubMed

Zhai, Hui

2015-02-01

This review focuses on recent developments in synthetic spin-orbit (SO) coupling in ultracold atomic gases. Two types of SO coupling are discussed. One is Raman process induced coupling between spin and motion along one of the spatial directions and the other is Rashba SO coupling. We emphasize their common features in both single-particle and two-body physics and the consequences of both in many-body physics. For instance, single particle ground state degeneracy leads to novel features of superfluidity and a richer phase diagram; increased low-energy density-of-state enhances interaction effects; the absence of Galilean invariance and spin-momentum locking gives rise to intriguing behaviours of superfluid critical velocity and novel quantum dynamics; and the mixing of two-body singlet and triplet states yields a novel fermion pairing structure and topological superfluids. With these examples, we show that investigating SO coupling in cold atom systems can, enrich our understanding of basic phenomena such as superfluidity, provide a good platform for simulating condensed matter states such as topological superfluids and more importantly, result in novel quantum systems such as SO coupled unitary Fermi gas and high spin quantum gases. Finally we also point out major challenges and some possible future directions.

Distal and Proximal Factors in Domestic Violence: A Test of an Integrated Model.

ERIC Educational Resources Information Center

DeMaris, Alfred; Benson, Michael L.; Fox, Greer L.; Hill, Terrence; Van Wyk, Judy

2003-01-01

Tests a model of couple violence drawn from several theoretical perspectives. The outcome distinguishes among nonviolent couples and those experiencing either physical aggression or intense male violence. According to the model, background characteristics of couples are related to relationship stressors, which affect the risk of violence via their…

Spousal Concordance in Attitudes toward Violence and Reported Physical Abuse in African Couples

ERIC Educational Resources Information Center

Alio, Amina P.; Clayton, Heather B.; Garba, Madeleine; Mbah, Alfred K.; Daley, Ellen; Salihu, Hamisu M.

2011-01-01

Purpose: We examined the potential association between African couples' concordance on attitudes toward violence (ATV) and risk for intimate partner violence (IPV). Method: Analyses included 13,837 couples from Demographic and Health Surveys conducted between 2003 and 2007, from six African countries. Concordance on ATV was defined as both spouses…

Second teaching: An exploration of cognitive factors in small group physics learning

NASA Astrophysics Data System (ADS)

Novemsky, Lisa Forman

This inquiry was focused on an exploration of introductory physics teaching. Alan Van Heuvelen's Overview Case Study (OCS) physics was the pedagogical approach involving guided small group problem solving and stressing concepts first, before mathematics. Second teaching is a new pedagogical construct based on Vygotsky's ideas. Structured small group activity follows traditional instruction facilitating learning for non-traditional students. It is a model of structured small group activity designed to follow traditional instruction to facilitate the learning process for students who find a physics optic (way of seeing) and physics language foreign. In informal small group settins students describe, explain, elaborate, test, and defend ideas in their own familiar vernacular as they collaborate in solving problems. Collective wisdom of a collaborative group, somewhat beyond the level for each individual member, is created then recreated through self-correction. Students improved significantly in physics knowledge. In a classroom setting, small groups of non-traditional physics students engaged in second teaching were observed. Written explanations to conceptual physics questions were analyzed. Development of language usage in relationship to introductory physics concept learning was studied. Overall physics learning correlated positively with gains in language clarity thus confirming the hypothesis that language development can be linked with gains in physics knowledge. Males and females were found to be significantly different in this respect. Male gains in language clarity were closely coupled with physics learning whereas female gains in the two measures were not coupled. Physics discourse, particularly in relationship to force and motion, seems to resonate with natural developmentally acquired sex-typical male but not female discourse. Thus, for males but not for females, physics learning proceeds in a seamless fashion wherein knowledge gains are coupled with language development. Average frequency in use of the indeterminate pronoun it per person decreased. Reificiation of qualifying terms appeared in the form of a word-form problem. In the process of reifying adjectival properties students may be recapitulating the language-bound history of natural science.

Cell-specific expression of connexins and evidence of restricted gap junctional coupling between glial cells and between neurons.

PubMed

Rash, J E; Yasumura, T; Dudek, F E; Nagy, J I

2001-03-15

The transmembrane connexin proteins of gap junctions link extracellularly to form channels for cell-to-cell exchange of ions and small molecules. Two primary hypotheses of gap junction coupling in the CNS are the following: (1) generalized coupling occurs between neurons and glia, with some connexins expressed in both neurons and glia, and (2) intercellular junctional coupling is restricted to specific coupling partners, with different connexins expressed in each cell type. There is consensus that gap junctions link neurons to neurons and astrocytes to oligodendrocytes, ependymocytes, and other astrocytes. However, unresolved are the existence and degree to which gap junctions occur between oligodendrocytes, between oligodendrocytes and neurons, and between astrocytes and neurons. Using light microscopic immunocytochemistry and freeze-fracture replica immunogold labeling of adult rat CNS, we investigated whether four of the best-characterized CNS connexins are each present in one or more cell types, whether oligodendrocytes also share gap junctions with other oligodendrocytes or with neurons, and whether astrocytes share gap junctions with neurons. Connexin32 (Cx32) was found only in gap junctions of oligodendrocyte plasma membranes, Cx30 and Cx43 were found only in astrocyte membranes, and Cx36 was only in neurons. Oligodendrocytes shared intercellular gap junctions only with astrocytes, with each oligodendrocyte isolated from other oligodendrocytes except via astrocyte intermediaries. Finally, neurons shared gap junctions only with other neurons and not with glial cells. Thus, the different cell types of the CNS express different connexins, which define separate pathways for neuronal versus glial gap junctional communication.

Dyadic analysis of self-efficacy and perceived support: the relationship of individual and spousal characteristics with physical activity among middle-aged and young-older adults.

PubMed

Ayotte, Brian J; Margrett, Jennifer A; Patrick, Julie Hicks

2013-06-01

The purpose of this study was to examine the associations among self-efficacy, perceived support, and physical activity in middle-aged and older married couples. A total of 116 middle-aged and older couples (M = 58.86 years, SD = 7.16, range 50-74) participated in the study. A dyadic approach to path modeling was taken. The final model indicated that for both husbands and wives, one's own self-efficacy was directly related to physical activity. In addition, husband self-efficacy was positively related to wive physical activity and indirectly related to wife physical activity through wife self-efficacy. Wife self-efficacy was indirectly related to husband physical activity via the level of husband perceived support. These results provide evidence for the importance of incorporating spousal characteristics in addition to individual characteristics when investigating physical activity during middle and later married life. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Coupling of small, low-loss hexapole mode with photonic crystal slab waveguide mode.

PubMed

Kim, Guk-Hyun; Lee, Yong-Hee; Shinya, Akihiko; Notomi, Masaya

2004-12-27

Coupling characteristics between the single-cell hexapole mode and the triangular-lattice photonic crystal slab waveguide mode is studied by the finite-difference time-domain method. The single-cell hexapole mode has a high quality factor (Q) of 3.3Chi106 and a small modal volume of 1.18(lambda/n)3. Based on the symmetry, three representative types of coupling geometries (shoulder-couple, butt-couple and side-couple structures) are selected and tested. The coupling efficiency shows strong dependence on the transverse overlap of the cavity mode and the waveguide mode over the region of the waveguide. The shoulder-couple structure shows best coupling characteristics among three tested structures. For example, two shouldercouple waveguides and a hexapole cavity result in a high performance resonant-tunneling-filter with Q of 9.7Chi105 and transmittance of 0.48. In the side-couple structure, the coupling strength is much weaker than that of the shoulder-couple structure because of the poor spatial overlap between the mode profiles. In the direct-couple structure, the energy transfer from the cavity to the waveguide is prohibited because of the symmetry mismatch and no coupling is observed.

Inflation scenario driven by a low energy physics inflaton

NASA Astrophysics Data System (ADS)

Ferreira, J. G.; Pires, C. A. de S.; Rodrigues, J. G.; Rodrigues da Silva, P. S.

2017-11-01

It is a longstanding desire of cosmologists, and particle physicists as well, to connect inflation to low energy physics, culminating, for instance, in what is known as Higgs inflation. The condition for the standard Higgs boson playing the role of the inflaton, and driving sucessfully inflation, is that it couples nonminimally with gravity. Nevertheless, cosmological constraints impose that the nonminimal coupling be large. This causes the loss of perturbative unitarity in a scale of energy far below the Planck one. Our aim in this work is to point out that inflaton potential containing a particular type of trilinear coupling involving the inflaton may circumvent this problem by realizing Higgs inflation with tiny nonminimal coupling of the inflaton with gravity. We then develop the idea within a toy model and implement it in the inverse type-II seesaw mechanism for small neutrinos masses.

On the phantom barrier crossing and the bounds on the speed of sound in non-minimal derivative coupling theories

NASA Astrophysics Data System (ADS)

Quiros, Israel; Gonzalez, Tame; Nucamendi, Ulises; García-Salcedo, Ricardo; Horta-Rangel, Francisco Antonio; Saavedra, Joel

2018-04-01

In this paper we investigate the so-called ‘phantom barrier crossing’ issue in a cosmological model based on the scalar–tensor theory with non-minimal derivative coupling to the Einstein tensor. Special attention will be paid to the physical bounds on the squared sound speed. The numeric results are geometrically illustrated by means of a qualitative procedure of analysis that is based on the mapping of the orbits in the phase plane onto the surfaces that represent physical quantities in the extended phase space, that is: the phase plane complemented with an additional dimension relative to the given physical parameter. We find that the cosmological model based on the non-minimal derivative coupling theory—this includes both the quintessence and the pure derivative coupling cases—has serious causality problems related to superluminal propagation of the scalar and tensor perturbations. Even more disturbing is the finding that, despite the fact that the underlying theory is free of the Ostrogradsky instability, the corresponding cosmological model is plagued by the Laplacian (classical) instability related with negative squared sound speed. This instability leads to an uncontrollable growth of the energy density of the perturbations that is inversely proportional to their wavelength. We show that, independent of the self-interaction potential, for positive coupling the tensor perturbations propagate superluminally, while for negative coupling a Laplacian instability arises. This latter instability invalidates the possibility for the model to describe the primordial inflation.

Coupled two-dimensional edge plasma and neutral gas modeling of tokamak scrape-off-layers

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

Maingi, Rajesh

1992-08-01

The objective of this study is to devise a detailed description of the tokamak scrape-off-layer (SOL), which includes the best available models of both the plasma and neutral species and the strong coupling between the two in many SOL regimes. A good estimate of both particle flux and heat flux profiles at the limiter/divertor target plates is desired. Peak heat flux is one of the limiting factors in determining the survival probability of plasma-facing-components at high power levels. Plate particle flux affects the neutral flux to the pump, which determines the particle exhaust rate. A technique which couples a two-dimensionalmore » (2-D) plasma and a 2-D neutral transport code has been developed (coupled code technique), but this procedure requires large amounts of computer time. Relevant physics has been added to an existing two-neutral-species model which takes the SOL plasma/neutral coupling into account in a simple manner (molecular physics model), and this model is compared with the coupled code technique mentioned above. The molecular physics model is benchmarked against experimental data from a divertor tokamak (DIII-D), and a similar model (single-species model) is benchmarked against data from a pump-limiter tokamak (Tore Supra). The models are then used to examine two key issues: free-streaming-limits (ion energy conduction and momentum flux) and the effects of the non-orthogonal geometry of magnetic flux surfaces and target plates on edge plasma parameter profiles.« less

Finite element procedures for coupled linear analysis of heat transfer, fluid and solid mechanics

NASA Technical Reports Server (NTRS)

Sutjahjo, Edhi; Chamis, Christos C.

1993-01-01

Coupled finite element formulations for fluid mechanics, heat transfer, and solid mechanics are derived from the conservation laws for energy, mass, and momentum. To model the physics of interactions among the participating disciplines, the linearized equations are coupled by combining domain and boundary coupling procedures. Iterative numerical solution strategy is presented to solve the equations, with the partitioning of temporal discretization implemented.

Kinetics of Microbial Reduction of Solid Phase U(VI)

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

Liu, Chongxuan; Jeon, Byong Hun; Zachara, John M.

2006-10-01

Sodium boltwoodite (NaUO2SiO3OH ?1.5H2O) was used to assess the kinetics of microbial reduction of solid phase U(VI) by a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1. The bioreduction kinetics was studied with Na-boltwoodite in suspension or within alginate beads. Concentrations of U(VI)tot and cell number were varied to evaluate the coupling of U(VI) dissolution, diffusion, and microbial activity. Batch experiments were performed in a non-growth medium with lactate as electron donor at pH 6.8 buffered with PIPES. Microscopic and spectroscopic analyses with transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), and laser-induced fluorescence spectroscopy (LIFS) collectively indicated that solidmore » phase U(VI) was first dissolved and diffused out of grain interiors before it was reduced on bacterial surfaces and/or within the periplasm. The kinetics of solid phase U(VI) bioreduction was well described by a coupled model of bicarbonate-promoted dissolution of Na-boltwoodite, intraparticle uranyl diffusion, and Monod type bioreduction kinetics with respect to dissolved U(VI) concentration. The results demonstrated the intimate coupling of biological, chemical, and physical processes in microbial reduction of solid phase U(VI).« less

Development of SSUBPIC code for modeling the neutral gas depletion effect in helicon discharges

NASA Astrophysics Data System (ADS)

Kollasch, Jeffrey; Sovenic, Carl; Schmitz, Oliver

2017-10-01

The SSUBPIC (steady-state unstructured-boundary particle-in-cell) code is being developed to model helicon plasma devices. The envisioned modeling framework incorporates (1) a kinetic neutral particle model, (2) a kinetic ion model, (3) a fluid electron model, and (4) an RF power deposition model. The models are loosely coupled and iterated until convergence to steady-state. Of the four required solvers, the kinetic ion and neutral particle simulation can now be done within the SSUBPIC code. Recent SSUBPIC modifications include implementation and testing of a Coulomb collision model (Lemons et al., JCP, 228(5), pp. 1391-1403) allowing efficient coupling of kineticly-treated ions to fluid electrons, and implementation of a neutral particle tracking mode with charge-exchange and electron impact ionization physics. These new simulation capabilities are demonstrated working independently and coupled to ``dummy'' profiles for RF power deposition to converge on steady-state plasma and neutral profiles. The geometry and conditions considered are similar to those of the MARIA experiment at UW-Madison. Initial results qualitatively show the expected neutral gas depletion effect in which neutrals in the plasma core are not replenished at a sufficient rate to sustain a higher plasma density. This work is funded by the NSF CAREER award PHY-1455210 and NSF Grant PHY-1206421.

Metabolic coupling and the Reverse Warburg Effect in cancer: Implications for novel biomarker and anticancer agent development.

PubMed

Wilde, Lindsay; Roche, Megan; Domingo-Vidal, Marina; Tanson, Katherina; Philp, Nancy; Curry, Joseph; Martinez-Outschoorn, Ubaldo

2017-06-01

Glucose is a key metabolite used by cancer cells to generate ATP, maintain redox state and create biomass. Glucose can be catabolized to lactate in the cytoplasm, which is termed glycolysis, or alternatively can be catabolized to carbon dioxide and water in the mitochondria via oxidative phosphorylation. Metabolic heterogeneity exists in a subset of human tumors, with some cells maintaining a glycolytic phenotype while others predominantly utilize oxidative phosphorylation. Cells within tumors interact metabolically with transfer of catabolites from supporting stromal cells to adjacent cancer cells. The Reverse Warburg Effect describes when glycolysis in the cancer-associated stroma metabolically supports adjacent cancer cells. This catabolite transfer, which induces stromal-cancer metabolic coupling, allows cancer cells to generate ATP, increase proliferation, and reduce cell death. Catabolites implicated in metabolic coupling include the monocarboxylates lactate, pyruvate, and ketone bodies. Monocarboxylate transporters (MCT) are critically necessary for release and uptake of these catabolites. MCT4 is involved in the release of monocarboxylates from cells, is regulated by catabolic transcription factors such as hypoxia inducible factor 1 alpha (HIF1A) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), and is highly expressed in cancer-associated fibroblasts. Conversely, MCT1 is predominantly involved in the uptake of these catabolites and is highly expressed in a subgroup of cancer cells. MYC and TIGAR, which are genes involved in cellular proliferation and anabolism, are inducers of MCT1. Profiling human tumors on the basis of an altered redox balance and intra-tumoral metabolic interactions may have important biomarker and therapeutic implications. Alterations in the redox state and mitochondrial function of cells can induce metabolic coupling. Hence, there is interest in redox and metabolic modulators as anticancer agents. Also, markers of metabolic coupling have been associated with poor outcomes in numerous human malignancies and may be useful prognostic and predictive biomarkers. Copyright © 2017 Elsevier Inc. All rights reserved.

Nyx: Adaptive mesh, massively-parallel, cosmological simulation code

NASA Astrophysics Data System (ADS)

Almgren, Ann; Beckner, Vince; Friesen, Brian; Lukic, Zarija; Zhang, Weiqun

2017-12-01

Nyx code solves equations of compressible hydrodynamics on an adaptive grid hierarchy coupled with an N-body treatment of dark matter. The gas dynamics in Nyx use a finite volume methodology on an adaptive set of 3-D Eulerian grids; dark matter is represented as discrete particles moving under the influence of gravity. Particles are evolved via a particle-mesh method, using Cloud-in-Cell deposition/interpolation scheme. Both baryonic and dark matter contribute to the gravitational field. In addition, Nyx includes physics for accurately modeling the intergalactic medium; in optically thin limits and assuming ionization equilibrium, the code calculates heating and cooling processes of the primordial-composition gas in an ionizing ultraviolet background radiation field.

Mesoscopic modeling of multi-physicochemical transport phenomena in porous media

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

Kang, Qinjin; Wang, Moran; Mukherjee, Partha P

2009-01-01

We present our recent progress on mesoscopic modeling of multi-physicochemical transport phenomena in porous media based on the lattice Boltzmann method. Simulation examples include injection of CO{sub 2} saturated brine into a limestone rock, two-phase behavior and flooding phenomena in polymer electrolyte fuel cells, and electroosmosis in homogeneously charged porous media. It is shown that the lattice Boltzmann method can account for multiple, coupled physicochemical processes in these systems and can shed some light on the underlying physics occuning at the fundamental scale. Therefore, it can be a potential powerful numerical tool to analyze multi-physicochemical processes in various energy, earth,more » and environmental systems.« less

A novel material screening platform for nanoporous gold-based neural electrodes

NASA Astrophysics Data System (ADS)

Chapman, Christopher Abbott Reece

Neural-electrical interfaces have emerged in the past decades as a promising modality to facilitate the understanding of the electropathophysiology of neurological disorders as well as the normal functioning of the central nervous system, and enable the treatment of neurological defects through electrical stimulation or electrically-controlled drug delivery. However, chronically implanted electrodes face a myriad of design challenges, including their coupling to neural tissue (biocompatibility), small form factor requirement, and their electrical properties (maintaining a low electrical impedance). Planar electrode materials such as planar platinum and gold experience a large increase in electrical impedance when electrode dimensions are reduced to increase spatial resolution of neural recordings. A decrease in electrode surface area reduces the total capacitance of the electrode double layer resulting in an increase in electrode impedance. This high impedance can reduce the signal amplitude and increase the thermal noise, resulting in degradation of signal-to-noise ratio. Conventionally, this increase in electrical impedance at small electrode dimensions has been mitigated by coatings with rough morphologies such as platinum black, conducting polymers, and titanium nitride. Porous surfaces have high effective surface area enabling low impedance at small electrode dimensions. However, achieving long-term stability of cellular coupling to the electrode surface has remained difficult. Designing electrodes that can physically couple with neurons successfully and maintain low impedance at small electrode dimensions necessitates consideration of novel electrode coatings, such as carbon nanotubes and gold nanopillars. Another promising material, and focus of this proposal, is thin film nanoporous gold (np-Au). Nanoporous gold is a promising material for addressing these limitations because of its inherently large effective surface area allows for lower impedances at small form factors, and its modifiable surface morphology can be used to control cell-electrode coupling. Additionally, thin film nanoporous gold is fabricated by traditional microfabrication methods, and thus can be directly adopted by the current state-of-the-art neural electrode fabrication processes. All these properties make thin film nanoporous gold a promising candidate for use in neural electrode surfaces. This dissertation seeks to characterize both the morphological and the electrical response of neural cells to thin film nanoporous gold morphologies using an in vitro electrode morphology screening platform. The specific aims for this proposal are to: (i) develop a electrode morphology library that displays varying topographies to study structure-property relationships of thin film nanoporous gold and cellular response, (ii) characterize neural cell response to identified nanoporous gold topographies that reduce adverse tissue response in vitro, and (iii) develop an electrophysiology platform to characterize neural coupling to each identified nanoporous gold topography.

The M sub 1 muscarinic receptor and its second messenger coupling in human neuroblastoma cells and transfected murine fibroblast cells

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

Mei, Lin.

1989-01-01

The data of this study indicate that pirenzepine (PZ)-high affinity muscarinic receptors (mAChRs) are coupled to the hydrolysis of inositol lipids and not to the adenylate cyclase system in human neuroblastoma SH-SY5Y cells. The maximal carbachol(CCh)-stimulated ({sup 3}H)IP{sub 1} accumulation in the SH-SY5Y cells was decreased in the presence of 1{mu}g/ml pertussis toxin, suggesting that a pertussis toxin sensitive G-protein may be involved in the coupling. Several cell clones which express only M{sub 1} mAChR were generated by transfecting the murine fibroblast B82 cells with the cloned rat genomic m{sub 1} gene. The transfected B82 cells (cTB10) showed specific ({supmore » 3}H)(-)QNB binding activity. The mAChRs in these cells are of the M{sub 1} type defined by their high affinity for PZ and low affinity for AF-DX 116 and coupled to hydrolysis of inositol lipids, possibly via a pertussis toxin sensitive G protein. The relationship between the M{sub 1} mAChR density and the receptor-mediated hydrolysis of inositol lipids was studied in 7 clones. The M{sub 1} mAChR densities in these cells characterized by ({sup 3}H)(-)MQNB binding ranged from 12 fmol/10{sup 6} cells in LK3-1 cells to 260 fmol/10{sup 6} cells in the LK3-8 cells.« less

Homocysteine activates T cells by enhancing endoplasmic reticulum-mitochondria coupling and increasing mitochondrial respiration.

PubMed

Feng, Juan; Lü, Silin; Ding, Yanhong; Zheng, Ming; Wang, Xian

2016-06-01

Hyperhomocysteinemia (HHcy) accelerates atherosclerosis by increasing proliferation and stimulating cytokine secretion in T cells. However, whether homocysteine (Hcy)-mediated T cell activation is associated with metabolic reprogramming is unclear. Here, our in vivo and in vitro studies showed that Hcy-stimulated splenic T-cell activation in mice was accompanied by increased levels of mitochondrial reactive oxygen species (ROS) and calcium, mitochondrial mass and respiration. Inhibiting mitochondrial ROS production and calcium signals or blocking mitochondrial respiration largely blunted Hcy-induced T-cell interferon γ (IFN-γ) secretion and proliferation. Hcy also enhanced endoplasmic reticulum (ER) stress in T cells, and inhibition of ER stress with 4-phenylbutyric acid blocked Hcy-induced T-cell activation. Mechanistically, Hcy increased ER-mitochondria coupling, and uncoupling ER-mitochondria by the microtubule inhibitor nocodazole attenuated Hcy-stimulated mitochondrial reprogramming, IFN-γ secretion and proliferation in T cells, suggesting that juxtaposition of ER and mitochondria is required for Hcy-promoted mitochondrial function and T-cell activation. In conclusion, Hcy promotes T-cell activation by increasing ER-mitochondria coupling and regulating metabolic reprogramming.

An implementation plan for priorities in solar-system space physics

NASA Technical Reports Server (NTRS)

Krimigis, Stamatios M.; Athay, R. Grant; Baker, Daniel; Fisk, Lennard A.; Fredricks, Robert W.; Harvey, John W.; Jokipii, Jack R.; Kivelson, Margaret; Mendillo, Michael; Nagy, Andrew F.

1985-01-01

The scientific objectives and implementation plans and priorities of the Space Science Board in areas of solar physics, heliospheric physics, magnetospheric physics, upper atmosphere physics, solar-terrestrial coupling, and comparative planetary studies are discussed and recommended programs are summarized. Accomplishments of Skylab, Solar Maximum Mission, Nimbus-7, and 11 other programs are highlighted. Detailed mission plans in areas of solar and heliospheric physics, plasma physics, and upper atmospheric physics are also described.

The Role of the Rab Coupling Protein in ErbB2-Driven Mammary Tumorigenesis and Metastasis

DTIC Science & Technology

2015-10-01

Epithelial Mesenchymal Transition , Cell junctions , Cell Proliferation 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF...Epithelial Mesenchymal Transition , Cell junctions and Cell Proliferation. 6 ACCOMPLISHMENTS The PI is reminded that the recipient organization is...oncogene. The potent transforming potential of ErbB2 in the mammary epithelium is thought to be due to its capacity to couple with a number of Src

BBU design of linear induction accelerator cells for radiography application

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

Shang, C.C.; Chen, Y.J.; Gaporaso, G.J.

1997-05-06

There is an ongoing effort to develop accelerating modules for high-current electron accelerators for advanced radiography application. Accelerating modules with low beam-cavity coupling impedances along with gap designs with acceptable field stresses comprise a set of fundamental design criteria. We examine improved cell designs which have been developed for accelerator application in several radiographic operating regimes. We evaluate interaction impedances, analyze the effects of beam structure coupling on beam dynamics (beam break-up instability and corkscrew motion). We also provide estimates of coupling through interesting new high-gradient insulators and evaluate their potential future application in induction cells.

Hidden sector behind the CKM matrix

NASA Astrophysics Data System (ADS)

Okawa, Shohei; Omura, Yuji

2017-08-01

The small quark mixing, described by the Cabibbo-Kobayashi-Maskawa (CKM) matrix in the standard model, may be a clue to reveal new physics around the TeV scale. We consider a simple scenario that extra particles in a hidden sector radiatively mediate the flavor violation to the quark sector around the TeV scale and effectively realize the observed CKM matrix. The lightest particle in the hidden sector, whose contribution to the CKM matrix is expected to be dominant, is a good dark matter (DM) candidate. There are many possible setups to describe this scenario, so that we investigate some universal predictions of this kind of model, focusing on the contribution of DM to the quark mixing and flavor physics. In this scenario, there is an explicit relation between the CKM matrix and flavor violating couplings, such as four-quark couplings, because both are radiatively induced by the particles in the hidden sector. Then, we can explicitly find the DM mass region and the size of Yukawa couplings between the DM and quarks, based on the study of flavor physics and DM physics. In conclusion, we show that DM mass in our scenario is around the TeV scale, and the Yukawa couplings are between O (0.01 ) and O (1 ). The spin-independent DM scattering cross section is estimated as O (10-9) [pb]. An extra colored particle is also predicted at the O (10 ) TeV scale.

The efficiency of driving chemical reactions by a physical non-equilibrium is kinetically controlled.

PubMed

Göppel, Tobias; Palyulin, Vladimir V; Gerland, Ulrich

2016-07-27

An out-of-equilibrium physical environment can drive chemical reactions into thermodynamically unfavorable regimes. Under prebiotic conditions such a coupling between physical and chemical non-equilibria may have enabled the spontaneous emergence of primitive evolutionary processes. Here, we study the coupling efficiency within a theoretical model that is inspired by recent laboratory experiments, but focuses on generic effects arising whenever reactant and product molecules have different transport coefficients in a flow-through system. In our model, the physical non-equilibrium is represented by a drift-diffusion process, which is a valid coarse-grained description for the interplay between thermophoresis and convection, as well as for many other molecular transport processes. As a simple chemical reaction, we consider a reversible dimerization process, which is coupled to the transport process by different drift velocities for monomers and dimers. Within this minimal model, the coupling efficiency between the non-equilibrium transport process and the chemical reaction can be analyzed in all parameter regimes. The analysis shows that the efficiency depends strongly on the Damköhler number, a parameter that measures the relative timescales associated with the transport and reaction kinetics. Our model and results will be useful for a better understanding of the conditions for which non-equilibrium environments can provide a significant driving force for chemical reactions in a prebiotic setting.

Cavity magnon polaritons with lithium ferrite and three-dimensional microwave resonators at millikelvin temperatures

NASA Astrophysics Data System (ADS)

Goryachev, Maxim; Watt, Stuart; Bourhill, Jeremy; Kostylev, Mikhail; Tobar, Michael E.

2018-04-01

Single crystal lithium ferrite (LiFe) spheres of sub-mm dimension are examined at mK temperatures, microwave frequencies, and variable dc magnetic field, for use in hybrid quantum systems and condensed matter and fundamental physics experiments. Strong coupling regimes of the photon-magnon interaction (cavity magnon polariton quasiparticles) were observed with coupling strength of up to 250 MHz at 9.5 GHz (2.6%) with magnon linewidths of order 4 MHz (with potential improvement to sub-MHz values). We show that the photon-magnon coupling can be significantly improved and exceed that of the widely used yttrium iron garnet crystal, due to the small unit cell of LiFe, allowing twice the spins per unit volume. Magnon mode softening was observed at low dc fields and, combined with the normal Zeeman effect, creates magnon spin-wave modes that are insensitive to first-order magnetic-field fluctuations. This effect is observed in the Kittel mode at 5.5 GHz (and another higher order mode at 6.5 GHz) with a dc magnetic field close to 0.19 tesla. We show that if the cavity is tuned close to this frequency, the magnon polariton particles exhibit an enhanced range of strong coupling and insensitivity to magnetic field fluctuations with both first-order and second-order insensitivity to magnetic field as a function of frequency (double magic point clock transition), which could potentially be exploited in cavity QED experiments.

Laser-direct-drive program: Promise, challenge, and path forward

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

Campbell, E. M.; Goncharov, V. N.; Sangster, T. C.

Along with laser-indirect (x-ray)-drive and magnetic-drive target concepts, laser direct drive is a viable approach to achieving ignition and gain with inertial confinement fusion. In the United States, a national program has been established to demonstrate and understand the physics of laser direct drive. The program utilizes the Omega Laser Facility to conduct implosion and coupling physics at the nominally 30-kJ scale and laser–plasma interaction and coupling physics at the MJ scale at the National Ignition Facility. This paper will discuss the motivation and challenges for laser direct drive and the broad-based program presently underway in the United States.

Laser-direct-drive program: Promise, challenge, and path forward

DOE PAGES

Campbell, E. M.; Goncharov, V. N.; Sangster, T. C.; ...

2017-03-19

Along with laser-indirect (x-ray)-drive and magnetic-drive target concepts, laser direct drive is a viable approach to achieving ignition and gain with inertial confinement fusion. In the United States, a national program has been established to demonstrate and understand the physics of laser direct drive. The program utilizes the Omega Laser Facility to conduct implosion and coupling physics at the nominally 30-kJ scale and laser–plasma interaction and coupling physics at the MJ scale at the National Ignition Facility. This paper will discuss the motivation and challenges for laser direct drive and the broad-based program presently underway in the United States.

Simulating biological processes: stochastic physics from whole cells to colonies.

PubMed

Earnest, Tyler M; Cole, John A; Luthey-Schulten, Zaida

2018-05-01

The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge that give rise to the complex forms and behaviors we see in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recent years have seen stochastic modeling grow into a major subdiscipline within biological physics. Here we review some of the major advances that have shaped our understanding of stochasticity in biology. We begin with some historical context, outlining a string of important experimental results that motivated the development of stochastic modeling. We then embark upon a fairly rigorous treatment of the simulation methods that are currently available for the treatment of stochastic biological models, with an eye toward comparing and contrasting their realms of applicability, and the care that must be taken when parameterizing them. Following that, we describe how stochasticity impacts several key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, before considering how the functions may be coupled into a comprehensive model of a 'minimal cell'. Finally, we close with our expectation for the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches in order to understand life across a range of length and time scales.

Diffusion of extracellular K+ can synchronize bursting oscillations in a model islet of Langerhans.

PubMed Central

Stokes, C L; Rinzel, J

1993-01-01

Electrical bursting oscillations of mammalian pancreatic beta-cells are synchronous among cells within an islet. While electrical coupling among cells via gap junctions has been demonstrated, its extent and topology are unclear. The beta-cells also share an extracellular compartment in which oscillations of K+ concentration have been measured (Perez-Armendariz and Atwater, 1985). These oscillations (1-2 mM) are synchronous with the burst pattern, and apparently are caused by the oscillating voltage-dependent membrane currents: Extracellular K+ concentration (Ke) rises during the depolarized active (spiking) phase and falls during the hyperpolarized silent phase. Because raising Ke depolarizes the cell membrane by increasing the potassium reversal potential (VK), any cell in the active phase should recruit nonspiking cells into the active phase. The opposite is predicted for the silent phase. This positive feedback system might couple the cells' electrical activity and synchronize bursting. We have explored this possibility using a theoretical model for bursting of beta-cells (Sherman et al., 1988) and K+ diffusion in the extracellular space of an islet. Computer simulations demonstrate that the bursts synchronize very quickly (within one burst) without gap junctional coupling among the cells. The shape and amplitude of computed Ke oscillations resemble those seen in experiments for certain parameter ranges. The model cells synchronize with exterior cells leading, though incorporating heterogeneous cell properties can allow interior cells to lead. The model islet can also be forced to oscillate at both faster and slower frequencies using periodic pulses of higher K+ in the medium surrounding the islet. Phase plane analysis was used to understand the synchronization mechanism. The results of our model suggest that diffusion of extracellular K+ may contribute to coupling and synchronization of electrical oscillations in beta-cells within an islet. Images FIGURE 1 PMID:8218890

Gβ Regulates Coupling between Actin Oscillators for Cell Polarity and Directional Migration

PubMed Central

Cai, Huaqing; Sun, Yaohui; Huang, Chuan-Hsiang; Freyre, Mariel; Zhao, Min; Devreotes, Peter N.; Weiner, Orion D.

2016-01-01

For directional movement, eukaryotic cells depend on the proper organization of their actin cytoskeleton. This engine of motility is made up of highly dynamic nonequilibrium actin structures such as flashes, oscillations, and traveling waves. In Dictyostelium, oscillatory actin foci interact with signals such as Ras and phosphatidylinositol 3,4,5-trisphosphate (PIP3) to form protrusions. However, how signaling cues tame actin dynamics to produce a pseudopod and guide cellular motility is a critical open question in eukaryotic chemotaxis. Here, we demonstrate that the strength of coupling between individual actin oscillators controls cell polarization and directional movement. We implement an inducible sequestration system to inactivate the heterotrimeric G protein subunit Gβ and find that this acute perturbation triggers persistent, high-amplitude cortical oscillations of F-actin. Actin oscillators that are normally weakly coupled to one another in wild-type cells become strongly synchronized following acute inactivation of Gβ. This global coupling impairs sensing of internal cues during spontaneous polarization and sensing of external cues during directional motility. A simple mathematical model of coupled actin oscillators reveals the importance of appropriate coupling strength for chemotaxis: moderate coupling can increase sensitivity to noisy inputs. Taken together, our data suggest that Gβ regulates the strength of coupling between actin oscillators for efficient polarity and directional migration. As these observations are only possible following acute inhibition of Gβ and are masked by slow compensation in genetic knockouts, our work also shows that acute loss-of-function approaches can complement and extend the reach of classical genetics in Dictyostelium and likely other systems as well. PMID:26890004

Self-organization: the fundament of cell biology.

PubMed

Wedlich-Söldner, Roland; Betz, Timo

2018-05-26

Self-organization refers to the emergence of an overall order in time and space of a given system that results from the collective interactions of its individual components. This concept has been widely recognized as a core principle in pattern formation for multi-component systems of the physical, chemical and biological world. It can be distinguished from self-assembly by the constant input of energy required to maintain order-and self-organization therefore typically occurs in non-equilibrium or dissipative systems. Cells, with their constant energy consumption and myriads of local interactions between distinct proteins, lipids, carbohydrates and nucleic acids, represent the perfect playground for self-organization. It therefore comes as no surprise that many properties and features of self-organized systems, such as spontaneous formation of patterns, nonlinear coupling of reactions, bi-stable switches, waves and oscillations, are found in all aspects of modern cell biology. Ultimately, self-organization lies at the heart of the robustness and adaptability found in cellular and organismal organization, and hence constitutes a fundamental basis for natural selection and evolution.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Magnetic Gold Nanoparticle-Labeled Heparanase Monoclonal Antibody and its Subsequent Application for Tumor Magnetic Resonance Imaging

NASA Astrophysics Data System (ADS)

Li, Ning; Jie, Meng-Meng; Yang, Min; Tang, Li; Chen, Si-Yuan; Sun, Xue-Mei; Tang, Bo; Yang, Shi-Ming

2018-04-01

Heparanase (HPA) is ubiquitously expressed in various metastatic malignant tumors; previous studies have demonstrated that HPA was a potential tumor-associated antigen (TAA) for tumor immunotherapy. We sought to evaluate the feasibility of HPA as a common TAA for magnetic resonance imaging (MRI) of tumor metastasis and its potential application in tumor molecular imaging. We prepared a targeted probe based on magnetic gold nanoparticles coupled with an anti-HPA antibody for the specific detection of HPA by MRI. The specificity of the targeted probe was validated in vitro by incubation of the probe with various tumor cells, and the probe was able to selectively detect HPA (+) cells. We found the probes displayed significantly reduced signal intensity in several tumor cells, and the signal intensity decreased significantly after the targeted probe was injected in tumor-bearing nude mice. In the study, we demonstrated that the HPA&GoldMag probe had excellent physical and chemical properties and immune activities and could specifically target many tumor cell tissues both in vitro and in vivo. This may provide an experimental base for molecular imaging of tumor highly expressing heparanase using HPA mAbs.

Selection of antigenic markers on a GFP-C{kappa} fusion scaffold with high sensitivity by eukaryotic ribosome display

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

Yang Yongmin; IgE Therapeutics, Inc., San Diego, CA 92121-2233; Barankiewicz, Teresa J.

2007-07-27

Ribosome display is a cell-free system permitting gene selection through the physical association of genetic material (mRNA) and its phenotypic (protein) product. While often used to select single-chain antibodies from large libraries by panning against immobilized antigens, we have adapted ribosome display for use in the 'reverse' format in order to select high affinity antigenic determinants against solid-phase antibody. To create an antigenic scaffold, DNA encoding green fluorescent protein (GFP) was fused to a light chain constant domain (C{kappa}) with stop codon deleted, and with 5' signals (T7 promoter, Kozak) enabling coupled transcription/translation in a eukaryotic cell-free system. Epitopes onmore » either GFP (5') or C{kappa} (3') were selected by anti-GFP or anti-C{kappa} antibodies, respectively, coupled to magnetic beads. After selection, mRNA was amplified directly from protein-ribosome-mRNA (PRM) complexes by in situ PCR followed by internal amplification and reassembly PCR. As little as 10 fg of the 1 kb DNA construct, i.e. approximately 7500 molecules, could be recovered following a single round of interaction with solid-phase anti-GFP antibody. This platform is highly specific and sensitive for the antigen-antibody interaction and may permit selection and reshaping of high affinity antigenic variants of scaffold proteins.« less

Electrocapturing flow cell

DOEpatents

Morozov, Victor [Manassas, VA

2011-04-05

A flow cell for electrophoretically-assisted capturing analytes from a flow. The flow cell includes a specimen chamber, a first membrane, a second membrane, a first electrode chamber, and a second electrode chamber. The specimen chamber may have a sample inlet and a sample outlet. A first portion of the first membrane may be coupled to a first portion of the specimen chamber. A first portion of the second membrane may be coupled to a second portion of the specimen chamber. The first electrode chamber may be configured to accept a charge. A portion of the first electrode chamber may be coupled to a second portion of the first membrane. A second electrode chamber may be configured to accept an opposite charge. A portion of the second electrode chamber may be coupled to a second portion of the second membrane.

Together and apart: a typology of re-partnering in old age.

PubMed

Koren, Chaya

2014-08-01

The human need for love, friendship, and physical contact, and the fear of loneliness do not diminish with age. Widowhood and late-life divorce and increased life expectancy are likely to lead to alternative relationships, such as re-partnering. The purpose of this paper is to explore interplays between emotional and physical components of re-partnering in old age. Theoretical sampling of 20 couples included men who re-partnered at the age of 65+ years and women at the age of 60+ years, following termination of lifelong marriages due to death or divorce. Living arrangements included married or unmarried cohabitation under the same roof or in separate homes. Forty semi-structured interviews were tape-recorded and transcribed verbatim. The couple was the unit of analysis. Interplays between physical and emotional dimensions were examined using five abductive parameters derived from data analysis resulting in a fourfold typology of emotional and physical closeness/distance in re-partnering in old age: (1) living together (physically and emotionally); (2) living apart (physically) together (emotionally); (3) living together (physically) apart (emotionally); and (4) living apart (physically and emotionally). Findings revealed types of partner relationships that are different from lifelong marriages. The typology could help professionals working with older persons regarding what to expect in re-partnering in old age and be included in developmental theories as an option in old age. A quantitative tool for research and therapy purposes, entitled The Re-partnering in Old Age Typology Scale (RPOAT Scale), based on abductive parameters, could be established for measuring re-partnering relationship quality and classifying re-partnering couples.

Intracellular subsurface imaging using a hybrid shear-force feedback/scanning quantitative phase microscopy technique

NASA Astrophysics Data System (ADS)

Edward, Kert

Quantitative phase microscopy (QPM) allows for the imaging of translucent or transparent biological specimens without the need for exogenous contrast agents. This technique is usually applied towards the investigation of simple cells such as red blood cells which are typically enucleated and can be considered to be homogenous. However, most biological cells are nucleated and contain other interesting intracellular organelles. It has been established that the physical characteristics of certain subsurface structures such as the shape and roughness of the nucleus is well correlated with onset and progress of pathological conditions such as cancer. Although the acquired quantitative phase information of biological cells contains surface information as well as coupled subsurface information, the latter has been ignored up until now. A novel scanning quantitative phase imaging system unencumbered by 2pi ambiguities is hereby presented. This system is incorporated into a shear-force feedback scheme which allows for simultaneous phase and topography determination. It will be shown how subsequent image processing of these two data sets allows for the extraction of the subsurface component in the phase data and in vivo cell refractometry studies. Both fabricated samples and biological cells ranging from rat fibroblast cells to malaria infected human erythrocytes were investigated as part of this research. The results correlate quite well with that obtained via other microscopy techniques.

Target of rapamycin complex 2 signals to downstream effector yeast protein kinase 2 (Ypk2) through adheres-voraciously-to-target-of-rapamycin-2 protein 1 (Avo1) in Saccharomyces cerevisiae.

PubMed

Liao, Hsien-Ching; Chen, Mei-Yu

2012-02-24

The conserved Ser/Thr kinase target of rapamycin (TOR) serves as a central regulator in controlling cell growth-related functions. There exist two distinct TOR complexes, TORC1 and TORC2, each coupling to specific downstream effectors and signaling pathways. In Saccharomyces cerevisiae, TORC2 is involved in regulating actin organization and maintaining cell wall integrity. Ypk2 (yeast protein kinase 2), a member of the cAMP-dependent, cGMP-dependent, and PKC (AGC) kinase family, is a TORC2 substrate known to participate in actin and cell wall regulation. Employing avo3(ts) mutants with defects in TORC2 functions that are suppressible by active Ypk2, we investigated the molecular interactions involved in mediating TORC2 signaling to Ypk2. GST pulldown assays in yeast lysates demonstrated physical interactions between Ypk2 and components of TORC2. In vitro binding assays revealed that Avo1 directly binds to Ypk2. In avo3(ts) mutants, the TORC2-Ypk2 interaction was reduced and could be restored by AVO1 overexpression, highlighting the important role of Avo1 in coupling TORC2 to Ypk2. The interaction was mapped to an internal region (amino acids 600-840) of Avo1 and a C-terminal region of Ypk2. Ypk2(334-677), a truncated form of Ypk2 containing the Avo1-interacting region, was able to interfere with Avo1-Ypk2 interaction in vitro. Overexpressing Ypk2(334-677) in yeast cells resulted in a perturbation of TORC2 functions, causing defective cell wall integrity, aberrant actin organization, and diminished TORC2-dependent Ypk2 phosphorylation evidenced by the loss of an electrophoretic mobility shift. Together, our data support the conclusion that the direct Avo1-Ypk2 interaction is crucial for TORC2 signaling to the downstream Ypk2 pathway.

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

PubMed

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

2015-11-01

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

Effect of Electrical Stimulation on Beta-Adrenergic Receptor Population and Coupling Efficiency in Chicken and Rat Skeleton Muscle Cell Cultures

NASA Technical Reports Server (NTRS)

Young, Ronald B.; Bridge, Kristin Y.; Strietzel, Catherine J.

1999-01-01

Expression of the beta-adrenergic receptor (bAR) and its coupling to cyclic AMP (cAMP) synthesis are important components of the signaling system that controls muscle atrophy and hypertrophy, and the goal of this study was to determine if electrical stimulation in a pattern simulating slow muscle contraction would alter the bAR response in primary cultures of avian and mammalian skeletal muscle cells. Specifically, chicken skeletal muscle cells and rat skeletal muscle cells that had been grown for seven days in culture were subjected to electrical stimulation for an additional two days at a pulse frequency of 0.5 pulses/sec and a pulse duration of 200 msec. In chicken skeletal muscle cells, the bAR population was not significantly affected by electrical stimulation; however, the ability of these cells to synthesize cyclic AMP was reduced by approximately one-half. Thus, in chicken muscle cells an enhanced level of contraction reduced the coupling efficiency of bAR for cyclic AMP production by approximately 55% compared to controls. In contrast, the bAR population in rat muscle cells was increased by approximately 25% by electrical stimulation, and the ability of these cells to synthesize cyclic AMP was also increased by almost two-fold. Thus, in rat muscle cells an enhanced level of contraction increased the coupling efficiency of bAR for cyclic AMP production by approximately 50% compared to controls. The basal levels of intracellular cyclic AMP in both rat muscle cells and chicken muscle cells were not affected by electrical stimulation.

Physical understanding of complex multiscale biochemical models via algorithmic simplification: Glycolysis in Saccharomyces cerevisiae

NASA Astrophysics Data System (ADS)

Kourdis, Panayotis D.; Steuer, Ralf; Goussis, Dimitris A.

2010-09-01

Large-scale models of cellular reaction networks are usually highly complex and characterized by a wide spectrum of time scales, making a direct interpretation and understanding of the relevant mechanisms almost impossible. We address this issue by demonstrating the benefits provided by model reduction techniques. We employ the Computational Singular Perturbation (CSP) algorithm to analyze the glycolytic pathway of intact yeast cells in the oscillatory regime. As a primary object of research for many decades, glycolytic oscillations represent a paradigmatic candidate for studying biochemical function and mechanisms. Using a previously published full-scale model of glycolysis, we show that, due to fast dissipative time scales, the solution is asymptotically attracted on a low dimensional manifold. Without any further input from the investigator, CSP clarifies several long-standing questions in the analysis of glycolytic oscillations, such as the origin of the oscillations in the upper part of glycolysis, the importance of energy and redox status, as well as the fact that neither the oscillations nor cell-cell synchronization can be understood in terms of glycolysis as a simple linear chain of sequentially coupled reactions.

Direct Interactions with the Integrin β1 Cytoplasmic Tail Activate the Abl2/Arg Kinase*

PubMed Central

Simpson, Mark A.; Bradley, William D.; Harburger, David; Parsons, Maddy; Calderwood, David A.; Koleske, Anthony J.

2015-01-01

Integrins are heterodimeric α/β extracellular matrix adhesion receptors that couple physically to the actin cytoskeleton and regulate kinase signaling pathways to control cytoskeletal remodeling and adhesion complex formation and disassembly. β1 integrins signal through the Abl2/Arg (Abl-related gene) nonreceptor tyrosine kinase to control fibroblast cell motility, neuronal dendrite morphogenesis and stability, and cancer cell invasiveness, but the molecular mechanisms by which integrin β1 activates Arg are unknown. We report here that the Arg kinase domain interacts directly with a lysine-rich membrane-proximal segment in the integrin β1 cytoplasmic tail, that Arg phosphorylates the membrane-proximal Tyr-783 in the β1 tail, and that the Arg Src homology domain then engages this phosphorylated region in the tail. We show that these interactions mediate direct binding between integrin β1 and Arg in vitro and in cells and activate Arg kinase activity. These findings provide a model for understanding how β1-containing integrins interact with and activate Abl family kinases. PMID:25694433

Numerical Propulsion System Simulation: An Overview

NASA Technical Reports Server (NTRS)

Lytle, John K.

2000-01-01

The cost of implementing new technology in aerospace propulsion systems is becoming prohibitively expensive and time consuming. One of the main contributors to the high cost and lengthy time is the need to perform many large-scale hardware tests and the inability to integrate all appropriate subsystems early in the design process. The NASA Glenn Research Center is developing the technologies required to enable simulations of full aerospace propulsion systems in sufficient detail to resolve critical design issues early in the design process before hardware is built. This concept, called the Numerical Propulsion System Simulation (NPSS), is focused on the integration of multiple disciplines such as aerodynamics, structures and heat transfer with computing and communication technologies to capture complex physical processes in a timely and cost-effective manner. The vision for NPSS, as illustrated, is to be a "numerical test cell" that enables full engine simulation overnight on cost-effective computing platforms. There are several key elements within NPSS that are required to achieve this capability: 1) clear data interfaces through the development and/or use of data exchange standards, 2) modular and flexible program construction through the use of object-oriented programming, 3) integrated multiple fidelity analysis (zooming) techniques that capture the appropriate physics at the appropriate fidelity for the engine systems, 4) multidisciplinary coupling techniques and finally 5) high performance parallel and distributed computing. The current state of development in these five area focuses on air breathing gas turbine engines and is reported in this paper. However, many of the technologies are generic and can be readily applied to rocket based systems and combined cycles currently being considered for low-cost access-to-space applications. Recent accomplishments include: (1) the development of an industry-standard engine cycle analysis program and plug 'n play architecture, called NPSS Version 1, (2) A full engine simulation that combines a 3D low-pressure subsystem with a 0D high pressure core simulation. This demonstrates the ability to integrate analyses at different levels of detail and to aerodynamically couple components, the fan/booster and low-pressure turbine, through a 3D computational fluid dynamics simulation. (3) Simulation of all of the turbomachinery in a modern turbofan engine on parallel computing platform for rapid and cost-effective execution. This capability can also be used to generate full compressor map, requiring both design and off-design simulation. (4) Three levels of coupling characterize the multidisciplinary analysis under NPSS: loosely coupled, process coupled and tightly coupled. The loosely coupled and process coupled approaches require a common geometry definition to link CAD to analysis tools. The tightly coupled approach is currently validating the use of arbitrary Lagrangian/Eulerian formulation for rotating turbomachinery. The validation includes both centrifugal and axial compression systems. The results of the validation will be reported in the paper. (5) The demonstration of significant computing cost/performance reduction for turbine engine applications using PC clusters. The NPSS Project is supported under the NASA High Performance Computing and Communications Program.

Proliferative activity of elastin-like-peptides depends on charge and phase transition.

PubMed

Yuan, Yuan; Koria, Piyush

2016-03-01

Elastin-like-peptides (ELPs) are stimulus-responsive protein-based polymers and are attractive biomaterials due to their biocompatibility and unique properties. This study shows that in addition to their physical properties, ELPs have biological activities that are conducive to tissue regeneration. Specifically, we found that ELPs induce fibroblast proliferation via cell surface heparan sulfate proteoglycans (HSPG). Furthermore, our data suggests that ELP based materials with differential proliferative potential can be designed by controlling the interaction of ELPs with HSPGs by incorporating either hydrophobic or positively charged residues within the ELP sequence. Fibroblast proliferation is important for granulation tissue formation which is important in chronic wounds as well as in healing of other tissues. The customizable biological activity of ELPs coupled with their unique physical properties will enable us to design novel, sustainable and cost effective therapies for different tissue regeneration applications. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 697-706, 2016. © 2015 Wiley Periodicals, Inc.

Electrochemical Transport Phenomena in Hybrid Pseudocapacitors under Galvanostatic Cycling

DOE PAGES

d'Entremont, Anna L.; Girard, Henri -Louis; Wang, Hainan; ...

2015-11-18

Here, this study aims to provide insights into the electrochemical transport and interfacial phenomena in hybrid pseudocapacitors under galvanostatic cycling. Pseudocapacitors are promising electrical energy storage devices for applications requiring large power density. They also involve complex, coupled, and multiscale physical phenomena that are difficult to probe experimentally. The present study performed detailed numerical simulations for a hybrid pseudocapacitor with planar electrodes and binary, asymmetric electrolyte under various cycling conditions, based on a first-principles continuum model accounting simultaneously for charge storage by electric double layer (EDL) formation and by faradaic reactions with intercalation. Two asymptotic regimes were identified corresponding tomore » (i) dominant faradaic charge storage at low current and low frequency or (ii) dominant EDL charge storage at high current and high frequency. Analytical expressions for the intercalated ion concentration and surface overpotential were derived for both asymptotic regimes. Features of typical experimentally measured cell potential were physically interpreted. These insights could guide the optimization of hybrid pseudocapacitors.« less

Ultrafast detection in particle physics and positron emission tomography using SiPMs

NASA Astrophysics Data System (ADS)

Dolenec, R.; Korpar, S.; Križan, P.; Pestotnik, R.

2017-12-01

Silicon photomultiplier (SiPM) photodetectors perform well in many particle and medical physics applications, especially where good efficiency, insensitivity to magnetic field and precise timing are required. In Cherenkov time-of-flight positron emission tomography the requirements for photodetector performance are especially high. On average only a couple of photons are available for detection and the best possible timing resolution is needed. Using SiPMs as photodetectors enables good detection efficiency, but the large sensitive area devices needed have somewhat limited time resolution for single photons. We have observed an additional degradation of the timing at very low light intensities due to delayed events in distribution of signals resulting from multiple fired micro cells. In this work we present the timing properties of AdvanSiD ASD-NUV3S-P-40 SiPM at single photon level picosecond laser illumination and a simple modification of the time-walk correction algorithm, that resulted in reduced degradation of timing resolution due to the delayed events.

Stability and Noise in the Cyanobacterial Circadian Clock

NASA Astrophysics Data System (ADS)

Mihalcescu, Irina

2008-03-01

Accuracy in cellular function has to be achieved despite random fluctuations (noise) in the concentrations of different molecular constituents inside and outside the cell. Single cell in vivo monitoring reveals that individual cells generate autonomous circadian rhythms in protein abundance. In multi-cellular organisms, the individual cell rhythms appear to be noisy with drifting phases and frequencies. However, the whole organism is significantly more accurate, the temporal precision being achieved most probably via intercellular coupling of the individual noisy oscillators. In cyanobacteria, we have shown that single cell oscillators are impressively stable and a first estimation rules out strong intercellular coupling. Interestingly, these prokaryotes also have the simplest molecular mechanism at the heart of their circadian clock. In the absence of transcriptional activity in vivo, as well alone in vitro, the three clock proteins KaiA, KaiB and KaiC generate a self-sustained circadian oscillation of autophosphorylation and dephosphorylation. Recent chemical kinetics models provide a possible understanding of the three-protein oscillator, but the measured in vivo stability remains yet unexplained. Is the clock stability a built-in property for each bacterium or does a weak intercellular coupling, make them appear like that? To address this question we first theoretically designed our experiment to be able to distinguish coupling, even weak, from phase diffusion. As the precision of our evaluation increases with the length of the experiments, we continuously monitor, for a couple of weeks, mixtures of cell populations with different initial phases. The inherent experimental noise contribution, initially dominant, is reduced by enhanced statistics. In addition, in situ entrainment experiments confirm our ability to detect a coupling of the circadian oscillator to an external force and to describe explicitly the dynamic change of the mean phase. We report a value of the coupling constant that is small compared to the diffusion constant. These results therefore confirm that the cyanobacterial clock stability is a built-in property: the cyanobacterian clock mechanism is not only the simplest but also the most robust.

Mechanical preconditioning enables electrophysiologic coupling of skeletal myoblast cells to myocardium

PubMed Central

Treskes, Philipp; Cowan, Douglas B.; Stamm, Christof; Rubach, Martin; Adelmann, Roland; Wittwer, Thorsten; Wahlers, Thorsten

2015-01-01

Objective The effect of mechanical preconditioning on skeletal myoblasts in engineered tissue constructs was investigated to resolve issues associated with conduction block between skeletal myoblast cells and cardiomyocytes. Methods Murine skeletal myoblasts were used to generate engineered tissue constructs with or without application of mechanical strain. After in vitro myotube formation, engineered tissue constructs were co-cultured for 6 days with viable embryonic heart slices. With the use of sharp electrodes, electrical coupling between engineered tissue constructs and embryonic heart slices was assessed in the presence or absence of pharmacologic agents. Results The isolation and expansion procedure for skeletal myoblasts resulted in high yields of homogeneously desmin-positive (97.1% ± 0.1%) cells. Mechanical strain was exerted on myotubes within engineered tissue constructs during gelation of the matrix, generating preconditioned engineered tissue constructs. Electrical coupling between preconditioned engineered tissue constructs and embryonic heart slices was observed; however, no coupling was apparent when engineered tissue constructs were not subjected to mechanical strain. Coupling of cells from engineered tissue constructs to cells in embryonic heart slices showed slower conduction velocities than myocardial cells with the embryonic heart slices (preconditioned engineered tissue constructs vs embryonic heart slices: 0.04 ± 0.02 ms vs 0.10 ± 0.05 ms, P = .011), lower stimulation frequencies (preconditioned engineered tissue constructs vs maximum embryonic heart slices: 4.82 ± 1.42 Hz vs 10.58 ± 1.56 Hz; P = .0009), and higher sensitivities to the gap junction inhibitor (preconditioned engineered tissue constructs vs embryonic heart slices: 0.22 ± 0.07 mmol/L vs 0.93 ± 0.15 mmol/L; P = .0004). Conclusions We have generated skeletal myoblast–based transplantable grafts that electrically couple to myocardium. PMID:22980065

Protein gradients in single cells induced by their coupling to "morphogen"-like diffusion

NASA Astrophysics Data System (ADS)

Nandi, Saroj Kumar; Safran, Sam A.

2018-05-01

One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not yet fully understood. One of the models for such gradient formation, based on differential diffusion, is limited to proteins with large ratios of their diffusion constants or to specific protein-large molecule interactions. We introduce a novel mechanism for gradient formation via the coupling of the proteins within a single cell with a molecule, that we call a "pronogen," whose action is similar to that of morphogens in multi-cell assemblies; the pronogen is produced with a fixed flux at one side of the cell. This coupling results in an effectively non-linear diffusion degradation model for the pronogen dynamics within the cell, which leads to a steady-state gradient of the protein concentration. We use stability analysis to show that these gradients are linearly stable with respect to perturbations.

Analysis of Anderson Acceleration on a Simplified Neutronics/Thermal Hydraulics System

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

Toth, Alex; Kelley, C. T.; Slattery, Stuart R

ABSTRACT A standard method for solving coupled multiphysics problems in light water reactors is Picard iteration, which sequentially alternates between solving single physics applications. This solution approach is appealing due to simplicity of implementation and the ability to leverage existing software packages to accurately solve single physics applications. However, there are several drawbacks in the convergence behavior of this method; namely slow convergence and the necessity of heuristically chosen damping factors to achieve convergence in many cases. Anderson acceleration is a method that has been seen to be more robust and fast converging than Picard iteration for many problems, withoutmore » significantly higher cost per iteration or complexity of implementation, though its effectiveness in the context of multiphysics coupling is not well explored. In this work, we develop a one-dimensional model simulating the coupling between the neutron distribution and fuel and coolant properties in a single fuel pin. We show that this model generally captures the convergence issues noted in Picard iterations which couple high-fidelity physics codes. We then use this model to gauge potential improvements with regard to rate of convergence and robustness from utilizing Anderson acceleration as an alternative to Picard iteration.« less

Variational multiscale models for charge transport.

PubMed

Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin

2012-01-01

This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle for chemo-electro-fluid systems. A number of computational algorithms is developed to implement the proposed new variational multiscale models in an efficient manner. A set of ten protein molecules and a realistic ion channel, Gramicidin A, are employed to confirm the consistency and verify the capability. Extensive numerical experiment is designed to validate the proposed variational multiscale models. A good quantitative agreement between our model prediction and the experimental measurement of current-voltage curves is observed for the Gramicidin A channel transport. This paper also provides a brief review of the field.

Variational multiscale models for charge transport

PubMed Central

Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin

2012-01-01

This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle for chemo-electro-fluid systems. A number of computational algorithms is developed to implement the proposed new variational multiscale models in an efficient manner. A set of ten protein molecules and a realistic ion channel, Gramicidin A, are employed to confirm the consistency and verify the capability. Extensive numerical experiment is designed to validate the proposed variational multiscale models. A good quantitative agreement between our model prediction and the experimental measurement of current-voltage curves is observed for the Gramicidin A channel transport. This paper also provides a brief review of the field. PMID:23172978

Thermodynamic Modeling and Dispatch of Distributed Energy Technologies including Fuel Cell -- Gas Turbine Hybrids

NASA Astrophysics Data System (ADS)

McLarty, Dustin Fogle

Distributed energy systems are a promising means by which to reduce both emissions and costs. Continuous generators must be responsive and highly efficiency to support building dynamics and intermittent on-site renewable power. Fuel cell -- gas turbine hybrids (FC/GT) are fuel-flexible generators capable of ultra-high efficiency, ultra-low emissions, and rapid power response. This work undertakes a detailed study of the electrochemistry, chemistry and mechanical dynamics governing the complex interaction between the individual systems in such a highly coupled hybrid arrangement. The mechanisms leading to the compressor stall/surge phenomena are studied for the increased risk posed to particular hybrid configurations. A novel fuel cell modeling method introduced captures various spatial resolutions, flow geometries, stack configurations and novel heat transfer pathways. Several promising hybrid configurations are analyzed throughout the work and a sensitivity analysis of seven design parameters is conducted. A simple estimating method is introduced for the combined system efficiency of a fuel cell and a turbine using component performance specifications. Existing solid oxide fuel cell technology is capable of hybrid efficiencies greater than 75% (LHV) operating on natural gas, and existing molten carbonate systems greater than 70% (LHV). A dynamic model is calibrated to accurately capture the physical coupling of a FC/GT demonstrator tested at UC Irvine. The 2900 hour experiment highlighted the sensitivity to small perturbations and a need for additional control development. Further sensitivity studies outlined the responsiveness and limits of different control approaches. The capability for substantial turn-down and load following through speed control and flow bypass with minimal impact on internal fuel cell thermal distribution is particularly promising to meet local demands or provide dispatchable support for renewable power. Advanced control and dispatch heuristics are discussed using a case study of the UCI central plant. Thermal energy storage introduces a time horizon into the dispatch optimization which requires novel solution strategies. Highly efficient and responsive generators are required to meet the increasingly dynamic loads of today's efficient buildings and intermittent local renewable wind and solar power. Fuel cell gas turbine hybrids will play an integral role in the complex and ever-changing solution to local electricity production.

A per-cent-level determination of the nucleon axial coupling from quantum chromodynamics.

PubMed

Chang, C C; Nicholson, A N; Rinaldi, E; Berkowitz, E; Garron, N; Brantley, D A; Monge-Camacho, H; Monahan, C J; Bouchard, C; Clark, M A; Joó, B; Kurth, T; Orginos, K; Vranas, P; Walker-Loud, A

2018-06-01

The axial coupling of the nucleon, g A , is the strength of its coupling to the weak axial current of the standard model of particle physics, in much the same way as the electric charge is the strength of the coupling to the electromagnetic current. This axial coupling dictates the rate at which neutrons decay to protons, the strength of the attractive long-range force between nucleons and other features of nuclear physics. Precision tests of the standard model in nuclear environments require a quantitative understanding of nuclear physics that is rooted in quantum chromodynamics, a pillar of the standard model. The importance of g A makes it a benchmark quantity to determine theoretically-a difficult task because quantum chromodynamics is non-perturbative, precluding known analytical methods. Lattice quantum chromodynamics provides a rigorous, non-perturbative definition of quantum chromodynamics that can be implemented numerically. It has been estimated that a precision of two per cent would be possible by 2020 if two challenges are overcome 1,2 : contamination of g A from excited states must be controlled in the calculations and statistical precision must be improved markedly 2-10 . Here we use an unconventional method 11 inspired by the Feynman-Hellmann theorem that overcomes these challenges. We calculate a g A value of 1.271 ± 0.013, which has a precision of about one per cent.

Electrical Stimulation Decreases Coupling Efficiency Between Beta-Adrenergic Receptors and Cyclic AMP Production in Cultured Muscle Cells

NASA Technical Reports Server (NTRS)

Young, R. B.; Bridge, K. Y.

1999-01-01

Electrical stimulation of skeletal muscle cells in culture is an effective way to simulate the effects of muscle contraction and its effects on gene expression in muscle cells. Expression of the beta-adrenergic receptor and its coupling to cyclic AMP synthesis are important components of the signaling system that controls muscle atrophy and hypertrophy, and the goal of this project was to determine if electrical stimulation altered the beta-adrenergic response in muscle cells. Chicken skeletal muscle cells that had been grown for seven days in culture were subjected to electrical stimulation for an additional two days at a pulse frequency of 0.5 pulses/sec and a pulse duration of 200 msec. At the end of this two-day stimulation period, beta-adrenergic receptor population was measured by the binding of tritium-labeled CGP-12177 to muscle cells, and coupling to cAMP synthesis was measured by Radioimmunoassay (RIA) after treating the cells for 10 min with the potent (beta)AR agonist, isoproterenol. The number of beta adrenergic receptors and the basal levels of intracellular cyclic AMP were not affected by electrical stimulation. However, the ability of these cells to synthesize cyclic AMP was reduced by approximately 50%. Thus, an enhanced level of contraction reduces the coupling efficiency of beta-adrenergic receptors for cyclic AMP production.

Electrical Coupling between the Myenteric Interstitial Cells of Cajal and Adjacent Muscle Layers in the Guinea-Pig Gastric Antrum

PubMed Central

Cousins, H M; Edwards, F R; Hickey, H; Hill, C E; Hirst, G D S

2003-01-01

Intracellular recordings were made from short segments of the muscular wall of the guinea-pig gastric antrum. Preparations were impaled using two independent microelectrodes, one positioned in the circular layer and the other either in the longitudinal layer, in the network of myenteric interstitial cells of Cajal (ICCmy) or in the circular layer. Cells in each layer displayed characteristic patterns of rhythmical activity, with the largest signals being generated by ICCmy. Current pulses injected into the circular muscle layer produced electrotonic potentials in each cell layer, indicating that the layers are electrically interconnected. The amplitudes of these electrotonic potentials were largest in the circular layer and smallest in the longitudinal layer. An analysis of electrical coupling between the three layers suggests that although the cells in each layer are well coupled to neighbouring cells, the coupling between either muscle layer and the network of ICCmy is relatively poor. The electrical connections between ICCmy and the circular layer did not rectify. In parallel immunohistochemical studies, the distribution of the connexins Cx40, Cx43 and Cx45 within the antral wall was determined. Only Cx43 was detected; it was widely distributed on ICCmy and throughout the circular smooth muscle layer, being concentrated around ICCIM, but was less abundant in the circular muscle layer immediately adjacent to ICCmy. Although the electrophysiological studies indicate that smooth muscle cells in the longitudinal muscle layer are electrically coupled to each other, none of the connexins examined were detected in this layer. PMID:12844505

Coupled Kelvin-Helmholtz and Tearing Mode Instabilities at the Mercury's Magnetopause

NASA Astrophysics Data System (ADS)

Ivanovski, S. L.; Milillo, A.; Kartalev, M.; Massetti, S.

2018-05-01

A MHD approach for numerical simulations of coupled Kelvin-Helmholtz and tearing mode instabilities has been applied to Mercury’s magnetopause and used to perform a physical parameters study constrained by the MESSENGER data.

The Coupled Harmonic Oscillator: Not Just for Seniors Anymore.

ERIC Educational Resources Information Center

Preyer, Norris W.

1996-01-01

Presents experiments that use Microcomputer Based Laboratory (MBL) techniques to enable freshmen physics students to investigate complex systems, such as nonlinear oscillators or coupled harmonic oscillators, at a level appropriate for an independent project. (JRH)

Agreement on reporting acts of aggression in couples in a community sample.

PubMed

Cuenca Montesino, María L; Graña Gómez, José L

2018-05-01

Agreement about acts of aggression in couples on the Conflict Tactics Scales (CTS-2) was evaluated. We conducted a quota sampling method to recruit a community sample of 590 heterosexual adult couples from the Region of Madrid (Spain). Prevalence rates based on the maximum dyadic report identified more aggressive behaviors than did individual reports of perpetration and victimization in men and women. Partner agreement about physical and psychological aggression was significant and moderate. However, partners agreed that Negotiation of Conflicts and Positive Behaviors assessed with the Dyadic Adjustment Scale were higher than the behaviors of the Physical Assault Scale. Correction factors are provided to estimate the prevalence of aggressive behavior and injuries when we only had individual reports of aggression. Partner agreement reveals the existence of variables at the individual level that significantly influence the assessment of aggression in the couple.

Real-time photoacoustic flow cytography and photothermolysis of single circulating melanoma cells in vivo

NASA Astrophysics Data System (ADS)

He, Yun; Wang, Lidai; Shi, Junhui; Yao, Junjie; Li, Lei; Zhang, Ruiying; Huang, Chih-Hsien; Zou, Jun; Wang, Lihong V.

2017-03-01

Metastasis is responsible for as many as 90% of cancer-related deaths, and the deadliest skin cancer, melanoma, has a high propensity for metastasis. Since hematogenous spread of circulating tumor cells (CTCs) is cancer's main route of metastasis, detecting and destroying CTCs can impede metastasis and improve patients' prognoses. Extensive studies employing exogenous agents to detect tumor-specific biomarkers and guide therapeutics to CTCs have achieved promising results, but biosafety remains a critical concern. Taking another approach, physical detection and destruction of CTCs is a safer way to evaluate and reduce metastasis risks. Melanoma cells strongly express melanosomes, providing a striking absorption contrast with the blood background in the red to near-infrared spectrum. Exploiting this intrinsic optical absorption contrast of circulating melanoma cells, we coupled dual-wavelength photoacoustic flow cytography with a nanosecond-pulsed laser killing mechanism that specifically targets melanoma CTCs. We have successfully achieved in vivo label-free imaging of rare single CTCs and CTC clusters in mice. Further, the photoacoustic signal from a CTC immediately hardware-triggers a lethal pinpoint laser irradiation that lyses it on the spot in a thermally confined manner. Our technology can facilitate early inhibition of metastasis by clearing circulating tumor cells from vasculature.

Novel electrical energy storage system based on reversible solid oxide cells: System design and operating conditions

NASA Astrophysics Data System (ADS)

Wendel, C. H.; Kazempoor, P.; Braun, R. J.

2015-02-01

Electrical energy storage (EES) is an important component of the future electric grid. Given that no other widely available technology meets all the EES requirements, reversible (or regenerative) solid oxide cells (ReSOCs) working in both fuel cell (power producing) and electrolysis (fuel producing) modes are envisioned as a technology capable of providing highly efficient and cost-effective EES. However, there are still many challenges and questions from cell materials development to system level operation of ReSOCs that should be addressed before widespread application. This paper presents a novel system based on ReSOCs that employ a thermal management strategy of promoting exothermic methanation within the ReSOC cell-stack to provide thermal energy for the endothermic steam/CO2 electrolysis reactions during charging mode (fuel producing). This approach also serves to enhance the energy density of the stored gases. Modeling and parametric analysis of an energy storage concept is performed using a physically based ReSOC stack model coupled with thermodynamic system component models. Results indicate that roundtrip efficiencies greater than 70% can be achieved at intermediate stack temperature (680 °C) and elevated stack pressure (20 bar). The optimal operating condition arises from a tradeoff between stack efficiency and auxiliary power requirements from balance of plant hardware.

Enzymatically Cross-linked Alginic-Hyaluronic acid Composite Hydrogels As Cell Delivery Vehicles

PubMed Central

Ganesh, Nitya; Hanna, Craig; Nair, Shantikumar V.; Nair, Lakshmi S.

2013-01-01

An injectable composite gel was developed from alginic and hyaluronic acid. The ezymatically cross-linked injectable gels were prepared via the oxidative coupling of tyramine modified sodium algiante and sodium hyaluronate in the presence of horse radish peroxidase (HRP) and hydrogen peroxide (H2O2). The composite gels were prepared by mixing equal parts of the two tryaminated polymer solutions in 10U HRP and treating with 1.0% H2O2. The properties of the alginate gels were significanly affected by the addition of hyaluronic acid. The percentage water absorption and storage modulus of the composite gels were found to be lower than the alginate gels. The alginate and composite gels showed lower protein release compared to hyaluronate gels in the absence of hyaluronidase. Even hyaluronate gels showed only approximately 10% protein release after 14 days incubation in phosphate buffer solution. ATDC-5 cells encapsulated in the injectable gels showed high cell viability. The composite gels showed the presence of enlarged spherical cells with significantly higher metabolic activity compared to cells in hyaluronic and alginic acid gels. The results suggest the potential of the composite approach to develop covalently cross-linked hydrogels with tuneable physical, mechanical, and biological properties. PMID:23357799

Polymeric nanofibrous substrates stimulate pluripotent stem cells to form three-dimensional multilayered patty-like spheroids in feeder-free culture and maintain their pluripotency.

PubMed

Alamein, Mohammad A; Wolvetang, Ernst J; Ovchinnikov, Dmitry A; Stephens, Sebastien; Sanders, Katherine; Warnke, Patrick H

2015-09-01

Expansion of pluripotent stem cells in defined media devoid of animal-derived feeder cells to generate multilayered three-dimensional (3D) bulk preparations or spheroids, rather than two-dimensional (2D) monolayers, is advantageous for many regenerative, biological or disease-modelling studies. Here we show that electrospun polymer matrices comprised of nanofibres that mimic the architecture of the natural fibrous extracellular matrix allow for feeder-free expansion of pluripotent human induced pluripotent stem cells (IPSCs) and human embryonic stem cells (HESCs) into multilayered 3D 'patty-like' spheroid structures in defined xeno-free culture medium. The observation that IPSCs and HESCs readily revert to 2D growth in the absence of the synthetic nanofibre membranes suggests that this 3D expansion behaviour is mediated by the physical microenvironment and artificial niche provided by the nanofibres only. Importantly, we could show that such 3D growth as patties maintained the pluripotency of cells as long as they were kept on nanofibres. The generation of complex multilayered 3D structures consisting of only pluripotent cells on biodegradable nanofibre matrices of the desired shape and size will enable both industrial-scale expansion and intricate organ-tissue engineering applications with human pluripotent stem cells, where simultaneous coupling of differentiation pathways of all germ layers from one stem cell source may be required for organ formation. Copyright © 2014 John Wiley & Sons, Ltd.

Magnetic characterization of isolated candidate vertebrate magnetoreceptor cells

PubMed Central

Eder, Stephan H.K.; Cadiou, Hervé; Muhamad, Airina; McNaughton, Peter A.; Kirschvink, Joseph L.; Winklhofer, Michael

2012-01-01

Over the past 50 y, behavioral experiments have produced a large body of evidence for the existence of a magnetic sense in a wide range of animals. However, the underlying sensory physiology remains poorly understood due to the elusiveness of the magnetosensory structures. Here we present an effective method for isolating and characterizing potential magnetite-based magnetoreceptor cells. In essence, a rotating magnetic field is employed to visually identify, within a dissociated tissue preparation, cells that contain magnetic material by their rotational behavior. As a tissue of choice, we selected trout olfactory epithelium that has been previously suggested to host candidate magnetoreceptor cells. We were able to reproducibly detect magnetic cells and to determine their magnetic dipole moment. The obtained values (4 to 100 fAm2) greatly exceed previous estimates (0.5 fAm2). The magnetism of the cells is due to a μm-sized intracellular structure of iron-rich crystals, most likely single-domain magnetite. In confocal reflectance imaging, these produce bright reflective spots close to the cell membrane. The magnetic inclusions are found to be firmly coupled to the cell membrane, enabling a direct transduction of mechanical stress produced by magnetic torque acting on the cellular dipole in situ. Our results show that the magnetically identified cells clearly meet the physical requirements for a magnetoreceptor capable of rapidly detecting small changes in the external magnetic field. This would also explain interference of ac powerline magnetic fields with magnetoreception, as reported in cattle. PMID:22778440

An Elevation in Physical Coupling of Type 1 IP3 Receptors to TRPC3 Channels Constricts Mesenteric Arteries in Genetic Hypertension

PubMed Central

Adebiyi, Adebowale; Thomas-Gatewood, Candice M.; Leo, M. Dennis; Kidd, Michael W.; Neeb, Zachary P.; Jaggar, Jonathan H.

2013-01-01

Hypertension is associated with an elevation in agonist-induced vasoconstriction, but mechanisms involved require further investigation. Many vasoconstrictors bind to phospholipase C-coupled receptors, leading to an elevation in inositol 1,4,5-trisphosphate (IP3) that activates sarcoplasmic reticulum (SR) IP3 receptors (IP3Rs). In cerebral artery myocytes, IP3Rs release SR Ca2+ and can physically couple to canonical transient receptor potential 3 (TRPC3) channels in a caveolin-1-containing macromolecular complex, leading to cation current (ICat) activation that stimulates vasoconstriction. Here, we investigated mechanisms by which IP3Rs control vascular contractility in systemic arteries and IP3R involvement in elevated agonist-induced vasoconstriction during hypertension. Total and plasma membrane-localized TRPC3 protein was ~2.7- and 2-fold higher in mesenteric arteries of hypertensive spontaneously hypertensive rats (SHR) than in Wistar-Kyoto (WKY) rat controls, respectively. In contrast, IP3R1, TRPC1, TRPC6, and caveolin-1 expression was similar. TRPC3 expression was also similar in arteries of pre-hypertensive SHR and WKY rats. Control, IP3- and endothelin-1 (ET-1)-induced FRET between IP3R1 and TRPC3 was higher in hypertensive SHR than WKY myocytes. IP3-induced ICat was ~3-fold larger in SHR myocytes. Pyr3, a selective TRPC3 channel blocker, and CIRBP-TAT, an IP3R-TRP physical coupling inhibitor, reduced IP3-induced ICat and ET-1-induced vasoconstriction more in SHR than WKY myocytes and arteries. Thapsigargin, a SR Ca2+-ATPase blocker, did not alter ET-1-stimulated vasoconstriction in SHR or WKY arteries. These data indicate that ET-1 stimulates physical coupling of IP3R1 to TRPC3 channels in mesenteric artery myocytes, leading to vasoconstriction. Furthermore, an elevation in IP3R1 to TRPC3 channel molecular coupling augments ET-1-induced vasoconstriction during hypertension. PMID:23045459

NASA's space physics theory program - An opportunity for collaboration

NASA Technical Reports Server (NTRS)

Vinas, Adolfo F.

1990-01-01

The field of theoretical space physics offers a unique opportunity to Latin American scientists for collaborative participation in NASA programs where the greatly increased complexity of both experimental observations and theoretical simulations requires in-depth comparisons between theory and observational data. The key problem areas identified by NASA for aggressive work in the decade of the 1990s are the nature of flows and turbulence, acceleration and transport of particles, the coupling of microphysics and macrophysics, the coupling of local and global dynamics, and nonclassical plasmas.

Grating-assisted surface acoustic wave directional couplers

NASA Astrophysics Data System (ADS)

Golan, G.; Griffel, G.; Seidman, A.; Croitoru, N.

1991-07-01

Physical properties of novel grating-assisted Y directional couplers are examined using the coupled-mode theory. A general formalism for the analysis of the lateral perturbed directional coupler properties is presented. Explicit expressions for waveguide key parameters such as coupling length, grating period, and other structural characterizations, are obtained. The influence of other physical properties such as time and frequency response or cutoff conditions are also analyzed. A plane grating-assisted directional coupler is presented and examined as a basic component in the integrated acoustic technology.

Lattice QCD studies on baryon interactions in the strangeness -2 sector with physical quark masses

NASA Astrophysics Data System (ADS)

Sasaki, Kenji; Aoki, Sinya; Doi, Takumi; Gongyo, Shinya; Hatsuda, Tetsuo; Ikeda, Yoichi; Inoue, Takashi; Iritani, Takumi; Ishii, Noriyoshi; Miyamoto, Takaya

2018-03-01

We investigate baryon-baryon (BB) interactions in the strangeness S = -2 sector via the coupled-channel HAL QCD method which enables us to extract the scattering observables from Nambu-Bethe-Salpeter (NBS) wave function on the lattice. The simulations are performed with (almost) physical quark masses (mπ = 146MeV) and a huge lattice volume of La = 8.1fm. We discuss the fate of H-dibaryon state through the ΛΛ and NΞ coupled-channel scatterings

Patterns of synchrony for feed-forward and auto-regulation feed-forward neural networks.

PubMed

Aguiar, Manuela A D; Dias, Ana Paula S; Ferreira, Flora

2017-01-01

We consider feed-forward and auto-regulation feed-forward neural (weighted) coupled cell networks. In feed-forward neural networks, cells are arranged in layers such that the cells of the first layer have empty input set and cells of each other layer receive only inputs from cells of the previous layer. An auto-regulation feed-forward neural coupled cell network is a feed-forward neural network where additionally some cells of the first layer have auto-regulation, that is, they have a self-loop. Given a network structure, a robust pattern of synchrony is a space defined in terms of equalities of cell coordinates that is flow-invariant for any coupled cell system (with additive input structure) associated with the network. In this paper, we describe the robust patterns of synchrony for feed-forward and auto-regulation feed-forward neural networks. Regarding feed-forward neural networks, we show that only cells in the same layer can synchronize. On the other hand, in the presence of auto-regulation, we prove that cells in different layers can synchronize in a robust way and we give a characterization of the possible patterns of synchrony that can occur for auto-regulation feed-forward neural networks.

Architecture and inherent robustness of a bacterial cell-cycle control system.

PubMed

Shen, Xiling; Collier, Justine; Dill, David; Shapiro, Lucy; Horowitz, Mark; McAdams, Harley H

2008-08-12

A closed-loop control system drives progression of the coupled stalked and swarmer cell cycles of the bacterium Caulobacter crescentus in a near-mechanical step-like fashion. The cell-cycle control has a cyclical genetic circuit composed of four regulatory proteins with tight coupling to processive chromosome replication and cell division subsystems. We report a hybrid simulation of the coupled cell-cycle control system, including asymmetric cell division and responses to external starvation signals, that replicates mRNA and protein concentration patterns and is consistent with observed mutant phenotypes. An asynchronous sequential digital circuit model equivalent to the validated simulation model was created. Formal model-checking analysis of the digital circuit showed that the cell-cycle control is robust to intrinsic stochastic variations in reaction rates and nutrient supply, and that it reliably stops and restarts to accommodate nutrient starvation. Model checking also showed that mechanisms involving methylation-state changes in regulatory promoter regions during DNA replication increase the robustness of the cell-cycle control. The hybrid cell-cycle simulation implementation is inherently extensible and provides a promising approach for development of whole-cell behavioral models that can replicate the observed functionality of the cell and its responses to changing environmental conditions.

Microwave-Assisted Synthesis of a MK2 Inhibitor by Suzuki-Miyaura Coupling for Study in Werner Syndrome Cells

PubMed Central

Bagley, Mark C.; Baashen, Mohammed; Chuckowree, Irina; Dwyer, Jessica E.; Kipling, David; Davis, Terence

2015-01-01

Microwave-assisted Suzuki-Miyaura cross-coupling reactions have been employed towards the synthesis of three different MAPKAPK2 (MK2) inhibitors to study accelerated aging in Werner syndrome (WS) cells, including the cross-coupling of a 2-chloroquinoline with a 3-pyridinylboronic acid, the coupling of an aryl bromide with an indolylboronic acid and the reaction of a 3-amino-4-bromopyrazole with 4-carbamoylphenylboronic acid. In all of these processes, the Suzuki-Miyaura reaction was fast and relatively efficient using a palladium catalyst under microwave irradiation. The process was incorporated into a rapid 3-step microwave-assisted method for the synthesis of a MK2 inhibitor involving 3-aminopyrazole formation, pyrazole C-4 bromination using N-bromosuccinimide (NBS), and Suzuki-Miyaura cross-coupling of the pyrazolyl bromide with 4-carbamoylphenylboronic acid to give the target 4-arylpyrazole in 35% overall yield, suitable for study in WS cells. PMID:26046488

Coupling molecular dynamics with lattice Boltzmann method based on the immersed boundary method

NASA Astrophysics Data System (ADS)

Tan, Jifu; Sinno, Talid; Diamond, Scott

2017-11-01

The study of viscous fluid flow coupled with rigid or deformable solids has many applications in biological and engineering problems, e.g., blood cell transport, drug delivery, and particulate flow. We developed a partitioned approach to solve this coupled Multiphysics problem. The fluid motion was solved by Palabos (Parallel Lattice Boltzmann Solver), while the solid displacement and deformation was simulated by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The coupling was achieved through the immersed boundary method (IBM). The code modeled both rigid and deformable solids exposed to flow. The code was validated with the classic problem of rigid ellipsoid particle orbit in shear flow, blood cell stretching test and effective blood viscosity, and demonstrated essentially linear scaling over 16 cores. An example of the fluid-solid coupling was given for flexible filaments (drug carriers) transport in a flowing blood cell suspensions, highlighting the advantages and capabilities of the developed code. NIH 1U01HL131053-01A1.

Parvalbumin-positive interneurons mediate neocortical-hippocampal interactions that are necessary for memory consolidation

PubMed Central

Xia, Frances; Richards, Blake A; Tran, Matthew M; Josselyn, Sheena A

2017-01-01

Following learning, increased coupling between spindle oscillations in the medial prefrontal cortex (mPFC) and ripple oscillations in the hippocampus is thought to underlie memory consolidation. However, whether learning-induced increases in ripple-spindle coupling are necessary for successful memory consolidation has not been tested directly. In order to decouple ripple-spindle oscillations, here we chemogenetically inhibited parvalbumin-positive (PV+) interneurons, since their activity is important for regulating the timing of spiking activity during oscillations. We found that contextual fear conditioning increased ripple-spindle coupling in mice. However, inhibition of PV+ cells in either CA1 or mPFC eliminated this learning-induced increase in ripple-spindle coupling without affecting ripple or spindle incidence. Consistent with the hypothesized importance of ripple-spindle coupling in memory consolidation, post-training inhibition of PV+ cells disrupted contextual fear memory consolidation. These results indicate that successful memory consolidation requires coherent hippocampal-neocortical communication mediated by PV+ cells. PMID:28960176

Simulations of coupled, Antarctic ice-ocean evolution using POP2x and BISICLES (Invited)

NASA Astrophysics Data System (ADS)

Price, S. F.; Asay-Davis, X.; Martin, D. F.; Maltrud, M. E.; Hoffman, M. J.

2013-12-01

We present initial results from Antarctic, ice-ocean coupled simulations using large-scale ocean circulation and land ice evolution models. The ocean model, POP2x is a modified version of POP, a fully eddying, global-scale ocean model (Smith and Gent, 2002). POP2x allows for circulation beneath ice shelf cavities using the method of partial top cells (Losch, 2008). Boundary layer physics, which control fresh water and salt exchange at the ice-ocean interface, are implemented following Holland and Jenkins (1999), Jenkins (1999), and Jenkins et al. (2010). Standalone POP2x output compares well with standard ice-ocean test cases (e.g., ISOMIP; Losch, 2008; Kimura et al., 2013) and with results from other idealized ice-ocean coupling test cases (e.g., Goldberg et al., 2012). The land ice model, BISICLES (Cornford et al., 2012), includes a 1st-order accurate momentum balance (L1L2) and uses block structured, adaptive-mesh refinement to more accurately model regions of dynamic complexity, such as ice streams, outlet glaciers, and grounding lines. For idealized test cases focused on marine-ice sheet dynamics, BISICLES output compares very favorably relative to simulations based on the full, nonlinear Stokes momentum balance (MISMIP-3d; Pattyn et al., 2013). Here, we present large-scale (southern ocean) simulations using POP2x with fixed ice shelf geometries, which are used to obtain and validate modeled submarine melt rates against observations. These melt rates are, in turn, used to force evolution of the BISICLES model. An offline-coupling scheme, which we compare with the ice-ocean coupling work of Goldberg et al. (2012), is then used to sequentially update the sub-shelf cavity geometry seen by POP2x.

Physical biology in cancer. 4. Physical cues guide tumor cell adhesion and migration.

PubMed

Stroka, Kimberly M; Konstantopoulos, Konstantinos

2014-01-15

As tumor cells metastasize from the primary tumor location to a distant secondary site, they encounter an array of biologically and physically heterogeneous microenvironments. While it is well established that biochemical signals guide all stages of the metastatic cascade, mounting evidence indicates that physical cues also direct tumor cell behavior, including adhesion and migration phenotypes. Physical cues acting on tumor cells in vivo include extracellular matrix mechanical properties, dimensionality, and topography, as well as interstitial flow, hydrodynamic shear stresses, and local forces due to neighboring cells. State-of-the-art technologies have recently enabled us and other researchers to engineer cell microenvironments that mimic specific physical properties of the cellular milieu. Through integration of these engineering strategies, along with physics, molecular biology, and imaging techniques, we have acquired new insights into tumor cell adhesion and migration mechanisms. In this review, we focus on the extravasation and invasion stages of the metastatic cascade. We first discuss the physical role of the endothelium during tumor cell extravasation and invasion and how contractility of endothelial and tumor cells contributes to the ability of tumor cells to exit the vasculature. Next, we examine how matrix dimensionality and stiffness coregulate tumor cell adhesion and migration beyond the vasculature. Finally, we summarize how tumor cells translate and respond to physical cues through mechanotransduction. Because of the critical role of tumor cell mechanotransduction at various stages of the metastatic cascade, targeting signaling pathways involved in tumor cell mechanosensing of physical stimuli may prove to be an effective therapeutic strategy for cancer patients.

Administration of sulfosuccinimidyl-4-[N-maleimidomethyl] cyclohexane-1-carboxylate conjugated GP100{sub 25–33} peptide-coupled spleen cells effectively mounts antigen-specific immune response against mouse melanoma

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

Chang, Xiaoli; Xia, Chang-Qing, E-mail: cqx65@yahoo.com; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL32610

It remains a top research priority to develop immunotherapeutic approaches to induce potent antigen-specific immune responses against tumors. However, in spite of some promising results, most strategies are ineffective because they generate low numbers of tumor-reactive cytotoxic T lymphocytes (CTLs). Here we designed a strategy to enhance antigen-specific immune response via administering sulfosuccinimidyl-4-[N-maleimidomethyl] cyclohexane-1-carboxylate (sulfo-SMCC)-conjugated melanoma tumor antigen GP100{sub 25–33} peptide-coupled syngeneic spleen cells in a mouse model of melanoma. We found that infusion of GP100{sub 25–33} peptide-coupled spleen cells significantly attenuated the growth of melanoma in prophylactic and therapeutic immunizations. Consistent with these findings, the adoptive transfer of spleenmore » cells from immunized mice to naïve syngeneic mice was able to transfer anti-tumor effect, suggesting that GP100{sub 25–33} peptide-specific immune response was induced. Further studies showed that, CD8+ T cell proliferation and the frequency of interferon (IFN)-γ-producing CD8+ T cells upon ex vivo stimulation by GP100{sub 25–33} were significantly increased compared to control groups. Tumor antigen, GP100{sub 25–23} specific immune response was also confirmed by ELISpot and GP100-tetramer assays. This approach is simple, easy-handled, and efficiently delivering antigens to lymphoid tissues. Our study offers an opportunity for clinically translating this approach into tumor immunotherapy. - Highlights: • Infusion of GP100{sub 25–33}-coupled spleen cells leads to potent anti-melanoma immunity. • GP100{sub 25–33}-coupled spleen cell treatment induces antigen-specific IFN-γ-producing CD8 T cells. • This approach takes advantage of homing nature of immune cells.« less

Inhibition of cadmium ion uptake in rice (Oryza sativa) cells by a wall-bound form of silicon.

PubMed

Liu, Jian; Ma, Jie; He, Congwu; Li, Xiuli; Zhang, Wenjun; Xu, Fangsen; Lin, Yongjun; Wang, Lijun

2013-11-01

The stresses acting on plants that are alleviated by silicon (Si) range from biotic to abiotic stresses, such as heavy metal toxicity. However, the mechanism of stress alleviation by Si at the single-cell level is poorly understood. We cultivated suspended rice (Oryza sativa) cells and protoplasts and investigated them using a combination of plant nutritional and physical techniques including inductively coupled plasma mass spectrometry (ICP-MS), the scanning ion-selective electrode technique (SIET) and X-ray photoelectron spectroscopy (XPS). We found that most Si accumulated in the cell walls in a wall-bound organosilicon compound. Total cadmium (Cd) concentrations in protoplasts from Si-accumulating (+Si) cells were significantly reduced at moderate concentrations of Cd in the culture medium compared with those from Si-limiting (-Si) cells. In situ measurement of cellular fluxes of the cadmium ion (Cd(2+) ) in suspension cells and root cells of rice exposed to Cd(2+) and/or Si treatments showed that +Si cells significantly inhibited the net Cd(2+) influx, compared with that in -Si cells. Furthermore, a net negative charge (charge density) within the +Si cell walls could be neutralized by an increase in the Cd(2+) concentration in the measuring solution. A mechanism of co-deposition of Si and Cd in the cell walls via a [Si-wall matrix]Cd co-complexation may explain the inhibition of Cd ion uptake, and may offer a plausible explanation for the in vivo detoxification of Cd in rice. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Modeling extracellular fields for a three-dimensional network of cells using NEURON.

PubMed

Appukuttan, Shailesh; Brain, Keith L; Manchanda, Rohit

2017-10-01

Computational modeling of biological cells usually ignores their extracellular fields, assuming them to be inconsequential. Though such an assumption might be justified in certain cases, it is debatable for networks of tightly packed cells, such as in the central nervous system and the syncytial tissues of cardiac and smooth muscle. In the present work, we demonstrate a technique to couple the extracellular fields of individual cells within the NEURON simulation environment. The existing features of the simulator are extended by explicitly defining current balance equations, resulting in the coupling of the extracellular fields of adjacent cells. With this technique, we achieved continuity of extracellular space for a network model, thereby allowing the exploration of extracellular interactions computationally. Using a three-dimensional network model, passive and active electrical properties were evaluated under varying levels of extracellular volumes. Simultaneous intracellular and extracellular recordings for synaptic and action potentials were analyzed, and the potential of ephaptic transmission towards functional coupling of cells was explored. We have implemented a true bi-domain representation of a network of cells, with the extracellular domain being continuous throughout the entire model. This has hitherto not been achieved using NEURON, or other compartmental modeling platforms. We have demonstrated the coupling of the extracellular field of every cell in a three-dimensional model to obtain a continuous uniform extracellular space. This technique provides a framework for the investigation of interactions in tightly packed networks of cells via their extracellular fields. Copyright © 2017 Elsevier B.V. All rights reserved.