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Sample records for cancer dynamic interface

  1. Molecular dynamics of interface rupture

    Science.gov (United States)

    Koplik, Joel; Banavar, Jayanth R.

    1993-01-01

    Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.

  2. Experiments showing dynamics of materials interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Benjamin, R.F. [Los Alamos National Lab., NM (United States). Dynamic Experimentation Div.

    1997-02-01

    The discipline of materials science and engineering often involves understanding and controlling properties of interfaces. The authors address the challenge of educating students about properties of interfaces, particularly dynamic properties and effects of unstable interfaces. A series of simple, inexpensive, hands-on activities about fluid interfaces provides students with a testbed to develop intuition about interface dynamics. The experiments highlight the essential role of initial interfacial perturbations in determining the dynamic response of the interface. The experiments produce dramatic, unexpected effects when initial perturbations are controlled and inhibited. These activities help students to develop insight about unstable interfaces that can be applied to analogous problems in materials science and engineering. The lessons examine ``Rayleigh-Taylor instability,`` an interfacial instability that occurs when a higher-density fluid is above a lower-density fluid.

  3. Molecular Dynamics Simulations of Interface Failure

    Science.gov (United States)

    Bachlechner, Martina E.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Swan, Wm. Trevor, III; Ducatman, Samuel C.

    2007-03-01

    The mechanical integrity of silicon/silicon nitride interfaces is of great importance in their applications in micro electronics and solar cells. Large-scale molecular dynamics simulations are an excellent tool to study mechanical and structural failure of interfaces subjected to externally applied stresses and strains. When pulling the system parallel to the interface, cracks in silicon nitride and slip and pit formation in silicon are typical failure mechanisms. Hypervelocity impact perpendicular to the interface plane leads to structural transformation and delamination at the interface. Influence of system temperature, strain rate, impact velocity, and system size on type and characteristics of failure will be discussed.

  4. User Interface Design For Dynamic Geometry Software

    Directory of Open Access Journals (Sweden)

    Ulrich Kortenkamp

    2010-06-01

    Full Text Available In this article we describe long-standing user interface issues with Dynamic Geometry Software and common approaches to address them. We describe first prototypes of multi-touch-capable DGS. We also give some hints on the educational benefits of proper user interface design.

  5. The dynamics of foams with mobile interfaces

    Science.gov (United States)

    Gratton, Michael B.; Davis, Stephen H.

    2011-11-01

    Using a novel technique for resolving nearly singular integrals, we investigate the dynamics of two-dimensional foams with mobile interfaces and an incompressible, inviscid gas phase by a boundary integral method. For foams with small liquid fractions (CMMI-0826703.

  6. DHMI: dynamic holographic microscopy interface

    Science.gov (United States)

    He, Xuefei; Zheng, Yujie; Lee, Woei Ming

    2016-12-01

    Digital holographic microscopy (DHM) is a powerful in-vitro biological imaging tool. In this paper, we report a fully automated off-axis digital holographic microscopy system completed with a graphical user interface in the Matlab environment. The interface primarily includes Fourier domain processing, phase reconstruction, aberration compensation and autofocusing. A variety of imaging operations such as region of interest selection, de-noising mode (filtering and averaging), low frame rate imaging for immediate reconstruction and high frame rate imaging routine ( 27 fps) are implemented to facilitate ease of use.

  7. Dynamically Generated Interfaces in XML Based Architecture

    CERN Document Server

    Gupta, Minit

    2009-01-01

    Providing on-line services on the Internet will require the definition of flexible interfaces that are capable of adapting to the user's characteristics. This is all the more important in the context of medical applications like home monitoring, where no two patients have the same medical profile. Still, the problem is not limited to the capacity of defining generic interfaces, as has been made possible by UIML, but also to define the underlying information structures from which these may be generated. The DIATELIC project deals with the tele-monitoring of patients under peritoneal dialysis. By means of XML abstractions, termed as "medical components", to represent the patient's profile, the application configures the customizable properties of the patient's interface and generates a UIML document dynamically. The interface allows the patient to feed the data manually or use a device which allows "automatic data acquisition". The acquired medical data is transferred to an expert system, which analyses the dat...

  8. Dynamics of swimming bacteria at complex interfaces

    CERN Document Server

    Lopez, Diego

    2014-01-01

    Flagellated bacteria exploiting helical propulsion are known to swim along circular trajectories near surfaces. Fluid dynamics predicts this circular motion to be clockwise (CW) above a rigid surface (when viewed from inside the fluid) and counter-clockwise (CCW) below a free surface. Recent experimental investigations showed that complex physicochemical processes at the nearby surface could lead to a change in the direction of rotation, both at solid surfaces absorbing slip-inducing polymers and interfaces covered with surfactants. Motivated by these results, we use a far-field hydrodynamic model to predict the kinematics of swimming near three types of interfaces: clean fluid-fluid interface, slipping rigid wall, and a fluid interface covered by incompressible surfactants. Representing the helical swimmer by a superposition of hydrodynamic singularities, we first show that in all cases the surfaces reorient the swimmer parallel to the surface and attract it, both of which are a consequence of the Stokes dip...

  9. Dynamic Morphologies of Microscale Droplet Interface Bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Mruetusatorn, Prachya [ORNL; Boreyko, Jonathan B [ORNL; Sarles, Stephen A [ORNL; Venkatesan, Guru [The University of Tennessee; Hayes, Douglas G [ORNL; Collier, Pat [ORNL

    2014-01-01

    Droplet interface bilayers (DIBs) are a powerful platform for studying the dynamics of synthetic cellular membranes; however, very little has been done to exploit the unique dynamical features of DIBs. Here, we generate microscale droplet interface bilayers ( DIBs) by bringing together femtoliter-volume water droplets in a microfluidic oil channel, and characterize morphological changes of the DIBs as the droplets shrink due to evaporation. By varying the initial conditions of the system, we identify three distinct classes of dynamic morphology. (1) Buckling and Fission: When forming DIBs using the lipid-out method (lipids in oil phase), lipids in the shrinking monolayers continually pair together and slide into the bilayer to conserve their mass. As the bilayer continues to grow, it becomes confined, buckles, and eventually fissions one or more vesicles. (2) Uniform Shrinking: When using the lipid-in method (lipids in water phase) to form DIBs, lipids uniformly transfer from the monolayers and bilayer into vesicles contained inside the water droplets. (3) Stretching and Unzipping: Finally, when the droplets are pinned to the wall(s) of the microfluidic channel, the droplets become stretched during evaporation, culminating in the unzipping of the bilayer and droplet separation. These findings offer a better understanding of the dynamics of coupled lipid interfaces.

  10. Dynamic actuation using nano-bio interfaces

    Directory of Open Access Journals (Sweden)

    Ian Y. Wong

    2010-06-01

    Full Text Available The nanoscale dimensions, sensitive electronic control, and flexible architecture of new generations of nanomaterials and nanofabrication techniques hold immense promise not only for electronic devices, but also biological interfaces. As the size scales of these materials approach biological species, interfaces with characteristics designed to emulate their nanoscale biological counterparts are becoming possible. These new systems have higher biocompatibility, functionality, and lower cell toxicity than their microscale predecessors. While stellar examples have been demonstrated for biomolecular detection and imaging, exciting new possibilities for long-term integration and dynamic stimulation are now emerging, including protein activation, membrane integration and intracellular delivery. These tailored interfaces may lead to improved regenerative medicine, gene therapy and neural prosthetics.

  11. A Natural-Product Switch for a Dynamic Protein Interface

    NARCIS (Netherlands)

    Scheepstra, Marcel; Nieto, Lidia; Hirsch, Anna K. H.; Fuchs, Sascha; Leysen, Seppe; Vinh Lam, Chan; Panhuis, Leslie In Het; van Boeckel, Constant A. A.; Wienk, Hans; Boelens, Rolf; Ottmann, Christian; Milroy, Lech-Gustav; Brunsveld, Luc

    2014-01-01

    Small ligands are a powerful way to control the function of protein complexes via dynamic binding interfaces. The classic example is found in gene transcription where small ligands regulate nuclear receptor binding to coactivator proteins via the dynamic activation function 2 (AF2) interface. Curren

  12. A natural-product switch for a dynamic protein interface

    NARCIS (Netherlands)

    Scheepstra, Marcel; Nieto, Lidia; Hirsch, Anna K H; Fuchs, Sascha; Leysen, Seppe; Lam, Chan Vinh; In Het Panhuis, Leslie; Van Boeckel, Constant A A; Wienk, Hans; Boelens, Rolf; Ottmann, Christian; Milroy, Lech Gustav; Brunsveld, Luc

    2014-01-01

    Small ligands are a powerful way to control the function of protein complexes via dynamic binding interfaces. The classic example is found in gene transcription where small ligands regulate nuclear receptor binding to coactivator proteins via the dynamic activation function 2 (AF2) interface. Curren

  13. Hypervelocity Impact on Interfaces: A Molecular-Dynamics Simulations Study

    Science.gov (United States)

    Bachlechner, Martina E.; Owens, Eli T.; Leonard, Robert H.; Cockburn, Bronwyn C.

    2008-03-01

    Silicon/silicon nitride interfaces are found in micro electronics and solar cells. In either application the mechanical integrity of the interface is of great importance. Molecular-dynamics simulations are performed to study the failure of interface materials under the influence of hypervelocity impact. Silicon nitride plates impacting on silicon/silicon nitride interface targets of different thicknesses result in structural phase transformation and delamination at the interface. Detailed analyses of atomic velocities, bond lengths, and bond angles are used to qualitatively examine the respective failure mechanisms.

  14. Dynamics of the YSZ-Pt Interface

    DEFF Research Database (Denmark)

    Bay, Lasse; Jacobsen, Torben

    1997-01-01

    Yttria stabilized zirconia (YSZ)-Pt point electrodes were examined by linear potential sweep, potential step and impedance measurements at 1000 degrees C in air. Inductive loops and hysteresis phenomena with long relaxation times were found. Atomic force microscopy showed changes of the interface...... between Pt and YSZ induced by the current passage. These changes involve transport of solid and are slow enough to explain the large time constants. The low frequency capacitance and inductive loop forming an entire circle indicate the presence of gas reservoirs at the YSZ-Pt interface....

  15. Dynamics of Complex Fluid-Fluid Interfaces

    NARCIS (Netherlands)

    Sagis, L.M.C.

    2016-01-01

    This chapter presents an overview of recent progress in modelling the behaviour of complex fluid–fluid interfaces with non-equilibrium thermodynamics. We will limit ourselves to frameworks employing the Gibbs dividing surface model, and start with a general discussion of the surface excess variables

  16. Agent-based Multimodal Interface for Dynamically Autonomous Mobile Robots

    Science.gov (United States)

    2003-01-01

    Agent-based Multimodal Interface for Dynamically Autonomous Mobile Robots Donald Sofge, Magdalena Bugajska, William Adams, Dennis...computing paradigm for integrated distributed artificial intelligence systems on autonomous mobile robots (Figure 1). Figure 1 – CoABS Grid...Architecture for Dynamically Autonomous Mobile Robots The remainder of the paper is organized as follows. Section 2 describes our integrated AI

  17. Polymer dynamics in nanoconfinement: Interfaces and interphases

    Directory of Open Access Journals (Sweden)

    Krutyeva Margarita

    2015-01-01

    Full Text Available The dynamics of polymers in nanoconfinement was studied by using neutron spectroscopy. A number of pronounced effects on different time and length scales for the polymers confined in nanopores of anodic aluminium oxide were observed. Local segmental dynamics was found to be dependent on the type of the interaction between the solid pore wall and polymer: attractive interactions lead to the formation of a surface layer with the dynamics slowed down as compared to the dynamics of pure polymer; neutral/repulsive interaction do not change the local dynamics. Attractive interactions cause anchoring of polymer segments on the surface creating an interphase between the polymer in close vicinity to the solid surface and pure polymer. In addition, at strong confinement conditions the dilution of the entanglement network is observed.

  18. Ultrafast excited-state dynamics at interfaces: fluorescent DNA probes at the dodecane/water interface

    Science.gov (United States)

    Licari, Giuseppe; Vauthey, Eric

    2015-08-01

    Although the interfaces between two isotropic media are of primary importance in many areas of science and technology, their properties are only partially understood. Our strategy to obtain an insight into these properties is to investigate the ultrafast excited-state dynamics of environment-sensitive molecular probes at liquid interfaces using time-resolved surface second harmonic generation, and to compare it with the dynamics of the same molecules in bulk solutions. Additionally, this approach gives rich information on how the chemical reactivity may change when going from the bulk phase to the interface. This is illustrated by an investigation performed with a series of fluorescent DNA probes at the dodecane/water interface without and with the presence of DNA in the aqueous phase. Substantial differences in the conformation of these cyanine dyes (aggregated or not) and in the excited-state dynamics are observed when going from bulk solutions to the interface. Moreover, the presence of double-stranded DNA in the aqueous phase induces some chirality at the interface.

  19. Oxide Interfaces: emergent structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Clarke, Roy [Univ. of Michigan, Ann Arbor, MI (United States)

    2016-08-16

    This Final Report describes the scientific accomplishments that have been achieved with support from grant DE-FG02-06ER46273 during the period 6/1/2012– 5/31/2016. The overall goals of this program were focused on the behavior of epitaxial oxide heterostructures at atomic length scales (Ångstroms), and correspondingly short time-scales (fs -ns). The results contributed fundamentally to one of the currently most active frontiers in condensed matter physics research, namely to better understand the intricate relationship between charge, lattice, orbital and spin degrees of freedom that are exhibited by complex oxide heterostructures. The findings also contributed towards an important technological goal which was to achieve a better basic understanding of structural and electronic correlations so that the unusual properties of complex oxides can be exploited for energy-critical applications. Specific research directions included: probing the microscopic behavior of epitaxial interfaces and buried layers; novel materials structures that emerge from ionic and electronic reconfiguration at epitaxial interfaces; ultrahigh-resolution mapping of the atomic structure of heterointerfaces using synchrotron-based x-ray surface scattering, including direct methods of phase retrieval; using ultrafast lasers to study the effects of transient strain on coherent manipulation of multi-ferroic order parameters; and investigating structural ordering and relaxation processes in real-time.

  20. Numerical simulation of particle dynamics at a fluid interface

    Science.gov (United States)

    Yue, Pengtao

    2016-11-01

    Particles straddling a fluid interface exhibit rich dynamics due to the coexistence of moving boundaries, fluid interfaces, and moving contact lines. For instance, as a particle falls onto a liquid surface, it may sink, float, or even bounce off depending on a wide range of parameters. To better understand the dynamics of such a multiphase system, we develop a finite-element based arbitrary Lagrangian-Eulerian-phase-field method. The governing equations for particles and fluids are solved in a unified variational framework that satisfies an energy law. We first validate our code by computing three problems found in literature: sinking of a horizontal cylinder through an air-water interface, sinking of a sphere through an air-oil interface at small Reynolds numbers, and bouncing of a sphere after its normal impact onto an air-water interface. Our numerical results show good agreements with experimental data. We then investigate the effect of wetting properties, including static contact angle, slip length, and wall energy relaxation, on particle dynamics at the fluid interface. This work is supported by NSF DMS-1522604.

  1. Dynamic interface pressure distributions of two transtibial prosthetic socket concepts.

    Science.gov (United States)

    Dumbleton, Tim; Buis, Arjan W P; McFadyen, Angus; McHugh, Brendan F; McKay, Geoff; Murray, Kevin D; Sexton, Sandra

    2009-01-01

    In this study, we investigated and compared the dynamic interface pressure distribution of hands-off and hands-on transtibial prosthetic systems by means of pressure mapping. Of the 48 established unilateral amputees recruited, half (n = 24) had been wearing pressure-cast prostheses (IceCast Compact) and the other half (n = 24) had been wearing hand-cast sockets of the patellar tendon bearing design. We measured the dynamic pressure profile of more than 90% of the area within each prosthetic socket by means of four Tekscan F-Scan socket transducer arrays. We compared the interface pressure between socket concepts. We found that the distribution of dynamic pressure at the limb-socket interface was similar for the two intervention (socket prescription) groups. However, a significant difference was found in the magnitude of the interface pressure between the two socket concepts; the interface pressures recorded in the hands-off sockets were higher than those seen in the hands-on concept. Despite the differences in interface pressure, the level of satisfaction with the sockets was similar between subject groups. The sockets instrumented for this study had been in daily use for at least 6 months, with no residual-limb health problems.

  2. New and general framework for adsorption processes on dynamic interfaces

    CERN Document Server

    Schmuck, Markus

    2013-01-01

    We introduce a new and general continuum thermodynamic framework for the mathematical analysis and computation of adsorption on dynamic interfaces. To the best of our knowledge, there is no formulation available that accounts for the coupled dynamics of interfaces and densities of adsorbants. Our framework leads to analytic adsorption isotherms which also take the interfacial geometry fully into account. We demonstrate the utility and physical consistency of our framework with a new computational multi-level discretization strategy. In the computations, we recover the experimentally observed feature that the adsorption of particles minimizes the interfacial tension.

  3. Ecohydrological Interfaces as Dynamic Hotspots of Biogeochemical Cycling

    Science.gov (United States)

    Krause, Stefan; Lewandowski, Joerg; Hannah, David; McDonald, Karlie; Folegot, Silvia; Baranov, Victor

    2016-04-01

    . Our results furthermore indicate that to fully understand spatial patterns and temporal dynamics of ecohydrological interface functioning, including hotspots and hot moments, detailed knowledge of the impacts of biological behavior on the physic-chemical ecosystem conditions, and vice-versa, is required.

  4. The Global Cancer Genomics Consortium: interfacing genomics and cancer medicine.

    Science.gov (United States)

    2012-08-01

    The Global Cancer Genomics Consortium (GCGC) is an international collaborative platform that amalgamates cancer biologists, cutting-edge genomics, and high-throughput expertise with medical oncologists and surgical oncologists; they address the most important translational questions that are central to cancer research and treatment. The annual GCGC symposium was held at the Advanced Centre for Treatment Research and Education in Cancer, Mumbai, India, from November 9 to 11, 2011. The symposium showcased international next-generation sequencing efforts that explore cancer-specific transcriptomic changes, single-nucleotide polymorphism, and copy number variations in various types of cancers, as well as the structural genomics approach to develop new therapeutic targets and chemical probes. From the spectrum of studies presented at the symposium, it is evident that the translation of emerging cancer genomics knowledge into clinical applications can only be achieved through the integration of multidisciplinary expertise. In summary, the GCGC symposium provided practical knowledge on structural and cancer genomics approaches, as well as an exclusive platform for focused cancer genomics endeavors.

  5. Nanoparticles at liquid interfaces: Rotational dynamics and angular locking

    Energy Technology Data Exchange (ETDEWEB)

    Razavi, Sepideh; Kretzschmar, Ilona [Department of Chemical Engineering, City College of City University of New York, New York, New York 10031 (United States); Koplik, Joel [Department of Physics and The Benjamin Levich Institute for Physico-chemical Hydrodynamics, City College of City University of New York, New York, New York 10031 (United States); Colosqui, Carlos E., E-mail: carlos.colosqui@stonybrook.edu [Department of Mechanical Engineering, Stony Brook University, Stony Brook, New York 11794 (United States)

    2014-01-07

    Nanoparticles with different surface morphologies that straddle the interface between two immiscible liquids are studied via molecular dynamics simulations. The methodology employed allows us to compute the interfacial free energy at different angular orientations of the nanoparticle. Due to their atomistic nature, the studied nanoparticles present both microscale and macroscale geometrical features and cannot be accurately modeled as a perfectly smooth body (e.g., spheres and cylinders). Under certain physical conditions, microscale features can produce free energy barriers that are much larger than the thermal energy of the surrounding media. The presence of these energy barriers can effectively “lock” the particle at specific angular orientations with respect to the liquid-liquid interface. This work provides new insights on the rotational dynamics of Brownian particles at liquid interfaces and suggests possible strategies to exploit the effects of microscale features with given geometric characteristics.

  6. Patterns and Interfaces in Dissipative Dynamics

    CERN Document Server

    Pismen, L.M

    2006-01-01

    Spontaneous pattern formation in nonlinear dissipative systems far from equilibrium is a paradigmatic case of emergent behaviour associated with complex systems. It is encountered in a great variety of settings, both in nature and technology, and has numerous applications ranging from nonlinear optics through solid and fluid mechanics, physical chemistry and chemical engineering to biology. Nature creates its variety of forms through spontaneous pattern formation and self-assembly, and this strategy is likely to be imitated by future biomorphic technologies. This book is a first-hand account by one of the leading players in this field, which gives in-depth descriptions of analytical methods elucidating the complex evolution of nonlinear dissipative systems, and brings the reader to the forefront of current research. The introductory chapter on the theory of dynamical systems is written with a view to applications of its powerful methods to spatial and spatio-temporal patterns. It is followed by two chapters t...

  7. Ultrafast dynamics of electrons at interfaces

    Energy Technology Data Exchange (ETDEWEB)

    McNeill, Jason Douglas [Univ. of California, Berkeley, CA (United States)

    1999-05-03

    Electronic states of a thin layer of material on a surface possess unique physical and chemical properties. Some of these properties arise from the reduced dimensionality of the thin layer with respect to the bulk or the properties of the electric field where two materials of differing dielectric constants meet at an interface. Other properties are related to the nature of the surface chemical bond. Here, the properties of excess electrons in thin layers of Xenon, Krypton, and alkali metals are investigated, and the bound state energies and effective masses of the excess electrons are determined using two-photon photoemission. For Xenon, the dependence of bound state energy, effective mass, and lifetime on layer thickness from one to nine layers is examined. Not all quantities were measured at each coverage. The two photon photoemission spectra of thin layers of Xenon on a Ag(111) substrate exhibit a number of sharp, well-defined peaks. The binding energy of the excess electronic states of Xenon layers exhibited a pronounced dependence on coverage. A discrete energy shift was observed for each additional atomic layer. At low coverage, a series of states resembling a Rydberg series is observed. This series is similar to the image state series observed on clean metal surfaces. Deviations from image state energies can be described in terms of the dielectric constant of the overlayer material and its effect on the image potential. For thicker layers of Xe (beyond the first few atomic layers), the coverage dependence of the features begins to resemble that of quantum well states. Quantum well states are related to bulk band states. However, the finite thickness of the layer restricts the perpendicular wavevector to a discrete set of values. Therefore, the spectrum of quantum well states contains a series of peaks which correspond to the various allowed values of the perpendicular wavevector. Analysis of the quantum well spectrum yields electronic band structure

  8. Molecular Dynamics Simulations of Adhesion at Epoxy Interfaces

    Science.gov (United States)

    Frankland, Sarah-Jane V.; Clancy, Thomas C.; Hinkley, J. A.; Gates. T. S.

    2008-01-01

    The effect of moisture on adhesives used in aerospace applications can be modeled with chemically specific techniques such as molecular dynamics simulation. In the present study, the surface energy and work of adhesion are calculated for epoxy surfaces and interfaces, respectively, by using molecular dynamics simulation. Modifications are made to current theory to calculate the work of adhesion at the epoxy-epoxy interface with and without water. Quantitative agreement with experimental values is obtained for the surface energy and work of adhesion at the interface without water. The work of adhesion agrees qualitatively with the experimental values for the interface with water: the magnitude is reduced 15% with respect to the value for the interface without water. A variation of 26% in the magnitude is observed depending on the water configuration at a concentration of 1.6 wt%. The methods and modifications to the method that are employed to obtain these values are expected to be applicable for other epoxy adhesives to determine the effects of moisture uptake on their work of adhesion.

  9. Adsorption dynamics of colloidal ellipsoids at oil-water interfaces

    Science.gov (United States)

    Wang, Anna; Rogers, W. Benjamin; Manoharan, Vinothan N.

    Nonspherical particles at immiscible fluid interfaces have strong interactions with each other and with the curvature of the host interface. However, the dynamics of nonspherical colloidal particles attaching to an interface have not yet been studied. We use digital holographic microscopy to image micron-sized polystyrene ellipsoids breaching an oil-water interface at hundreds of frames per second. We show that the particle height and polar angle have large fluctuations, but both change approximately logarithmic with time, likely due to contact line pinning on the surface of the particle. Equilibrium is reached on a timescale at least three orders of magnitude slower than that expected from Langevin dynamics simulations. We also find that all the trajectories collapse into straight lines when we plot particle polar angle as a function of particle height, unlike the trajectories seen in simulation. The differences between experiment and simulation suggest that contact line pinning and the shape of the three phase contact line may strongly influence the dynamics of particle adsorption.

  10. Molecular dynamics study of the water/n-alkane interface

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Molecular dynamics simulations on the interface between liquid water and liquid n-alkane (including octane, nonane, decane, undecane and dodecane) have been performed with the purpose to study the interfacial properties: (Ⅰ) density profile; (Ⅱ) molecular orientation; (Ⅲ) interfacial tension and the temperature effect on the interfacial tension. Simulation results show that at the interface the structures of both water and n-alkane are different from those in the bulk. Water has an orientational preference due to the number of hydrogen bonds per molecule maximized. N-alkane has a more lateral orientation with respect to the interface in order to be in close contact with water. The calculated individual phase bulk density and interfacial tension of water/n-alkane systems are in good agreement with the corresponding experimental ones.

  11. Dynamics of Polaron at Polymer/Polymer Interface

    Institute of Scientific and Technical Information of China (English)

    DI Bing; MENG Yan; AN Zhong; LI You-Cheng

    2008-01-01

    The migration of a polaron at polymer/polymer interface is believed to be of fundamental importance for the transport and light-emitting properties of conjugated polymer-based light emitting diodes.Based on the onedimensional tight-binding Su-Schrieffer-Heeger(SSH)model,we have investigated polaron dynamics in a onedimensional polymer/polymer system by using a nonadiabatic evolution method.In particular,we focus on how a polaron migrates through the conjugated polymer/polymer interface in the presence of external electric field.The results show that the migration of polaron at the interface depends sensitively on the hopping integrals,the potential barrier induced by the energy mismatch,and the strength of applied electric field which increases the polaron kinetic energy.

  12. Healing of polymer interfaces: Interfacial dynamics, entanglements, and strength.

    Science.gov (United States)

    Ge, Ting; Robbins, Mark O; Perahia, Dvora; Grest, Gary S

    2014-07-01

    Self-healing of polymer films often takes place as the molecules diffuse across a damaged region, above their melting temperature. Using molecular dynamics simulations we probe the healing of polymer films and compare the results with those obtained for thermal welding of homopolymer slabs. These two processes differ from each other in their interfacial structure since damage leads to increased polydispersity and more short chains. A polymer sample was cut into two separate films that were then held together in the melt state. The recovery of the damaged film was followed as time elapsed and polymer molecules diffused across the interface. The mass uptake and formation of entanglements, as obtained from primitive path analysis, are extracted and correlated with the interfacial strength obtained from shear simulations. We find that the diffusion across the interface is significantly faster in the damaged film compared to welding because of the presence of short chains. Though interfacial entanglements increase more rapidly for the damaged films, a large fraction of these entanglements are near chain ends. As a result, the interfacial strength of the healing film increases more slowly than for welding. For both healing and welding, the interfacial strength saturates as the bulk entanglement density is recovered across the interface. However, the saturation strength of the damaged film is below the bulk strength for the polymer sample. At saturation, cut chains remain near the healing interface. They are less entangled and as a result they mechanically weaken the interface. Chain stiffness increases the density of entanglements, which increases the strength of the interface. Our results show that a few entanglements across the interface are sufficient to resist interfacial chain pullout and enhance the mechanical strength.

  13. On the Interface Formation Model for Dynamic Triple Lines

    CERN Document Server

    Bothe, Dieter

    2015-01-01

    This paper revisits the theory of Y. Shikhmurzaev on forming interfaces as a continuum thermodynamical model for dynamic triple lines. We start with the derivation of the balances for mass, momentum, energy and entropy in a three-phase fluid system with full interfacial physics, including a brief review of the relevant transport theorems on interfaces and triple lines. Employing the entropy principle in the form given in [Bothe & Dreyer, Acta Mechanica, doi:10.1007/s00707-014-1275-1] but extended to this more general case, we arrive at the entropy production and perform a linear closure, except for a nonlinear closure for the sorption processes. Specialized to the isothermal case, we obtain a thermodynamically consistent mathematical model for dynamic triple lines and show that the total available energy is a strict Lyapunov function for this system.

  14. Molecular dynamics simulations of liquid crystals at interfaces

    CERN Document Server

    Shield, M

    2002-01-01

    Molecular dynamics simulations of an atomistic model of 4-n-octyl-4'-cyanobiphenyl (8CB) were performed for thin films of 8CB on solid substrates (a pseudopotential representation of the molecular topography of the (100) crystal surface of polyethylene (PE), a highly ordered atomistic model of a pseudo-crystalline PE surface and an atomistic model of a partially orientated film of PE), free standing thin films of 8CB and 8CB droplets in a hexagonal pit. The systems showed strong homeotropic anchoring at the free volume interface and planar anchoring at the solid interface whose strength was dependent upon the surface present. The free volume interface also demonstrated weak signs of smectic wetting of the bulk. Simulations of thin free standing films of liquid crystals showed the ordered nature of the liquid crystals at the two free volume interfaces can be adopted by the region of liquid crystal molecules between the homeotropic layer at each interface only if there is a certain number of liquid crystal mole...

  15. Dynamics at Solid State Surfaces and Interfaces Volume 2 Fundamentals

    CERN Document Server

    Bovensiepen, Uwe; Wolf, Martin

    2012-01-01

    This two-volume work covers ultrafast structural and electronic dynamics of elementary processes at solid surfaces and interfaces, presenting the current status of photoinduced processes. Providing valuable introductory information for newcomers to this booming field of research, it investigates concepts and experiments, femtosecond and attosecond time-resolved methods, as well as frequency domain techniques.The whole is rounded off by a look at future developments.

  16. Dynamic Stabilization of Metal Oxide–Water Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    McBriarty, Martin E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical Sciences Division; von Rudorff, Guido Falk [Univ. College London (United Kingdom). Dept. of Physics and Astronomy; Stubbs, Joanne E. [Univ. of Chicago, IL (United States). Center for Advanced Radiation Sources (CARS); Eng, Peter J. [Univ. of Chicago, IL (United States). Center for Advanced Radiation Sources (CARS); Blumberger, Jochen [Univ. College London (United Kingdom). Dept. of Physics and Astronomy; Rosso, Kevin M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical Sciences Division

    2017-02-08

    Metal oxide growth, dissolution, and redox reactivity depend on the structure and dynamics at the interface with aqueous solution. We present the most definitive analysis to date of the hydrated naturally abundant r-cut (11$\\bar{0}$2) termination of the iron oxide hematite (α-Fe2O3). In situ synchrotron X-ray scattering analysis reveals a ridged lateral arrangement of adsorbed water molecules hydrogen bonded to terminal aquo groups. Large-scale hybrid-functional density functional theory-based molecular dynamics (DFT-MD) simulations show how this structure is dynamically stabilized by picosecond exchange between aquo groups and adsorbed water, even under nominally dry conditions. Surface pKa prediction based on bond valence analysis suggests that water exchange may influence the proton transfer reactions associated with acid/base reactivity at the interface. Our findings rectify inconsistencies between existing models and may be extended to resolving more complex electrochemical phenomena at metal oxide-water interfaces.

  17. Structure and Dynamics of Water at Carbon-Based Interfaces

    Directory of Open Access Journals (Sweden)

    Jordi Martí

    2017-03-01

    Full Text Available Water structure and dynamics are affected by the presence of a nearby interface. Here, first we review recent results by molecular dynamics simulations about the effect of different carbon-based materials, including armchair carbon nanotubes and a variety of graphene sheets—flat and with corrugation—on water structure and dynamics. We discuss the calculations of binding energies, hydrogen bond distributions, water’s diffusion coefficients and their relation with surface’s geometries at different thermodynamical conditions. Next, we present new results of the crystallization and dynamics of water in a rigid graphene sieve. In particular, we show that the diffusion of water confined between parallel walls depends on the plate distance in a non-monotonic way and is related to the water structuring, crystallization, re-melting and evaporation for decreasing inter-plate distance. Our results could be relevant in those applications where water is in contact with nanostructured carbon materials at ambient or cryogenic temperatures, as in man-made superhydrophobic materials or filtration membranes, or in techniques that take advantage of hydrated graphene interfaces, as in aqueous electron cryomicroscopy for the analysis of proteins adsorbed on graphene.

  18. Dynamic Polymer Brush at Polymer/Water Interface

    Science.gov (United States)

    Yokoyama, Hideaki; Inoue, Kazuma; Ito, Kohzo; Inutsuka, Manabu; Tanaka, Keiji; Yamada, Norifumi

    2015-03-01

    A layer of polymer chains tethered by one end to a surface is called polymer brush and known to show various unique properties such as anti-fouling. The surface segregation phenomena of copolymers with surface-active blocks should be useful for preparing such a brush layer in spontaneous process. We report hydrophilic polymer brushes formed at the interface between water and polymer by the segregation of amphiphilic diblock copolymers blended in a crosslinked rubbery matrix and call it ``dynamic polymer brush.'' In this system, the hydrophilic block with high surface energy avoids air surface, but segregates to cover the interface between hydrophobic elastomer and water. The structures of the brush layers at D2O/polymer interfaces were measured by neutron reflectivity. The dynamic polymer brush layer surprisingly reached 75% of the contour length of the chain and 2.7 chains/nm2. The brush density was surprisingly comparable to the polymer brush fabricated by the ``grafting-from'' method. We will discuss the dependence of the brush structure on molecular weight and block fraction of amphiphilic block copolymers. Such a surprisingly thick and dense polymer brush were induced by the large enthalpy gain of hydration of hydrophilic block.

  19. Asymmetrical dynamic propagation problems on mode Ⅲ interface crack

    Institute of Scientific and Technical Information of China (English)

    L(U) Nian-chun; YANG Ding-ning; CHENG Yun-hong; CHENG Jin

    2007-01-01

    By the application of the theory of complex functions, asymmetrical dynamic propagation problems on mode Ⅲ interface crack are studied. The universal representations of analytical solutions are obtained by the approaches of serf-similar function. The problems researched can be facilely transformed into Riemann-Hilbert problems and analytical solution to an asymmetrical propagation crack under the condition of point loads and unit-step loads, respectively, is acquired. After those solutions were used by superposition theorem, the solutions of arbitrarily complex problems could be attained.

  20. Microscopic and Macroscopic Dynamic Interface Shapes and the Interpretation of Dynamic Contact Angles.

    Science.gov (United States)

    Ramé; Garoff

    1996-01-15

    We have studied shapes of dynamic fluid interfaces at distances contact line at capillary numbers (Ca) ranging from 10(-3) to 10(-1). Near the moving contact line where viscous deformation is important, an analysis valid to O(1) in Ca describes the shape of the fluid interface. Static capillarity should describe the interface shape far from the contact line. We have quantitatively determined the extent of the regions described by the analysis with viscous deformation and by a static shape as a function of Ca. We observe a third portion of the interface between the two regions cited above, which is not described by either the analysis with viscous deformation or a static shape. In this third region the interface shape is controlled by viscous and gravitational forces of comparable magnitude. We detect significant viscous deformation even far from the contact line at Ca approximately > 0.01. Our measured dynamic contact angle parameter extracted by fitting the analysis with viscous deformation to the shape near the moving contact line coincides with the contact angle of the static-like shape far from the contact line. We measure and explain the discrepancy between this dynamic contact angle parameter and the apparent contact angles based on meniscus or apex heights. Our observations of viscous effects at large distances from the contact line have implications for dynamic contact angle measurements in capillary tubes.

  1. Molecular dynamics of the water liquid-vapor interface

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

    1987-01-01

    The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

  2. Dynamic Stabilization of Metal Oxide–Water Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    McBriarty, Martin E.; von Rudorff, Guido Falk; Stubbs, Joanne E.; Eng, Peter J.; Blumberger, Jochen; Rosso, Kevin M.

    2017-02-08

    The interaction of water with metal oxide surfaces plays a crucial role in the catalytic and geochemical behavior of metal oxides. In a vast majority of studies, the interfacial structure is assumed to arise from a relatively static lowest energy configuration of atoms, even at room temperature. Using hematite (α-Fe2O3) as a model oxide, we show through a direct comparison of in situ synchrotron X-ray scattering with density functional theory-based molecular dynamics simulations that the structure of the (1102) termination is dynamically stabilized by picosecond water exchange. Simulations show frequent exchanges between terminal aquo groups and adsorbed water in locations and with partial residence times consistent with experimentally determined atomic sites and fractional occupancies. Frequent water exchange occurs even for an ultrathin adsorbed water film persisting on the surface under a dry atmosphere. The resulting time-averaged interfacial structure consists of a ridged lateral arrangement of adsorbed water molecules hydrogen bonded to terminal aquo groups. Surface pKa prediction based on bond valence analysis suggests that water exchange will influence the proton-transfer reactions underlying the acid/base reactivity at the interface. Our findings provide important new insights for understanding complex interfacial chemical processes at metal oxide–water interfaces.

  3. Dynamic Model of Contact Interface between Stator and Rotor

    Directory of Open Access Journals (Sweden)

    ZengHui Zhao

    2013-01-01

    Full Text Available Based on the equivalent principle, a linear spring contact model was established for the friction layer between stator and rotor. Different contact conditions were described by a distance index δ. Detailed analysis of the nonlinear contact behavior especially the static and dynamic slipping was carried on using a space-time equation. A contact deflection angle was proposed to quantitatively express the influence of friction force on the output performance. A more precision simulation model was established based on the theoretical analysis, and influences of different preload pressures and elastic modulus Em of friction layer on output performance were analyzed. The results showed the simulation results had very good consistency with experimental results, and the model could well reflect the output characteristics of contact interface.

  4. Ultrafast studies of electron dynamics at metal-dielectric interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ge, Nien-Hui [Univ. of California, Berkeley, CA (United States)

    1998-10-01

    Femtosecond time- and angle-resolved two-photon photoemission spectroscopy has been used to study fundamental aspects of excited electron dynamics at metal-dielectric interfaces, including layer-by-layer evolution of electronic structure and two-dimensional electron localization. On bare Ag(111), the lifetimes of image states are dominated by their position with respect to the projected bulk band structure. The n = 2 state has a shorter lifetime than the n = 1 state due to degeneracy with the bulk conduction band. As the parallel momentum of the n = 1 image electron increases, the lifetime decreases. With decreasing temperatures, the n = 1 image electrons, with zero or nonzero parallel momentum, all become longer lived. Adsorption of one to three layers of n-heptane results in an approximately exponential increase in lifetime as a function of layer thickness. This results from the formation of a tunneling barrier through which the interfacial electrons must decay, consistent with the repulsive bulk electron affinity of n-alkanes. The lifetimes of the higher quantum states indicate that the presence of the monolayer significantly reduces coupling of the image states to the bulk band structure. These results are compared with predictions of a dielectric continuum model. The study of electron lateral motion shows that optical excitation creates interfacial electrons in quasifree states for motion parallel to the n-heptane/Ag(111) interface. These initially delocalized electrons decay into a localized state within a few hundred femtoseconds. The localized electrons then decay back to the metal by tunneling through the adlayer potential barrier. The localization time depends strongly on the electron's initial parallel momentum and exhibits a non-Arrhenius temperature dependence. The experimental findings are consistent with a 2-D self-trapping process in which electrons become localized by interacting with the topmost plane of the alkane layer. The energy

  5. Nucleation and evolution of dynamic damage at Cu/Pb interfaces using molecular dynamics

    Science.gov (United States)

    Fensin, S. J.; Valone, S. M.; Cerreta, E. K.; Gray, G. T.; Shao, S.

    2017-01-01

    For ductile metals, the process of dynamic fracture occurs through nucleation, growth and coalescence of voids. For high purity single-phase metals, it has been observed by numerous investigators that voids tend to heterogeneously nucleate at grain boundaries and all grain boundaries are not equally susceptible to void nucleation. However, for materials of engineering significance, especially those with second phase particles, it is less clear if the type of bi-metal interface between the two phases will affect void nucleation and growth. To approach this problem in a systematic manner two bi-metal interfaces between Cu and Pb have been investigated: {111} and {100}. Qualitative and quantitative analysis of the collected data from molecular dynamics shock and spall simulations suggests that Pb becomes disordered during shock compression and is the preferred location for void nucleation under tension. Despite the interfaces being aligned with the spall plane (by design), they are not the preferred location for void nucleation irrespective of interface type.

  6. Slow dynamics of phospholipid monolayers at the air/water interface

    CERN Document Server

    Choi, Siyoung Q

    2009-01-01

    Phospholipid monolayers at the air-water interface serve as model systems for various biological interfaces, e.g. lung surfactant layers and outer leaflets of cell membranes. Although the dynamical (viscoelastic) properties of these interfaces may play a key role in stability, dynamics and function, the relatively weak rheological properties of most such monolayers have rendered their study difficult or impossible. A novel technique to measure the dynamical properties of fluid-fluid interfaces have developed accordingly. We microfabricate micron-scale ferromagnetic disks, place them on fluid-fluid interfaces, and use external electromagnets to exert torques upon them. By measuring the rotation that results from a known external torque, we compute the rotational drag, from which we deduce the rheological properties of the interface. Notably, our apparatus enable direct interfacial visualization while the probes are torqued. In this fluid dynamics video, we directly visualize dipalmitoylphosphatidylcholine(DPPC...

  7. Static and dynamic properties of curved vapour-liquid interfaces by massively parallel molecular dynamics simulation

    CERN Document Server

    Horsch, Martin T; Vrabec, Jadran; Glass, Colin W; Niethammer, Christoph; Bernreuther, Martin F; Müller, Erich A; Jackson, George

    2011-01-01

    Curved fluid interfaces are investigated on the nanometre length scale by molecular dynamics simulation. Thereby, droplets surrounded by a metastable vapour phase are stabilized in the canonical ensemble. Analogous simulations are conducted for cylindrical menisci separating vapour and liquid phases under confinement in planar nanopores. Regarding the emergence of nanodroplets during nucleation, a non-equilibrium phenomenon, both the non-steady dynamics of condensation processes and stationary quantities related to supersaturated vapours are considered. Results for the truncated and shifted Lennard-Jones fluid and for mixtures of quadrupolar fluids confirm the applicability of the capillarity approximation and the classical nucleation theory.

  8. Modeling and dynamic simulation of ultraviolet induced growing interfaces

    Science.gov (United States)

    Flicstein, J.; Guillonneau, E.; Pata, S.; Kee Chun, L. S.; Palmier, J. F.; Daguet, C.; Courant, J. L.

    1999-01-01

    A solid-on-solid (SOS) model to simulate SiN:H dynamic surface characteristics in ultraviolet chemical vapor deposition (CVD) onto indium phosphide is presented. It is recognized that the nucleation process occurs at an UV induced active charged center on the surface of the substrate. Photolysis rates are determined using bond dissociation energies for molecular processes to generate active adsorbed species. The microscopic activation energy in elementary processes depends on the configuration of neighbouring atoms. Monte Carlo-Metropolis method using microscopic activation energy barriers is taken into account in molecular processes by a three-dimensional algorithm. The model includes lattice coordination and atom-atom interactions out to third-nearest neighbours. The molecular events are chosen with a probability of occurrence that depends on the kinetic rates at each atomic site. Stable incorporation of main species is enabled. Three-dimensional simulation of a growing interface indicates validation of a thermally activated rough-smooth transition for submicronic thick layers in the Kardar-Parisi-Zhang model.

  9. Description of waste pretreatment and interfacing systems dynamic simulation model

    Energy Technology Data Exchange (ETDEWEB)

    Garbrick, D.J.; Zimmerman, B.D.

    1995-05-01

    The Waste Pretreatment and Interfacing Systems Dynamic Simulation Model was created to investigate the required pretreatment facility processing rates for both high level and low level waste so that the vitrification of tank waste can be completed according to the milestones defined in the Tri-Party Agreement (TPA). In order to achieve this objective, the processes upstream and downstream of the pretreatment facilities must also be included. The simulation model starts with retrieval of tank waste and ends with vitrification for both low level and high level wastes. This report describes the results of three simulation cases: one based on suggested average facility processing rates, one with facility rates determined so that approximately 6 new DSTs are required, and one with facility rates determined so that approximately no new DSTs are required. It appears, based on the simulation results, that reasonable facility processing rates can be selected so that no new DSTs are required by the TWRS program. However, this conclusion must be viewed with respect to the modeling assumptions, described in detail in the report. Also included in the report, in an appendix, are results of two sensitivity cases: one with glass plant water recycle steams recycled versus not recycled, and one employing the TPA SST retrieval schedule versus a more uniform SST retrieval schedule. Both recycling and retrieval schedule appear to have a significant impact on overall tank usage.

  10. Dynamics of cancerous tissue correlates with invasiveness

    Science.gov (United States)

    West, Ann-Katrine Vransø; Wullkopf, Lena; Christensen, Amalie; Leijnse, Natascha; Tarp, Jens Magelund; Mathiesen, Joachim; Erler, Janine Terra; Oddershede, Lene Broeng

    2017-01-01

    Two of the classical hallmarks of cancer are uncontrolled cell division and tissue invasion, which turn the disease into a systemic, life-threatening condition. Although both processes are studied, a clear correlation between cell division and motility of cancer cells has not been described previously. Here, we experimentally characterize the dynamics of invasive and non-invasive breast cancer tissues using human and murine model systems. The intrinsic tissue velocities, as well as the divergence and vorticity around a dividing cell correlate strongly with the invasive potential of the tissue, thus showing a distinct correlation between tissue dynamics and aggressiveness. We formulate a model which treats the tissue as a visco-elastic continuum. This model provides a valid reproduction of the cancerous tissue dynamics, thus, biological signaling is not needed to explain the observed tissue dynamics. The model returns the characteristic force exerted by an invading cell and reveals a strong correlation between force and invasiveness of breast cancer cells, thus pinpointing the importance of mechanics for cancer invasion. PMID:28262796

  11. Dynamics of cancerous tissue correlates with invasiveness

    Science.gov (United States)

    West, Ann-Katrine Vransø; Wullkopf, Lena; Christensen, Amalie; Leijnse, Natascha; Tarp, Jens Magelund; Mathiesen, Joachim; Erler, Janine Terra; Oddershede, Lene Broeng

    2017-03-01

    Two of the classical hallmarks of cancer are uncontrolled cell division and tissue invasion, which turn the disease into a systemic, life-threatening condition. Although both processes are studied, a clear correlation between cell division and motility of cancer cells has not been described previously. Here, we experimentally characterize the dynamics of invasive and non-invasive breast cancer tissues using human and murine model systems. The intrinsic tissue velocities, as well as the divergence and vorticity around a dividing cell correlate strongly with the invasive potential of the tissue, thus showing a distinct correlation between tissue dynamics and aggressiveness. We formulate a model which treats the tissue as a visco-elastic continuum. This model provides a valid reproduction of the cancerous tissue dynamics, thus, biological signaling is not needed to explain the observed tissue dynamics. The model returns the characteristic force exerted by an invading cell and reveals a strong correlation between force and invasiveness of breast cancer cells, thus pinpointing the importance of mechanics for cancer invasion.

  12. Interface

    DEFF Research Database (Denmark)

    Computerens interface eller grænseflade har spredt sig overalt. Mobiltelefoner, spilkonsoller, pc'er og storskærme indeholder computere – men computere indbygges også i tøj og andre hverdagslige genstande, så vi konstant har adgang til digitale data. Interface retter fokus mod, hvordan den digita...

  13. Molecular Dynamics of a Water-Lipid Bilayer Interface

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1994-01-01

    We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

  14. Presentation of dynamically overlapping auditory messages in user interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Papp, III, Albert Louis [Univ. of California, Davis, CA (United States)

    1997-09-01

    This dissertation describes a methodology and example implementation for the dynamic regulation of temporally overlapping auditory messages in computer-user interfaces. The regulation mechanism exists to schedule numerous overlapping auditory messages in such a way that each individual message remains perceptually distinct from all others. The method is based on the research conducted in the area of auditory scene analysis. While numerous applications have been engineered to present the user with temporally overlapped auditory output, they have generally been designed without any structured method of controlling the perceptual aspects of the sound. The method of scheduling temporally overlapping sounds has been extended to function in an environment where numerous applications can present sound independently of each other. The Centralized Audio Presentation System is a global regulation mechanism that controls all audio output requests made from all currently running applications. The notion of multimodal objects is explored in this system as well. Each audio request that represents a particular message can include numerous auditory representations, such as musical motives and voice. The Presentation System scheduling algorithm selects the best representation according to the current global auditory system state, and presents it to the user within the request constraints of priority and maximum acceptable latency. The perceptual conflicts between temporally overlapping audio messages are examined in depth through the Computational Auditory Scene Synthesizer. At the heart of this system is a heuristic-based auditory scene synthesis scheduling method. Different schedules of overlapped sounds are evaluated and assigned penalty scores. High scores represent presentations that include perceptual conflicts between over-lapping sounds. Low scores indicate fewer and less serious conflicts. A user study was conducted to validate that the perceptual difficulties predicted by

  15. Dynamics of particle accumulation at engineered and natural interfaces

    Science.gov (United States)

    Kim, Sechurl

    2000-08-01

    Investigation of the structure of particle aggregates and their morphology is crucial for understanding particle accumulation phenomena at solid-water interfaces. Engineering applications are often restricted by the lack of exact knowledge of this accumulation phenomenon. Natural processes are also not well understood for this reason. Among the wide spectrum of engineered and natural particle accumulation processes, the following important processes are considered in this study: the permeability and formation of fractal porous aggregates in aqueous systems, the solution structure of a dispersing medium, and the influence of hydrodynamic shear on deformable molecular assemblages. The Stokesian Dynamics technique was applied to particles in a suspension to elucidate the structural evolution and the permeability of aggregates. To reduce the computational effort, a special Stokesian dynamics method for a single moving particle in the geometrical environment was developed, and parallel computation with distributed memory scheme was employed for inverting the grand mobility matrix using a Linux cluster composed of 4 nodes. This technique was capable of generating aggregates with 300 primary particles by the processes of differential settling and turbulent shear. Simulated permeabilities of these particles and of synthetically generated aggregates agree well with values reported in the theoretical and experimental literature. The solution structure of a dispersion of charged solute particles was investigated by Monte Carlo simulation and integral equation theory with hypernetted chain closure. Two properties of the solution (dispersion), namely, osmotic pressure and sedimentation coefficient were obtained from the radial distribution function of the solute particles. Hydrodynamic mobility tensors were used to calculate the sedimentation coefficient, and the important effects of hydrodynamic interaction compared to interparticle interaction were demonstrated. Finally, the

  16. The development of an intelligent interface to a computational fluid dynamics flow-solver code

    Science.gov (United States)

    Williams, Anthony D.

    1988-01-01

    Researchers at NASA Lewis are currently developing an 'intelligent' interface to aid in the development and use of large, computational fluid dynamics flow-solver codes for studying the internal fluid behavior of aerospace propulsion systems. This paper discusses the requirements, design, and implementation of an intelligent interface to Proteus, a general purpose, three-dimensional, Navier-Stokes flow solver. The interface is called PROTAIS to denote its introduction of artificial intelligence (AI) concepts to the Proteus code.

  17. Molecular Dynamics of Peptide Folding at Aqueous Interfaces

    Science.gov (United States)

    Pohorille, Andrew; Chipot, Christophe; Chang, Sherwood (Technical Monitor)

    1997-01-01

    Even though most monomeric peptides are disordered in water they can adopt sequence-dependent, ordered structures, such as a-helices, at aqueous interfaces. This property is relevant to cellular signaling, membrane fusion, and the action of toxins and antibiotics. The mechanism of folding nonpolar peptides at the water-hexane interface was studied in the example of an 11-mer, of poly-L-leucine. Initially placed as a random coil on the water side of the interface, the peptide folded into an a-helix in 36 ns. Simultaneously, the peptide translocated into the hexane side of the interface. Folding was not sequential and involved a 3/10-helix as an intermediate. The folded peptide was either parallel to the interface or had its C-terminus exposed to water. An 11-mer, LQQLLQQLLQL, composed of leucine (L) and glutamine (G), was taken as a model amphiphilic peptide. It rapidly adopted an amphiphilic, disordered structure at the interface. Further folding proceeded through a series of amphiphilic intermediates.

  18. Oscillation theory for a pair of second order dynamic equations with a singular interface

    Directory of Open Access Journals (Sweden)

    Pallav Kumar Baruah

    2008-03-01

    Full Text Available In this paper we consider a pair of second order dynamic equations defined on the time scale $I = [a,c]cup [sigma(c,b]$. We impose matching interface conditions at the singular interface $c$. We prove a theorem regarding the relationship between the number of eigenvalues and zeros of the corresponding eigenfunctions.

  19. Influence of construction interfaces on dynamic characteristics of roller compacted concrete dams

    Institute of Scientific and Technical Information of China (English)

    顾冲时; 王少伟; 包腾飞

    2015-01-01

    To study the influence of construction interfaces on dynamic characteristics of roller compacted concrete dams (RCCDs), mechanical properties of construction interfaces are firstly analyzed. Then, the viscous-spring artificial boundary (VSAB) is adopted to simulate the radiation damping of their infinite foundations, and based on the Marc software, a simplified seismic motion input method is presented by the equivalent nodal loads. Finally, based on the practical engineering of a RCC gravity dam, effects of radiation damping and construction interfaces on the dynamic characteristics of dams are investigated in detail. Analysis results show that dynamic response of the RCC gravity dam significantly reduces about 25%when the radiation damping of infinite foundation is considered. Hot interfaces and the normal cold interfaces have little influence on the dynamic response of the RCC gravity dam. However, nonlinear fracture along the cold interfaces at the dam heel will occur under the designed earthquake if the cold interfaces are combined poorly. Therefore, to avoid the fractures along the construction interfaces under the potential super earthquakes, combination quality of the RCC layers should be significantly ensured.

  20. Probing Molecular Organization and Electronic Dynamics at Buried Organic Interfaces

    Science.gov (United States)

    Roberts, Sean

    2015-03-01

    Organic semiconductors are a promising class of materials due to their ability to meld the charge transport capabilities of semiconductors with many of the processing advantages of plastics. In thin film organic devices, interfacial charge transfer often comprises a crucial step in device operation. As molecular materials, the density of states within organic semiconductors often reflect their intermolecular organization. Truncation of the bulk structure of an organic semiconductor at an interface with another material can lead to substantial changes in the density of states near the interface that can significantly impact rates for interfacial charge and energy transfer. Here, we will present the results of experiments that utilize electronic sum frequency generation (ESFG) to probe buried interfaces in these materials. Within the electric dipole approximation, ESFG is only sensitive to regions of a sample that experience a breakage of symmetry, which occurs naturally at material interfaces. Through modeling of signals measured for thin organic films using a transfer matrix-based formalism, signals from buried interfaces between two materials can be isolated and used to uncover the interfacial density of states.

  1. Linear flow dynamics near a T/NT interface

    Science.gov (United States)

    Teixeira, Miguel; Silva, Carlos

    2011-11-01

    The characteristics of a suddenly-inserted T/NT interface separating a homogeneous and isotropic shear-free turbulence region from a non-turbulent flow region are investigated using rapid distortion theory (RDT), taking full account of viscous effects. Profiles of the velocity variances, TKE, viscous dissipation rate, turbulence length scales, and pressure statistics are derived, showing very good agreement with DNS. The normalized inviscid flow statistics at the T/NT interface do not depend on the form of the assumed TKE spectrum. In the non-turbulent region, where the flow is irrotational (except within a thin viscous boundary layer), the dissipation rate decays as z-6, where z is distance from the T/NT interface. The mean pressure exhibits a decrease towards the turbulence due to the associated velocity fluctuations, consistent with the generation of a mean entrainment velocity. The vorticity variance and dissipation rate display large maxima at the T/NT interface due to the existing inviscid discontinuities of the tangential velocity, and these maxima are quantitatively related to the thickness of the viscous boundary layer (VBL). At equilibrium, RDT suggests that the thickness of the T/NT interface scales on the Kolmogorov microscale. We acknowledge the financial support of FCT under Project PTDC/EME-MFE/099636/2008.

  2. A web based Radiation Oncology Dose Manager with a rich User Interface developed using AJAX, ruby, dynamic XHTML and the new Yahoo/EXT User Interface Library.

    Science.gov (United States)

    Vali, Faisal; Hong, Robert

    2007-10-11

    With the evolution of AJAX, ruby on rails, advanced dynamic XHTML technologies and the advent of powerful user interface libraries for javascript (EXT, Yahoo User Interface Library), developers now have the ability to provide truly rich interfaces within web browsers, with reasonable effort and without third-party plugins. We designed and developed an example of such a solution. The User Interface allows radiation oncology practices to intuitively manage different dose fractionation schemes by helping estimate total dose to irradiated organs.

  3. Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1991-01-01

    Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

  4. Elastic properties of surfactant monolayers at liquid-liquid interfaces: A molecular dynamics study

    DEFF Research Database (Denmark)

    Laradji, Mohamed; Mouritsen, Ole G.

    2000-01-01

    Using a simple molecular model based on the Lennard-Jones potential, we systematically study the elastic properties of liquid-liquid interfaces containing surfactant molecules by means of extensive and large-scale molecular dynamics simulations. The main elastic constants of the interface....... However, we found that the corresponding change in the bending rigidity is nonmonotonic. Specifically, we found that the bending rigidity decreases with increasing surfactant interfacial coverage for small surfactant interface coverages, but then it increases as the surfactant interface coverage...

  5. The interface dynamics of bicontinuous phase separating structure in a polymer blend

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Haruko; Yoshinaga, Masahiro; Mihara, Takaaki; Jinnai, Hiroshi [Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Kyoto 606-8585 (Japan); Nishi, Toshio, E-mail: n08a0001@kit.ac.j [World Premier International, Advanced Institute for Materials Research, Tohoku University, Katahira, Sendai 980-8577 (Japan)

    2009-08-01

    The time evolution of the phase separating pattern during the spinodal decomposition (SD) of a specimen was observed at the same volume of the specimen using X-ray computerized microtomography (X-ray CT). A careful examination of time-dependent three-dimensional (3D) images revealed that bridge-like domains played an important role in the phase separation dynamics. In the course of the SD, some bridge-like domains became thicker, while the others became thinner. It was found that the pressure difference across the interface, which is quantified through the mean curvature of the interface, influences such interface dynamics.

  6. Dynamics of crack penetration vs. branching at a weak interface: An experimental study

    Science.gov (United States)

    Sundaram, Balamurugan M.; Tippur, Hareesh V.

    2016-11-01

    In this paper, the dynamic crack-interface interactions and the related mechanics of crack penetration vs. branching at a weak interface are studied experimentally. The interface is oriented perpendicular to the incoming mode-I crack in an otherwise homogeneous bilayer. The focus of this investigation is on the effect of interface location and the associated crack-tip parameters within the bilayer on the mechanics of the ensuing fracture behavior based on the optical methodologies laid down in Ref. Sundaram and Tippur (2016). Time-resolved optical measurement of crack-tip deformations, velocity and stress intensity factor histories in different bilayer configurations is performed using Digital Gradient Sensing (DGS) technique in conjunction with high-speed photography. The results show that the crack path selection at the interface and subsequently the second layer are greatly affected by the location of the interface within the geometry. Using optically measured fracture parameters, the mechanics of crack penetration and branching are explained. Counter to the intuition, a dynamically growing mode-I approaching a weak interface at a lower velocity and stress intensity factor penetrates the interface whereas a higher velocity and stress intensity factor counterpart gets trapped by the interface producing branched daughter cracks until they kink out into the next layer. An interesting empirical observation based on measured crack-tip parameters for crack penetration and branching is also made.

  7. Ab initio study on the dynamics of furfural at the liquid-solid interfaces

    Science.gov (United States)

    Dang, Hongli; Xue, Wenhua; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2013-03-01

    Catalytic biomass conversion sometimes occurs at the liquid-solid interfaces. We report ab initio molecular dynamics simulations at finite temperatures for the catalytic reactions involving furfural at the water-Pd and water-Cu interfaces. We found that, during the dynamic process, the furan ring of furfural prefers to be parallel to the Pd surface and the aldehyde group tends to be away from the Pd surface. On the other hand, at the water-Cu(111) interface, furfural prefers to be tilted to the Cu surface while the aldehyde group is bonded to the surface. In both cases, interaction of liquid water and furfural is identified. The difference of dynamic process of furfural at the two interfaces suggests different catalytic reaction mechanisms for the conversion of furfural, consistent with the experimental investigations. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSED's and NERSC's supercomputers

  8. Runx3 at the interface of immunity, inflammation and cancer.

    Science.gov (United States)

    Lotem, Joseph; Levanon, Ditsa; Negreanu, Varda; Bauer, Omri; Hantisteanu, Shay; Dicken, Joseph; Groner, Yoram

    2015-04-01

    Inactivation of tumor suppressor genes (TSG) in normal cells provides a viability/growth advantage that contributes cell-autonomously to cancer. More than a decade ago claims arose that the RUNX3 member of the RUNX transcription factor family is a major TSG inactivated in gastric cancer, a postulate extended later to other cancers. However, evidence that Runx3 is not expressed in normal gastric and other epithelia has challenged the RUNX3-TSG paradigm. Here we critically re-appraise this paradigm in light of recent high-throughput, quantitative genome-wide studies on thousands of human samples of various tumors and new investigations of the role of Runx3 in mouse cancer models. Collectively, these studies unequivocally demonstrate that RUNX3 is not a bona fide cell-autonomous TSG. Accordingly, RUNX3 is not recognized as a TSG and is not included among the 2000 cancer genes listed in the "Cancer Gene Census" or "Network for Cancer Genes" repositories. In contrast, RUNX3 does play important functions in immunity and inflammation and may thereby indirectly influence epithelial tumor development.

  9. interfaces

    Directory of Open Access Journals (Sweden)

    Dipayan Sanyal

    2005-01-01

    macroscopic conservation equations with an order parameter which can account for the solid, liquid, and the mushy zones with the help of a phase function defined on the basis of the liquid fraction, the Gibbs relation, and the phase diagram with local approximations. Using the above formalism for alloy solidification, the width of the diffuse interface (mushy zone was computed rather accurately for iron-carbon and ammonium chloride-water binary alloys and validated against experimental data from literature.

  10. Decoding network dynamics in cancer

    DEFF Research Database (Denmark)

    Linding, Rune

    2014-01-01

    models through computational integration of systematic, large-scale, high-dimensional quantitative data sets. I will review our latest advances in methods for exploring phosphorylation networks. In particular I will discuss how the combination of quantitative mass-spectrometry, systems...... in comparative phospho-proteomics and network evolution [Tan et al. Science Signaling 2009, Tan et al. Science 2009, Tan et al. Science 2011]. Finally, I will discuss our most recent work in analyzing genomic sequencing data from NGS studies and how we have developed new powerful algorithms to predict the impact......Biological systems are composed of highly dynamic and interconnected molecular networks that drive biological decision processes. The goal of network biology is to describe, quantify and predict the information flow and functional behaviour of living systems in a formal language...

  11. Towards emotion modeling based on gaze dynamics in generic interfaces

    DEFF Research Database (Denmark)

    Vester-Christensen, Martin; Leimberg, Denis; Ersbøll, Bjarne Kjær

    2005-01-01

    Gaze detection can be a useful ingredient in generic human computer interfaces if current technical barriers are overcome. We discuss the feasibility of concurrent posture and eye-tracking in the context of single (low cost) camera imagery. The ingredients in the approach are posture and eye regi...... extraction based on active appearance modeling and eye tracking using a new fast and robust heuristic. The eye tracker is shown to perform well for low resolution image segments, hence, making it feasible to estimate gaze using a single generic camera.......Gaze detection can be a useful ingredient in generic human computer interfaces if current technical barriers are overcome. We discuss the feasibility of concurrent posture and eye-tracking in the context of single (low cost) camera imagery. The ingredients in the approach are posture and eye region...

  12. General framework for adsorption processes on dynamic interfaces

    Science.gov (United States)

    Schmuck, Markus; Kalliadasis, Serafim

    2016-03-01

    We propose a novel and general variational framework modelling particle adsorption mechanisms on evolving immiscible fluid interfaces. A by-product of our thermodynamic approach is that we systematically obtain analytic adsorption isotherms for given equilibrium interfacial geometries. We validate computationally our mathematical methodology by demonstrating the fundamental properties of decreasing interfacial free energies by increasing interfacial particle densities and of decreasing surface pressure with increasing surface area.

  13. Determining gastric cancer resectability by dynamic MDCT

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Zilai; Zhang, Huan; Du, Lianjun; Ding, Bei; Song, Qi; Ling, Huawei; Huang, Baisong; Chen, Kemin [Jiaotong University, Department of Radiology, Shanghai (China); Yan, Chao [Jiaotong University, Department of Surgery, Shanghai (China)

    2010-03-15

    Multi-detector row CT (MDCT) has been widely used to detect primary lesions and to evaluate TNM staging. In this study we evaluated the accuracy of dynamic MDCT in the preoperative determination of the resectability of gastric cancer. MDCT was used to image 350 cases of gastric cancer diagnosed by biopsy before surgery. MDCT findings regarding TNM staging and resectability were correlated with surgical and pathological findings. The accuracy of MDCT for staging gastric cancer was high, especially for tumour stage T1 (94.3%), lymph node stage N2 (87.3%), and for predicting distant metastases (>96.6%). When resectability was considered to be the outcome, the total accuracy of MDCT was 87.4%, sensitivity was 89.7% and specificity was 76.7%. Results showed high sensitivity for identifying peritoneal seeding (90.0%) and for predicting liver metastasis (80.0%). Dynamic enhanced MDCT is useful for TNM staging of gastric cancers and for predicting tumour respectability preoperatively. (orig.)

  14. Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin.

    Directory of Open Access Journals (Sweden)

    Julian E Fuchs

    Full Text Available Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.

  15. Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin.

    Science.gov (United States)

    Fuchs, Julian E; Huber, Roland G; Waldner, Birgit J; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

    2015-01-01

    Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.

  16. Dynamic Investigation of Interface Stress on Below-Knee Residual Limb in a Prosthetic Socket

    Institute of Scientific and Technical Information of China (English)

    贾晓红; 张明; 王人成; 金德闻

    2004-01-01

    The dynamic effects of inertial loads on the interface stresses between a residual limb and the trans-tibial prosthetic socket were investigated. A 3-D nonlinear finite element model, based on the actual geometry of the residual limb, including internal bones and socket liner, was developed to study the mechanical interaction between the socket and the residual limb during walking. To simulate the friction/slip boundary conditions between the skin and liner, automated surface-to-surface contact was used. The results show that interface pressure and shear stress have a similar double-peaked waveform shape in the stance phase. The average difference in interface stresses between the cases with and without consideration of inertial forces is 8.4% in the stance phase and 20.1% in the swing phase. The results suggest that the dynamic effects of inertial loads on interface stress distribution during walking must be considered in prosthetic socket design.

  17. Mechanical Strength of Silicon/Silicon Nitride Interfaces: A Molecular-Dynamics Study

    Science.gov (United States)

    Bachlechner, Martina E.; Knudsen, Steven R.; Schiffbauer, Jarrod E.; Wang, Ye; Zhang, Jennifer; Korakakis, Dimitris

    2004-03-01

    Molecular-dynamics simulations are performed on parallel computers to investigate failure mechanisms of the crystalline Si(111)/Si_3N_4(0001) interface as strain is applied parallel to the interface. Comparisons between different rates of strain and temperatures were studied. Increased temperatures were found to have an adverse effect on the mechanical strength of the material, and increased rates of strain caused the system to fail later than those that were stretched more slowly.

  18. The Silicon / Silicon Nitride Interface and Fracture in Si: Molecular Dynamics Simulations

    Science.gov (United States)

    Bachlechner, Martina E.; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar

    1997-03-01

    The interface structure of a Si_3N_4(0001) film on a Si(111) substrate is studied using the molecular dynamics (MD) method. Bulk Si is described by the Stillinger-Weber potential and Si_3N4 by a combination of two-body and three-body contributions. At the interface, the charge transfer from silicon to nitrogen is taken from LCAO electronic structure calculations. Using these Si, Si_3N4 and interface interactions in MD simulations, we determine structural correlations in the interfacial regions. Results for crack propagation in silicon will also be presented.

  19. The dynamic nature of autophagy in cancer.

    Science.gov (United States)

    Kimmelman, Alec C

    2011-10-01

    Macroautophagy (referred to hereafter as autophagy) is a highly regulated cellular process that serves to remove damaged proteins and organelles from the cell. Autophagy contributes to an array of normal and pathological processes, and has recently emerged as a key regulator of multiple aspects of cancer biology. The role of autophagy in cancer is complex and is likely dependent on tumor type, stage, and genetic context. This complexity is illustrated by the identification of settings where autophagy acts potently to either promote or inhibit tumorigenesis. In this review, I discuss the underlying basis for these opposing functions and propose a model suggesting a dynamic role for autophagy in malignancy. Collectively, the data point to autophagy as serving as a barrier to limit tumor initiation. Once neoplastic lesions are established, it appears that adaptive changes occur that now result in positive roles for autophagy in malignant progression and in subsequent tumor maintenance. Remarkably, constitutive activation of autophagy is critical for continued growth of some tumors, serving to both reduce oxidative stress and provide key intermediates to sustain cell metabolism. Autophagy is also induced in response to cancer therapies where it can function as a survival mechanism that limits drug efficacy. These findings have inspired significant interest in applying anti-autophagy therapies as an entirely new approach to cancer treatment. It is now apparent that aberrant control of autophagy is among the key hallmarks of cancer. While much needs to be learned about the regulation and context-dependent biological functions of autophagy, it seems clear that modulation of this process will be an attractive avenue for future cancer therapeutic approaches.

  20. Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

  1. i-PI: A Python interface for ab initio path integral molecular dynamics simulations

    CERN Document Server

    Ceriotti, Michele; Manolopoulos, David E

    2014-01-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high pressure water.

  2. Dynamics of non-spherical colloidal particles near and at oil-water interfaces

    Science.gov (United States)

    Wang, Anna; Dimiduk, Thomas G.; Fung, Jerome; Chaudhary, Kundan; Lewis, Jennifer A.; Razavi, Sepideh; Kretzschmar, Ilona; Manoharan, Vinothan N.

    2014-03-01

    Whereas much is known about how spherical colloidal particles interact with and at oil-water interfaces, not much is known about their non-spherical counterparts. The rotation of non-spherically symmetric particles adds extra degrees of freedom to how such particles interact with each other and the interface, so to study their three-dimensional dynamics we must first be able to image the rotation which has so far only been possible in viscous fluids or for particles with large aspect ratios. Here we track both the three-dimensional translation and the rotation of non-spherical colloidal particles at high speeds using the discrete dipole approximation in conjunction with digital holographic microscopy. We study the dynamics of such particles at an oil-water interface to determine interactions and dynamics prior to or after attachment. We aim to connect these measurements to the formation and stability of Pickering emulsions.

  3. Interface boundary conditions for dynamic magnetization and spin wave dynamics in a ferromagnetic layer with the interface Dzyaloshinskii-Moriya interaction

    Energy Technology Data Exchange (ETDEWEB)

    Kostylev, M. [School of Physics, M013, University of Western Australia, Crawley, Perth 6009, Western Australia (Australia)

    2014-06-21

    In this work, we derive the interface exchange boundary conditions for the classical linear dynamics of magnetization in ferromagnetic layers with the interface Dzyaloshinskii-Moriya interaction (IDMI). We show that IDMI leads to pinning of dynamic magnetization at the interface. An unusual peculiarity of the IDMI-based pinning is that its scales as the spin-wave wave number. We incorporate these boundary conditions into an existing numerical model for the dynamics of the Damon-Eshbach spin wave in ferromagnetic films. IDMI affects the dispersion and the frequency non-reciprocity of the travelling Damon-Eshbach spin wave. For a broad range of film thicknesses L and wave numbers, the results of the numerical simulations of the spin wave dispersion are in a good agreement with a simple analytical expression, which shows that the contribution of IDMI to the dispersion scales as 1/L, similarly to the effect of other types of interfacial anisotropy. Suggestions to experimentalists how to detect the presence of IDMI in a spin wave experiment are given.

  4. A comparison of molecular dynamics and diffuse interface model predictions of Lennard-Jones fluid evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)

    2014-12-09

    The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.

  5. Characterizing the inorganic/organic interface in cancer bone metastasis

    Science.gov (United States)

    Wu, Fei

    Bone metastasis frequently occurs in patients with advanced breast cancer and remains a major source of mortality. At the molecular level, bone is a nanocomposite composed of inorganic bone mineral deposited within an organic extracellular matrix (ECM). Although the exact mechanisms of bone metastasis remain unclear, the nanoscale materials properties of bone mineral have been implicated in this process. Bone apatite is closely related to synthetic hydroxyapatite (HAP, Ca10(PO4)6(OH)2) in terms of structural and mechanical properties. Additionally, although the primary protein content of bone is collagen I, the glycoprotein fibronectin (Fn) is essential in maintaining the overall integrity of the bone matrix. Importantly, in vivo, neither breast cancer cells nor normal bone cells interact directly with the bone mineral but rather with the protein film adsorbed onto the mineral surface. Therefore, we hypothesized that breast cancer cell functions were regulated by differential fibronectin adsorption onto hydroxyapatite, which led to pathological remodeling of the bone matrix and sustained bone metastasis. Three model systems containing HAP and Fn were developed for this thesis. In model system I, a library of synthetic HAP nanoparticles were utilized to investigate the effect of mineral size, shape, and crystallinity on Fn conformation, using Forster resonance energy transfer (FRET) spectroscopy. In model system II, Fn-functionalized large geologic HAP crystals were used instead of HAP nanoparticles to avoid cellular uptake when investigating subsequent cell functions. Overall our FRET analysis (models I and II) revealed that Fn conformation depended on size, surface chemistry, and roughness of underlying HAP. When breast cancer cells were seeded on the Fn-coated HAP crystal facets (model II), our data indicated high secretion levels of proangiogenic and proinflammatory factors associated with the presence of unfolded Fn conformations, likely caused by differential

  6. PREFACE: Liquid-solid interfaces: structure and dynamics from spectroscopy and simulations Liquid-solid interfaces: structure and dynamics from spectroscopy and simulations

    Science.gov (United States)

    Gaigeot, Marie-Pierre; Sulpizi, Marialore

    2012-03-01

    Liquid-solid interfaces play an important role in a number of phenomena encountered in biological, chemical and physical processes. Surface-induced changes of the material properties are not only important for the solid support but also for the liquid itself. In particular, it is now well established that water at the interface is substantially different from bulk water, even in the proximity of apparently inert surfaces such as a simple metal. The complex chemistry at liquid-solid interfaces is typically fundamental to heterogeneous catalysis and electrochemistry, and has become especially topical in connection with the search for new materials for energy production. A quite remarkable example is the development of cheap yet efficient solar cells, whose basic components are dye molecules grafted to the surface of an oxide material and in contact with an electrolytic solution. In life science, the most important liquid-solid interfaces are the water-cell-membrane interfaces. Phenomena occurring at the surface of phospholipid bilayers control the docking of proteins, the transmission of signals as well as transport of molecules in and out of the cell. Recently the development of bio-compatible materials has lead to research on the interface between bio-compatible material and lipid/proteins in aqueous solution. Gaining a microscopic insight into the processes occurring at liquid-solid interfaces is therefore fundamental to a wide range of disciplines. This special section collects some contributions to the CECAM Workshop 'Liquid/Solid interfaces: Structure and Dynamics from Spectroscopy and Simulations' which took place in Lausanne, Switzerland in June 2011. Our main aim was to bring together knowledge and expertise from different communities in order to advance our microscopic understanding of the structure and dynamics of liquids at interfaces. In particular, one of our ambitions was to foster discussion between the experimental and theoretical

  7. Dynamics of Photoexcitation and Photocatalysis at Nanostructured Carbon Interfaces

    Science.gov (United States)

    2015-07-14

    S) AND ADDRESS(ES) University of Wisconsin System Research and Sponsored Programs 21 N. Park Street, Suite 6401 Madison, WI 53715-1218 8...Detailed Accomplishments: 1. Dynamics of energy transport in coupled carbon nanotube materials for next generation solar cells In previous annual reports...isolated thin films and solar cells made from coupled nanotubes. First, we have used poly(fluorene) derivatives to isolate an intentionally polydisperse

  8. Dynamic Model of Contact Interface between Stator and Rotor

    OpenAIRE

    Zhao, Zenghui; Wang, Yuping; Yuan, YiKun; Zhao, Xiangdong

    2013-01-01

    Based on the equivalent principle, a linear spring contact model was established for the friction layer between stator and rotor. Different contact conditions were described by a distance index δ. Detailed analysis of the nonlinear contact behavior especially the static and dynamic slipping was carried on using a space-time equation. A contact deflection angle was proposed to quantitatively express the influence of friction force on the output performance. A more precision simulation model wa...

  9. Three-Dimensional Problems in the Dynamic Fracture Mechanics of Materials with Interface Cracks (Review)

    Science.gov (United States)

    Guz, A. N.; Guz, I. A.; Men'shikov, A. V.; Men'shikov, V. A.

    2013-01-01

    Three-dimensional problems in the dynamic fracture mechanics of materials with interface cracks are considered as nonclassical problems of fracture mechanics. Physically correct results in fracture mechanics in the case where the interaction of the crack edges must be taken into account are analyzed. The linear (classical) and nonlinear (nonclassical) problems of dynamic fracture mechanics for materials with interface cracks are formulated using the above approaches. A method for solving three-dimensional linear dynamic problems based on boundary integral equations for piecewise-homogeneous materials and the boundary-element method is outlined. This method can be used for incremental solution of nonlinear problems. The method involves the regularization of hypersingular integrals. New classes of three-dimensional linear dynamic problems for circular and elliptic interface cracks are solved. Numerical values of stress intensity factors obtained with the linear problem formulation are the first step toward calculating them in the nonlinear formulation. The first results obtained in solving nonlinear dynamic problems for interface cracks with interacting faces are briefly analyzed

  10. Phase-field investigation on the non-equilibrium interface dynamics of rapid alloy solidification

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jeong [Iowa State Univ., Ames, IA (United States)

    2011-01-01

    The research program reported here is focused on critical issues that represent conspicuous gaps in current understanding of rapid solidification, limiting our ability to predict and control microstructural evolution (i.e. morphological dynamics and microsegregation) at high undercooling, where conditions depart significantly from local equilibrium. More specifically, through careful application of phase-field modeling, using appropriate thin-interface and anti-trapping corrections and addressing important details such as transient effects and a velocity-dependent (i.e. adaptive) numerics, the current analysis provides a reasonable simulation-based picture of non-equilibrium solute partitioning and the corresponding oscillatory dynamics associated with single-phase rapid solidification and show that this method is a suitable means for a self-consistent simulation of transient behavior and operating point selection under rapid growth conditions. Moving beyond the limitations of conventional theoretical/analytical treatments of non-equilibrium solute partitioning, these results serve to substantiate recent experimental findings and analytical treatments for single-phase rapid solidification. The departure from the equilibrium solid concentration at the solid-liquid interface was often observed during rapid solidification, and the energetic associated non-equilibrium solute partitioning has been treated in detail, providing possible ranges of interface concentrations for a given growth condition. Use of these treatments for analytical description of specific single-phase dendritic and cellular operating point selection, however, requires a model for solute partitioning under a given set of growth conditions. Therefore, analytical solute trapping models which describe the chemical partitioning as a function of steady state interface velocities have been developed and widely utilized in most of the theoretical investigations of rapid solidification. However, these

  11. Substructurability: the effect of interface location on a real-time dynamic substructuring test

    Science.gov (United States)

    Terkovics, N.; Neild, S. A.; Lowenberg, M.; Szalai, R.; Krauskopf, B.

    2016-08-01

    A full-scale experimental test for large and complex structures is not always achievable. This can be due to many reasons, the most prominent one being the size limitations of the test. Real-time dynamic substructuring is a hybrid testing method where part of the system is modelled numerically and the rest of the system is kept as the physical test specimen. The numerical-physical parts are connected via actuators and sensors and the interface is controlled by advanced algorithms to ensure that the tested structure replicates the emulated system with sufficient accuracy. The main challenge in such a test is to overcome the dynamic effects of the actuator and associated controller, that inevitably introduce delay into the substructured system which, in turn, can destabilize the experiment. To date, most research concentrates on developing control strategies for stable recreation of the full system when the interface location is given a priori. Therefore, substructurability is mostly studied in terms of control. Here, we consider the interface location as a parameter and study its effect on the stability of the system in the presence of delay due to actuator dynamics and define substructurability as the system's tolerance to delay in terms of the different interface locations. It is shown that the interface location has a major effect on the tolerable delays in an experiment and, therefore, careful selection of it is necessary.

  12. Molecular dynamics, density functional theory of the metal--electrolyte interface

    Energy Technology Data Exchange (ETDEWEB)

    Price, D.L. [Department of Physics, University of Memphis, Memphis Tennessee 38152 (United States); Halley, J.W. [School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

    1995-04-22

    Quantitative, predictive theories for metal--electrolyte interfaces require an atomic-scale representation of the interface, which must include an accurate statistical description of a polar fluid in contact with a solid surface; and also a description of the electronic density and structure of a metal surface in contact with a fluid. Such a complex system presents a difficult computational problem, and has been dealt with in the past essentially by parts; either by molecular dynamics calculations of the fluid structure, or density functional calculations of the metal--surface electronic structure. A complete and self-consistent determination of the surface structure would, however, involve a simultaneous calculation of both the atomic and electronic structure of the interface. This suggests a combination of these two calculational techniques, and it is just this sort of molecular dynamics and density functional combination which comprises the Car--Parrinello, and related, methods. We have developed a Car--Parrinello type combination of molecular dynamics and density functional methods, suitable for application to the metal--electrolyte interface. We briefly describe this calculation and discuss our initial results for a fairly simple metal--water interface.

  13. Dynamic protein adsorption at the polyurethane copolymer/water interface

    Energy Technology Data Exchange (ETDEWEB)

    Yaseen, M; Lu, J R [Biological Physics Group, School of Physics and Astronomy, University of Manchester (United Kingdom); Salacinski, H J; Seifalian, A M [Biomaterial and Tissue Engineering Centre, Royal Free and University College Medical School, UCL (United Kingdom)], E-mail: j.lu@manchester.ac.uk

    2008-09-01

    Polyurethanes (PU) and their polymeric derivatives are widely used in the manufacturing of medical devices. It is important to understand how protein adsorbs onto PU materials as this molecular process directly implicates surface biocompatibility. In this work, we compared protein adsorption at the PU film surfaces with that from the hydrophilic silicon oxide. Two PU polymers were used, a commercial polyurethane (PUA) and a novel poly(carbonate-urea)urethane matrix containing silsesquioxanes (PU4). AFM imaging revealed micro-domain segregation on both PU surfaces, but the incorporation of pendent silsesquioxanes made the PU4 surface much rougher, with the outer surface comprised of soft upper PU segments and lower PU-silsesquioxane hard segments. It appeared that fibrinogen was preferable to adsorb onto the upper soft PU segments. The spectroscopic ellipsometry (SE) measurements at the PU film/solution interface showed that human serum albumin (HSA) adsorption was little affected by surface chemistry whilst fibrinogen adsorption was much greater on the two PU surfaces indicating a strong surface effect. Further studies revealed that HSA adsorption was reversible on hydrophilic SiO{sub 2} against changes in pH from 5 to 7, but irreversible on the two PU surfaces. In contrast, fibrinogen adsorption against the same pH cycling was found to be irreversible on all three surfaces. The different extent of irreversibility was clearly indicative of different interfacial interactions. Sequential protein adsorption revealed that the PU4 surface shared similar physiochemical properties to the SiO{sub 2} surface, demonstrating the success in incorporating the siloxane pendant nanocages. The knowledge of protein surface structure and behaviour may lead to the development of effective means to control surface biocompatibility.

  14. Dynamic contrast enhanced MRI in prostate cancer

    Energy Technology Data Exchange (ETDEWEB)

    Alonzi, Roberto [Marie Curie Research Wing, Mount Vernon Cancer Centre, Rickmansworth Road, Northwood, Middlesex, HA6 2RN (United Kingdom)], E-mail: robertoalonzi@btinternet.com; Padhani, Anwar R. [Paul Strickland Scanner Centre, Mount Vernon Cancer Centre, Rickmansworth Road, Northwood, Middlesex, HA6 2RN (United Kingdom); Synarc Inc. 575 Market Street, San Francisco, CA 94105 (United States)], E-mail: anwar.padhani@paulstrickland-scannercentre.org.uk; Allen, Clare [Department of Imaging, University College Hospital, London, 235 Euston Road, NW1 2BU (United Kingdom)], E-mail: clare.allen@uclh.nhs.uk

    2007-09-15

    Angiogenesis is an integral part of benign prostatic hyperplasia (BPH), is associated with prostatic intraepithelial neoplasia (PIN) and is key to the growth and for metastasis of prostate cancer. Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) using small molecular weight gadolinium chelates enables non-invasive imaging characterization of tissue vascularity. Depending on the technique used, data reflecting tissue perfusion, microvessel permeability surface area product, and extracellular leakage space can be obtained. Two dynamic MRI techniques (T{sub 2}*-weighted or susceptibility based and T{sub 1}-weighted or relaxivity enhanced methods) for prostate gland evaluations are discussed in this review with reference to biological basis of observations, data acquisition and analysis methods, technical limitations and validation. Established clinical roles of T{sub 1}-weighted imaging evaluations will be discussed including lesion detection and localisation, for tumour staging and for the detection of suspected tumour recurrence. Limitations include inadequate lesion characterisation particularly differentiating prostatitis from cancer, and in distinguishing between BPH and central gland tumours.

  15. Dynamics of monolayers adsorbed at the solid-liquid interface

    Energy Technology Data Exchange (ETDEWEB)

    Clarke, Stuart M. [BP Institute, Department of Chemistry, Univ. of Cambridge (United Kingdom); Inaba, Akira [Department of Chemistry, Osaka Univ., Osaka (Japan); Arnold, Thomas [Physical and Theoretical Chemistry Laboratory, Univ. of Oxford (United Kingdom); Thomas, Robert K.; Castro, Miguel A. [Instituto de Ciencia de Materiale de Sevilla, Avda. Americo Vespucio (Spain)

    2001-03-01

    Recently we have demonstrated, using a variety of techniques including calorimetry and neutron diffraction, the existence of translationally ordered two-dimensional phases of short chain n-alkanes (CnH2n+2) on the surface of graphite. Dodecane (n=12) is unusual in that it is found from diffraction experiments to adopt a structure with parallel molecules, similar to that seen for the odd alkanes, and exhibits a monolayer phase transition at 281 K, before the layer melts at 286 K. This additional transition is reminiscent of the rotator phase transitions seen in the longer bulk alkanes. In this work we present elastic incoherent neutron scattering (EISF) data which probe the dynamics of the monolayer and clearly demonstrate that the adsorbed layer is indeed far from static but has a high degree of rotational mobility. (author)

  16. Static and dynamic properties of poly(3-hexylthiophene) films at liquid/vacuum interfaces.

    Science.gov (United States)

    Yimer, Yeneneh Y; Tsige, Mesfin

    2012-11-28

    All-atom molecular dynamics simulations are used to study static and dynamic properties of poly(3-hexylthiophene) (P3HT) films at liquid/vacuum interfaces with regards to their dependence on both temperature and molecular weight. The static properties of the films are characterized by calculating specific volume, interfacial width, orientational ordering of the hexyl groups, and surface tension. The specific volume found to be a monotonically decreasing function of the molecular weight while its dependence on temperature follows the Simha-Somcynsky's equation of state. The orientational ordering calculations show the hexyl groups protruding from the vacuum side of the interface, where the degree of order at the interface is found to be strongly dependent on both temperature and molecular weight. The surface tension values show a linear dependence on temperature and the molecular weight dependence is equally described by both M(-2∕3) and M(-1) power law models. The dynamic properties are quantified by calculating diffusion coefficients for the chain centers-of-mass and thiophene ring segments as well as first-order and second-order end-to-end vector autocorrelations and chain backbone torsion autocorrelation. All calculated dynamic properties show strong dependence on both temperature and molecular weight. All the autocorrelations are well described by Kohlrausch-Williams-Watts equation. Our detailed analysis of the static and dynamic properties of P3HT films show that the calculated static and dynamic properties data can be fit with well-known polymer models.

  17. Real Time Dynamics of Laser Activated Interface Processes at the Molecular Scale

    Energy Technology Data Exchange (ETDEWEB)

    Eric Borguet

    2007-12-30

    Nanotechnology is one of the most interesting and challenging frontiers of science and technology. We are motivated by the belief that progress will come from improved understanding and control of structure, dynamics and reactivity at interfaces. First, we provide a summary of our projects and key findings. The following pages provide a more detailed account.

  18. Typelets - a rule-based evaluation model for dynamic, statically typed user interfaces

    DEFF Research Database (Denmark)

    Elsman, Martin; Schack-Nielsen, Anders

    2014-01-01

    -inference in MLFi, the features allow for type-level programming of user interfaces. The dynamic behavior of typelets are specified using declarative rules. The technique extends the flat spreadsheet programming model with higher-order rule composition techniques, extensive reuse, and type safety. A layout...

  19. Dynamics and applications inspired by bubble bursting at a compound interface

    Science.gov (United States)

    Feng, Jie

    Interfaces between two distinct phases typically include complex molecular and particulate structures. The properties of a complex interface are crucial to the response of many natural and practical systems, and also strongly govern the behaviors of particles near the interface. Therefore, the complex interface plays a key role in a wide range of phenomena involving mass and energy transport, and understanding the underlying physics remains a canonical problem. Inspired by bubble bursting at such a compound interface, this dissertation explores related dynamics and potential applications of the system, and investigates several other examples that highlight the role of the interface. In particular, we show that bubble bursting at the surface of an aqueous surfactant solution coated by an oil layer can disperse oil nanodroplets in the water. The dispersal results from the detachment of an oil spray from the bubble boundary when the bubble collapses, and the droplet size is set by physicochemical interactions between oil and surfactants. Motivated by this study, we propose a new platform to generate functional nanoemulsions. We demonstrate scaled-up synthesis and the capability of encapsulating functional nanomaterials with nanoemulsions. To study the hydrodynamic aspects of the system, we consider the stability of a long free film of liquid composed of two immiscible layers. The approach helps to interpret the behaviors of film rupture before a bubble bursts. Furthermore, the dynamics of bubble bouncing at the compound interface before the bubble comes to rest are then investigated with experiments, numerical simulations and a mass-spring-damper model. To further understand the role of a complex interface in other fluid systems, we use a reciprocal theorem to study the motion of a drop with surfactants immersed in a background flow. In addition, the dynamic response of the interface can be complicated by the surface topography, and an example is shown considering the

  20. Origin, fate and dynamics of macrophages at CNS interfaces

    Science.gov (United States)

    Goldmann, Tobias; Jordão, Marta Joana Costa; Wieghofer, Peter; Prutek, Fabiola; Hagemeyer, Nora; Frenzel, Kathrin; Staszewski, Ori; Kierdorf, Katrin; Amann, Lukas; Krueger, Martin; Locatelli, Giuseppe; Hochgarner, Hannah; Zeiser, Robert; Epelman, Slava; Geissmann, Frederic; Priller, Josef; Rossi, Fabio; Bechmann, Ingo; Kerschensteiner, Martin; Linnarsson, Sten; Jung, Steffen; Prinz, Marco

    2016-01-01

    Perivascular, meningeal and choroid plexus macrophages are non-parenchymal macrophages that mediate immune responses at brain boundaries. Although the origin of parenchymal microglia has recently been elucidated, much less is known about the precursors, the underlying transcriptional program and the dynamics of the other macrophages in the central nervous system (CNS). It has been assumed that they have a high turnover with blood-borne monocytes. However, large scale single-cell RNA-sequencing reveals a striking molecular overlap between perivascular macrophages and microglia but not monocytes. Using several fate mapping approaches and parabiosis we demonstrate that CNS macrophages arise from yolk sac precursors during embryonic development and remain a stable population. Notably, the generation of CNS macrophages relies on the transcription factor Pu.1 whereas myb, Batf3 and Nr4a1 are not required. Upon autoimmune inflammation, macrophages undergo extensive self-renewal by local proliferation. Our data provide challenging new insights into brains innate immune system. PMID:27135602

  1. Molecular Dynamics Investigations of the Ablator/Fuel Interface during Early Stages of Inertial Confinement Fusion

    Science.gov (United States)

    Stanton, Liam; Glosli, James; Murillo, Michael

    2016-10-01

    At the National Ignition Facility, high-powered laser beams are used to compress a small target to generate fusion reactions. A critical issue in achieving this is the understanding of mix at the ablator/fuel interface. Mixing occurs at various length scales, ranging from atomic inter-species diffusion to hydrodynamic instabilities. Because the interface is preheated by energy from the incoming shock, it is important to understand the dynamics before the shock arrives. The interface is in the warm dense matter phase with a deuterium/tritium fuel mixture on one side and a plastic mixture on the other. We would like to understand various aspects of the evolution, including the state of the interface when the main shock arrives, the role of electric field generation at the interface, and the character and time scales for diffusion. We present a multiscale approach to model these processes, which combines molecular dynamics to simulate the ionic degrees of freedom with orbital-free density functional theory to calculate the electronic structure. Simulation results are presented and connections to hydrodynamic models are discussed. This work is performed under the auspices of the U. S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  2. Modeling and numerical simulation of static and dynamic behavior of multilayered plates with interface effects

    Directory of Open Access Journals (Sweden)

    Zaki Smail

    2014-04-01

    Full Text Available In Multilayered structures the interface effects have a wide range of applications in aerospace, automotive and especially in civil engineering. The design and construction of these structures and the account for interface effects require special expertise in modeling, simulation and implementation. Many studies in this case were conducted to address these issues. The objective of this work is the modeling and numerical simulation of static and dynamic behaviors of beams and plates multilayered structures with different types of interfaces. The focus was on the prediction of the behavior of stresses; shears and displacements depending on thickness. The interface can be elastic or viscoelastic of small or large thickness. The state space method has been developed for this purpose. Various types of rolled arbitrary number of isotropic or anisotropic layers structures were considered. The three-dimensional behavior is obtained for different types of static and dynamic loading. The results were compared with those based on the model of Stroh and on the various existing theories of beams and plates. The methodological approach, developed here, will be applied to thick structures, functionally graded, bimorph or multilayer structures and possibly piezoelectric or viscoelastic layered structures with interface effect

  3. Lattice boltzmann study on the contact angle and contact line dynamics of liquid-vapor interfaces.

    Science.gov (United States)

    Zhang, Junfeng; Kwok, Daniel Y

    2004-09-14

    The moving contact line problem of liquid-vapor interfaces was studied using a mean-field free-energy lattice Boltzmann method recently proposed [Phys. Rev. E 2004, 69, 032602]. We have examined the static and dynamic interfacial behaviors by means of the bubble and capillary wave tests and found that both the Laplace equation of capillarity and the dispersion relation were satisfied. Dynamic contact angles followed the general trend of contact line velocity observed experimentally and can be described by Blake's theory. The velocity fields near the interface were also obtained and are in good agreement with fluid mechanics and molecular dynamics studies. Our simulations demonstrated that incorporating interfacial effects into the lattice Boltzmann model can be a valuable and powerful alternative in interfacial studies.

  4. Insulin Aggregation at a Dynamic Solid-Liquid-Air Triple Interface.

    Science.gov (United States)

    Frachon, Thibaut; Bruckert, Franz; Le Masne, Quentin; Monnin, Emmanuel; Weidenhaupt, Marianne

    2016-12-13

    Therapeutic proteins are privileged in drug development because of their exquisite specificity, which is due to their three-dimensional conformation in solution. During their manufacture, storage, and delivery, interactions with material surfaces and air interfaces are known to affect their stability. The growing use of automated devices for handling and injection of therapeutics increases their exposure to protocols involving intermittent wetting, during which the solid-liquid and liquid-air interfaces meet at a triple contact line, which is often dynamic. Using a microfluidic setup, we analyze the effect of a moving triple interface on insulin aggregation in real time over a hydrophobic surface. We combine thioflavin T fluorescence and reflection interference microscopy to concomitantly monitor insulin aggregation and the morphology of the liquid as it dewets the surface. We demonstrate that insulin aggregates in the region of a moving triple interface and not in regions submitted to hydrodynamic shear stress alone, induced by the moving liquid. During dewetting, liquid droplets form on the surface anchored by adsorbed proteins, and the accumulation of amyloid aggregates is observed exclusively as fluorescent rings growing eccentrically around these droplets. The fluorescent rings expand until the entire channel surface sweeped by the triple interface is covered by amyloid fibers. On the basis of our experimental results, we propose a model describing the growth mechanism of insulin amyloid fibers at a moving triple contact line, where proteins adsorbed at a hydrophobic surface are exposed to the liquid-air interface.

  5. Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.

  6. Real-time measurements to characterize dynamics of emulsion interface during simulated intestinal digestion.

    Science.gov (United States)

    Pan, Yuanjie; Nitin, N

    2016-05-01

    Efficient delivery of bioactives remains a critical challenge due to their limited bioavailability and solubility. While many encapsulation systems are designed to modulate the digestion and release of bioactives within the human gastrointestinal tract, there is limited understanding of how engineered structures influence the delivery of bioactives. The objective of this study was to develop a real-time quantitative method to measure structural changes in emulsion interface during simulated intestinal digestion and to correlate these changes with the release of free fatty acids (FFAs). Fluorescence resonant energy transfer (FRET) was used for rapid in-situ measurement of the structural changes in emulsion interface during simulated intestinal digestion. By using FRET, changes in the intermolecular spacing between the two different fluorescent probes labeled emulsifier were characterized. Changes in FRET measurements were compared with the release of FFAs. The results showed that bile salts and pancreatic lipase interacted immediately with the emulsion droplets and disrupted the emulsion interface as evidenced by reduction in FRET efficacy compared to the control. Similarly, a significant amount of FFAs was released during digestion. Moreover, addition of a second layer of polymers at emulsion interface decreased the extent of interface disruption by bile salts and pancreatic lipase and impacted the amount or rate of FFA release during digestion. These results were consistent with the lower donor/acceptor ratio of the labeled probes from the FRET result. Overall, this study provides a novel approach to analyze the dynamics of emulsion interface during digestion and their relationship with the release of FFAs.

  7. Structure and dynamics of plasma interfaces in laser-driven hohlraums

    Science.gov (United States)

    Li, C. K.; Sio, H.; Frenje, J. A.; Séguin, F. H.; Birkel, A.; Petrasso, R. D.; Wilks, S. C.; Amendt, P. A.; Remington, B. A.; Masson-Laborde, P.-E.; Laffite, S.; Tassin, V.; Betti, R.; Sanster, T. C.; Fitzsimmons, P.; Farrell, M.

    2016-10-01

    Understanding the structure and dynamics of plasma interfaces in laser-driven hohlraums is important because of their potential effects on capsule implosion dynamics. To that end, a series of experiments was performed to explore critical aspects of the hohlraum environment, with particular emphasis on the role of self-generated spontaneous electric and magnetic fields at plasma interfaces, including the interface between fill-gas and Au-blowoff. The charged fusion products (3-MeV DD protons and 14.7-MeV D3He protons generated in shock-driven, D3He filled backlighter capsule) pass through the subject hohlraum and form images on CR-39 nuclear track detectors, providing critical information. Important physics topics, including ion diffusive mix and Rayleigh-Taylor instabilities, will be studied to illuminate ion kinetic dynamics and hydrodynamic instability at plasma interfaces in laser-driven hohlraums. This work was supported in part by LLE, the U.S. DoE (NNSA, NLUF) and LLNL.

  8. Dynamics of a solid sphere bouncing on or penetrating through a liquid-air interface

    Science.gov (United States)

    Kim, Seong Jin; Jung, Sunghwan; Lee, Sungyon

    2014-11-01

    In this study, we investigate the dynamics of a solid particle moving from liquid to air through a liquid-air interface. The experimental setup consists of an air-piston system that shoots a solid particle into water towards the free surface from below. Experimental results indicate that the particle either penetrates or bounces back depending on the particle size, impact speed, and surface tension. In particular, the particle needs to overcome the resistive interfacial forces in order to penetrate through the liquid-air interface. This transition from bouncing to penetration regimes is captured theoretically by conducting a simple force balance and is further compared with experiments.

  9. The dynamic histopathologic spectrum of lung cancer.

    Science.gov (United States)

    Yesner, R

    1981-01-01

    The APUD concept has postulated that pulmonary carcinoids and small cell carcinomas arise from the neural crest. In development from hypothesis to tautology is traced, and evidence is presented that all pulmonary epithelial tumors arise from the primitive endoderm. Morphologic studies show that a dynamic spectrum exists. Not only do various cell types appear within a single section, but cell types may change from biopsy to autopsy with or without chemotherapy. The spectrum is sustained at the ultramicroscopic level in regard to organelles such as desmosomes, tonofibrils, and dense core granules. Secretory products such as ACTH and L-dopa decarboxylase also show that all lung cancers are related. Epidemiologic evidence indicates that small cell carcinomas in uranium miners occur after prolonged squamous cell dysplasia, and that carcinoids occur independently of external carcinogens, but show transitions to other tumors. Finally, experimental evidence indicates that the K cells, to which carcinoids are most closely related, are of local origin.

  10. Dynamics of rigid microparticles at the interface of co-flowing immiscible liquids in a microchannel.

    Science.gov (United States)

    Jayaprakash, K S; Banerjee, U; Sen, A K

    2017-05-01

    We report the dynamical migration behavior of rigid polystyrene microparticles at an interface of co-flowing streams of primary CP1 (aqueous) and secondary CP2 (oils) immiscible phases at low Reynolds numbers (Re) in a microchannel. The microparticles initially suspended in the CP1 either continue to flow in the bulk CP1 or migrate across the interface into CP2, when the stream width of the CP1 approaches the diameter of the microparticles. Experiments were performed with different secondary phases and it is found that the migration criterion depends on the sign of the spreading parameter S and the presence of surfactant at the interface. To substantiate the migration criterion, experiments were also carried out by suspending the microparticles in CP2 (oil phase). Our study reveals that in case of aqueous-silicone oil combination, the microparticles get attached to the interface since S90°. For complete detachment of microparticles from the interface into the secondary phase, additional energy ΔG is needed. We discuss the role of interfacial perturbation, which causes detachment of microparticles from the interface. In case of mineral and olive oils, the surfactants present at the interface prevents attachment of the microparticles to the interface due to the repulsive disjoining pressure. Finally, using a aqueous-silicone oil system, we demonstrate size based sorting of microparticles of size 25μm and 15μm respectively from that of 15μm and 10μm and study the variation of separation efficiency η with the ratio of the width of the aqueous stream to the diameter of the microparticles ρ.

  11. Tumor clone dynamics in lethal prostate cancer.

    Science.gov (United States)

    Carreira, Suzanne; Romanel, Alessandro; Goodall, Jane; Grist, Emily; Ferraldeschi, Roberta; Miranda, Susana; Prandi, Davide; Lorente, David; Frenel, Jean-Sebastien; Pezaro, Carmel; Omlin, Aurelius; Rodrigues, Daniel Nava; Flohr, Penelope; Tunariu, Nina; S de Bono, Johann; Demichelis, Francesca; Attard, Gerhardt

    2014-09-17

    It is unclear whether a single clone metastasizes and remains dominant over the course of lethal prostate cancer. We describe the clonal architectural heterogeneity at different stages of disease progression by sequencing serial plasma and tumor samples from 16 ERG-positive patients. By characterizing the clonality of commonly occurring deletions at 21q22, 8p21, and 10q23, we identified multiple independent clones in metastatic disease that are differentially represented in tissue and circulation. To exemplify the clinical utility of our studies, we then showed a temporal association between clinical progression and emergence of androgen receptor (AR) mutations activated by glucocorticoids in about 20% of patients progressing on abiraterone and prednisolone or dexamethasone. Resistant clones showed a complex dynamic with temporal and spatial heterogeneity, suggesting distinct mechanisms of resistance at different sites that emerged and regressed depending on treatment selection pressure. This introduces a management paradigm requiring sequential monitoring of advanced prostate cancer patients with plasma and tumor biopsies to ensure early discontinuation of agents when they become potential disease drivers.

  12. Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study

    Science.gov (United States)

    Benjamin, Ilan; Pohorille, Andrew

    1993-01-01

    The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.

  13. Crack propagation through adhesive interface in glass driven by dynamic loading

    Science.gov (United States)

    Park, Hwun

    Dynamic crack behaviors at glass interfaces were investigated to understand dynamic failure mechanisms of glass. To produce highly intensive and rapidly increasing loading, glass specimens jointed with epoxy adhesive in edge-to-edge configurations were impacted on their notched edges with plastic projectiles. Cracks developed from the notch and propagated into the interfaces between glass plates at the maximum speed. The patterns of crack propagation through the interfaces were observed to depend on the interface's conditions. Crack propagation stops at the interface where no adhesive was applied. The crack penetrates through the interface where two glass plates were bonded directly without any space. If the interface has finite thickness of an adhesive layer, a crack passing through the interface branches into multiple cracks immediately when it extends to the second glass plate. Both of the slow crack speed in the epoxy adhesive and resistance for crack initiation in the second glass account for the delay in crack propagation at the interface. The surface conditions of glass at the interface affect the resistance for crack initiation. Mirror-like polished surfaces have better resistance than rough surfaces trimmed by a water jet. If the polished surface is etched with hydrofluoric acid to remove surface flaws, the glass surfaces have higher strength and resistance for damage. This etched glass even ceases crack propagation completely with a sufficiently thick adhesive layer. Crack branching has been an open topic. Exact explanation has not been given yet. As the consistent shape of crack branching are created with the proposed method, diagnostics experiments were conducted to reveal the nature of crack branching. To investigate interaction between stress propagation and crack branching, stress histories synchronizing with high speed images were measured. Two types of specimen were used to vary stress distribution during crack propagation. The apex angle of

  14. Nonlinear dynamics theory on the steady state interface pattern during solidification of a dilute binary alloy

    Institute of Scientific and Technical Information of China (English)

    王自东; 胡汉起

    1997-01-01

    The nonlinear dynamics equations of the time dependence of the perturbation amplitude of the solid/ liquid interface during unidirectional solidification of a dilute binary alloy are established. The solutions to these equations are obtained, and the condition of the initial steady state growth of the cellular and dendritic structure after the planar solid/liquid interface bifurcates (mGc> G) with the increase of the growth rate is given. The condition of the steady state growth of fine cellular and dendritic structure in the beginning after the coarse dendrites bifurcate ( mGc<Γw2 + G) under the rapid solidification is obtained. The relationship of the steady state cell and dendrite tip radius, the perturbation amplitude and wavelength at the solid/liquid interface is presented.

  15. A bidirectional brain-machine interface connecting alert rodents to a dynamical system.

    Science.gov (United States)

    Boi, Fabio; Semprini, Marianna; Mussa Ivaldi, Ferdinando A; Panzeri, Stefano; Vato, Alessandro

    2015-01-01

    We present a novel experimental framework that implements a bidirectional brain-machine interface inspired by the operation of the spinal cord in vertebrates that generates a control policy in the form of a force field. The proposed experimental set-up allows connecting the brain of freely moving rats to an external device. We tested this apparatus in a preliminary experiment with an alert rat that used the interface for acquiring a food reward. The goal of this approach to bidirectional interfaces is to explore the role of voluntary neural commands in controlling a dynamical system represented by a small cart moving on vertical plane and connected to a water/pellet dispenser.

  16. Nonequilibrium population dynamics of phenotype conversion of cancer cells.

    Directory of Open Access Journals (Sweden)

    Joseph Xu Zhou

    Full Text Available Tumorigenesis is a dynamic biological process that involves distinct cancer cell subpopulations proliferating at different rates and interconverting between them. In this paper we proposed a mathematical framework of population dynamics that considers both distinctive growth rates and intercellular transitions between cancer cell populations. Our mathematical framework showed that both growth and transition influence the ratio of cancer cell subpopulations but the latter is more significant. We derived the condition that different cancer cell types can maintain distinctive subpopulations and we also explain why there always exists a stable fixed ratio after cell sorting based on putative surface markers. The cell fraction ratio can be shifted by changing either the growth rates of the subpopulations (Darwinism selection or by environment-instructed transitions (Lamarckism induction. This insight can help us to understand the dynamics of the heterogeneity of cancer cells and lead us to new strategies to overcome cancer drug resistance.

  17. The Silica-Water Interface from the Analysis of Molecular Dynamic Simulations

    KAUST Repository

    Lardhi, Sheikha F.

    2013-05-01

    Surface chemistry is an emerging field that can give detailed insight about the elec- tronic properties and the interaction of complex material surfaces with their neigh- bors. This is for both solid-solid and solid-liquid interfaces. Among the latter class, the silica-water interface plays a major role in nature. Silica is among the most abundant materials on earth, as well in advanced technological applications such as catalysis and nanotechnology. This immediately indicates the relevance of a detailed understanding of the silica-water interface. In this study, we investigate the details of this interaction at microscopic level by analyzing trajectories obtained with ab initio molecular dynamic simulations. The system we consider consists of bulk liquid water confined between two β-cristobalite silica surfaces. The molecular dynamics were generated with the CP2K, an ab initio molecular dynamic simulation tool. The simulations are 25 picoseconds long, and the CP2K program was run on 64 cores on a supercomputer cluster. During the simulations the program integrates Newton’s equations of motion for the system and generates the trajectory for analysis. For analysis, we focused on the following properties that characterize the silica water interface. We calculated the density profile of the water layers from the silica surface, and we also calculated the radial distribution function (RDF) of the hydrogen bond at the silanols on the silica surface. The main focus of this thesis is to write the programs for calculating the atom density profile and the RDF from the generated MD trajectories. The atomic probability density profile shows that water is strongly adsorbed on the (001) cristobalite surface, while the RDF indicates differently ad- sorbed water molecules in the first adsorption layer. As final remark, the protocol and the tools developed in this thesis can be applied to the study of basically any crystal-water interface.

  18. First-Principles Simulation of Hot Electron Dynamics at Silicon-Molecule Interfaces

    Science.gov (United States)

    Li, Lesheng; Kanai, Yosuke; Kanai Group Team

    2015-03-01

    Hot carrier relaxation process at an interface between semiconductor and molecular ligands is of great importance for a number of technological applications ranging from photo-electrochemical cells to quantum-dot light emitting diodes. Although a number of spectroscopic experiments suggest important role of molecular ligands at surface in the hot carrier relaxation, a quantitative understanding has not been developed. We investigate the hot electron relaxation process through synergetic use of first-principles molecular dynamics (FPMD), fewest switch surface hopping (FSSH) algorithm, and GW calculations. Using FSSH stochastic dynamics simulation based on non-adiabatic couplings from FPMD and quasi-particle energy level alignment at the interface, we investigate the role of molecular passivation at silicon (111) surface as a representative example. We will discuss how different types of molecules influence the relaxation process and elucidate important factors controlling the relaxation time scale.

  19. Shape-Tunable Charge Carrier Dynamics at the Interfaces between Perovskite Nanocrystals and Molecular Acceptors

    KAUST Repository

    Ahmed, Ghada H.

    2016-09-19

    Hybrid organic/inorganic perovskites have recently emerged as an important class of materials and have exhibited remarkable performance in photovoltaics. To further improve their device efficiency, an insightful understanding of the interfacial charge transfer (CT) process is required. Here, we report the first direct experimental observation of the tremendous effect that the shape of perovskite nanocrystals (NCs) has on interfacial CT in the presence of a molecular acceptor. A dramatic change in CT dynamics at the interfaces of three different NC shapes, spheres, platelets, and cubes, is recorded. Our results clearly demonstrate that the mechanism of CT is significantly affected by the NC shape. More importantly, the results demonstrate that complexation on the NC surface acts as an additional driving force not only to tune the CT dynamics but also to control the reaction mechanism at the interface. This observation opens a new venue for further developing perovskite NCs-based applications.

  20. Capturing the transient species at the electrode-electrolyte interface by in situ dynamic molecular imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Jiachao; Zhou, Yufan; Hua, Xin; Liu, Songqin; Zhu, Zihua; Yu, Xiao-Ying

    2016-09-01

    The electrochemical interface between the solid electrode and liquid electrolyte has long been studied because of its importance in electrical energy storage, material synthesis, catalysis, and energy conversions.1 However, such interfaces are complex and extremely difficult to observe directly and are poorly under-stood due to lack of true in situ tools.2 Although electrochemical techniques have been widely used to investigate such interfaces, they are based on macroscopic models or current changes that could not provide direct ionic and molecular information of the interfacial structure. Many in situ and ex situ spectroscopy and microscopy techniques have been used to study the solid–liquid (s–l) interface.3,4 In situ TEM in sealed liquid cells has notably become a popular choice to provide structural information of s–l at the atomic level.5,6 However, real-time spatial mapping of the ionic and molecular intermediate species at the dynamic inter-face still remains a key challenge.

  1. An extensible interface for QM/MM molecular dynamics simulations with AMBER.

    Science.gov (United States)

    Götz, Andreas W; Clark, Matthew A; Walker, Ross C

    2014-01-15

    We present an extensible interface between the AMBER molecular dynamics (MD) software package and electronic structure software packages for quantum mechanical (QM) and mixed QM and classical molecular mechanical (MM) MD simulations within both mechanical and electronic embedding schemes. With this interface, ab initio wave function theory and density functional theory methods, as available in the supported electronic structure software packages, become available for QM/MM MD simulations with AMBER. The interface has been written in a modular fashion that allows straight forward extensions to support additional QM software packages and can easily be ported to other MD software. Data exchange between the MD and QM software is implemented by means of files and system calls or the message passing interface standard. Based on extensive tests, default settings for the supported QM packages are provided such that energy is conserved for typical QM/MM MD simulations in the microcanonical ensemble. Results for the free energy of binding of calcium ions to aspartate in aqueous solution comparing semiempirical and density functional Hamiltonians are shown to demonstrate features of this interface.

  2. Waste pretreatment and interfacing system dynamic simulation model (ITHINK model) FY-96 year-end report

    Energy Technology Data Exchange (ETDEWEB)

    Harmsen, R.W.

    1996-09-30

    The Waste Pretreatment and Interfacing Systems Dynamic Simulation (ITHINK) Model (see WHC-SD-WM-DR-013) was originally created to investigate the required pretreatment facility processing rates required to meet the Tri-Party Agreement (TPA) waste vitrification milestones. The TPA milestones are satisfied by retrieving the TX tank farm (salt cake) single-shell tanks (SSTs)first and by utilizing a relatively constant retrieval rate to the year 2018 when retrieval is completed.

  3. Dynamics at Solid State Surfaces and Interfaces, Volume 1 Current Developments

    CERN Document Server

    Bovensiepen, Uwe; Wolf, Martin

    2010-01-01

    This two-volume work covers ultrafast structural and electronic dynamics of elementary processes at solid surfaces and interfaces, presenting the current status of photoinduced processes. Providing valuable introductory information for newcomers to this booming field of research, it investigates concepts and experiments, femtosecond and attosecond time-resolved methods, as well as frequency domain techniques. The whole is rounded off by a look at future developments.

  4. Molecular dynamics study of the Cu-water interface in the presence of chlorine

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Y.; Mazzolo, A.; Halley, J.W. [Univ. of Minnesota, Minneapolis, MN (United States). School of Physics and Astronomy; Price, D.L. [Univ. of Memphis, TN (United States). Dept. of Physics

    1998-05-01

    As part of a program to model and explain the sensitivity of electron transfer reactions at metal interfaces to trace amounts of chloride in aqueous solutions, preliminary results on a direct dynamics model for the adsorption of chloride ion on a copper 100 surface in water are reported. The model predicts the charge state of the chlorine in water and vacuum correctly, but gives a solvation energy which is too large. Possible reasons for this are discussed.

  5. DYNAMIC PROPAGATION PROBLEM ON DUGDALE MODEL OF MODE Ⅲ INTERFACE CRACK

    Institute of Scientific and Technical Information of China (English)

    L(U) Nian-chun; CHENG Yun-hong; TIAN Xiu-bo; CHENG Jin

    2005-01-01

    By the theory of complex functions, the dynamic propagation problem on Dugdale model of mode Ⅲ interface crack for nonlinear characters of materials was studied. The general expressions of analytical solutions are obtained by the methods of self-similar functions. The problems dealt with can be easily transformed into RiemannHilbert problems and their closed solutions are attained rather simply by this approach.After those solutions were utilized by superposition theorem, the solutions of arbitrarily complex problems could be obtained.

  6. Dynamics of surfactant sorption at the air/water interface: continuous-flow tensiometry.

    Science.gov (United States)

    Svitova, T F; Wetherbee, M J; Radke, C J

    2003-05-01

    Dynamic interfacial tensiometry, gauged by axisymmetric drop shape analysis of static drops or bubbles, provides useful information on surfactant adsorption kinetics. However, the traditional pendant-drop methodology is not readily amenable to the study of desorption kinetics. Thus, the question of sorption reversibility is difficult to assess by this technique. We extend classical pendant/sessile drop dynamic tensiometry by immersing a sessile bubble in a continuously mixed optical cell. Ideal-mixed conditions are established by stirring and by constant flow through the cell. Aqueous surface-active-agent solutions are either supplied to the cell (loading) or removed from the cell by flushing with water (washout), thereby allowing study of both adsorption and desorption kinetics. Well-mixed conditions and elimination of any mass transfer resistance permit direct identification of sorption kinetic barriers to and from the external aqueous phase with time constants longer than the optical-cell residence time. The monodisperse nonionic surfactant ethoxy dodecyl alcohol (C(12)E(5)), along with cationic cetyltrimethyl ammonium bromide (CTAB) in the presence of added salt, adsorbs and desorbs instantaneously at the air/water interface. In these cases, the experimentally observed dynamic-tension curves follow the local-equilibrium model precisely for both loading and washout. Accordingly, these surfactants below their critical micelle concentrations (CMC) exhibit no detectable sorption-activation barriers on time scales of order a min. However, the sorption dynamics of dilute CTAB in the absence of electrolyte is markedly different from that in the presence of KBr. Here CTAB desorption occurs at local equilibrium, but the adsorption rate is kinetically limited, most likely due to an electrostatic barrier arising as the charged surfactant accumulates at the interface. The commercial, polydisperse nonionic surfactant ethoxy nonylphenol (NP9) loads in good agreement with

  7. Computer simulation study of surface wave dynamics at the crystal--melt interface

    CERN Document Server

    Benet, Jorge; Sanz, Eduardo

    2014-01-01

    We study, by means of computer simulations, the crystal-melt interface of three different systems: hard-spheres, Lennard Jones and the TIP4P/2005 water model. In particular, we focus on the dynamics of surface waves. We observe that the processes involved in the relaxation of surface waves are characterized by distinct time scales: a slow one related to the continuous recrystallization and melting, that is governed by capillary forces; and a fast one which we suggest to be due to a combination of processes that quickly cause small perturbations to the shape of the interface (like e. g. Rayleigh waves, subdiffusion, or attachment/detachment of particles to/from the crystal). The relaxation of surface waves becomes dominated by the slow process as the wavelength increases. Moreover, we see that the slow relaxation is not influenced by the details of the microscopic dynamics. In a time scale characteristic for the diffusion of the liquid phase, the relaxation dynamics of the crystal-melt interface of water is ar...

  8. Phase-field investigation on the non-equilibrium interface dynamics of rapid alloy solidification

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jeong [Iowa State Univ., Ames, IA (United States)

    2011-01-01

    The research program reported here is focused on critical issues that represent conspicuous gaps in current understanding of rapid solidification, limiting our ability to predict and control microstructural evolution (i.e. morphological dynamics and microsegregation) at high undercooling, where conditions depart significantly from local equilibrium. More specifically, through careful application of phase-field modeling, using appropriate thin-interface and anti-trapping corrections and addressing important details such as transient effects and a velocity-dependent (i.e. adaptive) numerics, the current analysis provides a reasonable simulation-based picture of non-equilibrium solute partitioning and the corresponding oscillatory dynamics associated with single-phase rapid solidification and show that this method is a suitable means for a self-consistent simulation of transient behavior and operating point selection under rapid growth conditions. Moving beyond the limitations of conventional theoretical/analytical treatments of non-equilibrium solute partitioning, these results serve to substantiate recent experimental findings and analytical treatments for single-phase rapid solidification. The departure from the equilibrium solid concentration at the solid-liquid interface was often observed during rapid solidification, and the energetic associated non-equilibrium solute partitioning has been treated in detail, providing possible ranges of interface concentrations for a given growth condition. Use of these treatments for analytical description of specific single-phase dendritic and cellular operating point selection, however, requires a model for solute partitioning under a given set of growth conditions. Therefore, analytical solute trapping models which describe the chemical partitioning as a function of steady state interface velocities have been developed and widely utilized in most of the theoretical investigations of rapid solidification. However, these

  9. Protein dynamics governed by interfaces of high polarity and low packing density.

    Directory of Open Access Journals (Sweden)

    Vladimir Espinosa Angarica

    Full Text Available The folding pathway, three-dimensional structure and intrinsic dynamics of proteins are governed by their amino acid sequences. Internal protein surfaces with physicochemical properties appropriate to modulate conformational fluctuations could play important roles in folding and dynamics. We show here that proteins contain buried interfaces of high polarity and low packing density, coined as LIPs: Light Interfaces of high Polarity, whose physicochemical properties make them unstable. The structures of well-characterized equilibrium and kinetic folding intermediates indicate that the LIPs of the corresponding native proteins fold late and are involved in local unfolding events. Importantly, LIPs can be identified using very fast and uncomplicated computational analysis of protein three-dimensional structures, which provides an easy way to delineate the protein segments involved in dynamics. Since LIPs can be retained while the sequences of the interacting segments diverge significantly, proteins could in principle evolve new functional features reusing pre-existing encoded dynamics. Large-scale identification of LIPS may contribute to understanding evolutionary constraints of proteins and the way protein intrinsic dynamics are encoded.

  10. Dynamic infrared imaging for skin cancer screening

    Science.gov (United States)

    Godoy, Sebastián E.; Ramirez, David A.; Myers, Stephen A.; von Winckel, Greg; Krishna, Sanchita; Berwick, Marianne; Padilla, R. Steven; Sen, Pradeep; Krishna, Sanjay

    2015-05-01

    Dynamic thermal imaging (DTI) with infrared cameras is a non-invasive technique with the ability to detect the most common types of skin cancer. We discuss and propose a standardized analysis method for DTI of actual patient data, which achieves high levels of sensitivity and specificity by judiciously selecting pixels with the same initial temperature. This process compensates the intrinsic limitations of the cooling unit and is the key enabling tool in the DTI data analysis. We have extensively tested the methodology on human subjects using thermal infrared image sequences from a pilot study conducted jointly with the University of New Mexico Dermatology Clinic in Albuquerque, New Mexico (ClinicalTrials ID number NCT02154451). All individuals were adult subjects who were scheduled for biopsy or adult volunteers with clinically diagnosed benign condition. The sample size was 102 subjects for the present study. Statistically significant results were obtained that allowed us to distinguish between benign and malignant skin conditions. The sensitivity and specificity was 95% (with a 95% confidence interval of [87.8% 100.0%]) and 83% (with a 95% confidence interval of [73.4% 92.5%]), respectively, and with an area under the curve of 95%. Our results lead us to conclude that the DTI approach in conjunction with the judicious selection of pixels has the potential to provide a fast, accurate, non-contact, and non-invasive way to screen for common types of skin cancer. As such, it has the potential to significantly reduce the number of biopsies performed on suspicious lesions.

  11. i-PI: A Python interface for ab initio path integral molecular dynamics simulations

    Science.gov (United States)

    Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

    2014-03-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic

  12. Dynamics of two-phase interfaces and surface tensions: A density-functional theory perspective

    Science.gov (United States)

    Yatsyshin, Petr; Sibley, David N.; Duran-Olivencia, Miguel A.; Kalliadasis, Serafim

    2016-11-01

    Classical density functional theory (DFT) is a statistical mechanical framework for the description of fluids at the nanoscale, where the inhomogeneity of the fluid structure needs to be carefully accounted for. By expressing the grand free-energy of the fluid as a functional of the one-body density, DFT offers a theoretically consistent and computationally accessible way to obtain two-phase interfaces and respective interfacial tensions in a ternary solid-liquid-gas system. The dynamic version of DFT (DDFT) can be rigorously derived from the Smoluchowsky picture of the dynamics of colloidal particles in a solvent. It is generally agreed that DDFT can capture the diffusion-driven evolution of many soft-matter systems. In this context, we use DDFT to investigate the dynamic behaviour of two-phase interfaces in both equilibrium and dynamic wetting and discuss the possibility of defining a time-dependent surface tension, which still remains in debate. We acknowledge financial support from the European Research Council via Advanced Grant No. 247031 and from the Engineering and Physical Sciences Research Council of the UK via Grants No. EP/L027186 and EP/L020564.

  13. Molecular dynamics of phenol at the liquid-vapor interface of water

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1991-01-01

    Results of molecular dynamics calculations on phenol at the water liquid-vapor interface are presented. The density profile of the center of mass of phenol exhibits a maximum 1 A from the Gibbs surface toward the vapor phase, indicating that the molecule is surface-active. Changes in the profile caused by the interface extend 6 A from the Gibbs surface into the liquid, significantly more than change in the density profile of water. The most probable orientation of the solute at the surface is such that its symmetry axis is perpendicular to the interface with the OH substituent pointing toward the liquid. An additional simulation with benzene shows that this molecule at the surface most often adopts orientations parallel to the interface. Deeper in the liquid all the solutes are preferentially ordered perpendicular to the surface. In the interfacial region the orientational preferences of the solute are primarily determined by cavity formation needed to accommodate the hydrophobic portion of the dissolved molecule.

  14. Dynamic Evolution of the Evaporating Liquid-Vapor Interface in Micropillar Arrays.

    Science.gov (United States)

    Antao, Dion S; Adera, Solomon; Zhu, Yangying; Farias, Edgardo; Raj, Rishi; Wang, Evelyn N

    2016-01-19

    Capillary assisted passively pumped thermal management devices have gained importance due to their simple design and reduction in energy consumption. The performance of these devices is strongly dependent on the shape of the curved interface between the liquid and vapor phases. We developed a transient laser interferometry technique to investigate the evolution of the shape of the liquid-vapor interface in micropillar arrays during evaporation heat transfer. Controlled cylindrical micropillar arrays were fabricated on the front side of a silicon wafer, while thin-film heaters were deposited on the reverse side to emulate a heat source. The shape of the meniscus was determined using the fringe patterns resulting from interference of a monochromatic beam incident on the thin liquid layer. We studied the evolution of the shape of the meniscus on these surfaces under various operating conditions including varying the micropillar geometry and the applied heating power. By monitoring the transient behavior of the evaporating liquid-vapor interface, we accurately measured the absolute location and shape of the meniscus and calculated the contact angle and the maximum capillary pressure. We demonstrated that the receding contact angle which determines the capillary pumping limit is independent of the microstructure geometry and the rate of evaporation (i.e., the applied heating power). The results of this study provide fundamental insights into the dynamic behavior of the liquid-vapor interface in wick structures during phase-change heat transfer.

  15. Effects of Structured Ionomer Interfaces on Water Diffusion: Molecular Dynamics Simulation Insight

    Science.gov (United States)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary

    The dynamics of solvent molecules across structured ionomers interfaces is crucial to innovative technologies with selective controlled transport. These polymers consist of ionizable blocks facilitating transport tethered to mechanical stability enhancing ones, where their incompatibility drives compounded interfaces. Here water penetration through the interface of an A-B-C-B-A co-polymer is probed by atomistic molecular dynamics simulations where C is a randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55, B is poly (ethylene-r-propylene) and A is poly (t-butyl styrene). For f>0, a two-step process with slow diffusion at the early stages is observed where water molecules transverse the hydrophobic rich surface before reaching the hydrophilic regime. Water molecules then diffuse along the percolating network of the ionic center block. Increasing the temperature and sulfonation fraction enhances both the rate of diffusion and the overall water uptake. This work is partially supported by DOE: DE-SC007908.

  16. Characterisation of dynamic couplings at lower limb residuum/socket interface using 3D motion capture.

    Science.gov (United States)

    Tang, Jinghua; McGrath, Michael; Laszczak, Piotr; Jiang, Liudi; Bader, Dan L; Moser, David; Zahedi, Saeed

    2015-12-01

    Design and fitting of artificial limbs to lower limb amputees are largely based on the subjective judgement of the prosthetist. Understanding the science of three-dimensional (3D) dynamic coupling at the residuum/socket interface could potentially aid the design and fitting of the socket. A new method has been developed to characterise the 3D dynamic coupling at the residuum/socket interface using 3D motion capture based on a single case study of a trans-femoral amputee. The new model incorporated a Virtual Residuum Segment (VRS) and a Socket Segment (SS) which combined to form the residuum/socket interface. Angular and axial couplings between the two segments were subsequently determined. Results indicated a non-rigid angular coupling in excess of 10° in the quasi-sagittal plane and an axial coupling of between 21 and 35 mm. The corresponding angular couplings of less than 4° and 2° were estimated in the quasi-coronal and quasi-transverse plane, respectively. We propose that the combined experimental and analytical approach adopted in this case study could aid the iterative socket fitting process and could potentially lead to a new socket design.

  17. Aqueous interfaces with hydrophobic room-temperature ionic liquids: a molecular dynamics study.

    Science.gov (United States)

    Chaumont, A; Schurhammer, R; Wipff, G

    2005-10-13

    We report a molecular dynamics study of the interface between water and (macroscopically) water-immiscible room-temperature ionic liquids "ILs", composed of PF6(-) anions and butyl- versus octyl-substituted methylimidazolium+ cations (noted BMI+ and OMI+). Because the parameters used to simulate the pure ILs were found to exaggerate the water/IL mixing, they have been modified by scaling down the atomic charges, leading to better agreement with the experiment. The comparison of [OMI][PF6] versus [BMI][PF6] ILs demonstrates the importance of the N-alkyl substituent on the extent of solvent mixing and on the nature of the interface. With the most hydrophobic [OMI][PF6] liquid, the "bulk" IL phase is dryer than with the [BMI][PF6] liquid. At the interface, the OMI+ cations retain direct contacts with the bulk IL, whereas the more hydrophilic PF6(-) anions gradually dilute in the local water micro-environment and are thus isolated from the "bulk" IL. The interfacial OMI+ cations are ordered with their imidazolium moiety pointing toward the aqueous side and their octyl chains toward the IL side of the interface. With the [BMI][PF6] liquid, the system gradually evolves from an IL-rich to a water-rich medium, leading to an ill-defined interfacial domain with high intersolvent mixing. As a result, the BMI+ cations are isotropically oriented "at the interface". Because the imidazolium cations are more hydrophobic than the PF6(-) anions, the charge distribution at the interface is heterogeneous, leading to a positive electrostatic potential at the interface with the two studied ILs. Mixing-demixing simulations on [BMI][PF6]/water mixtures are also reported, comparing Ewald versus reaction field treatments of electrostatics. Phase separation is very slow (at least 30 ns), in marked contrast with mixtures involving classical organic liquids, which separate in less than 0.5 ns at the microscopic level. The results allow us to better understand the specificity of the aqueous

  18. Molecular dynamics simulations of the mechanical strength of Si/ Si3 N4 interfaces

    Science.gov (United States)

    Bachlechner, Martina E.; Zhang, Jennifer; Wang, Ye; Schiffbauer, Jarrod; Knudsen, Steven R.; Korakakis, Dimitris

    2005-09-01

    Molecular dynamics simulations are performed on parallel computers to investigate the crystalline Si(111)/Si3N4(0001) interface that is modeled as an eight-component system. The average total energy per particle and the average kinetic energy per particle of the subsystems are monitored during the preparation of the system. The Young’s modulus of the interface is compared with that of the silicon part alone and that of the silicon-nitride film, respectively. The results for one extended simulation feature a crack in the silicon-nitride film and dislocated atoms in silicon below the crack. Simulations at rates of strain ranging from 0.00125to0.05ps-1 show that for lower strain rates, the systems stretched faster reach their ultimate strength at a higher strain value than those that were stretched more slowly. At the highest strain rates, however, the failure mechanisms change qualitatively indicative of a more ductile behavior.

  19. High density gas state at water/graphite interface studied by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Wang Chun-Lei; Li Zhao-Xia; Li Jing-Yuan; Xiu Peng; Hu Jun; Fang Hai-Ping

    2008-01-01

    In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results: gas films (pancake-like) for a larger ratio and nanobubbles for a Smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film (pancake-like) and nanobubbles.

  20. SOCIAL INTERFACE DYNAMICS IN FOOD PRODUCTION PROGRAM "ZERO HUNGER" OF NICARAGUA

    Directory of Open Access Journals (Sweden)

    Beverly Castillo Herrera

    2015-07-01

    Full Text Available This article uses the concept of social interface, coined by Norman Long (2007, to answer the question: How do the processes of planned intervention come into the world of life of individuals and groups? This concept is discussed in the dynamics of the “Zero Hunger“ Food Production Program implemented in Nicaragua since 2007. This research is qualitative. Interviews with women protagonists of the program in the north-central region were applied. The article shows how the concept of social interface permits to analyze the moments of discrepancies between planned and executed social programs, because the various stakeholders are involved in social interactions where interests, needs, power relations, interpretations, symbols and accumulated knowledge are circulating and interacting.

  1. The Dynamic Organic/Inorganic Interface of Colloidal PbS Quantum Dots.

    Science.gov (United States)

    Grisorio, Roberto; Debellis, Doriana; Suranna, Gian Paolo; Gigli, Giuseppe; Giansante, Carlo

    2016-06-01

    Colloidal quantum dots are composed of nanometer-sized crystallites of inorganic semiconductor materials bearing organic molecules at their surface. The organic/inorganic interface markedly affects forms and functions of the quantum dots, therefore its description and control are important for effective application. Herein we demonstrate that archetypal colloidal PbS quantum dots adapt their interface to the surroundings, thus existing in solution phase as equilibrium mixtures with their (metal-)organic ligand and inorganic core components. The interfacial equilibria are dictated by solvent polarity and concentration, show striking size dependence (leading to more stable ligand/core adducts for larger quantum dots), and selectively involve nanocrystal facets. This notion of ligand/core dynamic equilibrium may open novel synthetic paths and refined nanocrystal surface-chemistry strategies.

  2. Spontaneous assembly of HSP90 inhibitors at water/octanol interface: A molecular dynamics simulation study

    Science.gov (United States)

    Zolghadr, Amin Reza; Boroomand, Samaneh

    2017-02-01

    Drug absorption at an acceptable dose depends on the pair of solubility and permeability. There are many potent therapeutics that are not active in vivo, presumably due to the lack of capability to cross the cell membrane. Molecular dynamics simulation of radicicol, diol-radicicol, cyclopropane-radicicol and 17-DMAG were performed at water/octanol interface to suggest interfacial activity as a physico-chemical characteristic of these heat shock protein 90 (HSP90) inhibitors. We have observed that orally active HSP90 inhibitors form aggregates at the water/octanol and DPPC-lipid/water interfaces by starting from an initial configuration with HSP90 inhibitors embedded in the water matrix.

  3. Structure and dynamics of single hydrophobic/ionic heteropolymers at the vapor-liquid interface of water.

    Science.gov (United States)

    Vembanur, Srivathsan; Venkateshwaran, Vasudevan; Garde, Shekhar

    2014-04-29

    We focus on the conformational stability, structure, and dynamics of hydrophobic/charged homopolymers and heteropolymers at the vapor-liquid interface of water using extensive molecular dynamics simulations. Hydrophobic polymers collapse into globular structures in bulk water but unfold and sample a broad range of conformations at the vapor-liquid interface of water. We show that adding a pair of charges to a hydrophobic polymer at the interface can dramatically change its conformations, stabilizing hairpinlike structures, with molecular details depending on the location of the charged pair in the sequence. The translational dynamics of homopolymers and heteropolymers are also different, whereas the homopolymers skate on the interface with low drag, the tendency of charged groups to remain hydrated pulls the heteropolymers toward the liquid side of the interface, thus pinning them, increasing drag, and slowing the translational dynamics. The conformational dynamics of heteropolymers are also slower than that of the homopolymer and depend on the location of the charged groups in the sequence. Conformational dynamics are most restricted for the end-charged heteropolymer and speed up as the charge pair is moved toward the center of the sequence. We rationalize these trends using the fundamental understanding of the effects of the interface on primitive pair-level interactions between two hydrophobic groups and between oppositely charged ions in its vicinity.

  4. Epigenetic mechanisms and cancer: an interface between the environment and the genome.

    Science.gov (United States)

    Herceg, Zdenko; Vaissière, Thomas

    2011-07-01

    Although epidemiological studies support the role of environment in a wide range of human cancers, the precise mechanisms by which environmental exposures promote cancer development and progression remain poorly understood. Environmental factors have been proposed to promote the development of malignancies by eliciting epigenetic changes; however, it is only with recent advances in epigenetics and epigenomics that target genes and the mechanisms underlying environmental influences are beginning to be elucidated. Because epigenetic mechanisms may function as an interface between environmental factors and the genome, deregulation of the epigenome by environmental stressors is likely to disrupt different cellular processes and contribute to cancer risk. In addition, the early appearance and ubiquity of epigenetic changes in virtually all steps of tumor development and progression in most, if not all, human neoplasms, make them attractive targets for biomarker discovery and targeted prevention. At the cellular level, aberrant epigenetic changes associated with environmental exposures may deregulate key cellular processes (including transcriptional control, DNA repair, cell cycle control, and carcinogen detoxification), which can be further modulated by environmental stressors, thus defining not only the phenotype of the disease but also potential biomarkers. This review summarizes recent progress in our understanding of the epigenetic mechanisms through which environmental factors may promote tumor development, with a particular focus on human lung cancer.

  5. Dislocation Emission at the Silicon/Silicon Nitride Interface: A Million Atom Molecular Dynamics Simulation on Parallel Computers

    Science.gov (United States)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam

    2000-01-01

    Mechanical behavior of the Si\\(111\\)/Si3N4\\(0001\\) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the \\(1¯ 1¯1\\) plane of the silicon substrate with a speed of 500 \\(+/-100\\) m/s. Time evolution of the dislocation emission and nature of defects is studied.

  6. Dislocation Emission at the Silicon/Silicon Nitride Interface: A Million Atom Molecular Dynamics Simulation on Parallel Computers

    Energy Technology Data Exchange (ETDEWEB)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjoe, Ingvar; Madhukar, Anupam

    2000-01-10

    Mechanical behavior of the Si(111)/Si{sub 3}N{sub 4} (0001) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the (1 11) plane of the silicon substrate with a speed of 500 ({+-}100) m/s . Time evolution of the dislocation emission and nature of defects is studied. (c) 2000 The American Physical Society.

  7. Molecular dynamics study on condensation/evaporation coefficients of chain molecules at liquid-vapor interface.

    Science.gov (United States)

    Nagayama, Gyoko; Takematsu, Masaki; Mizuguchi, Hirotaka; Tsuruta, Takaharu

    2015-07-07

    The structure and thermodynamic properties of the liquid-vapor interface are of fundamental interest for numerous technological implications. For simple molecules, e.g., argon and water, the molecular condensation/evaporation behavior depends strongly on their translational motion and the system temperature. Existing molecular dynamics (MD) results are consistent with the theoretical predictions based on the assumption that the liquid and vapor states in the vicinity of the liquid-vapor interface are isotropic. Additionally, similar molecular condensation/evaporation characteristics have been found for long-chain molecules, e.g., dodecane. It is unclear, however, whether the isotropic assumption is valid and whether the molecular orientation or the chain length of the molecules affects the condensation/evaporation behavior at the liquid-vapor interface. In this study, MD simulations were performed to study the molecular condensation/evaporation behavior of the straight-chain alkanes, i.e., butane, octane, and dodecane, at the liquid-vapor interface, and the effects of the molecular orientation and chain length were investigated in equilibrium systems. The results showed that the condensation/evaporation behavior of chain molecules primarily depends on the molecular translational energy and the surface temperature and is independent of the molecular chain length. Furthermore, the orientation at the liquid-vapor interface was disordered when the surface temperature was sufficiently higher than the triple point and had no significant effect on the molecular condensation/evaporation behavior. The validity of the isotropic assumption was confirmed, and we conclude that the condensation/evaporation coefficients can be predicted by the liquid-to-vapor translational length ratio, even for chain molecules.

  8. Dynamic and spatial behavior of a corrugated interface in the driven lattice gas model

    Science.gov (United States)

    Saracco, Gustavo P.; Albano, Ezequiel V.

    2010-09-01

    The spatiotemporal behavior of an initially corrugated interface in the two-dimensional driven lattice gas (DLG) model with attractive nearest-neighbors interactions is investigated via Monte Carlo simulations. By setting the system in the ordered phase, with periodic boundary conditions along the external field axis. i.e. horizontal, and open along the vertical directions respectively, an initial interface was imposed, that consists in a series of sinusoidal profiles with amplitude A0 and wavelength λ set parallel to the applied driving field axis. We studied the dynamic behavior of its statistical width or roughness W(t), defined as the root mean square of the interface position. We found that W(t) decays exponentially for all λ and lattice longitudinal sizes Lx, i.e., the lattice side that runs along the axis of the external field. We determined its relaxation time τ, and found that depends on λ as a power law τ∝λp, where p depends on the temperature and Lx. At low T’s ( T≪Tc(E)) and large Lx, p approaches to p=3/2. At intermediate T’s ( Tinterface stabilizes faster than in the equilibrium model, i. e. the Ising lattice gas (E=0) where p=3. At higher T’s p increases for T≲Tc(E), and the finite size dependence is recovered. Also, if T is fixed, p increases with Lx until it saturates at large values of it, while this regime is vanishing at T≲Tc(E). In this way, the dynamic relaxation process of a sinusoidal interface is improved by the external driving field with respect to its equilibrium counterpart, if the system is set in an intermediate temperature stage far from Tc(E) and in a lattice with a sufficiently large longitudinal side. The behavior of τ was also investigated as a function of E and in the intermediate stage T

  9. Rupture dynamics along bimaterial interfaces: a parametric study of the shear-normal traction coupling

    Science.gov (United States)

    Scala, Antonio; Festa, Gaetano; Vilotte, Jean-Pierre

    2017-01-01

    Earthquake ruptures often develop along faults separating materials with dissimilar elastic properties. Due to the broken symmetry, the propagation of the rupture along the bimaterial interface is driven by the coupling between interfacial sliding and normal traction perturbations. We numerically investigate in-plane rupture growth along a planar interface, under slip weakening friction, separating two dissimilar isotropic linearly elastic half-spaces, and we perform a parametric study of the classical Prakash-Clifton regularisation, for different material contrasts. In particular the mesh-dependence and the regularisation-dependence of the numerical solutions are analysed in this parameter space. When the regularisation involves a slip-rate dependent relaxation time, a characteristic sliding distance is identified below which numerical solutions no longer depend on the regularisation parameter, i.e. they are physically well-posed solutions. Such regularisation provides an adaptive high-frequency filter of the slip-induced normal traction perturbations, following the dynamic shrinking of the dissipation zone during the acceleration phase. In contrast, a regularisation involving a constant relaxation time leads to numerical solutions that always depend on the regularisation parameter since it fails in adapting to the shrinking of the process zone. Dynamic regularisation is further investigated using a non-local regularisation based on a relaxation time that depends on the dynamic length of the dissipation zone. Such reformulation is shown to provide similar results as the dynamic time scale regularisation proposed by Prakash-Clifton when the slip rate is replaced by the maximum slip rate along the sliding interface. This leads to the identification of a dissipative length scale associated with the coupling between interfacial sliding and normal traction perturbations, together with a scaling law between the maximum slip rate and the dynamic size of the process zone

  10. Paraelectric-ferroelectric interface dynamics induced by latent heat transfer and irreversibility of ferroelectric phase transitions

    Institute of Scientific and Technical Information of China (English)

    Ai Shu-Tao

    2006-01-01

    The temperature gradients that arise in the paraelectric-ferroelectric interface dynamics induced by the latent heat transfer are studied from the point of view that a ferroelectric phase transition is a stationary, thermal-electric coupled transport process. The local entropy production is derived for a ferroelectric phase transition system from the Gibbs equation. Three types of regions in the system are described well by using the Onsager relations and the principle of minimum entropy production. The theoretical results coincides with the experimental ones.

  11. Dynamic Study of Gemini Surfactant and Single-chain Surfactant at Air/Water Interface

    Institute of Scientific and Technical Information of China (English)

    Yi Jian CHEN; Gui Ying XU; Shi Ling YUAN; Hai Ying SUN

    2005-01-01

    Molecular dynamics (MD) simulation are used to study the properties of gemini surfactant of ethyl-α,ω-bis(dodecyldimethylammonium bromide) (C12C2C12) and dodecyltrimethylammonium bromide (DTAB) at the air/water interface, respectively. In the two systems,the surfactant concentrations are both 28 wt. %, and other conditions are also the same. After reaching the thermodynamic equilibrium, the concentration profiles, the radial distributions functions (RDF) and the mean squared displacement (MSD) are investigated. Theresults reveal that the surface activity of C12C2C12 suffactant is higher than DTAB surfactant.

  12. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    Science.gov (United States)

    Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra

    2015-01-01

    The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362

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

    KAUST Repository

    Sprittles, J.E.

    2013-01-01

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

  14. Interface dynamics of a metastable mass-conserving spatially extended diffusion

    CERN Document Server

    Berglund, Nils

    2015-01-01

    We study the metastable dynamics of a discretised version of the mass-conserving stochastic Allen-Cahn equation. Consider a periodic one-dimensional lattice with $N$ sites, and attach to each site a real-valued variable, which can be interpreted as a spin, as the concentration of one type of metal in an alloy, or as a particle density. Each of these variables is subjected to a local force deriving from a symmetric double-well potential, to a weak ferromagnetic coupling with its nearest neighbours, and to independent white noise. In addition, the dynamics is constrained to have constant total magnetisation or mass. Using tools from the theory of metastable diffusion processes, we show that the long-term dynamics of this system is similar to a Kawasaki-type exchange dynamics, and determine explicit expressions for its transition probabilities. This allows us to describe the system in terms of the dynamics of its interfaces, and to compute an Eyring-Kramers formula for its spectral gap. In particular, we obtain ...

  15. Finite Element Simulation of Dynamic Wetting Flows as an Interface Formation Process

    CERN Document Server

    Sprittles, James

    2012-01-01

    A mathematically challenging model of dynamic wetting as a process of interface formation has been, for the first time, fully incorporated into a numerical code based on the finite element method and applied, as a test case, to the problem of capillary rise. The motivation for this work comes from the fact that, as discovered experimentally more than a decade ago, the key variable in dynamic wetting flows -the dynamic contact angle - depends not just on the velocity of the three-phase contact line but on the entire flow field/geometry. Hence, to describe this effect, it becomes necessary to use the mathematical model that has this dependence as its integral part. A new physical effect, termed the `hydrodynamic resist to dynamic wetting', is discovered where the influence of the capillary's radius on the dynamic contact angle, and hence on the global flow, is computed. The capabilities of the numerical framework are then demonstrated by comparing the results to experiments on the unsteady capillary rise, where...

  16. Hematite(001)-liquid water interface from hybrid density functional-based molecular dynamics

    Science.gov (United States)

    Falk von Rudorff, Guido; Jakobsen, Rasmus; Rosso, Kevin M.; Blumberger, Jochen

    2016-10-01

    The atom-scale characterisation of interfaces between transition metal oxides and liquid water is fundamental to our mechanistic understanding of diverse phenomena ranging from crystal growth to biogeochemical transformations to solar fuel production. Here we report on the results of large-scale hybrid density functional theory-based molecular dynamics simulations for the hematite(001)-liquid water interface. A specific focus is placed on understanding how different terminations of the same surface influence surface solvation. We find that the two dominant terminations for the hematite(001) surface exhibit strong differences both in terms of the active species formed on the surface and the strength of surface solvation. According to present simulations, we find that charged oxyanions (-O-) and doubly protonated oxygens (-OH2+ ) can be formed on the iron terminated layer via autoionization of neutral -OH groups. No such charged species are found for the oxygen terminated surface. In addition, the missing iron sublayer in the iron terminated surface strongly influences the solvation structure, which becomes less well ordered in the vicinity of the interface. These pronounced differences are likely to affect the reactivity of the two surface terminations, and in particular the energetics of excess charge carriers at the surface.

  17. Molecular dynamics simulation of structural change at metal/semiconductor interface induced by nanoindenter

    Science.gov (United States)

    Zhao, Bing-Bing; Wang, Ying; Liu, Chang; Wang, Xiao-Chun

    2016-11-01

    The structures of the Si/Cu heterogenous interface impacted by a nanoindenter with different incident angles and depths are investigated in detail using molecular dynamics simulation. The simulation results suggest that for certain incident angles, the nanoindenter with increasing depth can firstly increase the stress of each atom at the interface and it then introduces more serious structural deformation of the Si/Cu heterogenous interface. A nanoindenter with increasing incident angle (absolute value) can increase the length of the Si or Cu extended atom layer. It is worth mentioning that when the incident angle of the nanoindenter is between -45° and 45°, these Si or Cu atoms near the nanoindenter reach a stable state, which has a lower stress and a shorter length of the Si or Cu extended atom layer than those of the other incident angles. This may give a direction to the planarizing process of very large scale integration circuits manufacture. Project supported by the Tribology Science Fund of State Key Laboratory of Tribology, China (Grant No. SKLTKF12A01), the National Natural Science Foundation of China (Grant No. 11474123), the Natural Science Foundation of Jilin Province of China (Grant No. 20130101011JC), and the Fundamental Research Funds for Central Universities at Jilin University, China.

  18. Control of valley dynamics in silicon quantum dots in the presence of an interface step

    Science.gov (United States)

    Boross, Péter; Széchenyi, Gábor; Culcer, Dimitrie; Pályi, András

    2016-07-01

    Recent experiments on silicon nanostructures have seen breakthroughs toward scalable, long-lived quantum information processing. The valley degree of freedom plays a fundamental role in these devices, and the two lowest-energy electronic states of a silicon quantum dot can form a valley qubit. In this paper, we show that a single-atom high step at the silicon/barrier interface induces a strong interaction of the qubit and in-plane electric fields and that the strength of this interaction can be controlled by varying the relative position of the electron and the step. We analyze the consequences of this enhanced interaction on the dynamics of the qubit. The charge densities of the qubit states are deformed differently by the interface step, allowing nondemolition qubit readout via valley-to-charge conversion. A gate-induced in-plane electric field together with the interface step enables fast control of the valley qubit via electrically driven valley resonance. We calculate single- and two-qubit gate times, as well as relaxation and dephasing times, and present predictions for the parameter range where the gate times can be much shorter than the relaxation time and dephasing is reduced.

  19. The Effect of Water on the Work of Adhesion at Epoxy Interfaces by Molecular Dynamics Simulation

    Science.gov (United States)

    Hinkley, J.A.; Frankland, S.J.V.; Clancy, T.C.

    2009-01-01

    Molecular dynamics simulation can be used to explore the detailed effects of chemistry on properties of materials. In this paper, two different epoxies found in aerospace resins are modeled using molecular dynamics. The first material, an amine-cured tetrafunctional epoxy, represents a composite matrix resin, while the second represents a 177 C-cured adhesive. Surface energies are derived for both epoxies and the work of adhesion values calculated for the epoxy/epoxy interfaces agree with experiment. Adding water -- to simulate the effect of moisture exposure -- reduced the work of adhesion in one case, and increased it in the other. To explore the difference, the various energy terms that make up the net work of adhesion were compared and the location of the added water was examined.

  20. Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins

    Science.gov (United States)

    Lebard, David N.; Matyushov, Dmitry V.

    2008-12-01

    Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein-water interface, allowing large-amplitude collective fluctuations of the water density in the protein’s first solvation shell. On top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at ≃220K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line or undergoing a weak first-order transition.

  1. First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent

    CERN Document Server

    Sanchez, Veronica M; Scherlis, Damian A

    2009-01-01

    Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a DFT framework, using plane-waves basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [J. Chem. Phys. 124, 74103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions, by introducing new term in the Kohn-Sham potential which becomes unphysically large at the interfacial region, seriously affecting the convergence. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics ...

  2. Bio-Inspired Composite Interfaces: Controlling Hydrogel Mechanics via Polymer-Nanoparticle Coordination Bond Dynamics

    Science.gov (United States)

    Holten-Andersen, Niels

    2015-03-01

    In soft nanocomposite materials, the effective interaction between polymer molecules and inorganic nanoparticle surfaces plays a critical role in bulk mechanical properties. However, controlling these interfacial interactions remains a challenge. Inspired by the adhesive chemistry in mussel threads, we present a novel approach to control composite mechanics via polymer-particle interfacial dynamics; by incorporating iron oxide nanoparticles (Fe3O4 NPs) into a catechol-modified polymer network the resulting hydrogels are crosslinked via reversible coordination bonds at Fe3O4 NP surfaces thereby providing a dynamic gel network with robust self-healing properties. By studying the thermally activated composite network relaxation processes we have found that the polymer-NP binding energy can be controlled by engineering both the organic and inorganic side of the interface.

  3. Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins

    CERN Document Server

    LeBard, David N

    2008-01-01

    Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein/water interface allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On the top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line.

  4. Dynamic contact with friction of an ultra-low flying head-disk interface with thermal protrusion

    NARCIS (Netherlands)

    Vakis, A.I.; Lee, S.-C.; Polycarpou, A.A.

    2009-01-01

    A dynamic two-degree-of-freedom contact with friction model of the head-disk interface (HDI) is presented accounting for slider thermal protrusion and its influence on the HDI dynamics. Using this model, which includes roughness, the applied power to the thermal protrusion is calculated that leads t

  5. Metapopulation dynamics and spatial heterogeneity in cancer

    OpenAIRE

    2002-01-01

    With the advent of drugs targeting specific molecular defects in cancerous cells [Gorre, M. E., et al. (2001) Science 293, 876–880], it is important to understand the degree of genetic heterogeneity present in tumor cell populations and the rules that govern microdiversity in human cancer. Here, we first show that populations with different genotypes in genes influencing cell growth and programmed cell death coexist in advanced malignant tumors of the colon, exhibiting microsatellite instabil...

  6. Segregation of ions at the interface: molecular dynamics studies of the bulk and liquid-vapor interface structure of equimolar binary mixtures of ionic liquids.

    Science.gov (United States)

    Palchowdhury, Sourav; Bhargava, B L

    2015-08-14

    The structures of three different equimolar binary ionic liquid mixtures and their liquid-vapor interface have been studied using atomistic molecular dynamics simulations. Two of these binary mixtures were composed of a common cation 1-n-butyl-3-methylimidazolium and varying anions (chloride and hexafluorophosphate in one of the mixtures and chloride and trifluoromethanesulfonate in the other) and the third binary mixture was composed of a common anion, trifluoromethanesulfonate and two imidazolium cations with ethyl and octyl side chains. Binary mixtures with common cations are found to be homogeneous. The anions are preferentially located near the ring hydrogen atoms due to H-bonding interactions. Segregation of ions is observed at the interface with an enrichment of the liquid-vapor interface layer by longer alkyl chains and bigger anions with a distributed charge. The surface composition is drastically different from that of the bulk composition, with the longer alkyl tail groups and bigger anions populating the outermost layer of the interface. The longer alkyl chains of the cations and trifluoromethanesulfonate anions with a smaller charge density show orientational ordering at the liquid-vapor interface.

  7. Structure and dynamics of interfaces in organic and inorganic materials using atomic level simulation

    Science.gov (United States)

    Lee, Donghwa

    Interfaces in materials play a key role for industrial applications. The structures and dynamics at various interfaces including ferroelectric domain walls, gas-organic interface, organic-semiconductor interface and metal-gas interface are investigated with different atomic levels of simulation approaches. Ferroelectricity: Due to their unique ferroelectric and nonlinear optical properties, trigonal ferroelectrics such as LiNbO3 and LiTaO 3, are of wide interest for their potential applications in optoelectronics and nonlinear optics. The properties of these materials are heavily influenced by the shape of ferroelectric domains and domain walls. Therefore, investigation of the local structure and energetics of the ferroelectric domain walls and their interaction with defects on atomic scales, which is not clearly understood, is extremely important. The structure and energetics of ferroelectric domain walls in LiNbO 3 are examined using density functional theory (DFT) and molecular dynamics (MD) methods. The energetically favorable structures of 180° domain walls and the activation energy for domain wall motion are determined by atomic level simulations. The variation of polarization due to the presence of domain walls is also discussed. Defects can be pinned by domain walls. Various defects-domain walls interactions and the effects on domain wall motion are described using atomic level simulation methods. Although the structure of LiTaO3 is very similar with LiNbO3, it has been said experimentally that the shapes of domain walls are different with the presence of particular defects. Using both DFT and a newly developed interatomic potential for LiTaO 3, the differences in domain wall structure are understood in terms of the difference in energetics of domain walls between two materials. Polymerization: Surface polymerization by ion-assisted deposition (SPIAD) enables the control of thin film chemistry and morphology on the nanoscale during growth of conductive

  8. Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry.

    Science.gov (United States)

    Xiao, Yiming; Konermann, Lars

    2015-08-01

    Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N(2) bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N(2) bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N(2) sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, "semi-unfolded" ↔ "native" ↔ "globally unfolded" → "aggregated". This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS.

  9. Energy Partition During In-plane Dynamic Rupture on a Frictional Interface

    Science.gov (United States)

    Needleman, A.; Shi, Z.; Ben-Zion, Y.

    2007-12-01

    We study properties of dynamic ruptures and the partition of energy between radiation and dissipative mechanisms using two-dimensional in-plane calculations with the finite element method. The model consists of two identical isotropic elastic media separated by an interface governed by rate- and state-dependent friction. Rupture is initiated by gradually overstressing a localized nucleation zone. Our simulations with model parameters representative of Homalite-100 indicate that different values of parameters controlling the velocity dependence of friction, the strength excess parameter and the length of the nucleation zone, can lead to the following four rupture modes: supershear crack-like rupture, subshear crack-like rupture, subshear single pulse and supershear train of pulses. High initial shear stress and weak velocity dependence of friction favor crack-like ruptures, while the opposite conditions favor the pulse mode. The rupture mode can switch from a subshear single pulse to a supershear train of pulses when the width of the nucleation zone increases. The elastic strain energy released over the same propagation distance by the different rupture modes has the following order: supershear crack, subshear crack, supershear train of pulses and subshear single pulse. The same order applies also to the ratio of kinetic energy (radiation) to total change of elastic energy for the different rupture modes. Decreasing the dynamic coefficient of friction increases the fraction of stored energy that is converted to kinetic energy. In the current study we use model parameters representative of rocks instead of Homalite-100, by modeling recent results of Kilgore et al. (2007) who measured and estimated various energy components in laboratory friction experiments with granite. We are also incorporating into the code ingredients that will allow us to study rupture properties and energy partition for cases with a bimaterial interface and dynamic generation of plastic strain

  10. Mechanisms of pit formation at strained crystalline Si(111)/Si3N4(0001) interfaces: Molecular-dynamics simulations

    Science.gov (United States)

    Bachlechner, Martina E.; Srivastava, Deepak; Owens, Eli T.; Schiffbauer, Jarrod; Anderson, Jonas T.; Burky, Melissa R.; Ducatman, Samuel C.; Gripper, Adam M.; Guffey, Eric J.; Ramos, Fernando Serrano

    2006-08-01

    Molecular-dynamics simulations of the crystalline silicon-silicon nitride interfaces are performed to investigate the mechanical failure mechanisms at the interfaces under external strain. At 8% applied tensile strain, parallel to the interface, regular crack initiation and propagation in silicon nitride and dislocation emission and propagation in silicon are observed. At larger 16% strain, however, the formation of a pit similar to that in experiments with lattice-mismatched systems is observed. The simulation results suggest the primary mechanism of pit formation is interaction of a local compressional pinch of the film at the interface with the close proximity to the arrival of a dislocation at the interface in the highly strained silicon.

  11. A Model Study of Inclusions Deposition, Macroscopic Transport, and Dynamic Removal at Steel-Slag Interface for Different Tundish Designs

    Science.gov (United States)

    Chen, Chao; Ni, Peiyuan; Jonsson, Lage Tord Ingemar; Tilliander, Anders; Cheng, Guoguang; Jönsson, Pär Göran

    2016-06-01

    This paper presents computational fluid dynamics (CFD) simulation results of inclusions macroscopic transport as well as dynamic removal in tundishes. A novel treatment was implemented using the deposition velocity calculated by a revised unified Eulerian deposition model to replace the widely used Stokes rising velocity in the boundary conditions for inclusions removal at the steel-slag interface in tundishes. In this study, the dynamic removal for different size groups of inclusions at different steel-slag interfaces (smooth or rough) with different absorption conditions at the interface (partially or fully absorbed) in two tundish designs was studied. The results showed that the dynamic removal ratios were higher for larger inclusions than for smaller inclusions. Besides, the dynamic removal ratio was higher for rough interfaces than for smooth interfaces. On the other hand, regarding the cases when inclusions are partially or fully absorbed at a smooth steel-slag interface, the removal ratio values are proportional to the absorption proportion of inclusions at the steel-slag interface. Furthermore, the removal of inclusions in two tundish designs, i.e., with and without a weir and a dam were compared. Specifically, the tundish with a weir and a dam exhibited a better performance with respect to the removal of bigger inclusions (radii of 5, 7, and 9 μm) than that of the case without weir and dam. That was found to be due to the strong paralleling flow near the middle part of the top surface. However, the tundish without weir and dam showed a higher removal ratio of smaller inclusions (radius of 1 μm). The reason could be the presence of a paralleling flow near the inlet zone, where the inclusions deposition velocities were much higher than in other parts.

  12. Dynamic modeling efforts for system interface studies for nuclear hydrogen production.

    Energy Technology Data Exchange (ETDEWEB)

    Vilim, R. B.; Nuclear Engineering Division

    2007-08-15

    System interface studies require not only identifying economically optimal equipment configurations, which involves studying mainly full power steady-state operation, but also assessing the operability of a design during load change and startup and assessing safety-related behavior during upset conditions. This latter task is performed with a dynamic simulation code. This report reviews the requirements of such a code. It considers the types of transients that will need to be simulated, the phenomena that will be present, the models best suited for representing the phenomena, and the type of numerical solution scheme for solving the models to obtain the dynamic response of the combined nuclear-hydrogen plant. Useful insight into plant transient behavior prior to running a dynamics code is obtained by some simple methods that take into account component time constants and energy capacitances. Methods for determining reactor stability, plant startup time, and temperature response during load change, and tripping of the reactor are described. Some preliminary results are presented.

  13. Personalized keystroke dynamics for self-powered human--machine interfacing.

    Science.gov (United States)

    Chen, Jun; Zhu, Guang; Yang, Jin; Jing, Qingshen; Bai, Peng; Yang, Weiqing; Qi, Xuewei; Su, Yuanjie; Wang, Zhong Lin

    2015-01-27

    The computer keyboard is one of the most common, reliable, accessible, and effective tools used for human--machine interfacing and information exchange. Although keyboards have been used for hundreds of years for advancing human civilization, studying human behavior by keystroke dynamics using smart keyboards remains a great challenge. Here we report a self-powered, non-mechanical-punching keyboard enabled by contact electrification between human fingers and keys, which converts mechanical stimuli applied to the keyboard into local electronic signals without applying an external power. The intelligent keyboard (IKB) can not only sensitively trigger a wireless alarm system once gentle finger tapping occurs but also trace and record typed content by detecting both the dynamic time intervals between and during the inputting of letters and the force used for each typing action. Such features hold promise for its use as a smart security system that can realize detection, alert, recording, and identification. Moreover, the IKB is able to identify personal characteristics from different individuals, assisted by the behavioral biometric of keystroke dynamics. Furthermore, the IKB can effectively harness typing motions for electricity to charge commercial electronics at arbitrary typing speeds greater than 100 characters per min. Given the above features, the IKB can be potentially applied not only to self-powered electronics but also to artificial intelligence, cyber security, and computer or network access control.

  14. Dynamic covalent chemistry of bisimines at the solid/liquid interface monitored by scanning tunnelling microscopy

    Science.gov (United States)

    Ciesielski, Artur; El Garah, Mohamed; Haar, Sébastien; Kovaříček, Petr; Lehn, Jean-Marie; Samorì, Paolo

    2014-11-01

    Dynamic covalent chemistry relies on the formation of reversible covalent bonds under thermodynamic control to generate dynamic combinatorial libraries. It provides access to numerous types of complex functional architectures, and thereby targets several technologically relevant applications, such as in drug discovery, (bio)sensing and dynamic materials. In liquid media it was proved that by taking advantage of the reversible nature of the bond formation it is possible to combine the error-correction capacity of supramolecular chemistry with the robustness of covalent bonding to generate adaptive systems. Here we show that double imine formation between 4-(hexadecyloxy)benzaldehyde and different α,ω-diamines as well as reversible bistransimination reactions can be achieved at the solid/liquid interface, as monitored on the submolecular scale by in situ scanning tunnelling microscopy imaging. Our modular approach enables the structurally controlled reversible incorporation of various molecular components to form sophisticated covalent architectures, which opens up perspectives towards responsive multicomponent two-dimensional materials and devices.

  15. Automatic dynamic mask extraction for PIV images containing an unsteady interface, bubbles, and a moving structure

    Science.gov (United States)

    Dussol, David; Druault, Philippe; Mallat, Bachar; Delacroix, Sylvain; Germain, Grégory

    2016-07-01

    When performing Particle Image Velocimetry (PIV) measurements in complex fluid flows with moving interfaces and a two-phase flow, it is necessary to develop a mask to remove non-physical measurements. This is the case when studying, for example, the complex bubble sweep-down phenomenon observed in oceanographic research vessels. Indeed, in such a configuration, the presence of an unsteady free surface, of a solid-liquid interface and of bubbles in the PIV frame, leads to generate numerous laser reflections and therefore spurious velocity vectors. In this note, an image masking process is developed to successively identify the boundaries of the ship and the free surface interface. As the presence of the solid hull surface induces laser reflections, the hull edge contours are simply detected in the first PIV frame and dynamically estimated for consecutive ones. As for the unsteady surface determination, a specific process is implemented like the following: i) the edge detection of the gradient magnitude in the PIV frame, ii) the extraction of the particles by filtering high-intensity large areas related to the bubbles and/or hull reflections, iii) the extraction of the rough region containing these particles and their reflections, iv) the removal of these reflections. The unsteady surface is finally obtained with a fifth-order polynomial interpolation. The resulted free surface is successfully validated from the Fourier analysis and by visualizing selected PIV images containing numerous spurious high intensity areas. This paper demonstrates how this data analysis process leads to PIV images database without reflections and an automatic detection of both the free surface and the rigid body. An application of this new mask is finally detailed, allowing a preliminary analysis of the hydrodynamic flow.

  16. On the implementation of error handling in dynamic interfaces to scientific codes

    Energy Technology Data Exchange (ETDEWEB)

    Solomon, C.J.

    1993-11-01

    With the advent of powerful workstations with windowing systems, the scientific community has become interested in user friendly interfaces as a means of promoting the distribution of scientific codes to colleagues. Distributing scientific codes to a wider audience can, however, be problematic because scientists, who are familiar with the problem being addressed but not aware of necessary operational details, are encouraged to use the codes. A more friendly environment that not only guides user inputs, but also helps catch errors is needed. This thesis presents a dynamic graphical user interface (GUI) creation system with user controlled support for error detection and handling. The system checks a series of constraints defining a valid input set whenever the state of the system changes and notifies the user when an error has occurred. A naive checking scheme was implemented that checks every constraint every time the system changes. However, this method examines many constraints whose values have not changed. Therefore, a minimum evaluation scheme that only checks those constraints that may have been violated was implemented. This system was implemented in a prototype and user testing was used to determine if it was a success. Users examined both the GUI creation system and the end-user environment. The users found both to be easy to use and efficient enough for practical use. Moreover, they concluded that the system would promote distribution.

  17. Molecular dynamics simulations of the adsorption of amino acids on the hydroxyapatite {100}-water interface

    Institute of Scientific and Technical Information of China (English)

    Zhi-sen ZHANG; Hai-hua PAN; Rui-kang TANG

    2008-01-01

    The understanding of interfaces and interaction of organic molecules and inorganic materials are the important issues in biomineralization. Experimentally, it has been found that amino acids (AA) can regulate the morphology of hydroxyapatite (HAP) crystals significantly. In this study, molecular dynamics simulation is employed to investigate the detailed adsorption behavior of polar, ionic, and hydrophobic AA on the {100} face of HAP at the atomic level. The results indicate that various AA are adsorbed on the HAP crystal surface mainly by amino and carboxylate groups at the specific sites. Multiple inter-action points are found for polar and ionic AA. The adsorbed AA molecules occupy the Ca and P sites of the HAP surfaces which may inhibit and regulate the HAP growth. The adsorbed amino acid layer can also change the interfacial hydration layer and influence the transporta-tion of ions in and out of HAP, which may be another strategy of biological control in biomineralization.

  18. Interfacing polymeric scaffolds with primary pancreatic ductal adenocarcinoma cells to develop 3D cancer models.

    Science.gov (United States)

    Ricci, Claudio; Mota, Carlos; Moscato, Stefania; D'Alessandro, Delfo; Ugel, Stefano; Sartoris, Silvia; Bronte, Vincenzo; Boggi, Ugo; Campani, Daniela; Funel, Niccola; Moroni, Lorenzo; Danti, Serena

    2014-01-01

    We analyzed the interactions between human primary cells from pancreatic ductal adenocarcinoma (PDAC) and polymeric scaffolds to develop 3D cancer models useful for mimicking the biology of this tumor. Three scaffold types based on two biocompatible polymeric formulations, such as poly(vinyl alcohol)/gelatin (PVA/G) mixture and poly(ethylene oxide terephthalate)/poly(butylene terephthalate) (PEOT/PBT) copolymer, were obtained via different techniques, namely, emulsion and freeze-drying, compression molding followed by salt leaching, and electrospinning. In this way, primary PDAC cells interfaced with different pore topographies, such as sponge-like pores of different shape and size or nanofiber interspaces. The aim of this study was to investigate the influence played by the scaffold architecture over cancerous cell growth and function. In all scaffolds, primary PDAC cells showed good viability and synthesized tumor-specific metalloproteinases (MMPs) such as MMP-2, and MMP-9. However, only sponge-like pores, obtained via emulsion-based and salt leaching-based techniques allowed for an organized cellular aggregation very similar to the native PDAC morphological structure. Differently, these cell clusters were not observed on PEOT/PBT electrospun scaffolds. MMP-2 and MMP-9, as active enzymes, resulted to be increased in PVA/G and PEOT/PBT sponges, respectively. These findings suggested that spongy scaffolds supported the generation of pancreatic tumor models with enhanced aggressiveness. In conclusion, primary PDAC cells showed diverse behaviors while interacting with different scaffold types that can be potentially exploited to create stage-specific pancreatic cancer models likely to provide new knowledge on the modulation and drug susceptibility of MMPs.

  19. Interface between platinum(111) and liquid isopropanol (2-propanol): a model for molecular dynamics studies.

    Science.gov (United States)

    Tarmyshov, Konstantin B; Müller-Plathe, Florian

    2007-02-21

    A molecular dynamics model and its parametrization procedure are devised and used to study adsorption of isopropanol on platinum(111) (Pt(111)) surface in unsaturated and oversaturated coverages regimes. Static and dynamic properties of the interface between Pt(111) and liquid isopropanol are also investigated. The magnitude of the adsorption energy at unsaturated level increases at higher coverages. At the oversaturated coverage (multilayer adsorption) the adsorption energy reduces, which coincides with findings by Panja et al. in their temperature-programed desorption experiment [Surf. Sci. 395, 248 (1998)]. The density analysis showed a strong packing of molecules at the interface followed by a depletion layer and then by an oscillating density profile up to 3 nm. The distribution of individual atom types showed that the first adsorbed layer forms a hydrophobic methyl "brush." This brush then determines the distributions further from the surface. In the second layer methyl and methine groups are closer to the surface and followed by the hydroxyl groups; the third layer has exactly the inverted distribution. The alternating pattern extends up to about 2 nm from the surface. The orientational structure of molecules as a function of distance of molecules is determined by the atom distribution and surprisingly does not depend on the electrostatic or chemical interactions of isopropanol with the metal surface. However, possible formation of hydrogen bonds in the first layer is notably influenced by these interactions. The surface-adsorbate interactions influence the mobility of isopropanol molecules only in the first layer. Mobility in the higher layers is independent of these interactions.

  20. Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations

    Directory of Open Access Journals (Sweden)

    Qin Haina

    2012-01-01

    Full Text Available Abstract Background The role of dynamics in protein functions including signal transduction is just starting to be deciphered. Eph receptors with 16 members divided into A- and B- subclasses are respectively activated by 9 A- and B-ephrin ligands. EphA4 is the only receptor capable of binding to all 9 ephrins and small molecules with overlapped interfaces. Results We first determined the structures of the EphA4 ligand binding domain (LBD in two crystals of P1 space group. Noticeably, 8 EphA4 molecules were found in one asymmetric unit and consequently from two crystals we obtained 16 structures, which show significant conformational variations over the functionally critical A-C, D-E, G-H and J-K loops. The 16 new structures, together with previous 9 ones, can be categorized into two groups: closed and open forms which resemble the uncomplexed and complexed structures of the EphA4 LBD respectively. To assess whether the conformational diversity over the loops primarily results from the intrinsic dynamics, we initiated 30-ns molecular dynamics (MD simulations for both closed and open forms. The results indicate that the loops do have much higher intrinsic dynamics, which is further unravelled by NMR H/D exchange experiments. During simulations, the open form has the RMS deviations slightly larger than those of the closed one, suggesting the open form may be less stable in the absence of external contacts. Furthermore, no obvious exchange between two forms is observed within 30 ns, implying that they are dynamically separated. Conclusions Our study provides the first experimental and computational result revealing that the intrinsic dynamics are most likely underlying the conformational diversity observed for the EphA4 LBD loops mediating the binding affinity and specificity. Interestingly, the open conformation of the EphA4 LBD is slightly unstable in the absence of it natural ligand ephrins, implying that the conformational transition from the

  1. Dynamic impedance model of the skin-electrode interface for transcutaneous electrical stimulation.

    Directory of Open Access Journals (Sweden)

    José Luis Vargas Luna

    Full Text Available Transcutaneous electrical stimulation can depolarize nerve or muscle cells applying impulses through electrodes attached on the skin. For these applications, the electrode-skin impedance is an important factor which influences effectiveness. Various models describe the interface using constant or current-depending resistive-capacitive equivalent circuit. Here, we develop a dynamic impedance model valid for a wide range stimulation intensities. The model considers electroporation and charge-dependent effects to describe the impedance variation, which allows to describe high-charge pulses. The parameters were adjusted based on rectangular, biphasic stimulation pulses generated by a stimulator, providing optionally current or voltage-controlled impulses, and applied through electrodes of different sizes. Both control methods deliver a different electrical field to the tissue, which is constant throughout the impulse duration for current-controlled mode or have a very current peak for voltage-controlled. The results show a predominant dependence in the current intensity in the case of both stimulation techniques that allows to keep a simple model. A verification simulation using the proposed dynamic model shows coefficient of determination of around 0.99 in both stimulation types. The presented method for fitting electrode-skin impedance can be simple extended to other stimulation waveforms and electrode configuration. Therefore, it can be embedded in optimization algorithms for designing electrical stimulation applications even for pulses with high charges and high current spikes.

  2. Assembling structures and dynamics properties of perfluorooctane sulfonate (PFOS) at water-titanium oxide interfaces.

    Science.gov (United States)

    He, Guangzhi; Pan, Gang; Zhang, Meiyi

    2013-09-01

    The surface-associated structures and growth modes of perfluorooctane sulfonate (PFOS) at water-rutile TiO2 interfaces were defined by molecular dynamics (MD) simulations. The results showed that a compact PFOS layer was generated at the rutile surfaces, and the assembling structures and dynamic profiles were crystal-face-dependent. PFOS molecules were attached to the (110) and (001) surfaces mainly by the sulfonate headgroups. A well-defined monolayer was formed on the (110) surface with the perfluorinated alkyl chains nearly perpendicular to the substrate, whereas the C-F chains were inclined at an angle (30-75°) and formed a hemicylinder-like configuration on the (001) surface. On the other hand, the perfluorinated amphiphiles interacted with the (100) plane through both the sulfonate headgroups (relatively strong electrostatic attraction) and the C-F tailgroups (weak van der Waals forces) and yielded an irregular assembling pattern. Water molecules were mostly concentrated more than 17.0 Å away from the solid surfaces and formed a continuous solvent layer, suggesting the super hydrophobicity of perfluorinated alkyl chains. A counterion-bridging mechanism suggested in surfactant adsorption was observed at the molecular scale, where the sulfonate headgroups were linked together by the potassium ions at the surfaces and caused the formation of surface aggregates.

  3. First principles molecular dynamics of metal/water interfaces under bias potential

    Science.gov (United States)

    Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre; Fernandez-Serra, Marivi

    2014-03-01

    Understanding the interaction of the water-metal system at an atomic level is extremely important in electrocatalysts for fuel cells, photocatalysis among other systems. The question of the interface energetics involves a detailed study of the nature of the interactions between water-water and water-substrate. A first principles description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemically processes. In this work we describe, using first principles molecular dynamics simulations, the dynamics of a combined surface(Au and Pd)/water system both in the presence and absence of an external bias potential applied to the electrodes, as one would come across in electrochemistry. This is accomplished using a combination of density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), thus accounting for the fact that one is dealing with an out-of-equilibrium open system, with and without van der Waals interactions. DOE Early Career Award No. DE-SC0003871.

  4. Evaluating the quality of colorectal cancer care across the interface of healthcare sectors.

    Directory of Open Access Journals (Sweden)

    Sabine Ludt

    Full Text Available BACKGROUND: Colorectal cancer (CRC has a high prevalence in western countries. Diagnosis and treatment of CRC is complex and requires multidisciplinary collaboration across the interface of health care sectors. In Germany, a new nationwide established program aims to provide quality information of healthcare delivery across different sectors. Within this context, this study describes the development of a set of quality indicators charting the whole pathway of CRC-care including data specifications that are necessary to operationalize these indicators before practice testing. METHODS: Indicators were developed following a systematic 10 step modified 'RAND/UCLA Appropriateness Method' which involved a multidisciplinary panel of thirteen participants. For each indicator in the final set, data specifications relating to sources of quality information, data collection procedures, analysis and feedback were described. RESULTS: The final indicator set included 52 indicators covering diagnostic procedures (11 indicators, therapeutic management (28 indicators and follow-up (6 indicators. In addition, 7 indicators represented patient perspectives. Primary surgical tumor resection and pre-operative radiation (rectum carcinoma only were perceived as most useful tracer procedures initiating quality data collection. To assess the quality of CRC care across sectors, various data sources were identified: medical records, administrative inpatient and outpatient data, sickness-funds billing code systems and patient survey. CONCLUSION: In Germany, a set of 52 quality indicators, covering necessary aspects across the interfaces and pathways relevant to CRC-care has been developed. Combining different sectors and sources of health care in quality assessment is an innovative and challenging approach but reflects better the reality of the patient pathway and experience of CRC-care.

  5. MULTIPLE SCATTERING AND DYNAMIC STRESS ANALYSIS OF ELASTIC WAVES IN A FIBER—REINFORCED COMPOSITE WITH INTERFACES

    Institute of Scientific and Technical Information of China (English)

    李凤明; 胡超; 徐敏强; 黄文虎

    2003-01-01

    Based on the theory of elastic dynamics, multiple scattering of elastic waves anddynamic stress concentrations in fiber-reinforced composite are studied. The analytical expressions ofelastic waves in different regions are presented. The mode coefficients of elastic waves are determinedin accordance with the continuous conditions of displacement and stress on the boundary of the multi-interfaces. By using the addition theorem of Hankel functions, the formula of scattered wave fields indifferent local coordinates are transformed into those in one local coordinate to determine the unknowncoefficients and dynamic stress concentration factors (DSCFs). The influences of the distance betweentwo inclusions, material properties and structural size on the DSCFs near the interfaces are analyzed.As examples, the numerical results of DSCFs near the interfaces for two kinds of fiber-reinforcedcomposites are presented and discussed.

  6. MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

    KAUST Repository

    Abdel-Azeim, Safwat

    2014-05-06

    Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

  7. Dynamic analysis of structures with elastomers using substructuring with non-matched interfaces and improved modeling of elastomer properties

    Science.gov (United States)

    Lin, Hejie

    A variety of engineering structures are composed of linear structural components connected by elastomers. The components are commonly analyzed using large-scale finite element models. Examples include engine crankshafts with torsional dampers, engine structures with an elastomeric gasket between the head and the block, engine-vehicle structures using elastomeric engine mounts, etc. An analytical method is presented in this research for the dynamic analysis of large-scale structures with elastomers. The dissertation has two major parts. In the first part, a computationally efficient substructuring method is developed for substructures with non-matched interface meshes. The method is based on the conventional fixed-interface, Craig-Bampton component mode synthesis (CMS) method. However, its computational efficiency is greatly enhanced with the introduction of interface modes. Kriging interpolation at the interfaces between substructures ensures compatibility of deformation. In the second part, a series of dynamic measurements of mechanical properties of elastomers is presented. Dynamic stiffness as a function of frequency under controlled temperature and vibrational amplitude is measured. Also, the strain and stress relaxation behavior is tested to investigate the linearity and histeresis of an elastomer. The linearity of dynamic stiffness is studied and discussed in detail through the strain and stress relaxation test. The dynamic stiffness of elastomers is measured at different conditions such as temperature, frequency, and amplitude. The relationships between dynamic stiffness and temperature, and frequency and amplitude are discussed. After the dynamic properties of an elastomer are measured, a mathematical model is presented for characterizing the frequency and temperature-dependent properties of elastomers from the fundamental features of the molecular chains forming them. Experimental observations are used in the model development to greatly enhance the

  8. MULTIPLE SCATTERING AND DYNAMIC STRESS ANALYSIS OF ELASTIC WAVES IN A FIBER-REINFORCED COMPOSITE WITH INTERFACES

    Institute of Scientific and Technical Information of China (English)

    李凤明; 胡超; 徐敏强; 黄文虎

    2003-01-01

    Based on the theory of elastic dynamics,multiple scattering of elastic waves and dynamic stress concentrations in fiber-reinforced composite are studied.The analytical expressions of elastic waves in different regions are presented.The mode coefficients of elastic waves are determined in accordance with the continuous conditions of displacement and stress on the boundary of the multiinterfaces.By using the addition theorem of Hankel functions,the formula of scattered wave fields in different local coordinates are transformed into those in one local coordinate to determine the unknown coefficients and dynamic stress concentration factors (DSCFs).The influences of the distance between two inclusions,material properties and structural size on the DSCFs near the interfaces are analyzed.As examples,the numerical results of DSCFs near the interfaces for two kinds of fiber-reinforced composites are presented and discussed.

  9. HiRISE Mission to Address the Dynamical Chromosphere-Corona Interface

    Science.gov (United States)

    Damé, Luc; Lamy, Philippe; von Fay-Siebenburgen (Erdélyi), Robert

    Several ground facilities and space missions are currently dedicated to the study of the Sun at high resolution and of the solar corona in particular. However, and despite significant progress with the advent of space missions and UV, EUV and XUV direct observations of the hot chro-mosphere and million degrees coronal plasma, much is yet to be achieved in the understanding of these high temperatures, fine dissipative structures and of the coronal heating in general. Recent missions have shown the definite role of waves and of the magnetic field deep in the inner corona, at the chromosphere-corona interface, where dramatic changes occur. The dynamics of the chromosphere and corona is controlled by the emerging magnetic field, guided by the coronal magnetic field. Accordingly, the direct measurement of the chromospheric and coronal magnetic fields is of prime importance. The solar corona consists of many thin loops or threads with the plasmas brightening and fading independently. The dynamics in each thread is believed to be related to the formation of filaments, each one being dynamic, in a non-equilibrium state. The mechanism sustaining that dynamics, oscillations or waves (Alfvén or MHD?), require both very high-cadence, multi-spectral observations, and high resolution. This is foreseen in the future Space Mission HiRISE, the ultimate new generation ultrahigh resolution, interferomet-ric and coronagraphic, Solar Physics Mission, proposed for ESA Cosmic Vision (pre-selected in 2007, and under preparation for 2012 second call). HiRISE (High Resolution Imaging and Spectroscopy Explorer), at the L1 Lagrangian point, provides meter class FUV imaging and spectro-imaging, EUV and XUV imaging and spectroscopy, and ultimate coronagraphy by a remote external occulter (satellites in formation flying 280 m apart) allowing to characterize temperature, densities and velocities in the solar upper chromosphere, transition zone and inner corona with, in particular, 2D very high

  10. METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

    Science.gov (United States)

    Biarnés, Xevi; Pietrucci, Fabio; Marinelli, Fabrizio; Laio, Alessandro

    2012-01-01

    We present a new computational tool, METAGUI, which extends the VMD program with a graphical user interface that allows constructing a thermodynamic and kinetic model of a given process simulated by large-scale molecular dynamics. The tool is specially designed for analyzing metadynamics based simulations. The huge amount of diverse structures generated during such a simulation is partitioned into a set of microstates (i.e. structures with similar values of the collective variables). Their relative free energies are then computed by a weighted-histogram procedure and the most relevant free energy wells are identified by diagonalization of the rate matrix followed by a commitor analysis. All this procedure leads to a convenient representation of the metastable states and long-time kinetics of the system which can be compared with experimental data. The tool allows to seamlessly switch between a collective variables space representation of microstates and their atomic structure representation, which greatly facilitates the set-up and analysis of molecular dynamics simulations. METAGUI is based on the output format of the PLUMED plugin, making it compatible with a number of different molecular dynamics packages like AMBER, NAMD, GROMACS and several others. The METAGUI source files can be downloaded from the PLUMED web site ( http://www.plumed-code.org). Program summaryProgram title: METAGUI Catalogue identifier: AEKH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 117 545 No. of bytes in distributed program, including test data, etc.: 8 516 203 Distribution format: tar.gz Programming language: TK/TCL, Fortran Computer: Any computer with a VMD installation and capable of running an executable produced by a gfortran compiler Operating

  11. Molecular dynamics simulation analysis of ion irradiation effects on plasma-liquid interface

    Science.gov (United States)

    Minagawa, Yudai; Shirai, Naoki; Uchida, Satoshi; Tochikubo, Fumiyoshi

    2013-09-01

    Nonthermal atmospheric plasmas are used in a wide range of fields because the high-density plasma can be easily irradiated to various substances such as solid, liquid, biological object and so on. On the other hand, the mechanisms of physical and chemical phenomena at the plasma-liquid interface are not well understood yet. To investigate the effects of ion impact from plasma on water surface, we analyzed behavior of liquid water by classical molecular dynamics simulation. Simulation system consists of an irradiation particle in gas phase and 2000 water molecules in liquid phase. O+ ion with 10 eV or 100 eV was impinged on the water surface. Ion impact induced increasing water temperature and ejection of water molecules. The averaged number of evaporated water molecules by ion impact is 0.6 molecules at 10 eV and 7.0 molecules at 100 eV. The maximum ion penetration depth was 1.14 nm at 10 eV and 2.75 nm at 100 eV. Ion entering into water disturbs the stable hydrogen bonding configurations between water molecules and gives energy to water molecules. Some water molecules rotated and moved by ion interaction impact on other water molecules one after another. When the water molecule near the surface received strongly repulsive force, it released into gas phase. This work was supported financially in part by a Grant-in-Aid for Scientific Research on Innovation Areas (No21110007) from MEXT, Japan.

  12. Interface dynamics and crystal phase switching in GaAs nanowires

    Science.gov (United States)

    Jacobsson, Daniel; Panciera, Federico; Tersoff, Jerry; Reuter, Mark C.; Lehmann, Sebastian; Hofmann, Stephan; Dick, Kimberly A.; Ross, Frances M.

    2016-03-01

    Controlled formation of non-equilibrium crystal structures is one of the most important challenges in crystal growth. Catalytically grown nanowires are ideal systems for studying the fundamental physics of phase selection, and could lead to new electronic applications based on the engineering of crystal phases. Here we image gallium arsenide (GaAs) nanowires during growth as they switch between phases as a result of varying growth conditions. We find clear differences between the growth dynamics of the phases, including differences in interface morphology, step flow and catalyst geometry. We explain these differences, and the phase selection, using a model that relates the catalyst volume, the contact angle at the trijunction (the point at which solid, liquid and vapour meet) and the nucleation site of each new layer of GaAs. This model allows us to predict the conditions under which each phase should be observed, and use these predictions to design GaAs heterostructures. These results could apply to phase selection in other nanowire systems.

  13. Molecular dynamics computer simulation studies of aqueous solutions in clusters, in bulk, and at interfaces

    Science.gov (United States)

    Yeh, In-Chul

    1999-10-01

    This dissertation investigates the structural and dynamical properties of aqueous solutions in clusters, in bulk, and at interfaces using molecular dynamics computer simulations. First, the photodetachment spectra of Cl- (H 2O)n (n = 2,3,...15) clusters have been calculated. The dependence of the spectra on the variations in the temperature of the clusters, the potential parameter for the postejected ion, and the type of the potential (pair-wise non-polarizable vs. many-body polarizable) has been investigated. Next, I have compared structural and dynamical properties of bulk water calculated by the simple point charge (SPC) and extended simple point charge (SPC/E) models. Tetrahedral network in SPC water is found to be weaker than those in SPC/E water due to smaller point charges, resulting in a larger self-diffusion coefficient. As a model interfacial system, I discuss the structure of water next to metal surfaces: Pt(100) and Pt(111). The two dimensional Ewald summation technique has been used for the calculation of long range Coulombic forces. Water next to an uncharged metallic surface is perturbed to a distance of 1 nm. Next to the charged surface water is reorienting and when the external field is strong, undergoes a layering transition. The dielectric constant of water as a function of electric fields has been also calculated. Simulations of water between walls and bulk water have been done to confirm the macroscopic nature of the dielectric constant. Calculated dielectric constants have been compared with those obtained by a theoretical prediction and a recent simulation study. Distance dependent density profiles of water near charged Ag(111) surfaces have been calculated and compared with experimental profiles. The effect of ionic screening is accounted for by an exponetially decaying electric field. Finally, I propose a modification in the three dimensional Ewald summation technique for calculations of long-range Coulombic forces for systems with a slab

  14. Abnormal enhancement of interface trap generation under dynamic oxide field stress at MHz region

    OpenAIRE

    Zhu, Shiyang; Nakajima, Anri

    2005-01-01

    By stressing metal-oxide-semiconductor field-effect transistors with ultrathin silicon dioxide or oxynitride gate dielectrics under square wave form voltage at the MHz region, an abnormal enhancement of interface trap generation in the midchannel region has been observed at some special frequencies. A hypothesis, including self-accelerating interface trap generation originated from the positive feedback of a charge pumping current to be contributed by the stress-induced near-interface oxide t...

  15. ENABLE (Exportable Notation and Bookmark List Engine): an Interface to Manage Tumor Measurement Data from PACS to Cancer Databases.

    Science.gov (United States)

    Goyal, Nikhil; Apolo, Andrea B; Berman, Eliana D; Bagheri, Mohammad Hadi; Levine, Jason E; Glod, John W; Kaplan, Rosandra N; Machado, Laura B; Folio, Les R

    2017-01-10

    Oncologists evaluate therapeutic response in cancer trials based on tumor quantification following selected "target" lesions over time. At our cancer center, a majority of oncologists use Response Evaluation Criteria in Solid Tumors (RECIST) v1.1 quantifying tumor progression based on lesion measurements on imaging. Currently, our oncologists handwrite tumor measurements, followed by multiple manual data transfers; however, our Picture Archiving Communication System (PACS) (Carestream Health, Rochester, NY) has the ability to export tumor measurements, making it possible to manage tumor metadata digitally. We developed an interface, "Exportable Notation and Bookmark List Engine" (ENABLE), which produces prepopulated RECIST v1.1 worksheets and compiles cohort data and data models from PACS measurement data, thus eliminating handwriting and manual data transcription. We compared RECIST v1.1 data from eight patients (16 computed tomography exams) enrolled in an IRB-approved therapeutic trial with ENABLE outputs: 10 data fields with a total of 194 data points. All data in ENABLE's output matched with the existing data. Seven staff were taught how to use the interface with a 5-min explanatory instructional video. All were able to use ENABLE successfully without additional guidance. We additionally assessed 42 metastatic genitourinary cancer patients with available RECIST data within PACS to produce a best response waterfall plot. ENABLE manages tumor measurements and associated metadata exported from PACS, producing forms and data models compatible with cancer databases, obviating handwriting and the manual re-entry of data. Automation should reduce transcription errors and improve efficiency and the auditing process.

  16. A Dynamic Model for the Interaction Between an Insoluble Particle and an Advancing Solid/Liquid Interface

    Science.gov (United States)

    Catalina, A. V.; Mukherjee, S.; Stefanescu, D. M.

    2000-01-01

    Most models that describe the interaction of an insoluble particle with an advancing solid-liquid interface are based on the assumption of steady state. However, as demonstrated by experimental work, the process does not reach steady state until the particle is pushed for a while by the interface. In this work, a dynamic mathematical model was developed. The dynamic model demonstrates that this interaction is essentially non-steady state and that steady state eventually occurs only when solidification is conducted at sub-critical velocities. The model was tested for three systems: aluminum-zirconia particles, succinonitrilepolystyrene particles, and biphenyl-glass particles. The calculated values for critical velocity of the pushing/engulfment transition were in same range with the experimental ones.

  17. DYNAMIC BEHAVIOR OF TWO UNEQUAL PARALLEL PERMEABLE INTERFACE CRACKS IN A PIEZOELECTRIC LAYER BONDED TO TWO HALF PIEZOELECTRIC MATERIALS PLANES

    Institute of Scientific and Technical Information of China (English)

    SUN Jian-liang; ZHOU Zhen-gong; WANG Biao

    2005-01-01

    The dynamic behavior of two unequal parallel permeable interface cracks in a piezoelectric layer bonded to two half-piezoelectric material planes subjected to harmonic anti-plane shear waves is investigated. By using the Fourier transform, the problem can be solved with the help of two pairs of dual integral equations in which the unknown variables were the jumps of the displacements across the crack surfaces. Numerical results are presented graphically to show the effects of the geometric parameters, the frequency of the incident wave on the dynamic stress intensity factors and the electric displacement intensity factors. Especially, the present problem can be returned to static problem of two parallel permeable interface cracks. Compared with the solutions of impermeable crack surface condition, it is found that the electric displacement intensity factors for the permeable crack surface conditions are much smaller.

  18. A thermal-mechanical constitutive model for b-HMX single crystal and cohesive interface under dynamic high pressure loading

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Due to the significant thermal-mechanical effects during hot spot formation in PBX explosives,a thermodynamic constitutive model has been constructed for HMX anisotropic single crystal subjected to dynamic impact loading. The crystal plasticity model based on dislocation dynamics theory was employed to describe the anisotropic plastic behavior along the preferential slip systems. A modified equation of state (EOS) was introduced into the constitutive equations through the decomposing stress tensor and the nonlinear elasticity for materials was taken into account. The one-dimensional strain impact simulations for HMX single crystal and quasi-bicrystal were performed respectively,in which the cohesive elements were inserted over the interface areas for the latter. The predicted particle velocities for the single crystal sample agreed well with the experimental results in the literature. Furthermore,the effects of crystal orientations,interface,misorientations on localized strain,stress and temperature distributions were predicted and discussed.

  19. In Situ Mass Spectrometric Monitoring of the Dynamic Electrochemical Process at the Electrode–Electrolyte Interface: a SIMS Approach

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhaoying; Zhang, Yanyan; Liu, Bingwen; Wu, Kui; Thevuthasan, Suntharampillai; Baer, Donald R.; Zhu, Zihua; Yu, Xiao-Ying; Wang, Fuyi

    2017-01-03

    The in situ molecular characterization of reaction intermediates and products at electrode-electrolyte interfaces is central to mechanistic studies of complex electrochemical processes, yet a great challenge. The coupling of electrochemistry (EC) and mass spectrometry (MS) has seen rapid development and found broad applicability in tackling challenges in analytical and bioanalytical chemistry. However, few truly in situ and real-time EC-MS studies have been reported at electrode-electrolyte interfaces. An innovative EC-MS coupling method named in situ liquid secondary ion mass spectrometry (SIMS) was recently developed by combining SIMS with a vacuum compatible microfluidic electrochemical device. Using this novel capability we report the first in situ elucidation of the electro-oxidation mechanism of a biologically significant organic compound, ascorbic acid (AA), at the electrode-electrolyte interface. The short-lived radical intermediate was successfully captured, which had not been detected directly before. Moreover, we demonstrated the power of this new technique in real-time monitoring of the formation and dynamic evolution of electrical double layers at the electrode-electrolyte interface. This work suggests further promising applications of in situ liquid SIMS in studying more complex chemical and biological events at the electrode-electrolyte interface.

  20. Structure and dynamics of egg white ovalbumin adsorbed at the air/water interface

    NARCIS (Netherlands)

    Kudryashova, E.V.; Meinders, M.B.J.; Visser, A.J.W.G.; Hoek, A. van; Jongh, H.H.J. de

    2003-01-01

    The molecular properties of egg white ovalbumin adsorbed at the air/water interface were studied using infrared reflection absorption spectroscopy (IRRAS) and time-resolved fluorescence anisotropy (TRFA) techniques. Ovalbumin adsorbed at the air/ water interface adopts a characteristic partially unf

  1. Role of Structural Dynamics at the Receptor G Protein Interface for Signal Transduction.

    Directory of Open Access Journals (Sweden)

    Alexander S Rose

    Full Text Available GPCRs catalyze GDP/GTP exchange in the α-subunit of heterotrimeric G proteins (Gαßγ through displacement of the Gα C-terminal α5 helix, which directly connects the interface of the active receptor (R* to the nucleotide binding pocket of G. Hydrogen-deuterium exchange mass spectrometry and kinetic analysis of R* catalysed G protein activation have suggested that displacement of α5 starts from an intermediate GDP bound complex (R*•GGDP. To elucidate the structural basis of receptor-catalysed displacement of α5, we modelled the structure of R*•GGDP. A flexible docking protocol yielded an intermediate R*•GGDP complex, with a similar overall arrangement as in the X-ray structure of the nucleotide free complex (R*•Gempty, however with the α5 C-terminus (GαCT forming different polar contacts with R*. Starting molecular dynamics simulations of GαCT bound to R* in the intermediate position, we observe a screw-like motion, which restores the specific interactions of α5 with R* in R*•Gempty. The observed rotation of α5 by 60° is in line with experimental data. Reformation of hydrogen bonds, water expulsion and formation of hydrophobic interactions are driving forces of the α5 displacement. We conclude that the identified interactions between R* and G protein define a structural framework in which the α5 displacement promotes direct transmission of the signal from R* to the GDP binding pocket.

  2. Role of Structural Dynamics at the Receptor G Protein Interface for Signal Transduction.

    Science.gov (United States)

    Rose, Alexander S; Zachariae, Ulrich; Grubmüller, Helmut; Hofmann, Klaus Peter; Scheerer, Patrick; Hildebrand, Peter W

    2015-01-01

    GPCRs catalyze GDP/GTP exchange in the α-subunit of heterotrimeric G proteins (Gαßγ) through displacement of the Gα C-terminal α5 helix, which directly connects the interface of the active receptor (R*) to the nucleotide binding pocket of G. Hydrogen-deuterium exchange mass spectrometry and kinetic analysis of R* catalysed G protein activation have suggested that displacement of α5 starts from an intermediate GDP bound complex (R*•GGDP). To elucidate the structural basis of receptor-catalysed displacement of α5, we modelled the structure of R*•GGDP. A flexible docking protocol yielded an intermediate R*•GGDP complex, with a similar overall arrangement as in the X-ray structure of the nucleotide free complex (R*•Gempty), however with the α5 C-terminus (GαCT) forming different polar contacts with R*. Starting molecular dynamics simulations of GαCT bound to R* in the intermediate position, we observe a screw-like motion, which restores the specific interactions of α5 with R* in R*•Gempty. The observed rotation of α5 by 60° is in line with experimental data. Reformation of hydrogen bonds, water expulsion and formation of hydrophobic interactions are driving forces of the α5 displacement. We conclude that the identified interactions between R* and G protein define a structural framework in which the α5 displacement promotes direct transmission of the signal from R* to the GDP binding pocket.

  3. Effects of interface slip and viscoelasticity on the dynamic response of droplet quartz crystal microbalances.

    Science.gov (United States)

    Zhuang, Han; Lu, Pin; Lim, Siak Piang; Lee, Heow Pueh

    2008-10-01

    In the present paper we first present a derivation based on the time-dependent perturbation theory to develop the dynamical equations which can be applied to model the response of a droplet quartz crystal microbalance (QCM) in contact with a single viscoelastic media. Moreover, the no-slip boundary condition across the device-viscoelastic media interface has been relaxed in the present model by using the Ellis-Hayward slip length approach. The model is then used to illustrate the characteristic changes in the frequency and attenuation of the QCM with and without the boundary slippage due to the changes in viscoelasticity as the coated media varies from Newtonian liquid to solid. To complement the theory, experiments have been conducted with microliter droplets of aqueous glycerol solutions and silicone oils with a viscosity in the range of 50 approximately 10,000 cS. The results have confirmed the Newtonian characteristics of the glycerol solutions. In contrast, the acoustic properties of the silicones oils as reflected in the impedance analysis are different from the glycerol solutions. More importantly, it was found that for the silicone oils the frequency steadily increased for several hours and even exceeded the initial value of the unloaded crystal as reflected in the positive frequency shift. Collaborative effects of interfacial slippage and viscoelasticity have been introduced to qualitatively interpret the measured frequency up-shifts for the silicone oils. The present work shows the potential importance of the combined effects of viscoelasticity and interfacial slippage when using the droplet QCM to investigate the rheological behavior of more complex fluids.

  4. Global dynamics of a colorectal cancer treatment model with cancer stem cells.

    Science.gov (United States)

    Abernathy, Kristen; Abernathy, Zachary; Brown, Kelsey; Burgess, Claire; Hoehne, Rebecca

    2017-02-01

    We present and analyze a mathematical model of the treatment of colorectal cancer using a system of nonlinear ordinary differential equations. The model describes the effectiveness of immunotherapy and chemotherapy for treatment of tumor cells and cancer stem cells (CSCs). The effects of CD8(+)T cells, natural killer cells, and interleukin proteins on tumor cells and CSCs under the influence of treatment are also illustrated. Using the method of localization of compact invariant sets, we present conditions on treatment parameters to guarantee a globally attracting tumor clearance state. Numerical simulations using estimated parameters from the literature are included to showcase various global dynamics of the model.

  5. Influence of temperature on the structure and dynamics of the [BMIM][PF(6)] ionic liquid/graphite interface.

    Science.gov (United States)

    Kislenko, Sergey A; Amirov, Ravil H; Samoylov, Igor S

    2010-10-07

    The influence of temperature on the structure and dynamics of the [BMIM][PF(6)] ionic liquid/graphite interface has been investigated by molecular dynamics simulations. The performed simulations cover a 100 K wide temperature interval, ranging from 300 K to 400 K. It was shown that the magnitudes of density peaks of anions in the vicinity of the surface decrease with increasing temperature while in the case of cations anomalous temperature behaviour of the density profile is observed: the magnitude of the second peak of cations increases with the increase of temperature. To characterize interface dynamics the local self-diffusion coefficients D(x) of ions in the normal direction to the surface and the residence time of ions in the first and second interfacial layer have been estimated. It was shown that the local self-diffusion coefficients in the vicinity of the surface correlate with the local ion density; the maxima of the function D(x)(x) for the cations (anions) coincide with the regions of reduced cation (anion) density and vice versa. Finally, the influence of temperature on the screening potential in the vicinity of a charged graphite surface has been studied. It was shown that the increase of temperature from 300 K to 400 K induces the decrease of the potential drop across the interface that implies the increase of the capacitance of the electrical double layer.

  6. Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

    Science.gov (United States)

    Lísal, Martin; Izák, Pavel

    2013-07-01

    Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf2N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 μmol/m2 at 300 K. For [bmim][Tf2N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are ±0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf2N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

  7. Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

    Energy Technology Data Exchange (ETDEWEB)

    Lisal, Martin [Institute of Chemical Process Fundamentals of the ASCR, v. v. i., 165 02 Prague 6-Suchdol (Czech Republic); Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Usti n. Lab. (Czech Republic); Izak, Pavel [Institute of Chemical Process Fundamentals of the ASCR, v. v. i., 165 02 Prague 6-Suchdol (Czech Republic)

    2013-07-07

    Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf{sub 2}N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 {mu}mol/m{sup 2} at 300 K. For [bmim][Tf{sub 2}N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are {+-}0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf{sub 2}N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

  8. Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface.

    Science.gov (United States)

    Lísal, Martin; Izák, Pavel

    2013-07-07

    Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf2N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 μmol/m(2) at 300 K. For [bmim][Tf2N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are ±0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf2N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

  9. Reactivity of aldehydes at the air-water interface. Insights from molecular dynamics simulations and ab initio calculations.

    Science.gov (United States)

    Martins-Costa, Marilia T C; García-Prieto, Francisco F; Ruiz-López, Manuel F

    2015-02-14

    Understanding the influence of solute-solvent interactions on chemical reactivity has been a subject of intense research in the last few decades. Theoretical studies have focused on bulk solvation phenomena and a variety of models and methods have been developed that are now widely used by both theoreticians and experimentalists. Much less attention has been paid, however, to processes that occur at liquid interfaces despite the important role such interfaces play in chemistry and biology. In this study, we have carried out sequential molecular dynamics simulations and quantum mechanical calculations to analyse the influence of the air-water interface on the reactivity of formaldehyde, acetaldehyde and benzaldehyde, three simple aldehydes of atmospheric interest. The calculated free-energy profiles exhibit a minimum at the interface, where the average reactivity indices may display large solvation effects. The study emphasizes the role of solvation dynamics, which are responsible for large fluctuations of some molecular properties. We also show that the photolysis rate constant of benzaldehyde in the range 290-308 nm increases by one order of magnitude at the surface of a water droplet, from 2.7 × 10(-5) s(-1) in the gas phase to 2.8 × 10(-4) s(-1) at the air-water interface, and we discuss the potential impact of this result on the chemistry of the troposphere. Experimental data in this domain are still scarce and computer simulations like those presented in this work may provide some insights that can be useful to design new experiments.

  10. Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab-Initio Molecular Dynamics Simulations

    CERN Document Server

    Kessler, Jan; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D

    2015-01-01

    The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab-initio molecular dynamics simulations in conjunction with an instantaneous surface definition [A. P. Willard and D. Chandler, J. Phys. Chem. B 114, 1954 (2010)]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

  11. Dynamic Distribution and Layouting of Model-Based User Interfaces in Smart Environments

    Science.gov (United States)

    Roscher, Dirk; Lehmann, Grzegorz; Schwartze, Veit; Blumendorf, Marco; Albayrak, Sahin

    The developments in computer technology in the last decade change the ways of computer utilization. The emerging smart environments make it possible to build ubiquitous applications that assist users during their everyday life, at any time, in any context. But the variety of contexts-of-use (user, platform and environment) makes the development of such ubiquitous applications for smart environments and especially its user interfaces a challenging and time-consuming task. We propose a model-based approach, which allows adapting the user interface at runtime to numerous (also unknown) contexts-of-use. Based on a user interface modelling language, defining the fundamentals and constraints of the user interface, a runtime architecture exploits the description to adapt the user interface to the current context-of-use. The architecture provides automatic distribution and layout algorithms for adapting the applications also to contexts unforeseen at design time. Designers do not specify predefined adaptations for each specific situation, but adaptation constraints and guidelines. Furthermore, users are provided with a meta user interface to influence the adaptations according to their needs. A smart home energy management system serves as running example to illustrate the approach.

  12. Ligand-protein docking: cancer research at the interface between biology and chemistry.

    Science.gov (United States)

    Glen, R C; Allen, S C

    2003-05-01

    years. For example, some methods rely on complex molecular dynamics simulations while others use less costly graph matching approaches. There is generally a compromise between speed and accuracy, with some methods giving much more information and insight into the nature of the protein/ligand interactions and other methods optimised for speed of docking thousands of putative ligands. We will describe some of the more common methods and algorithms used to solve the docking problem and in particular, we will review recent applications in cancer research.

  13. Atomic structure and thermal stability of interfaces between metallic glass and embedding nano-crystallites revealed by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gao, X.Z.; Yang, G.Q.; Xu, B.; Qi, C.; Kong, L.T., E-mail: konglt@sjtu.edu.cn; Li, J.F.

    2015-10-25

    Molecular dynamics simulations were performed to investigate the atomic structure and thermal stability of interfaces formed between amorphous Cu{sub 50}Zr{sub 50} matrix and embedding B2 CuZr nano-crystallites. The interfaces are found to be rather abrupt, and their widths show negligible dependence on the nano-crystallite size. Local atomic configuration in the interfacial region is dominated by geometry characterized by Voronoi polyhedra <0,5,2,6> and <0,4,4,6>, and the contents of these polyhedra also exhibit apparent size dependence, which in turn results in an increasing trend in the interfacial energy against the nano-crystallite size. Annealing of the interface models at elevated temperatures will also enrich these characterizing polyhedra. While when the temperature is as high as the glass transition temperature of the matrix, growth of the nano-crystallites will be appreciable. The growth activation energy also shows size dependence, which is lower for larger nano-crystallites, suggesting that large nano-crystallites are prone to grow upon thermal disturbance. - Highlights: • Special clusters characterizing the local geometry are abundant in the interfaces. • Their content varies with the size of the embedding nano-crystallite. • In turn, size dependences in interfacial thermodynamics and kinetics are observed.

  14. Molecular Dynamics Study of the Separation Behavior at the Interface between PVDF Binder and Copper Current Collector

    Directory of Open Access Journals (Sweden)

    Seungjun Lee

    2016-01-01

    Full Text Available In Li-ion batteries, the mechanical strengths at the interfaces of binder/particle and binder/current collector play an important role in maintaining the mechanical integrity of the composite electrode. In this work, the separation behaviors between polyvinylidene fluoride (PVDF binders and copper current collectors are studied in the opening and sliding modes using molecular dynamics (MD simulations. The simulation shows that the separation occurs inside the PVDF rather than at the interface due to the strong adhesion between PVDF and copper. This fracture behavior is different from the behavior of the PVDF/graphite basal plane that shows a clear separation at the interface. The results suggest that the adhesion strength of the PVDF/copper is stronger than that of the PVDF/graphite basal plane. The methodology used in MD simulation can directly evaluate the adhesion strength at the interfaces of various materials between binders, substrates, and particles at the atomic scales. The proposed method can therefore provide a guideline for the design of the electrode in order to enhance the mechanical integrity for better battery performance.

  15. Dynamic Mass Transfer of Hemoglobin at the Aqueous/Ionic-Liquid Interface Monitored with Liquid Core Optical Waveguide.

    Science.gov (United States)

    Chen, Xuwei; Yang, Xu; Zeng, Wanying; Wang, Jianhua

    2015-08-04

    Protein transfer from aqueous medium into ionic liquid is an important approach for the isolation of proteins of interest from complex biological samples. We hereby report a solid-cladding/liquid-core/liquid-cladding sandwich optical waveguide system for the purpose of monitoring the dynamic mass-transfer behaviors of hemoglobin (Hb) at the aqueous/ionic liquid interface. The optical waveguide system is fabricated by using a hydrophobic IL (1,3-dibutylimidazolium hexafluorophosphate, BBimPF6) as the core, and protein solution as one of the cladding layer. UV-vis spectra are recorded with a CCD spectrophotometer via optical fibers. The recorded spectra suggest that the mass transfer of Hb molecules between the aqueous and ionic liquid media involve accumulation of Hb on the aqueous/IL interface followed by dynamic extraction/transfer of Hb into the ionic liquid phase. A part of Hb molecules remain at the interface even after the accomplishment of the extraction/transfer process. Further investigations indicate that the mass transfer of Hb from aqueous medium into the ionic liquid phase is mainly driven by the coordination interaction between heme group of Hb and the cationic moiety of ionic liquid, for example, imidazolium cation in this particular case. In addition, hydrophobic interactions also contribute to the transfer of Hb.

  16. Influence of surface polarity on water dynamics at the water/rutile TiO₂(110) interface.

    Science.gov (United States)

    Ohto, Tatsuhiko; Mishra, Ankur; Yoshimune, Seiji; Nakamura, Hisao; Bonn, Mischa; Nagata, Yuki

    2014-06-18

    We report molecular dynamics (MD) simulations of the water/clean rutile TiO2 (110) interface using polarizable and non-surface polarity force field models. The effect of surface polarity on the water dynamics near the TiO2(110) surface is addressed, specifically by calculating the water hydrogen bond and reorientational dynamics. The hydrogen bond lifetime of interfacial water molecules is several times longer than that of bulk water due to the strong water-TiO2 interactions. A comparison of the dynamics simulated with the polarizable and non-surface polarity models shows that, while the hydrogen bond lifetime between the interfacial water and TiO2 surface is insensitive to the surface polarity, the reorientational dynamics around this hydrogen bond axis is significantly influenced by the surface polarity; the surface polarity of the TiO2 increases the water-TiO2 interactions, stabilizing the local structure of the interfacial water molecules and restricting their rotational motion. This reorientation occurs predominantly by rotation around the O-H group hydrogen bonded to the TiO2 surface. Furthermore, we correlate the dynamics of the induced charge on the TiO2 surface with the interfacial water dynamics. Our results show that the timescale of correlations of the atom charges induced by the local electric field in bulk water is influenced by the rotational motion, hydrogen bond rearrangement and translational motion, while the induced charge dynamics of the TiO2 surface is governed primarily by the rotational dynamics of the interfacial water molecules. This study demonstrates that the solid surface polarity has a significant impact on the dynamics of water molecules near TiO2 surfaces.

  17. Dynamic Fluctuation of Circulating Tumor Cells during Cancer Progression

    Directory of Open Access Journals (Sweden)

    Mazen A. Juratli

    2014-01-01

    Full Text Available Circulating tumor cells (CTCs are a promising diagnostic and prognostic biomarker for metastatic tumors. We demonstrate that CTCs’ diagnostic value might be increased through real-time monitoring of CTC dynamics. Using preclinical animal models of breast cancer and melanoma and in vivo flow cytometry with photoacoustic and fluorescence detection schematics, we show that CTC count does not always correlate with the primary tumor size. Individual analysis elucidated many cases where the highest level of CTCs was detected before the primary tumor starts progressing. This phenomenon could be attributed to aggressive tumors developing from cancer stem cells. Furthermore, real-time continuous monitoring of CTCs reveals that they occur at highly variable rates in a detection point over a period of time (e.g., a range of 0–54 CTCs per 5 min. These same fluctuations in CTC numbers were observed in vivo in epithelial and non-epithelial metastatic tumors, in different stages of tumor progression, and in different vessels. These temporal CTC fluctuations can explain false negative results of a one-time snapshot test in humans. Indeed, we observed wide variations in the number of CTCs in subsequent blood samples taken from the same metastatic melanoma patient, with some samples being CTC-free. If these phenomena are confirmed in our ongoing in vivo clinical trials, this could support a personalized strategy of CTC monitoring for cancer patients.

  18. Dynamic Fluctuation of Circulating Tumor Cells during Cancer Progression

    Energy Technology Data Exchange (ETDEWEB)

    Juratli, Mazen A.; Sarimollaoglu, Mustafa; Nedosekin, Dmitry A. [Phillips Classic Laser and Nanomedicine Laboratories, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Melerzanov, Alexander V. [Moscow Institute of Physics and Technology (MIPT), Moscow Region, 141700 (Russian Federation); Zharov, Vladimir P. [Phillips Classic Laser and Nanomedicine Laboratories, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Arkansas Nanomedicine Center, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States); Moscow Institute of Physics and Technology (MIPT), Moscow Region, 141700 (Russian Federation); Galanzha, Ekaterina I., E-mail: egalanzha@uams.edu [Phillips Classic Laser and Nanomedicine Laboratories, University of Arkansas for Medical Sciences, Little Rock, AR 72205 (United States)

    2014-01-15

    Circulating tumor cells (CTCs) are a promising diagnostic and prognostic biomarker for metastatic tumors. We demonstrate that CTCs’ diagnostic value might be increased through real-time monitoring of CTC dynamics. Using preclinical animal models of breast cancer and melanoma and in vivo flow cytometry with photoacoustic and fluorescence detection schematics, we show that CTC count does not always correlate with the primary tumor size. Individual analysis elucidated many cases where the highest level of CTCs was detected before the primary tumor starts progressing. This phenomenon could be attributed to aggressive tumors developing from cancer stem cells. Furthermore, real-time continuous monitoring of CTCs reveals that they occur at highly variable rates in a detection point over a period of time (e.g., a range of 0–54 CTCs per 5 min). These same fluctuations in CTC numbers were observed in vivo in epithelial and non-epithelial metastatic tumors, in different stages of tumor progression, and in different vessels. These temporal CTC fluctuations can explain false negative results of a one-time snapshot test in humans. Indeed, we observed wide variations in the number of CTCs in subsequent blood samples taken from the same metastatic melanoma patient, with some samples being CTC-free. If these phenomena are confirmed in our ongoing in vivo clinical trials, this could support a personalized strategy of CTC monitoring for cancer patients.

  19. Subtraction and dynamic MR images of breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Murakami, Yoshitaka; Aoki, Manabu; Harada, Junta (Jikei Univ., Tokyo (Japan). School of Medicine)

    1993-04-01

    The purpose of this study was to evaluate the diagnostic effectiveness of subtraction and dynamic MR imaging in patients with breast masses. In 23 breast cancers and six fibroadenomas, spin echo T1 images were obtained at 0.2 Tesla before and every minute after intravenous injection of Gd-DTPA (0.1 or 0.2 mmol/kg). Subtraction images were obtained sequentially on the CRT monitor. All breast masses were enhanced after gadolinium and stood out as bright lesions on subtraction images. The tumor margin and its extension were more precisely evaluated on subtraction MR images than on conventional postcontrast MR images. Breast cancer showed a characteristic time-intensity curve with an early peak, in contrast to fibroadenoma, which showed a gradual increase in signal intensity. Subtraction MR imaging is a simple method for the evaluation of breast masses, and further, the time-intensity curve obtained by dynamic study is helpful in the differential diagnosis of lesions. (author).

  20. Thermodynamics and intrinsic structure of the Al-Pb liquid-liquid interface: a molecular dynamics simulation study.

    Science.gov (United States)

    Yang, Yang; Laird, Brian B

    2014-07-17

    We examine the thermodynamics and intrinsic structure of the Al-Pb liquid-liquid interface using molecular dynamics simulation and embedded atom method potentials. The instantaneous interfacial positions, from which the intrinsic structure and the capillary fluctuation spectrum are determined, are calculated using a grid-based method. The interfacial free energy extracted from the capillary fluctuation spectrum is shown to be in excellent agreement with that calculated mechanically by integrating the stress profile. The intrinsic liquid-liquid interfacial density profile shows structural oscillations in the liquid phases in the interfacial region that are shown to be quantitatively similar to the radial distribution functions of the bulk liquid, consistent with theoretical predictions from classical density functional theory and with earlier simulations on liquid-liquid and liquid-vapor interfaces. In addition, we show the mean interfacial density profile for this system is well described as a convolution of the intrinsic density profile and the probability distribution of interfacial position.

  1. Calculation of transient dynamic stress intensity factors at bimaterial interface cracks using a SBFEMbased frequency-domain approach

    Institute of Scientific and Technical Information of China (English)

    Z.J.YANG; A.J.DEEKS

    2008-01-01

    A frequency-domain approach based on the semi-analytical scaled boundary finite element method (SBFEM) was developed to calculate dynamic stress intensity factors (DSIFs) at bimaterial interface cracks subjected to transient loading. Be-cause the stress solutions of the SBFEM in the frequency domain are analytical in the radial direction, and the complex stress singularity at the bimaterial interface crack tip is explicitly represented in the stress solutions, the mixed-mode DSIFs were calculated directly by definition. The complex frequency-response functions of DSIFs were then used by the fast Fourier transform (FFT) and the inverse FFT to calculate time histories of DSIFs. A benchmark example was modelled. Good re-sults were obtained by modelling the example with a small number of degrees of freedom due to the semi-analytical nature of the SBFEM.

  2. Mechanical responses of the bio-nano interface: A molecular dynamics study of graphene-coated lipid membrane

    Directory of Open Access Journals (Sweden)

    Zhigong Song

    2015-11-01

    Full Text Available Bio-nano interfaces between biological materials and functional nanodevices are of vital importance in relevant energy and information exchange processes, which thus demand an in-depth understanding. One of the critical issues from the application viewpoint is the stability of the bio-nano hybrid under mechanical perturbations. In this work we explore mechanical responses of the interface between lipid bilayer and graphene under hydrostatic pressure or indentation loads. We find that graphene coating provides remarkable resistance to the loads, and the intercalated water layer offers additional protection. These findings are discussed based on molecular dynamics simulation results that elucidate the molecular level mechanisms, which provide a basis for the rational design of bionanotechnology-enabled applications such as biomedical devices and nanotherapeutics.

  3. Femtosecond Hydrogen Bond Dynamics of Bulk-like and Bound Water at Positively and Negatively Charged Lipid Interfaces Revealed by 2D HD-VSFG Spectroscopy.

    Science.gov (United States)

    Singh, Prashant Chandra; Inoue, Ken-Ichi; Nihonyanagi, Satoshi; Yamaguchi, Shoichi; Tahara, Tahei

    2016-08-26

    Interfacial water in the vicinity of lipids plays an important role in many biological processes, such as drug delivery, ion transportation, and lipid fusion. Hence, molecular-level elucidation of the properties of water at lipid interfaces is of the utmost importance. We report the two-dimensional heterodyne-detected vibrational sum frequency generation (2D HD-VSFG) study of the OH stretch of HOD at charged lipid interfaces, which shows that the hydrogen bond dynamics of interfacial water differ drastically, depending on the lipids. The data indicate that the spectral diffusion of the OH stretch at a positively charged lipid interface is dominated by the ultrafast (dynamics, while the dynamics at a negatively charged lipid interface exhibit sub-picosecond dynamics almost exclusively, implying that fast hydrogen bond fluctuation is prohibited. These results reveal that the ultrafast hydrogen bond dynamics at the positively charged lipid-water interface are attributable to the bulk-like property of interfacial water, whereas the slow dynamics at the negatively charged lipid interface are due to bound water, which is hydrogen-bonded to the hydrophilic head group.

  4. Allosteric analysis of glucocorticoid receptor-DNA interface induced by cyclic Py-Im polyamide: a molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Yaru Wang

    Full Text Available BACKGROUND: It has been extensively developed in recent years that cell-permeable small molecules, such as polyamide, can be programmed to disrupt transcription factor-DNA interfaces and can silence aberrant gene expression. For example, cyclic pyrrole-imidazole polyamide that competes with glucocorticoid receptor (GR for binding to glucocorticoid response elements could be expected to affect the DNA dependent binding by interfering with the protein-DNA interface. However, how such small molecules affect the transcription factor-DNA interfaces and gene regulatory pathways through DNA structure distortion is not fully understood so far. METHODOLOGY/PRINCIPAL FINDINGS: In the present work, we have constructed some models, especially the ternary model of polyamides+DNA+GR DNA-binding domain (GRDBD dimer, and carried out molecular dynamics simulations and free energy calculations for them to address how polyamide molecules disrupt the GRDBD and DNA interface when polyamide and protein bind at the same sites on opposite grooves of DNA. CONCLUSIONS/SIGNIFICANCE: We found that the cyclic polyamide binding in minor groove of DNA can induce a large structural perturbation of DNA, i.e. a >4 Å widening of the DNA minor groove and a compression of the major groove by more than 4 Å as compared with the DNA molecule in the GRDBD dimer+DNA complex. Further investigations for the ternary system of polyamides+DNA+GRDBD dimer and the binary system of allosteric DNA+GRDBD dimer revealed that the compression of DNA major groove surface causes GRDBD to move away from the DNA major groove with the initial average distance of ∼4 Å to the final average distance of ∼10 Å during 40 ns simulation course. Therefore, this study straightforward explores how small molecule targeting specific sites in the DNA minor groove disrupts the transcription factor-DNA interface in DNA major groove, and consequently modulates gene expression.

  5. Contact angle and adsorption energies of nanoparticles at the air-liquid interface determined by neutron reflectivity and molecular dynamics

    Science.gov (United States)

    Reguera, Javier; Ponomarev, Evgeniy; Geue, Thomas; Stellacci, Francesco; Bresme, Fernando; Moglianetti, Mauro

    2015-03-01

    Understanding how nanomaterials interact with interfaces is essential to control their self-assembly as well as their optical, electronic, and catalytic properties. We present here an experimental approach based on neutron reflectivity (NR) that allows the in situ measurement of the contact angles of nanoparticles adsorbed at fluid interfaces. Because our method provides a route to quantify the adsorption and interfacial energies of the nanoparticles in situ, it circumvents problems associated with existing indirect methods, which rely on the transport of the monolayers to substrates for further analysis. We illustrate the method by measuring the contact angle of hydrophilic and hydrophobic gold nanoparticles, coated with perdeuterated octanethiol (d-OT) and with a mixture of d-OT and mercaptohexanol (MHol), respectively. The contact angles were also calculated via atomistic molecular dynamics (MD) computations, showing excellent agreement with the experimental data. Our method opens the route to quantify the adsorption of complex nanoparticle structures adsorbed at fluid interfaces featuring different chemical compositions.Understanding how nanomaterials interact with interfaces is essential to control their self-assembly as well as their optical, electronic, and catalytic properties. We present here an experimental approach based on neutron reflectivity (NR) that allows the in situ measurement of the contact angles of nanoparticles adsorbed at fluid interfaces. Because our method provides a route to quantify the adsorption and interfacial energies of the nanoparticles in situ, it circumvents problems associated with existing indirect methods, which rely on the transport of the monolayers to substrates for further analysis. We illustrate the method by measuring the contact angle of hydrophilic and hydrophobic gold nanoparticles, coated with perdeuterated octanethiol (d-OT) and with a mixture of d-OT and mercaptohexanol (MHol), respectively. The contact angles were

  6. Influence of a lipid interface on protein dynamics in a fungal lipase

    DEFF Research Database (Denmark)

    Peters, Günther H.j.; Bywater, R. P.

    2001-01-01

    Lipases catalyze lipolytic reactions and for optimal activity they require a lipid interface. To study the effect of a lipid aggregate on the behavior of the enzyme at the interfacial plane and how the aggregate influences an attached substrate or product molecule in time and space, we have...

  7. Dynamic behavior of two collinear interface cracks between two dissimilar functionally graded piezoelectric/piezomagnetic material strips

    Institute of Scientific and Technical Information of China (English)

    ZHANG Pei-wei; ZHOU Zhen-gong; WANG Biao

    2007-01-01

    The dynamic interaction oftwo collinear interface cracks between two dislar.functionally graded piezoelectric/piezomagnetic material strips subjected to the anti-plane shear harmonic stress waves was investigated.By using the Fourier transform, unknown variable is jump of displacement across the crack surfaces.These equations are solved using the Schmidt method.Numerical examples are provided to show the effect of the functionally graded parameter,the circular frequency of the incident waves and the thickness of the strip upon stress,electric displacement and magnetic flux intensity factors of cracks.

  8. Molecular dynamics studies of simple membrane-water interfaces: Structure and functions in the beginnings of cellular life

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    1995-01-01

    Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience 'interfacial resistance' to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

  9. Molecular Dynamics Simulation: The Behavior of Asphaltene in Crude Oil and at the Oil/Water Interface

    KAUST Repository

    Gao, Fengfeng

    2014-12-18

    Carboxyl asphaltene is commonly discussed in the petroleum industry. In most conditions, electroneutral carboxyl asphaltene molecules can be deprotonated to become carboxylate asphaltenes. Both in crude oil and at the oil/water interface, the characteristics of anionic carboxylate asphaltenes are different than those of the carboxyl asphaltenes. In this paper, molecular dynamics (MD) simulations are utilized to study the structural features of different asphaltene molecules, namely, C5 Pe and anionic C5 Pe, at the molecular level. In crude oil, the electroneutral C5 Pe molecules prefer to form a steady face-to-face stacking, while the anionic C5 Pe molecules are inclined to form face-to-face stacking and T-shaped II stacking because of the repulsion of the anionic headgroups. Anionic C5 Pe has a distinct affinity to the oil/water interface during the simulation, while the C5 Pe molecules persist in the crude oil domain. A three-stage model of anionic C5 Pe molecules adsorbed at the oil/water interface is finally developed.

  10. Molecular dynamics simulation of protein adsorption at fluid interfaces: a comparison of all-atom and coarse-grained models.

    Science.gov (United States)

    Euston, Stephen R

    2010-10-11

    The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.

  11. Study of the dynamical approach to the interface localization-delocalization transition of the confined Ising model

    Energy Technology Data Exchange (ETDEWEB)

    Albano, Ezequiel V [Instituto de Investigaciones Fisicoquimicas Teoricas y Aplicadas (INIFTA), UNLP, CONICET, Casilla de Correo 16, Sucursal 4 (1900) La Plata (Argentina); Virgiliis, Andres de [Instituto de Investigaciones Fisicoquimicas Teoricas y Aplicadas (INIFTA), UNLP, CONICET, Casilla de Correo 16, Sucursal 4 (1900) La Plata (Argentina); Mueller, Marcus [Institut fuer Physik, WA331, Johannes Gutenberg Universitaet, Staudingerweg 7, D-55099 Mainz (Germany); Binder, Kurt [Institut fuer Physik, WA331, Johannes Gutenberg Universitaet, Staudingerweg 7, D-55099 Mainz (Germany)

    2004-06-16

    Confined magnetic Ising films in a L x D geometry (L << D), with short-range competing magnetic fields (h) acting at opposite walls along the D-direction, exhibit a slightly rounded localization-delocalization transition of the interface between domains of different orientations that runs parallel to the walls. This transition is the precursor of a wetting transition that occurs in the limit of infinite film thickness (L {yields} {infinity}) at the critical curve T{sub w}(h). For TT{sub w}(h)) such an interface is bounded (unbounded) to the walls, while right at T{sub w}(h) the interface is freely fluctuating around the centre of the film. Starting from disordered configurations, corresponding to T {yields} {infinity}, we quench to the wetting critical temperature and study the dynamics of the approach to the stationary regime by means of extensive Monte Carlo simulations. It is found that for all layers parallel to the wall (rows), the row magnetizations exhibit a peak at a time {tau}{sub max} {proportional_to} L{sup 2} and subsequently relax to the stationary, equilibrium behaviour. The characteristic time for such a relaxation scales as {tau}{sub R} {proportional_to} L{sup 4}, as expected from theoretical arguments, that are discussed in detail.

  12. Dynamic contrast-enhanced CT in patients with pancreatic cancer

    DEFF Research Database (Denmark)

    Lauridsen, Carsten Ammitzbøl; Eriksen, Rie Østbjerg; Strauch, Louise Søborg;

    2016-01-01

    tissue, compared with measurements in pancreatic tissue outside of tumor, or normal pancreatic tissue in control groups of healthy volunteers. The studies were heterogeneous in the number of patients enrolled and scan protocols. Perfusion parameters measured and analyzed by DCE-CT might be useful......The aim of this systematic review is to provide an overview of the use of Dynamic contrast-enhanced Computed Tomography (DCE-CT) in patients with pancreatic cancer. This study was composed according to the PRISMA guidelines 2009. The literature search was conducted in PubMed, Cochrane Library...... in the investigation of characteristic vascular patterns of pancreatic exocrine tumors. Further clinical studies are desired for investigating the potential of DCE-CT in pancreatic tumors. Keywords:...

  13. Refinements of water parameters for molecular dynamics: Simulations of adsorption at the clay mineral/aqueous solution interface

    DEFF Research Database (Denmark)

    Schäfer, L.; Yu, C.; Teppen, B.J.;

    1999-01-01

    In the context of a long-term program involving molecular dynamics simulations of adsorption phenomena at the clay mineral/aqueous solution interface, we are testing the viability of combining a force field that we developed specificially for clays with other, independently derived potential...... parameters for molecular species which are important in clay adsorption. For the current study the importance of variations in the potential parameters of water were investigated and polarization effects on oxygen studied as a function of intermolecular interactions. For this purpose ab initio MP2/6-311GG...... atomic charges were determined for several oligomers of water and for the water dimer at different intermolecular separations. Charge variations of up to ~0.1 electron charge unit on oxygen are found and, together with changes in van der Waals constants, their significance for dynamics simulations...

  14. Supramolecular 1-D polymerization of DNA origami through a dynamic process at the 2-dimensionally confined air-water interface.

    Science.gov (United States)

    Yonamine, Yusuke; Cervantes-Salguero, Keitel; Minami, Kosuke; Kawamata, Ibuki; Nakanishi, Waka; Hill, Jonathan P; Murata, Satoshi; Ariga, Katsuhiko

    2016-05-14

    In this study, a Langmuir-Blodgett (LB) system has been utilized for the regulation of polymerization of a DNA origami structure at the air-water interface as a two-dimensionally confined medium, which enables dynamic condensation of DNA origami units through variation of the film area at the macroscopic level (ca. 10-100 cm(2)). DNA origami sheets were conjugated with a cationic lipid (dioctadecyldimethylammonium bromide, 2C18N(+)) by electrostatic interaction and the corresponding LB-film was prepared. By applying dynamic pressure variation through compression-expansion processes, the lipid-modified DNA origami sheets underwent anisotropic polymerization forming a one-dimensionally assembled belt-shaped structure of a high aspect ratio although the thickness of the polymerized DNA origami was maintained at the unimolecular level. This approach opens up a new field of mechanical induction of the self-assembly of DNA origami structures.

  15. A study of the breast cancer dynamics in North Carolina.

    Science.gov (United States)

    Christakos, G; Lai, J J

    1997-11-01

    This work is concerned with the study of breast cancer incidence in the State of North Carolina. Methodologically, the current analysis illustrates the importance of spatiotemporal random field modelling and introduces a mode of reasoning that is based on a combination of inductive and deductive processes. The composite space/time analysis utilizes the variability characteristics of incidence and the mathematical features of the random field model to fit it to the data. The analysis is significantly general and can efficiently represent non-homogeneous and non-stationary characteristics of breast cancer variation. Incidence predictions are produced using data at the same time period as well as data from other time periods and disease registries. The random field provides a rigorous and systematic method for generating detailed maps, which offer a quantitative description of the incidence variation from place to place and from time to time, together with a measure of the accuracy of the incidence maps. Spatiotemporal mapping accounts for the geographical locations and the time instants of the incidence observations, which is not usually the case with most empirical Bayes methods. It is also more accurate than purely spatial statistics methods, and can offer valuable information about the breast cancer risk and dynamics in North Carolina. Field studies could be initialized in high-rate areas identified by the maps in an effort to uncover environmental or life-style factors that might be responsible for the high risk rates. Also, the incidence maps can help elucidate causal mechanisms, explain disease occurrences at a certain scale, and offer guidance in health management and administration.

  16. Dynamics of tissue topology during cancer invasion and metastasis

    Science.gov (United States)

    Munn, Lance L.

    2013-12-01

    During tumor progression, cancer cells mix with other cell populations including epithelial and endothelial cells. Although potentially important clinically as well as for our understanding of basic tumor biology, the process of mixing is largely a mystery. Furthermore, there is no rigorous, analytical measure available for quantifying the mixing of compartments within a tumor. I present here a mathematical model of tissue repair and tumor growth based on collective cell migration that simulates a wide range of observed tumor behaviors with correct tissue compartmentalization and connectivity. The resulting dynamics are analyzed in light of the Euler characteristic number (χ), which describes key topological features such as fragmentation, looping and cavities. The analysis predicts a number of regimes in which the cancer cells can encapsulate normal tissue, form a co-interdigitating mass, or become fragmented and encapsulated by endothelial or epithelial structures. Key processes that affect the topological changes are the production of provisional matrix in the tumor, and the migration of endothelial or epithelial cells on this matrix. Furthermore, the simulations predict that topological changes during tumor invasion into blood vessels may contribute to metastasis. The topological analysis outlined here could be useful for tumor diagnosis or monitoring response to therapy and would only require high resolution, 3D image data to resolve and track the various cell compartments.

  17. Phosphate DIstribution and Movement in Soil—Root Interface Zone:Ⅲ.Dynamics

    Institute of Scientific and Technical Information of China (English)

    XUMING-GANG; ZHANGYI-PING; 等

    1995-01-01

    The depletion rate of phosphate in the soil-root interface zone increased along with growth and phosphate uptske of wheat or maize,which indicated that the phosphate distribution in soil near the root surface agreed well with the phosphate movement in rhizosphere and phosphate uptake by plant,The relative accumulation zone of phosphate within 0.5mm apart from the root surface developed at the 15th day or so after cultivating wheat or maize since the root phosphate secretion increased gradually in this stage.The phosphate distribution in the soil-root interface zone against the growing time(t)and the distance from the root plane(x) could be described by the non-linear regression equation with the third powers of x and t.

  18. Studies by Near Edge X-ray Absorption Spectroscopies of Bonding Dynamics at the Graphene/Guanine Interface - A Proposal for High Mobility, Organic Graphene Field Effect Transistors

    Science.gov (United States)

    2015-07-01

    AFRL-AFOSR-UK-TR-2015-0034 Studies by Near Edge X-ray Absorption Spectroscopies of Bonding Dynamics at the Graphene/Guanine...April 2015 4. TITLE AND SUBTITLE Studies by Near Edge X-ray Absorption Spectroscopies of Bonding Dynamics at the Graphene/Guanine Interface - A

  19. Mesoscale Structures at Complex Fluid-Fluid Interfaces: a Novel Lattice Boltzmann / Molecular Dynamics Coupling

    OpenAIRE

    Sega, Marcello; Sbragaglia, Mauro; Kantorovich, Sofia Sergeevna; Ivanov, Alexey Olegovich

    2013-01-01

    Complex fluid-fluid interfaces featuring mesoscale structures with adsorbed particles are key components of newly designed materials which are continuously enriching the field of soft matter. Simulation tools which are able to cope with the different scales characterizing these systems are fundamental requirements for efficient theoretical investigations. In this paper we present a novel simulation method, based on the approach of Ahlrichs and D\\"unweg [Ahlrichs and D\\"unweg, Int. J. Mod. Phy...

  20. Charge transfer reactions at interfaces between neutral gas and plasma: Dynamical effects and X-ray emission

    Science.gov (United States)

    Provornikova, E.; Izmodenov, V. V.; Lallement, R.

    2012-04-01

    Charge-transfer is the main process linking neutrals and charged particles in the interaction regions of neutral (or partly ionized) gas with a plasma. In this paper we illustrate the importance of charge-transfer with respect to the dynamics and the structure of neutral gas-plasma interfaces. We consider the following phenomena: (1) the heliospheric interface - region where the solar wind plasma interacts with the partly-ionized local interstellar medium (LISM) and (2) neutral interstellar clouds embedded in a hot, tenuous plasma such as the million degree gas that fills the so-called ``Local Bubble". In (1), we discuss several effects in the outer heliosphere caused by charge exchange of interstellar neutral atoms and plasma protons. In (2) we describe the role of charge exchange in the formation of a transition region between the cloud and the surrounding plasma based on a two-component model of the cloud-plasma interaction. In the model the cloud consists of relatively cold and dense atomic hydrogen gas, surrounded by hot, low density, fully ionized plasma. We discuss the structure of the cloud-plasma interface and the effect of charge exchange on the lifetime of interstellar clouds. Charge transfer between neutral atoms and minor ions in the plasma produces X-ray emission. Assuming standard abundances of minor ions in the hot gas surrounding the cold interstellar cloud, we estimate the X-ray emissivity consecutive to the charge transfer reactions. Our model shows that the charge-transfer X-ray emission from the neutral cloud-plasma interface may be comparable to the diffuse thermal X-ray emission from the million degree gas cavity itself.

  1. Tomography-based characterization of ice-air interface dynamics of temperature gradient snow metamorphism under advective conditions

    Science.gov (United States)

    Ebner, Pirmin Philipp; Andreoli, Christian; Schneebeli, Martin; Steinfeld, Aldo

    2015-12-01

    Snow at or close to the surface commonly undergoes temperature gradient metamorphism under advective flow, which alters its microstructure and physical properties. A functional understanding of this process is essential for many disciplines, from modeling the effects of snow on regional and global climate to assessing avalanche formation. Time-lapse X-ray microtomography was applied to investigate the structural dynamics of temperature gradient snow metamorphism exposed to an advective airflow in controlled laboratory conditions. Experiments specifically analyzed sublimation and deposition of water vapor on the ice structure. In addition, an analysis of the ice-air interface dynamics was carried out using a macroscopic equivalent model of heat and water vapor transport through a snow layer. The results indicate that sublimation of the ice matrix dominated for flow rates surface area and thus suggest a change of the physical and optical properties of the snow. The estimated values of the curvature effect of the ice crystals and the interface kinetic coefficient are in good agreement with previously published values.

  2. Dynamic single-interface hollow fiber liquid phase microextraction of Cr(VI) using ionic liquid containing supported liquid membrane.

    Science.gov (United States)

    Pimparu, Rungaroon; Nitiyanontakit, Sira; Miró, Manuel; Varanusupakul, Pakorn

    2016-12-01

    The concept of dynamic single-interface hollow fiber membrane liquid-phase microextraction (HF-LPME), where the target analyte was extracted on-line and eluted inside the lumen of the HF membrane, was explored. An ionic liquid containing supported liquid membrane was used for the trace determination of Cr(VI) as a model compound. Since the extraction took place on-line inside the hollow fiber membrane, the mass transfer behavior was described and discussed in comparison with the conventional HF-LPME. The extraction efficiency was improved by a recirculation configuration of the sample solution at relatively high sampling flow rates as a result of the increased effective contact area. The positive pressure observed to be built up during extraction was overcome by a flow-balancing pressure design. The dynamic single-interface HF-LPME method with an enrichment factor of 41, a detection limit of 1.2µgL(-1) and determination limit of 4.0µgL(-1) was successfully applied to the reliable determination of Cr(VI) from environmental water samples. The quantification limit is below the maximum contaminant level in drinking water, set at 10µgL(-1) of hexavalent chromium by the California Environmental Protection Agency.

  3. The interface of SrTiO3 and H2O from density functional theory molecular dynamics

    Science.gov (United States)

    Holmström, E.; Spijker, P.; Foster, A. S.

    2016-09-01

    We use dispersion-corrected density functional theory molecular dynamics simulations to predict the ionic, electronic and vibrational properties of the SrTiO3/H2O solid-liquid interface. Approximately 50% of surface oxygens on the planar SrO termination are hydroxylated at all studied levels of water coverage, the corresponding number being 15% for the planar TiO2 termination and 5% on the stepped TiO2-terminated surface. The lateral ordering of the hydration structure is largely controlled by covalent-like surface cation to H2O bonding and surface corrugation. We find a featureless electronic density of states in and around the band gap energy region at the solid-liquid interface. The vibrational spectrum indicates redshifting of the O-H stretching band due to surface-to-liquid hydrogen bonding and blueshifting due to high-frequency stretching vibrations of OH fragments within the liquid, as well as strong suppression of the OH stretching band on the stepped surface. We find highly varying rates of proton transfer above different SrTiO3 surfaces, owing to differences in hydrogen bond strength and the degree of dissociation of incident water. Trends in proton dynamics and the mode of H2O adsorption among studied surfaces can be explained by the differential ionicity of the Ti-O and Sr-O bonds in the SrTiO3 crystal.

  4. Molecular dynamics study of growth and interface structure during aluminum deposition on Ni(1 0 0) substrate

    Energy Technology Data Exchange (ETDEWEB)

    Hassani, A., E-mail: a.hassani.uh1@gmail.com [Univ Hassan 1" e" r, Laboratory of Radiation and Matter, Faculty of Science and Technology, 26000 Settat (Morocco); Univ Hassan 1" e" r, Laboratory LS3M, Faculté Polydisciplinaire of Khouribga, 26000 Settat (Morocco); Makan, A. [Laboratory of Water and Environment, Faculty of Science, Univ. Chouaib Doukkali, 24000 El Jadida (Morocco); Sbiaai, K., E-mail: ksbiaai@gmail.com [Univ Hassan 1" e" r, Laboratory LS3M, Faculté Polydisciplinaire of Khouribga, 26000 Settat (Morocco); Tabyaoui, A. [Univ Hassan 1" e" r, Laboratory of Radiation and Matter, Faculty of Science and Technology, 26000 Settat (Morocco); Hasnaoui, A. [Univ Hassan 1" e" r, Laboratory LS3M, Faculté Polydisciplinaire of Khouribga, 26000 Settat (Morocco)

    2015-09-15

    Highlights: • Aluminum thin film growth on Ni(1 0 0) substrate was investigated. • Molecular dynamics simulation based on EAM interaction potential was considered. • Hexagonal and fourfold structures coexisted in the first layer. • Interface mismatch was revealed by wavy effect occurring in both lateral directions. • Film growth followed a layer-by-layer mode only in the first three deposited layers. - Abstract: We investigate aluminum thin film growth on Ni(1 0 0) substrate by means of molecular dynamics simulation. Embedded Atom Method interaction potential is considered. The simulation is performed at 300 K using an incident energy of 1 eV. The substrate-grown film interface shows the coexistence of hexagonal and fourfold structures in the first layer during the initial stage of deposition. As the deposition proceeds, the hexagonal geometry transforms to fourfold one which becomes dominant toward the end of deposition. The coverage of this layer exceeded 100%. Moreover, the deposited Al atoms with fourfold geometry adopt the lattice parameter of Ni as the thickness of deposited film increases. The interface mismatch investigation revealed that the roughness is dictated by how the Al(1 1 1) fits to the Ni(1 0 0) substrate, which may be reflected by a wavy effect occurring in both lateral directions. Furthermore, the film grows by a layer-by-layer mode with a coverage rate greater than 66.7% in the first three layers, while it follows an island mode with a coverage rate lower than the previous value (66.7%) beyond the third layer. Overall, a detailed analysis of each layer growth has established a relationship between the number of deposited atoms and the coverage rate of each layer.

  5. Molecular dynamics simulations of the aqueous interface with the [BMI][PF6] ionic liquid: Comparison of different solvent models.

    Science.gov (United States)

    Chevrot, G; Schurhammer, R; Wipff, G

    2006-09-28

    We report a Molecular Dynamics (MD) study of the interface between water and the hygroscopic room temperature Ionic Liquid "IL" [BMI][PF6] (1-butyl-3-methyl-imidazolium hexafluorophosphate), comparing the TIP3P, SPC/E and TIP5P models for water and two IL models where the ions are +/-1 or +/-0.9 charged. A recent MD study (A. Chaumont, R. Schurhammer and G. Wipff, J. Phys. Chem. B, 2005, 109, 18964) showed that using TIP3P water in conjunction with the IL(+/-1) model led to water-IL mixing without forming an interface, whereas a biphasic system could be obtained with the IL(+/-0.9) model. With the TIP5P and SPC/E models, the juxtaposed aqueous and IL phases are found to remain distinct for at least 20 ns. The resulting IL humidity, exaggerated with the IL(+/-1) model, is in better agreement with experiment using the IL(+/-0.9) model. We also report demixing simulations on the "randomly mixed" liquids, using the IL(+/-0.9) model for the ionic liquid. With the three tested water models, the phases separate very slowly ( approximately 20 ns or more) compared to "classical" chloroform-water mixtures (less than 1 ns), leading to biphasic systems similar to those obtained after equilibration of the juxtaposed liquids. The characteristics of the interface (size, polarity, ion orientation, electrostatic potential) are compared with the different models. Possible reasons why, among the three tested water models, the widely-used TIP3P model exaggerates the inter-solvent mixing, are analyzed. The difficulty in computationally and experimentally equilibrating water-IL mixtures is attributed to the slow dynamics and micro-heterogeneity of the IL and to the different states of water in the IL phase.

  6. Spatial-Temporal Study of Rab1b Dynamics and Function at the ER-Golgi Interface.

    Science.gov (United States)

    Martinez, Hernán; García, Iris A; Sampieri, Luciana; Alvarez, Cecilia

    2016-01-01

    The GTPase Rab1b is involved in ER to Golgi transport, with multiple Rab1b effectors (located at ERES, VTCs and the Golgi complex) being required for its function. In this study, we performed live-cell dual-expression studies to analyze the dynamics of Rab1b and some effectors located at the ERES-Golgi interface. Rab1b occupied widely distributed mobile punctate and tubular structures, displaying a transient overlaps with its effectors and showing that these overlaps occurred at the same time in spatially distinct steps of ER to Golgi transport. In addition, we assessed Rab1b dynamics during cargo sorting by analyzing the concentration at ERES of a Golgi protein (SialT2-CFP) during Brefeldin A washout (BFA WO). Rab1b was associated to most of the ERES structures, but at different times during BFA WO, and recurrently SialT2-CFP was sorted in the ERES-Rab1b positive structures. Furthermore, we reveal for first time that Rab1b localization time at ERES depended on GBF1, a Rab1b effector that acts as the guanine nucleotide exchange factor of Arf1, and that Rab1b membrane association/dissociation dynamics at ERES was dependent on the GBF1 membrane association and activity, which strongly suggests that GBF1 activity modulates Rab1b membrane cycling dynamic.

  7. Spatial-Temporal Study of Rab1b Dynamics and Function at the ER-Golgi Interface

    Science.gov (United States)

    Martinez, Hernán; García, Iris A.; Sampieri, Luciana

    2016-01-01

    The GTPase Rab1b is involved in ER to Golgi transport, with multiple Rab1b effectors (located at ERES, VTCs and the Golgi complex) being required for its function. In this study, we performed live-cell dual-expression studies to analyze the dynamics of Rab1b and some effectors located at the ERES-Golgi interface. Rab1b occupied widely distributed mobile punctate and tubular structures, displaying a transient overlaps with its effectors and showing that these overlaps occurred at the same time in spatially distinct steps of ER to Golgi transport. In addition, we assessed Rab1b dynamics during cargo sorting by analyzing the concentration at ERES of a Golgi protein (SialT2-CFP) during Brefeldin A washout (BFA WO). Rab1b was associated to most of the ERES structures, but at different times during BFA WO, and recurrently SialT2-CFP was sorted in the ERES-Rab1b positive structures. Furthermore, we reveal for first time that Rab1b localization time at ERES depended on GBF1, a Rab1b effector that acts as the guanine nucleotide exchange factor of Arf1, and that Rab1b membrane association/dissociation dynamics at ERES was dependent on the GBF1 membrane association and activity, which strongly suggests that GBF1 activity modulates Rab1b membrane cycling dynamic. PMID:27500526

  8. Dynamics and Interactions in Room Temperature Ionic Liquids, Surfaces and Interfaces

    Science.gov (United States)

    2016-01-13

    quantifying spectral diffusion. To elucidate the detailed structural dynamics with accurate time constants, FFCF decays were monitored to 60 ps, a major...heterodyne detected optical Kerr effect (OHD-OKE) experiments that addressed the relationship between RTIL dynamics and structure . Metal -organic frame works...were also studied. A unique aspect of metal -organic frameworks (MOFs) is their structural "flexibility" coexisting with a degree of regularity

  9. Ledge-flow-controlled catalyst interface dynamics during Si nanowire growth

    DEFF Research Database (Denmark)

    Hofmann, S; Sharma, R; Wirth, CT;

    2008-01-01

    and the overall mechanism is largely unresolved. Here, we present a video-rate environmental transmission electron microscopy study of Si nanowire formation from Pd silicide crystals under disilane exposure. A Si crystal nucleus forms by phase separation, as observed for the liquid Au–Si system, which we use...... as a comparative benchmark. The dominant coherent Pd silicide/Si growth interface subsequently advances by lateral propagation of ledges, driven by catalytic dissociation of disilane and coupled Pd and Si diffusion. Our results establish an atomistic framework for nanowire assembly from solid catalysts, relevant...

  10. Interfacing polymeric scaffolds with primary pancreatic ductal adenocarcinoma cells to develop 3D cancer models

    NARCIS (Netherlands)

    Ricci, C.; Mota, C.M.; Moscato, S.; Alessandro, D' D.; Ugel, S.; Sartoris, S.; Bronte, V.; Boggi, U.; Campani, D.; Funel, N.; Moroni, L.; Danti, S.

    2014-01-01

    We analyzed the interactions between human primary cells from pancreatic ductal adenocarcinoma (PDAC) and polymeric scaffolds to develop 3D cancer models useful for mimicking the biology of this tumor. Three scaffold types based on two biocompatible polymeric formulations, such as poly(vinyl alcohol

  11. On the transition between two-phase and single-phase interface dynamics in multicomponent fluids at supercritical pressures

    Science.gov (United States)

    Dahms, Rainer N.; Oefelein, Joseph C.

    2013-09-01

    A theory that explains the operating pressures where liquid injection processes transition from exhibiting classical two-phase spray atomization phenomena to single-phase diffusion-dominated mixing is presented. Imaging from a variety of experiments have long shown that under certain conditions, typically when the pressure of the working fluid exceeds the thermodynamic critical pressure of the liquid phase, the presence of discrete two-phase flow processes become diminished. Instead, the classical gas-liquid interface is replaced by diffusion-dominated mixing. When and how this transition occurs, however, is not well understood. Modern theory still lacks a physically based model to quantify this transition and the precise mechanisms that lead to it. In this paper, we derive a new model that explains how the transition occurs in multicomponent fluids and present a detailed analysis to quantify it. The model applies a detailed property evaluation scheme based on a modified 32-term Benedict-Webb-Rubin equation of state that accounts for the relevant real-fluid thermodynamic and transport properties of the multicomponent system. This framework is combined with Linear Gradient Theory, which describes the detailed molecular structure of the vapor-liquid interface region. Our analysis reveals that the two-phase interface breaks down not necessarily due to vanishing surface tension forces, but due to thickened interfaces at high subcritical temperatures coupled with an inherent reduction of the mean free molecular path. At a certain point, the combination of reduced surface tension, the thicker interface, and reduced mean free molecular path enter the continuum length scale regime. When this occurs, inter-molecular forces approach that of the multicomponent continuum where transport processes dominate across the interfacial region. This leads to a continuous phase transition from compressed liquid to supercritical mixture states. Based on this theory, a regime diagram for

  12. A molecular dynamics study of Ni/Cu(0 0 1) interfaces

    CERN Document Server

    Jimenez-Saez, J C; Jimenez-Rodriguez, J J; Perez-Martin, A M C

    2002-01-01

    This work is focused mainly on the analysis of effects related to a lattice misfit at a metallic interface. The system studied is the Ni/Cu(0 0 1) which exhibits a misfit of 2.6%. For this structure, the adjustment between the lattice parameters of a Ni crystal layer over Cu(0 0 1) substrate is analysed. To avoid edge effects a large enough substrate is taken while the Ni crystal set on top has smaller dimensions than the substrate. We have studied structures of one, two, four and ten monolayers of Ni set on top of the Cu substrate. It is shown how the stabilisation of different interface structures on an atomic scale is achieved; especially, the type of processes that help to accomplish a gradual change in the atomic distances. The main conclusion is the anisotropy of the coupling provokes that a cubic becomes a tetragonal lattice. The rearrangement of atoms and the strain field induced by the coupling are studied in detail.

  13. The Si/Si_3N4 Interface and Si/Si_3N4 Submicron Mesa: A Multi-million Atom Molecular Dynamics Study

    Science.gov (United States)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam

    1998-03-01

    Using molecular dynamics simulations on parallel computers, the interface structure, stress distribution, crack propagation and fracture in a Si_3N4 film on Si substrate are studied. Bulk Si is described by Stillinger-Weber potential and Si_3N4 is represented by a combination of two- and three-body covalent interactions. At the interface, the charge transfer is taken from LCAO electronic structure calculations (G.-L. Zhao and M.E. Bachlechner, Europhys. Lett. 36, 287 (1997)). Results for structural correlations at the interface and 3D stress distribution for the submicron mesa are presented.

  14. Research on Dynamic Modeling and Application of Kinetic Contact Interface in Machine Tool

    Directory of Open Access Journals (Sweden)

    Dan Xu

    2016-01-01

    Full Text Available A method is presented which is a kind of combining theoretic analysis and experiment to obtain the equivalent dynamic parameters of linear guideway through four steps in detail. From statics analysis, vibration model analysis, dynamic experiment, and parameter identification, the dynamic modeling of linear guideway is synthetically studied. Based on contact mechanics and elastic mechanics, the mathematic vibration model and the expressions of basic mode frequency are deduced. Then, equivalent stiffness and damping of guideway are obtained in virtue of single-freedom-degree mode fitting method. Moreover, the investigation above is applied in a certain gantry-type machining center; and through comparing with simulation model and experiment results, both availability and correctness are validated.

  15. Selective optical switching of interface-coupled relaxation dynamics in carbon nanotube-Si heterojunctions

    KAUST Repository

    Ponzoni, Stefano

    2014-10-16

    By properly tuning the photon energy of a femtosecond laser pump, we disentangle, in carbon nanotube-Si (CNT/Si) heterojunctions, the fast relaxation dynamics occurring in CNT from the slow repopulation dynamics due to hole charge transfer at the junction. In this way we are able to track the transfer of the photogenerated holes from the Si depletion layer to the CNT layer, under the action of the built-in heterojunction potential. This also clarifies that CNT play an active role in the junction and do not act only as channels for charge collection and transport.

  16. Structure and Dynamics of Forsterite-scCO2/H2O Interfaces as a Function of Water Content

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien N.; Weare, John H.; Felmy, Andrew R.

    2012-05-01

    Molecular dynamics (MD) simulations of forsterite surfaces in contact with supercritical carbon dioxide (scCO2) fluids of varying water content were performed to determine the partition of water between the scCO2 fluid and the mineral surface, the nature of CO2 and H2O bonding at the interface, and the regions of the interface that may be conducive to HxCO3(2-x)- formation. Calculations of the free energy of the associative adsorption of water onto the (010) forsterite surface from the scCO2 phase indicated that the formation of a water film up to three-monolayer thick can be exothermic even for water contents below the water saturation concentration of the scCO2 fluid. In MD simulations of scCO2/H2O mixtures in contact with the (010) forsterite surface, H2O was found to readily displace CO2 at the surface and, therefore, CO2 directly contacted the surface only for water coverages below two monolayers. For thicker water films, a two-monolayer hydration layer formed that CO2 could not penetrate. Simulations of the hydroxylated (010) surface and of the (011) surface suggested that this conclusion can be extended to forsterite surfaces with different surface structures and/or compositions. The density, diffusion, and degree of hydration of CO2 as well as the extent of CO2/H2O mixing at the interface were all predicted to depend strongly on the thickness of the water-rich film, i.e., on the water content of the scCO2 fluid.

  17. Structure and dynamics of forsterite-scCO2/H2O interfaces as a function of water content

    Science.gov (United States)

    Kerisit, Sebastien; Weare, John H.; Felmy, Andrew R.

    2012-05-01

    Molecular dynamics (MD) simulations of forsterite surfaces in contact with supercritical carbon dioxide (scCO2) fluids of varying water content were performed to determine the partition of water between the scCO2 fluid and the mineral surface, the nature of CO2 and H2O bonding at the interface, and the regions of the interface that may be conducive to HCO3(2-x)- formation. Calculations of the free energy of the associative adsorption of water onto the (0 1 0) forsterite surface from the scCO2 phase indicated that the formation of a water film up to three-monolayer thick can be exothermic even for water contents below the water saturation concentration of the scCO2 fluid. In MD simulations of scCO2/H2O mixtures in contact with the (0 1 0) forsterite surface, H2O was found to readily displace CO2 at the surface and, therefore, CO2 directly contacted the surface only for water coverages below two monolayers. For thicker water films, a two-monolayer hydration layer formed that CO2 could not penetrate. The MD simulations thus suggest that, in the presence of sufficient water, HCO3(2-x)- formation occurs in the water films and not via direct reaction of CO2 with the forsterite surface. Simulations of the hydroxylated (0 1 0) surface and of the (0 1 1) surface suggested that this conclusion can be extended to forsterite surfaces with different surface structures and/or compositions. The density, diffusion, and degree of hydration of CO2 as well as the extent of CO2/H2O mixing at the interface were all predicted to depend strongly on the thickness of the water-rich film, i.e., on the water content of the scCO2 fluid.

  18. Strong electric fields at a prototypical oxide/water interface probed by ab initio molecular dynamics: MgO(001).

    Science.gov (United States)

    Laporte, Sara; Finocchi, Fabio; Paulatto, Lorenzo; Blanchard, Marc; Balan, Etienne; Guyot, François; Saitta, Antonino Marco

    2015-08-21

    We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field. In particular, we observe that the bare MgO(001) surface, although charge-neutral and defectless, has an intense electric field on the Å scale. The MgO(001) surface covered with 1 water monolayer (1 ML) is investigated via a supercell accounting for the experimentally-observed (2 × 3) reconstruction, stable at ambient temperature, and in which two out of six water molecules are dissociated. This 1 ML-hydrated surface is also found to have a high, albeit short-ranged, normal component of the field. Finally, the oxide/water interface is studied via room-temperature ab initio molecular dynamics (AIMD) using 34 H2O molecules between two MgO(001) surfaces. To our best knowledge this is the first AIMD study of the MgO(001)/liquid water interface in which all atoms are treated using DFT and including several layers above the first adsorbed layer. We observe that the surface electric field, averaged over the AIMD trajectories, is still very strong on the fully-wet surface, peaking at about 3 V Å(-1). Even in the presence of bulk-like water, the structure of the first layer in contact with the surface remains similar to the (2 × 3)-reconstructed ice ad-layer on MgO(001). Moreover, we observe proton exchange within the first layer, and between the first and second layers - indeed, the O-O distances close to the surface are found to be distributed towards shorter distances, a property which has been shown to directly promote proton transfer.

  19. Charge-transfer dynamics at the dye-semiconductor interface of photocathodes for solar energy applications.

    Science.gov (United States)

    Black, Fiona A; Wood, Christopher J; Ngwerume, Simbarashe; Summers, Gareth H; Clark, Ian P; Towrie, Michael; Camp, Jason E; Gibson, Elizabeth A

    2017-03-13

    This article describes a comparison between the photophysical properties of two charge-transfer dyes adsorbed onto NiO via two different binding moieties. Transient spectroscopy measurements suggest that the structure of the anchoring group affects both the rate of charge recombination between the dye and NiO surface and the rate of dye regeneration by an iodide/triiodide redox couple. This is consistent with the performance of the dyes in p-type dye sensitised solar cells. A key finding was that the recombination rate differed in the presence of the redox couple. These results have important implications on the study of electron transfer at dye|semiconductor interfaces for solar energy applications.

  20. Nonlinear dynamics at the interface of two-layer stratified flows over pronounced obstacles

    CERN Document Server

    Cabeza, C; Bove, I; Freire, D; Marti, Arturo C; Sarasua, L G; Usera, G; Montagne, R; Araújo, M

    2008-01-01

    The flow of a two--layer stratified fluid over an abrupt topographic obstacle, simulating relevant situations in oceanographic problems, is investigated numerically and experimentally in a simplified two--dimensional situation. Experimental results and numerical simulations are presented at low Froude numbers in a two-layer stratified flow and for two abrupt obstacles, semi--cylindrical and prismatic. We find four different regimes of the flow immediately past the obstacles: sub-critical (I), internal hydraulic jump (II), Kelvin-Helmholtz at the interface (III) and shedding of billows (IV). The critical condition for delimiting the experiments is obtained using the hydraulic theory. Moreover, the dependence of the critical Froude number on the geometry of the obstacle are investigated. The transition from regime III to regime IV is explained with a theoretical stability analysis. The results from the stability analysis are confirmed with the DPIV measurements. In regime (IV), when the velocity upstream is lar...

  1. Transport theory at the nanoscale. II. Interface dynamics for film growth.

    Science.gov (United States)

    ten Bosch, A

    2006-03-01

    Conditions for surface nucleation and growth of a film are determined in a diffuse interface model. A method is given, derived from a Fokker-Planck equation for the nonequilibrium particle distribution, which links atomic and mesoscopic events in a rheological description similar to the classical continuum theory of fluid flow. Film nucleation and growth are modeled by the spatially inhomogeneous continuous evolution of the instantaneous density profile which measures the average number of particles or molecules at given time and position. It is shown how an alteration in the distribution of particles in the vicinity of the boundary between parent and product phases induces transient film growth and damped vibrations at the surface. The method is general but as an illustration, the condensation of a simple classical fluid on cooling is considered in detail.

  2. Crawling Ajax-based Web Applications through Dynamic Analysis of User Interface State Changes

    NARCIS (Netherlands)

    Mesbah, A.; Van Deursen, A.; Lenselink, S.

    2011-01-01

    Using JavaScript and dynamic DOM manipulation on the client-side of web applications is becoming a widespread approach for achieving rich interactivity and responsiveness in modern web applications. At the same time, such techniques, collectively known as Ajax, shatter the metaphor of web ‘pages’ wi

  3. Equation of state and adsorption dynamics of soft microgel particles at an air-water interface

    NARCIS (Netherlands)

    Deshmukh, Omkar S.; Maestro, Armando; Duits, Michel H.G.; Ende, van den Dirk; Cohen Stuart, Martien; Mugele, Frieder

    2014-01-01

    Understanding the adsorption dynamics of soft microgel particles is a key step in designing such particles for potential applications as stimuli-responsive Pickering stabilizers for foams or emulsions. In this study we experimentally determine an equation of state (EOS) for poly (N-isopropylacrylami

  4. Heterogeneous growth of calcite at aragonite {001}- and vaterite {001}-melt interfaces: A molecular dynamics simulation study

    Science.gov (United States)

    Nada, Hiroki; Nishimura, Tatsuya; Sakamoto, Takeshi; Kato, Takashi

    2016-09-01

    Crystal growth at the interface between a calcium carbonate (CaCO3) crystal and its melt at a high temperature of 1500 K is investigated by means of a molecular dynamics simulation. The simulation is performed for the interfaces of a calcite {104} plane, aragonite {001}, {100}, and {010} planes, and vaterite {001}, {110}, and {100} planes. The growth from a pure melt and that from a melt containing Mg2+ are examined. Calcite growth occurs on the calcite {104} plane, aragonite growth occurs on the aragonite {100}, and {010} planes, and vaterite growth occurs on the vaterite {110} and {100} planes. However, the heterogeneous growth of calcite occurs on the {001} plane of aragonite and vaterite, irrespective of the presence of Mg2+. The results advance our understanding of geological processes that occur at high temperature, such as the formation of CaCO3 crystals from carbonatite magma and the formation of marble. Moreover, the results provide useful information for the control of CaCO3 crystal formation in material design.

  5. Solvation Dynamics of CO₂(g) by Monoethanolamine at the Gas-Liquid Interface: A Molecular Mechanics Approach.

    Science.gov (United States)

    Huang, I-Shou; Li, Jia-Jen; Tsai, Ming-Kang

    2016-12-23

    A classical force field approach was used to characterize the solvation dynamics of high-density CO₂(g) by monoethanolamine (MEA) at the air-liquid interface. Intra- and intermolecular CO₂ and MEA potentials were parameterized according to the energetics calculated at the MP2 and BLYP-D2 levels of theory. The thermodynamic properties of CO₂ and MEA, such as heat capacity and melting point, were consistently predicted using this classical potential. An approximate interfacial simulation for CO₂(g)/MEA(l) was performed to monitor the depletion of the CO₂(g) phase, which was influenced by amino and hydroxyl groups of MEA. There are more intramolecular hydrogen bond interactions notably identified in the interfacial simulation than the case of bulk MEA(l) simulation. The hydroxyl group of MEA was found to more actively approach CO₂ and overpower the amino group to interact with CO₂ at the air-liquid interface. With artificially reducing the dipole moment of the hydroxyl group, CO₂-amino group interaction was enhanced and suppressed CO₂(g) depletion. The hydroxyl group of MEA was concluded to play dual but contradictory roles for CO₂ capture.

  6. Facet-dependent trapping and dynamics of excess electrons at anatase TiO2 surfaces and aqueous interfaces

    Science.gov (United States)

    Selcuk, Sencer; Selloni, Annabella

    2016-10-01

    Excess electrons from intrinsic defects, dopants and photoexcitation play a key role in many of the properties of TiO2. Understanding their behaviour is important for improving the performance of TiO2 in energy-related applications. We focus on anatase, the TiO2 polymorph most relevant in photocatalysis and solar energy conversion. Using first-principles simulations, we investigate the states and dynamics of excess electrons from different donors near the most common anatase (101) and (001) surfaces and aqueous interfaces. We find that the behaviour of excess electrons depends strongly on the exposed anatase surface, the environment and the character of the electron donor. Whereas no electron trapping is observed on the (101) surface in vacuo, an excess electron at the aqueous (101) interface can trigger water dissociation and become trapped into a stable surface Ti3+-bridging OH complex. By contrast, electrons avoid the (001) surface, indicating that oxidation reactions are favoured on this surface. Our results provide a bridge between surface science experiments and observations of crystal-face-dependent photocatalysis on anatase, and support the idea that optimization of the ratio between {101} and {001} facets could provide a way to enhance the photocatalytic activity of this material.

  7. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1993-01-01

    A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

  8. Molecular dynamics simulations of peptides at the air-water interface: influencing factors on peptide-templated mineralization.

    Science.gov (United States)

    Jain, Alok; Jochum, Mara; Peter, Christine

    2014-12-30

    Biomineralization is the intricate, biomedically highly relevant process by which living organisms deposit minerals on biological matrices to stiffen tissues and build skeletal structures and shells. Rapaport and coworkers ( J. Am. Chem. Soc. 2000 , 122 , 12523 ; Adv. Funct. Mater. 2008 , 18 , 2889 ; Acta Biomater. 2012 , 8 , 2466 ) have designed a class of self-assembling amphiphilic peptides that are capable of forming hydrogels and attracting ions from the environment, generating structures akin to the extracellular matrix and promoting bone regeneration. The air-water interface serves both in experiment and in simulations as a model hydrophobic surface to mimic the cell's organic-aqueous interface and to investigate the organization of the peptide matrix into ordered β-pleated monolayers and the subsequent onset of biomineral formation. To obtain insight into the underlying molecular mechanism, we have used molecular dynamics simulations to study the effect of peptide sequence on aggregate stability and ion-peptide interactions. We find-in excellent agreement with experimental observations-that the nature of the peptide termini (proline vs phenylalanine) affect the aggregate order, while the nature of the acidic side chains (aspartic vs glutamic acid) affect the aggregate's stability in the presence of ions. These simulations provide valuable microscopic insight into the way ions and peptide templates mutually affect each other during the early stages of biomineralization preceding nucleation.

  9. Atomistic simulations of a solid/liquid interface: a combined force field and first principles approach to the structure and dynamics of acetonitrile near an anatase surface

    Energy Technology Data Exchange (ETDEWEB)

    Schiffmann, Florian; Hutter, Juerg; VandeVondele, Joost [Physical Chemistry Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich (Switzerland)

    2008-02-13

    The acetonitrile/anatase(101) interface can be considered a prototypical interface between an oxide and a polar aprotic liquid, and is common in dye sensitized solar cells. Using first principles molecular dynamics simulations of a slab of TiO{sub 2} in contact with neat acetonitrile (MeCN), the liquid structure near this interface has been characterized. Furthermore, in order to investigate properties that require extensive sampling, a classical force field to describe the MeCN/TiO{sub 2} interaction has been optimized, and we show that this force field accurately describes the structure near the interface. We find a surprisingly strong interaction of MeCN with TiO{sub 2}, which leads to an ordered first MeCN layer displaying a significantly enhanced molecular dipole. The strong dipolar interactions between solvent molecules lead to pronounced layering further away from the interface, each successive layer having an alternate orientation of the molecular dipoles. At least seven distinct solvent layers (approximately 12 A) can be discerned in the orientational distribution function. The observed structure also strongly suppresses diffusion parallel to the interface in the first nanometer of the liquid. These results show that the properties of the liquid near the interface differ from those in the bulk, which suggests that solvation near the interface will be distinctly different from solvation in the bulk.

  10. Synthesis of a Two-Dimensional Covalent Organic Monolayer through Dynamic Imine Chemistry at the Air/Water Interface.

    Science.gov (United States)

    Dai, Wenyang; Shao, Feng; Szczerbiński, Jacek; McCaffrey, Ryan; Zenobi, Renato; Jin, Yinghua; Schlüter, A Dieter; Zhang, Wei

    2016-01-01

    A two-dimensional covalent organic monolayer was synthesized from simple aromatic triamine and dialdehyde building blocks by dynamic imine chemistry at the air/water interface (Langmuir-Blodgett method). The obtained monolayer was characterized by optical microscopy, scanning electron microscopy, and atomic force microscopy, which unambiguously confirmed the formation of a large (millimeter range), unimolecularly thin aromatic polyimine sheet. The imine-linked chemical structure of the obtained monolayer was characterized by tip-enhanced Raman spectroscopy, and the peak assignment was supported by spectra simulated by density functional theory. Given the modular nature and broad substrate scope of imine formation, the work reported herein opens up many new possibilities for the synthesis of customizable 2D polymers and systematic studies of their structure-property relationships.

  11. Swing Friction Behavior of the Contact Interface Between CoCrMo and UHMWPE Under Dynamic Loading

    Science.gov (United States)

    Chen, Kai; Zhang, Dekun; Yang, Xuehui; Zhang, Xin; Wang, Qingliang; Qi, Jianwei

    2016-12-01

    CoCrMo alloy and UHMWPE have been widely used in knee joint prosthesis implantation materials. In this paper, swing friction behavior of the contact interface between CoCrMo alloy and UHMWPE is studied under dynamic loading. Swing friction characteristic and damage mechanism are discussed. The results show that swing friction coefficients increase with the rising of maximum normal load and swing angular amplitude. Unloading-standing could play alleviative roles in friction and wear to a large degree. As the cycle number gradually increases, the surface roughness of UHMWPE decreases, while the roughness of CoCrMo increases. During the swing friction, the main damage mechanism of CoCrMo is abrasive wear and the main damage mechanisms of UHMWPE are abrasive wear, fatigue wear and plastic deformation. Besides, it is easier to generate surface damages with small angle and heavy load.

  12. The structure and dynamics of Nano Particles encapsulated by the SDS monolayer collapse at the water/TCE interface

    Science.gov (United States)

    Shi, Wenxiong

    2016-11-01

    The super-saturated surfactant monolayer collapses with the nanoparticles (NPs) at the water/trichloroethylene (TCE) interface are investigated using molecular dynamics (MD) simulations. The results show that sodium alkyl sulfate (SDS) monolayer collapse is initiated by buckling and followed primarily by budding and the bud encapsulating the NPs and oil molecules. The developed bud detaches from the monolayer into a water phase and forms the swollen micelle emulsion with NPs and oil molecules. We investigate the wavelength of the initial budding and the theoretical description of the budding process. The wavelength of the monolayer increases with bending modulus. The energy barrier of the budding can be easily overcome by thermal fluctuation energy, which indicates that budding process proceeds rapidly.

  13. Non-equilibrium magnetic colloidal dispersions at liquid-air interfaces: dynamic patterns, magnetic order and self-assembled swimmers.

    Science.gov (United States)

    Snezhko, Alexey

    2011-04-20

    Colloidal dispersions of interacting particles subjected to an external periodic forcing often develop nontrivial self-assembled patterns and complex collective behavior. A fundamental issue is how collective ordering in such non-equilibrium systems arises from the dynamics of discrete interacting components. In addition, from a practical viewpoint, by working in regimes far from equilibrium new self-organized structures which are generally not available through equilibrium thermodynamics can be created. In this review spontaneous self-assembly phenomena in magnetic colloidal dispersions suspended at liquid-air interfaces and driven out of equilibrium by an alternating magnetic field are presented. Experiments reveal a new type of nontrivially ordered self-assembled structures emerging in such systems in a certain range of excitation parameters. These dynamic structures emerge as a result of the competition between magnetic and hydrodynamic forces and have complex unconventional magnetic ordering. Nontrivial self-induced hydrodynamic fields accompany each out-of-equilibrium pattern. Spontaneous symmetry breaking of the self-induced surface flows leading to a formation of self-propelled microstructures has been discovered. Some features of the self-localized structures can be understood in the framework of the amplitude equation (Ginzburg-Landau type equation) for parametric waves coupled to the conservation law equation describing the evolution of the magnetic particle density and the Navier-Stokes equation for hydrodynamic flows. To understand the fundamental microscopic mechanisms governing self-assembly processes in magnetic colloidal dispersions at liquid-air interfaces a first-principle model for a non-equilibrium self-assembly is presented. The latter model allows us to capture in detail the entire process of out-of-equilibrium self-assembly in the system and reproduces most of the observed phenomenology.

  14. Geocadabra Construction Box: A dynamic geometry interface within a 3D visualization teaching-learning trajectory for elementary learners

    Directory of Open Access Journals (Sweden)

    Jacqueline Sack

    2013-07-01

    Full Text Available This study focuses on the integration of a 3-D dynamic geometry interface to enhance the 3-D visualization capacity of 8-9-year-old children who attend an after-school program. Each year, all third grade children, who attend a dual-language urban elementary school, are invited to participate, typically beginning with 20-25 participants. The program runs for one hour per week for the duration of the academic year. The research team (a university researcher and one or more classroom teachers uses design research principles (Cobb, et al., 2003 to develop and refine teaching-learning trajectories for the program. They use socially mediated instructional strategies, constantly challenging learners to find multiple solutions and explanations to a wide variety ofspatial problems. Learners work with figures made from wooden cubes, 2-D pictures that resemble these figures, and with iconic representations (such as top-view numeric or top, side and front plane views that do not directly resemble the figures. Through the integration of Geocadabra (Lecluse, 2005, the 3-D dynamic digital interface, learners move easily among the different representations and then can mentally abstract properties of these figures. They were able to visualize and accurately enumerate cubes of a complex 2-D conventional picture, but were also able to determine multiple solutions for given sets of front, side and top view diagrams, which do not always correlate with only one 3-D solution. With the current curricular focus on predominantly symbolic numeration, systematic integration of visualization, even as a representation tool for number work, into the elementary curriculum is problematic.

  15. Motor cortical prediction of EMG: evidence that a kinetic brain-machine interface may be robust across altered movement dynamics.

    Science.gov (United States)

    Cherian, A; Krucoff, M O; Miller, L E

    2011-08-01

    During typical movements, signals related to both the kinematics and kinetics of movement are mutually correlated, and each is correlated to some extent with the discharge of neurons in the primary motor cortex (M1). However, it is well known, if not always appreciated, that causality cannot be inferred from correlations. Although these mutual correlations persist, their nature changes with changing postural or dynamical conditions. Under changing conditions, only signals directly controlled by M1 can be expected to maintain a stable relationship with its discharge. If one were to rely on noncausal correlations for a brain-machine interface, its generalization across conditions would likely suffer. We examined this effect, using multielectrode recordings in M1 as input to linear decoders of both end point kinematics (position and velocity) and proximal limb myoelectric signals (EMG) during reaching. We tested these decoders across tasks that altered either the posture of the limb or the end point forces encountered during movement. Within any given task, the accuracy of the kinematic predictions tended to be somewhat better than the EMG predictions. However, when we used the decoders developed under one task condition to predict the signals recorded under different postural or dynamical conditions, only the EMG decoders consistently generalized well. Our results support the view that M1 discharge is more closely related to kinetic variables like EMG than it is to limb kinematics. These results suggest that brain-machine interface applications using M1 to control kinetic variables may prove to be more successful than the more standard kinematic approach.

  16. Dynamic Contrast-Enhanced CT in Patients with Pancreatic Cancer

    Directory of Open Access Journals (Sweden)

    Rie Ø. Eriksen

    2016-09-01

    Full Text Available The aim of this systematic review is to provide an overview of the use of Dynamic Contrast-enhanced Computed Tomography (DCE-CT in patients with pancreatic cancer. This study was composed according to the PRISMA guidelines 2009. The literature search was conducted in PubMed, Cochrane Library, EMBASE, and Web of Science databases to identify all relevant publications. The QUADAS-2 tool was implemented to assess the risk of bias and applicability concerns of each included study. The initial literature search yielded 483 publications. Thirteen articles were included. Articles were categorized into three groups: nine articles concerning primary diagnosis or staging, one article about tumor response to treatment, and three articles regarding scan techniques. In exocrine pancreatic tumors, measurements of blood flow in eight studies and blood volume in seven studies were significantly lower in tumor tissue, compared with measurements in pancreatic tissue outside of tumor, or normal pancreatic tissue in control groups of healthy volunteers. The studies were heterogeneous in the number of patients enrolled and scan protocols. Perfusion parameters measured and analyzed by DCE-CT might be useful in the investigation of characteristic vascular patterns of exocrine pancreatic tumors. Further clinical studies are desired for investigating the potential of DCE-CT in pancreatic tumors.

  17. Cancer

    Science.gov (United States)

    ... cancer Non-Hodgkin lymphoma Ovarian cancer Pancreatic cancer Testicular cancer Thyroid cancer Uterine cancer Symptoms Symptoms of cancer ... tumor Obesity Pancreatic cancer Prostate cancer Stomach cancer Testicular cancer Throat or larynx cancer Thyroid cancer Patient Instructions ...

  18. Dynamical spin injection at a quasi-one-dimensional ferromagnet-graphene interface

    Energy Technology Data Exchange (ETDEWEB)

    Singh, S.; Ahmadi, A.; Mucciolo, E. R.; Barco, E. del [Department of Physics, University of Central Florida, Orlando, Florida 32816 (United States); Cherian, C. T. [Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542 (Singapore); Graphene Research Center, National University of Singapore, Singapore 117542 (Singapore); Özyilmaz, B. [Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542 (Singapore); NanoCore, 4 Engineering Drive 3, National University of Singapore, Singapore 117576 (Singapore); Graphene Research Center, National University of Singapore, Singapore 117542 (Singapore); NUS Graduate School for Integrative Sciences and Engineering (NGS), National University of Singapore, Singapore 117456 (Singapore)

    2015-01-19

    We present a study of dynamical spin injection from a three-dimensional ferromagnet into two-dimensional single-layer graphene. Comparative ferromagnetic resonance (FMR) studies of ferromagnet/graphene strips buried underneath the central line of a coplanar waveguide show that the FMR linewidth broadening is the largest when the graphene layer protrudes laterally away from the ferromagnetic strip, indicating that the spin current is injected into the graphene areas away from the area directly underneath the ferromagnet being excited. Our results confirm that the observed damping is indeed a signature of dynamical spin injection, wherein a pure spin current is pumped into the single-layer graphene from the precessing magnetization of the ferromagnet. The observed spin pumping efficiency is difficult to reconcile with the expected backflow of spins according to the standard spin pumping theory and the characteristics of graphene, and constitutes an enigma for spin pumping in two-dimensional structures.

  19. Dynamics at the Polymer/Nanoparticle Interface in Poly(2-vinylpyridine)/Silica Nanocomposites.

    Energy Technology Data Exchange (ETDEWEB)

    Holt, Adam P [ORNL; Griffin, Phillip [University of Tennessee (UTK) and Oak Ridge National Laboratory (ORNL); Bocharova, Vera [ORNL; Agapov, Alexander L [ORNL; Imel, Adam E [ORNL; Dadmun, Mark D [ORNL; Sangoro, Joshua R [ORNL; Sokolov, Alexei P [ORNL

    2014-01-01

    The static and dynamic properties of poly(2-vinylpyridine)/silica nanocomposites are investigated by temperature modulated differential scanning calorimetry, broadband dielectric spectroscopy (BDS), small-angle X-ray scattering (SAXS), and transmission electron microscopy. Both BDS and SAXS detect the existence of an interfacial polymer layer on the surface of nanoparticles. The results show that whereas the calorimetric glass transition temperature varies only weakly with nanoparticle loading, the segmental mobility of the polymer interfacial layer is slower than the bulk polymer by 2 orders of magnitude. Detailed analysis of BDS and SAXS data reveal that the interfacial layer has a thickness of 4 6 nm irrespective of the nanoparticle concentration. These results demonstrate that in contrast to some recent articles on polymer nanocomposites, the interfacial polymer layer is by no means a dead layer . However, its existence might provide some explanation for controversies surrounding the dynamics of polymer nanocomposites.

  20. Polarizability effects in molecular dynamics simulations of the graphene-water interface

    Science.gov (United States)

    Ho, Tuan A.; Striolo, Alberto

    2013-02-01

    The importance of including the polarizability of both water and graphene in molecular dynamics simulations of the water/graphene system was quantified. A thin film of either rigid single point charge extended (SPC/E) water or polarizable simple 4-site water model with Drude polarizability (SWM4_DP) water on non-polarizable and polarizable graphene surfaces was simulated. The graphene surface was either maintained neutral or charged, positively and negatively. The results suggest that SPC/E and SWM4_DP water models yield very similar predictions for the water structural properties on neutral non-polarizable graphene, although they yield slightly different dynamical properties of interfacial water on neutral non-polarizable graphene. More pronounced were the differences obtained when graphene was modeled with a polarizable force field. In particular, the polarizability of graphene was found to enhance the number of interfacial SWM4_DP water molecules pointing one of their OH bonds towards the neutral surface. Despite this structural difference, the dynamical properties predicted for the interfacial SWM4_DP water were found to be independent on polarizability as long as the polarizability of a carbon atom is smaller than α = 0.878 Å. On charged graphene surfaces, the effect of polarizability of graphene on structural properties and some dynamical properties of SWM4_DP water is negligible because electrostatic forces due to surface charge dominate polarization forces, as expected. For all cases, our results suggest that the hydrogen bond network is insensitive to the polarizability of both water and graphene. Understanding how these effects will determine the accumulation of ions near neutral or charged graphene could have important implications for applications in the fields of energy storage and water desalination.

  1. ADHESION EFFECTS WITHIN THE HARD MATTER – SOFT MATTER INTERFACE: MOLECULAR DYNAMICS

    OpenAIRE

    2016-01-01

    In the present study three soft matter – hard matter systems consisting of different nanomaterials and organic molecules were studied using the steered molecular dynamics approach in order to reveal regularities in the formation of organic-inorganic hybrids and the stability of multimolecular complexes, as well as to analyze the energy aspects of adhesion between bio-molecules and layered ceramics. The combined process free energy estimation (COPFEE) procedure was used for quantitative and qu...

  2. Dynamic contrast-enhanced MRI for monitoring response to neoadjuvant chemotherapy in breast cancer

    OpenAIRE

    Loo, C E

    2016-01-01

    The general aim of this thesis is to investigate the role of dynamic contrast-enhanced MRI in monitoring response of breast cancer during neoadjuvant chemotherapy. The role of MRI with respect to achieving personalized breast cancer treatment by improving response monitoring is examined. Our findings demonstrate the potential clinical relevance of contrast-enhanced MRI for monitoring response of breast cancer during and after neoadjuvant chemotherapy. We defined MRI criteria ( reduction < 25%...

  3. Applying dynamic data collection to improve dry electrode system performance for a P300-based brain-computer interface

    Science.gov (United States)

    Clements, J. M.; Sellers, E. W.; Ryan, D. B.; Caves, K.; Collins, L. M.; Throckmorton, C. S.

    2016-12-01

    Objective. Dry electrodes have an advantage over gel-based ‘wet’ electrodes by providing quicker set-up time for electroencephalography recording; however, the potentially poorer contact can result in noisier recordings. We examine the impact that this may have on brain-computer interface communication and potential approaches for mitigation. Approach. We present a performance comparison of wet and dry electrodes for use with the P300 speller system in both healthy participants and participants with communication disabilities (ALS and PLS), and investigate the potential for a data-driven dynamic data collection algorithm to compensate for the lower signal-to-noise ratio (SNR) in dry systems. Main results. Performance results from sixteen healthy participants obtained in the standard static data collection environment demonstrate a substantial loss in accuracy with the dry system. Using a dynamic stopping algorithm, performance may have been improved by collecting more data in the dry system for ten healthy participants and eight participants with communication disabilities; however, the algorithm did not fully compensate for the lower SNR of the dry system. An analysis of the wet and dry system recordings revealed that delta and theta frequency band power (0.1-4 Hz and 4-8 Hz, respectively) are consistently higher in dry system recordings across participants, indicating that transient and drift artifacts may be an issue for dry systems. Significance. Using dry electrodes is desirable for reduced set-up time; however, this study demonstrates that online performance is significantly poorer than for wet electrodes for users with and without disabilities. We test a new application of dynamic stopping algorithms to compensate for poorer SNR. Dynamic stopping improved dry system performance; however, further signal processing efforts are likely necessary for full mitigation.

  4. Dynamic contrast-enhanced MRI for monitoring response to neoadjuvant chemotherapy in breast cancer

    NARCIS (Netherlands)

    Loo, C.E.

    2016-01-01

    The general aim of this thesis is to investigate the role of dynamic contrast-enhanced MRI in monitoring response of breast cancer during neoadjuvant chemotherapy. The role of MRI with respect to achieving personalized breast cancer treatment by improving response monitoring is examined. Our finding

  5. Dynamic response of cancer under the influence of immunological activity and therapy

    NARCIS (Netherlands)

    De Vladar, H.P.; Gonzalez, J.A.

    2004-01-01

    The dynamical basis of tumoral growth has been controversial. Many models have been proposed to explain cancer development. The descriptions employ exponential, potential, logistic or Gompertzian growth laws. Some of these models are concerned with the interaction between cancer and the immunologica

  6. [?]Nonlinear Issues in the Aerothermochemistry of Gases and Materials and the Associated Physics and Dynamics of Interfaces

    Science.gov (United States)

    Johnson, Joseph A., III

    1996-01-01

    Our research and technology are focused on nonlinear issues in the aerothermochemistry of gases and materials and the associated physics and dynamics of interfaces. Our program is now organized to aggressively support the NASA Aeronautics Enterprise so as to: (a) develop a new generation of environmentally compatible, economic subsonic aircraft; (b) develop the technology base for an economically viable and environmentally compatible high-speed civil transport; (c) develop the technology options for new capabilities in high-performance aircraft; (d) develop hypersonic technologies for air-breathing flight; and (e) develop advanced concepts, understanding of physical phenomena, and theoretical, experimental, and computational tools for advanced aerospace systems. The implications from our research for aeronautical and aerospace technology have been both broad and deep. For example, using advanced computational techniques, we have determined exact solutions for the Schrodinger equation in electron-molecule scattering allowing us to evaluate atmospheric models important to reentry physics. We have also found a new class of exact solutions for the Navier Stokes equations. In experimental fluid dynamics, we have found explicit evidence of turbulence modification of droplet sizes in shock tube flow with condensation. We have developed a new diagnostic tool for the direct estimation of flow velocities at MHz sampling rates in quasi-one dimensional turbulent flow. This procedure suggests an unexpected confirmation of the possibility of 'natural' closure in Reynolds stresses with deep implications for the development of turbulent models. A transient increase is observed in both the spectral energy decay rate and the degree of chaotic complexity at the interface of a shock wave and a turbulent ionized gas. Even though the gas is apparently brought to rest by the shock wave, no evidence is found either of the expected relaminarization. A unique diamond-shaped nozzle has been

  7. Ultrafast Hydration Dynamics Probed by Tryptophan at Protein Surface and Protein-DNA Interface

    Science.gov (United States)

    Qin, Yangzhong

    As we all live in a special water planet Earth, the significance of water to life has been universally recognized. The reason why water is so important to life has intrigued many researchers. This dissertation will focus on the ultrafast dynamics of protein surface water and protein-DNA interfacial water which have direct importance to the protein structure and function. Using tryptophan as an intrinsic fluorescence probe, combined with site-directed mutagenesis and ultrafast fluorescence up-conversion spectroscopy, we can achieve single residue spatial resolution and femtosecond temporal resolution. We can also precisely determine the local hydration water dynamics by monitoring the Stokes shift of tryptophan one at a time. Previously, the protein surface hydration has been extensively studied by our group. In this thesis, we will provide more details on the methods we are using to extract the hydration dynamics, and also validate our methods from both experimental and theoretical perspectives. To further interrogate the interfacial water hydration dynamics relative to the protein surface hydration, we studied two DNA polymerases: DNA Polymerase IV (Dpo4) and DNA Polymerase Beta (Pol beta). Both proteins show typical surface hydration pattern with three distinct time components including: (i) the ultrafast sub-picosecond component reflects the bulk type water motion; (ii) a few picoseconds component shows the inner water relaxation mainly corresponding to the local libration and reorientation; (iii) the tens to hundred picoseconds component represents the water-protein coupled motion involving the whole water network reorganization. Dpo4, a loosely DNA binding protein, exhibits very flexible interfacial water which resembles its surface water yet with a significantly reduced ultrafast component. Such dynamic interfacial water not only maintains interfacial flexibility, but also contributes to the low fidelity of the protein. In contrast to the Dpo4, pol beta

  8. Dynamics in Sunspot Umbra as Seen in New Solar Telescope and Interface Region Imaging Spectrograph Data

    CERN Document Server

    Yurchyshyn, Vasyl; Kilcik, Ali

    2014-01-01

    We analyse sunspot oscillations using Interface Region Imaging Spectrograph (IRIS) slit-jaw and spectral data and narrow-band chromospheric images from the New Solar Telescope (NST) for the main sunspot in NOAA AR 11836. We report that the difference between the shock arrival times as measured the Mg II k 2796.35\\AA\\ and Si IV 1393.76\\AA\\ line formation levels changes during the observed period and peak-to-peak delays may range from 40~s to zero. The intensity of chromospheric shocks also displays a long term (about 20~min) variations. NST's high spatial resolution \\ha\\ data allowed us to conclude that in this sunspot umbral flashes (UFs) appeared in the form of narrow bright lanes stretched along the light bridges and around clusters of umbral bright points. Time series also suggested that UFs preferred to appear on the sunspot-center side of light bridges, which may indicate the existence of a compact sub-photospheric driver of sunspot oscillations. The sunspot's umbra as seen in the IRIS chromospheric and ...

  9. Multi-solid and multi-fluid diffuse interface model: Applications to dynamic fracture and fragmentation

    Energy Technology Data Exchange (ETDEWEB)

    Ndanou, S., E-mail: serge.ndanou@univ-amu.fr; Favrie, N., E-mail: nicolas.favrie@univ-amu.fr; Gavrilyuk, S., E-mail: sergey.gavrilyuk@univ-amu.fr

    2015-08-15

    We extend the model of diffuse solid–fluid interfaces developed earlier by authors of this paper to the case of arbitrary number of interacting hyperelastic solids. Plastic transformations of solids are taken into account through a Maxwell type model. The specific energy of each solid is given in separable form: it is the sum of a hydrodynamic part of the energy depending only on the density and the entropy, and an elastic part of the energy which is unaffected by the volume change. It allows us to naturally pass to the fluid description in the limit of vanishing shear modulus. In spite of a large number of governing equations, the model has a quite simple mathematical structure: it is a duplication of a single visco-elastic model. The model is well posed both mathematically and thermodynamically: it is hyperbolic and compatible with the second law of thermodynamics. The resulting model can be applied in the situations involving an arbitrary number of fluids and solids. In particular, we show the ability of the model to describe spallation and penetration phenomena occurring during high velocity impacts.

  10. Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    R. James Kirkpatrick; Andrey G. Kalinichev

    2008-11-25

    Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches to important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, and reactivity at mineral-water interfaces and for oxy-ions in solution, but has traditionally been difficult to model with molecular dynamics (MD). Our ultimate objective is to develop this capability, because MD is much less computationally demanding than quantum-chemical approaches. We have also extended our previous MD simulations of metal binding to natural organic matter (NOM) to a much longer time scale (up to 10 ns) for

  11. Dynamic Microenvironment Induces Phenotypic Plasticity of Esophageal Cancer Cells Under Flow

    Science.gov (United States)

    Calibasi Kocal, Gizem; Güven, Sinan; Foygel, Kira; Goldman, Aaron; Chen, Pu; Sengupta, Shiladitya; Paulmurugan, Ramasamy; Baskin, Yasemin; Demirci, Utkan

    2016-12-01

    Cancer microenvironment is a remarkably heterogeneous composition of cellular and non-cellular components, regulated by both external and intrinsic physical and chemical stimuli. Physical alterations driven by increased proliferation of neoplastic cells and angiogenesis in the cancer microenvironment result in the exposure of the cancer cells to elevated levels of flow-based shear stress. We developed a dynamic microfluidic cell culture platform utilizing eshopagael cancer cells as model cells to investigate the phenotypic changes of cancer cells upon exposure to fluid shear stress. We report the epithelial to hybrid epithelial/mesenchymal transition as a result of decreasing E-Cadherin and increasing N-Cadherin and vimentin expressions, higher clonogenicity and ALDH positive expression of cancer cells cultured in a dynamic microfluidic chip under laminar flow compared to the static culture condition. We also sought regulation of chemotherapeutics in cancer microenvironment towards phenotypic control of cancer cells. Such in vitro microfluidic system could potentially be used to monitor how the interstitial fluid dynamics affect cancer microenvironment and plasticity on a simple, highly controllable and inexpensive bioengineered platform.

  12. A molecular-dynamics study of defects and failure mechanisms in strained heteroepitaxial interfaces

    Science.gov (United States)

    Schiffbauer, Jarrod E.; Bachlechner, Martina E.

    2006-03-01

    The formation and growth of pits and pit-like structures through a delamination-driven mechanism have been observed in the analysis of comprehensive molecular dynamics simulations of a laterally strained Si(111)/Si3N4(0001) interfacial system. These phenomena contribute to the ultimate mechanical failure of the simulated samples. Several factors play a key role the nucleation and growth of the pits including temperature and strain rate. Here we present an overview of the dependence of pit nucleation and morphology on both global and local conditions for a representative range of temperatures and applied strain rates.

  13. The study of Cu/Nb interface diffusion using molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    Ivan V. Nelasov

    2016-06-01

    Full Text Available The peculiarities of interfacial boundary diffusion where the boundary goes between nonmiscible metals with body-centered cubic (BCC and face-centered cubic (FCC lattices have been studied taking, as a case in point, the Cu/Nb system, and using the molecular dynamics method. The diffusion atomic displacements were shown to occur mainly near the mismatch dislocations and their intersections. The diffusion of the high-melting component was found to be characterized by high anisotropy with the predominant atomic displacement along the dense-packed direction in the interfacial boundary plane being common to FCC and BCC lattices with the Kurdyumov–Sachs mutual orientation.

  14. A graphical interface based model for wind turbine drive train dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Manwell, J.F.; McGowan, J.G.; Abdulwahid, U.; Rogers, A. [Univ. of Massachusetts, Amherst, MA (United States); McNiff, B. [McNiff Light Industry, Blue Hill, ME (United States)

    1996-12-31

    This paper presents a summary of a wind turbine drive train dynamics code that has been under development at the University of Massachusetts, under National Renewable Energy Laboratory (NREL) support. The code is intended to be used to assist in the proper design and selection of drive train components. This work summarizes the development of the equations of motion for the model, and discusses the method of solution. In addition, a number of comparisons with analytical solutions and experimental field data are given. The summary includes conclusions and suggestions for future work on the model. 13 refs., 10 figs.

  15. Dynamic properties of cationic diacyl-glycerol-arginine-based surfactant/phospholipid mixtures at the air/water interface.

    Science.gov (United States)

    Lozano, Neus; Pinazo, Aurora; Pérez, Lourdes; Pons, Ramon

    2010-02-16

    In this Article, we study the binary surface interactions of 1,2-dimyristoyl-rac-glycero-3-O-(N(alpha)-acetyl-L-arginine) hydrochloride (1414RAc) with 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) on 0.1 M sodium chloride solutions. 1414RAc is a novel monocationic surfactant that has potential applications as an antimicrobial agent, is biodegradable, and shows a toxicity activity smaller than that of other commercial cationic surfactants. DPPC phospholipid was used as a model membrane component. The dynamic surface tension of 1414RAc/DPPC aqueous dispersions injected into the saline subphase was followed by tensiometry. The layer formation for the mixtures is always accelerated with respect to DPPC, and surprisingly, the surface tension reduction is faster and reaches lower surface tension values at surfactant concentration below its critical micellar concentration (cmc). Interfacial dilational rheology properties of mixed films spread on the air/water interface were determined by the dynamic oscillation method using a Langmuir trough. The effect of surfactant mole fraction on the rheological parameters of 1414RAc/DPPC mixed monolayers was studied at a relative amplitude of area deformation of 5% and a frequency of 50 mHz. The monolayer viscoelasticity shows a nonideal mixing behavior with predominance of the surfactant properties. This nonideal behavior has been attributed to the prevalence of electrostatic interactions.

  16. Thermal stability of interface voids in Cu grain boundaries with molecular dynamic simulations

    Science.gov (United States)

    Xydou, A.; Parviainen, S.; Aicheler, M.; Djurabekova, F.

    2016-09-01

    By means of molecular dynamic simulations, the stability of cylindrical voids is examined with respect to the diffusion bonding procedure. To do this, the effect of grain boundaries between the grains of different crystallographic orientations on the void closing time was studied at high temperatures from 0.7 up to 0.94 of the bulk melting temperature ({{T}\\text{m}} ). The diameter of the voids varied from 3.5 to 6.5 nm. A thermal instability occurring at high temperatures at the surface of the void placed in a grain boundary triggered the eventual closure of the void at all examined temperatures. The closing time has an exponential dependence on the examined temperature values. A model based on the defect diffusion theory is developed to predict the closing time for voids of macroscopic size. The diffusion coefficient within the grain boundaries is found to be overall higher than the diffusion coefficient in the region around the void surface. The activation energy for the diffusion in the grain boundary is calculated based on molecular dynamic simulations. This value agrees well with the experimental given in the Ashby maps for the creep in copper via Coble GB diffusion.

  17. Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces

    Science.gov (United States)

    Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos

    2016-08-01

    Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.

  18. Numerical Modeling and In-Situ Observations of the Dynamics of the Solid/Liquid Interface Morphology During Directional Solidification of Alloys

    Science.gov (United States)

    Catalina, Adrian V.; Stefanescu, Doru M.; Sen, Subhayu; Curreri, Peter A.; Kaukler, W. F.

    1999-01-01

    The departure from interface planarity and the subsequent evolution to a periodic array of cells or dendrites is a fundamental process that characterizes most microstructures in solidified alloys. The growing demand for high quality alloys and semiconductor crystals requires a precise methodology to predict and subsequently control both the interface morphology and the distribution of impurities, additives, and phases in the grown crystal. Apart from its practical significance, the study of morphological evolution has also been viewed as a means to unearth a general paradigm for pattern formation in nature. A previously developed 2D numerical model for the solid/liquid interface tracking has been further refined and used to simulate the time-evolution of the perturbations on the interface. The dynamics of the local growth velocity, interface undercooling and solute concentration at the interface has been theoretically predicted by means of the numerical model for Al-Cu and Pb-Sn alloys. The model shows that perturbations with a wavelengths, lambda greater than a critical wavelength lambda(sub c) continue to grow in time whereas perturbations with lambda < lambda(sub c) cease to propagate. The model further predicts that under certain conditions perturbation can also propagate along the interface. Comparison of these predictions with existing theories of pattern formation and experimental results will be discussed.

  19. Numerical Modeling and In-Situ Observations of the Dynamics of the Solid/Liquid Interface Morphology During Directional Solidification of Alloys

    Science.gov (United States)

    Catalina, Adrian V.; Stefanescu, Doru M.; Sen, Subhayu; Curreri, Peter A.; Kaukler, W. F.

    1999-01-01

    The departure from interface planarity and the subsequent evolution to a periodic array of cells or dendrites is a fundamental process that characterizes most microstructures in solidified alloys. The growing demand for high quality alloys and semiconductor crystals requires a precise methodology to predict and subsequently control both the interface morphology and the distribution of impurities, additives, and phases in the grown crystal. Apart from its practical significance, the study of morphological evolution has also been viewed as a means to unearth a general paradigm for pattern formation in nature. A previously developed 2D numerical model for the solid/liquid interface tracking has been further refined and used to simulate the time-evolution of the perturbations on the interface. The dynamics of the local growth velocity, interface undercooling and solute concentration at the interface has been theoretically predicted by means of the numerical model for Al-Cu and Pb-Sn alloys. The model shows that perturbations with a wavelengths, lambda greater than a critical wavelength lambda(sub c) continue to grow in time whereas perturbations with lambda interface. Comparison of these predictions with existing theories of pattern formation and experimental results will be discussed.

  20. Probing Dynamics at Interfaces: Molecular Motions in Lipid Bilayers studied by Neutron Backscattering

    CERN Document Server

    Rheinstädter, M C; Salditt, T; Rheinst\\"adter, Maikel C.; Seydel, Tilo; Salditt, Tim

    2004-01-01

    Lipid membranes in a physiological context cannot be understood without taking into account their mobile environment. Here, we report on a high energy-resolution neutron backscattering study to investigate slow motions on nanosecond time scales in highly oriented solid supported phospholipid bilayers of the model system DMPC -d54 (deuterated 1,2-dimyristoyl-sn-glycero-3-phoshatidylcholine). This technique allows discriminating the Q-dependent onset of mobility and provides a benchmark test regarding the feasibility of dynamical neutron scattering investigations on these sample systems. Apart from freezing of the lipid acyl-chains, we could observe a second freezing temperature that we attribute to the hydration water in between the membrane stacks. The freezing is lowered several degrees as compared to (heavy) bulk water.

  1. Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories.

    Science.gov (United States)

    Koukos, Panagiotis I; Glykos, Nicholas M

    2013-10-05

    We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross-platform, Perl/Tk-based front-end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user-friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root-meansquare deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free-open source software available immediately for download.

  2. STM “molecular tracer” dynamics at the solid-solution interface.

    Science.gov (United States)

    Padowitz, David

    2001-03-01

    We have measured rates of adsorption-desorption at equilibrium for single molecules in a monolayer in contact with solution. Long-chain alkanes, ethers, and thioethers were adsorbed on a graphite surface from solution. Matched length pairs of molecules co-crystallize but are readily distinguishable in scanning tunneling microscope images due to strong contrast between sulfur atoms and methylene or oxygen groups. Thioether molecules were seen to continually enter and leave the well-ordered crystalline monolayer. Residence times were on the order of seconds, depending on chain length and temperature. The rates were less sensitive to solvent and solution concentration. Each exchange event is completed within a few milliseconds. We are also using tracers to follow molecular rearrangements at domain boundaries. The results appear relevant to tribology and the growth of molecular crystals and organic thin films. With careful selection the method should be applicable to dynamics in molecules such as lipids and liquid crystals.

  3. Towards a naturalistic brain-machine interface: hybrid torque and position control allows generalization to novel dynamics.

    Directory of Open Access Journals (Sweden)

    Pratik Y Chhatbar

    Full Text Available Realization of reaching and grasping movements by a paralytic person or an amputee would greatly facilitate her/his activities of daily living. Towards this goal, control of a computer cursor or robotic arm using neural signals has been demonstrated in rodents, non-human primates and humans. This technology is commonly referred to as a Brain-Machine Interface (BMI and is achieved by predictions of kinematic parameters, e.g. position or velocity. However, execution of natural movements, such as swinging baseball bats of different weights at the same speed, requires advanced planning for necessary context-specific forces in addition to kinematic control. Here we show, for the first time, the control of a virtual arm with representative inertial parameters using real-time neural control of torques in non-human primates (M. radiata. We found that neural control of torques leads to ballistic, possibly more naturalistic movements than position control alone, and that adding the influence of position in a hybrid torque-position control changes the feedforward behavior of these BMI movements. In addition, this level of control was achievable utilizing the neural recordings from either contralateral or ipsilateral M1. We also observed changed behavior of hybrid torque-position control under novel external dynamic environments that was comparable to natural movements. Our results demonstrate that inclusion of torque control to drive a neuroprosthetic device gives the user a more direct handle on the movement execution, especially when dealing with novel or changing dynamic environments. We anticipate our results to be a starting point of more sophisticated algorithms for sensorimotor neuroprostheses, eliminating the need of fully automatic kinematic-to-dynamic transformations as currently used by traditional kinematic-based decoders. Thus, we propose that direct control of torques, or other force related variables, should allow for more natural

  4. Dynamics and hydrodynamic mixing of reactive solutes at stable fresh-salt interfaces

    Science.gov (United States)

    van der Zee, Sjoerd E. A. T. M.; Eeman, Sara; Cirkel, Gijsbert; Leijnse, Toon

    2014-05-01

    In coastal zones with saline groundwater, but also in semi-arid regions, fresh groundwater lenses may form due to infiltration of rain water. The thickness of both the lens and the mixing zone, determines fresh water availability for plant growth. Due to recharge variation, the thickness of the lens and the mixing zone are not constant, which may adversely affect agricultural and natural vegetation if saline water reaches the root zone during the growing season. A similar situation is found in situations where groundwater is not saline, but has a different chemical signature than rainwater-affected groundwater. Then also, vegetation patches and botanic biodiversity may depend sensitively on the depth of the interface between different types of groundwater. In this presentation, we study the response of thin lenses and their mixing zone to variation of recharge. The recharge is varied using sinusoids with a range of amplitudes and frequencies. We vary lens properties by varying the Rayleigh number and Mass flux ratio of saline and fresh water, as these dominate on the thickness of thin lenses and their mixing zone. Numerical results show a linear relation between the normalised lens volume and the main lens and recharge characteristics, enabling an empirical approximation of the variation of lens thickness. Increase of the recharge amplitude causes increase and the increase of recharge frequency causes a decrease in the variation of lens thickness. The average lens thickness is not significantly influenced by these variations in recharge, contrary to the mixing zone thickness. The mixing zone thickness is compared to that of a Fickian mixing regime. A simple relation between the travelled distance of the centre of the mixing zone position due to variations in recharge and the mixing zone thickness is shown to be valid for both a sinusoidal recharge variation and actual records of irregularly varying daily recharge data. Starting from a step response function

  5. A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in FIREBALL

    Science.gov (United States)

    Keith, J. Brandon; Fennick, Jacob R.; Junkermeier, Chad E.; Nelson, Daniel R.; Lewis, James P.

    2009-03-01

    FIREBALL is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access FIREBALL's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation. Program summaryProgram title: FireballUI Catalogue identifier: AECF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 279 784 No. of bytes in distributed program, including test data, etc.: 12 836 145 Distribution format: tar.gz Programming language: Java Computer: PC and workstation Operating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package. RAM: 512 MB Word size: 32 or 64 bits Classification: 4.14 Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations. Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are

  6. Isotopic and impurity element probes of mesoscale chemical dynamics at mineral fluid interfaces

    Science.gov (United States)

    DePaolo, D. J.

    2012-12-01

    Mesoscale interactions control important Earth processes including the growth of minerals from aqueous solutions and silicate liquids, the diffusion of ions in solids and silicate liquids, and the solid-state deformation and recrystallization that constitutes metamorphism. Most of these processes are typically understood from the classical side in terms of macroscopic physical and thermodynamic properties and classical kinetics, and from the molecular side in terms of single molecule or nearest-neighbor interactions. However, in many cases the controlling processes occur at intermediate scales of both length and time, and involve complex interactions among multiple chemical species. A major limitation has been in characterizing and modeling the dynamic processes that lead to the macroscopic properties and behavior. Advanced microscopy techniques allow phase changes, for example, to be monitored at high resolution, and this capability continues to improve. However, other important information about the phase changes, such as the molecular exchange fluxes between phases and the detailed mechanisms of reaction, are not revealed by microscopy. High-resolution isotopic characterization now allows the molecular exchange fluxes to be quantified, and models suggest that the incorporation of impurity elements is directly tied to these fluxes. One of the main advances is that precise isotopic measurements have recently been extended to include major stoichiometric cations such as Ca, Mg, Fe, and K, as well as key impurity elements such as U, Cd, Mo, and Sr. Isotopic analysis at the nano- to microscale would further clarify the detailed dynamics of mineral chemistry controls but are not yet possible except in a few instances. Impurity element concentrations are more easily measured at these small scales, and they are a key bridge between isotopic measurements and microscopy.Other limitations to advancing our knowledge of the chemical and isotopic effects associated with

  7. Dynamics of cancer progression and suppression: A novel evolutionary game theory based approach.

    Science.gov (United States)

    Banerjee, Jeet; Ranjan, Tanvi; Layek, Ritwik Kumar

    2015-01-01

    In this paper, a novel mathematical approach is proposed for the dynamics of progression and suppression of cancer. We define mutant cell density, ρ(μ) (μ × ρ), as a primary factor in cancer dynamics, and use logistic growth model and replicator equation for defining the dynamics of total cell density (ρ) and mutant fraction (μ), respectively. Furthermore, in the proposed model, we introduce an analytical expression for a control parameter D (drug), to suppress the proliferation of mutants with extra fitness level σ. Lastly, we present a comparison of the proposed model with some existing models of tumour growth.

  8. Forest Management and the Evolution of Project Design in Dynamic Wildland Urban Interface Fire Environments

    Science.gov (United States)

    Conway, S.

    2014-12-01

    The Truckee Ranger District on the Tahoe National Forest, in the heart of the Sierra Nevada Mountains, has a rich history of human activities. Native American influences, comstock-era logging, fire suppression, development, and recreation have all shaped the natural environment into what it is today. Like much of our national forests in California, forest conditions that have developed are generally much more homogenous and less resistant to disturbance from fire, insect, and disease than they might have been without the myriad of human influences. However, in order to improve the resiliency of our forests to stand replacing disturbances like high severity fire, while managing for integrated anthropomorphic values, it is imperative that management evolve to meet those dynamic needs. Recent advances in remote sensing and GIS allow land managers more access to forest information and can inform site specific prescriptions to change site specific undesirable conditions. It is ecologically and politically complex, yet our forests deserve that microscope. This particular presentation will focus on how the Truckee Ranger District began this process of incorporating several values, generated from stakeholder collaboration, into one project's goals and how those lessons learned informed their most recent project.

  9. High-resolution isotope measurements resolve rapid ecohydrological dynamics at the soil-plant interface.

    Science.gov (United States)

    Volkmann, Till H M; Haberer, Kristine; Gessler, Arthur; Weiler, Markus

    2016-05-01

    Plants rely primarily on rainfall infiltrating their root zones - a supply that is inherently variable, and fluctuations are predicted to increase on most of the Earth's surface. Yet, interrelationships between water availability and plant use on short timescales are difficult to quantify and remain poorly understood. To overcome previous methodological limitations, we coupled high-resolution in situ observations of stable isotopes in soil and transpiration water. We applied the approach along with Bayesian mixing modeling to track the fate of (2) H-labeled rain pulses following drought through soil and plants of deciduous tree ecosystems. We resolve how rainwater infiltrates the root zones in a nonequilibrium process and show that tree species differ in their ability to quickly acquire the newly available source. Sessile oak (Quercus petraea) adjusted root uptake to vertical water availability patterns under drought, but readjustment toward the rewetted topsoil was delayed. By contrast, European beech (Fagus sylvatica) readily utilized water from all soil depths independent of water depletion, enabling faster uptake of rainwater. Our results demonstrate that species-specific plasticity and responses to water supply fluctuations on short timescales can now be identified and must be considered to predict vegetation functional dynamics and water cycling under current and future climatic conditions.

  10. Forced oscillations dynamic tribometer with real-time insights of lubricated interfaces

    Science.gov (United States)

    Yahiaoui, M.; Rigaud, E.; Mazuyer, D.; Cayer-Barrioz, J.

    2017-03-01

    This paper presents an innovative forced oscillations dynamic tribometer, the CHRONOS tribometer, with a lubricated ball-on-flat contact configuration fitted out with an in situ optical visualization system and a triggered high-speed camera. The CHRONOS tribometer generates controlled oscillating kinematics by means of a shaker with a range of strokes from 5 μm to 2.5 mm and an oscillation frequency which can be adjusted from 5 Hz to 250 Hz. Displacement and velocity are measured using a vibrometer. The ball-on-flat mean contact pressure is set between 200 MPa and 600 MPa. During motion, the instantaneous normal and friction forces and the interfacial film thickness distribution (in the nanometer scale) are simultaneously measured. In addition to this instantaneous approach, a more macroscopic approach is developed in terms of moving averages of friction and velocity. Another parameter, the friction-velocity tilt angle, is also introduced. This last parameter may give information on the friction-velocity dependence. Eventually, the experiments performed on the CHRONOS device lead to the representation of synchronized temporal signals of displacement/velocity, friction, and lubricant central film thickness. This superimposition of key parameters reveals time effects introduced by the periodical fluid squeeze and flow in the contact.

  11. Brownian nanoimaging of interface dynamics and ligand-receptor binding at cell surfaces in 3-D.

    Science.gov (United States)

    Kuznetsov, Igor R; Evans, Evan A

    2013-04-01

    We describe a method for nanoimaging interfacial dynamics and ligand-receptor binding at surfaces of live cells in 3-D. The imaging probe is a 1-μm diameter glass bead confined by a soft laser trap to create a "cloud" of fluctuating states. Using a facile on-line method of video image analysis, the probe displacements are reported at ~10 ms intervals with bare precisions (±SD) of 4-6 nm along the optical axis (elevation) and 2 nm in the transverse directions. We demonstrate how the Brownian distributions are analyzed to characterize the free energy potential of each small probe in 3-D taking into account the blur effect of its motions during CCD image capture. Then, using the approach to image interactions of a labeled probe with lamellae of leukocytic cells spreading on cover-glass substrates, we show that deformations of the soft distribution in probe elevations provide both a sensitive long-range sensor for defining the steric topography of a cell lamella and a fast telemetry for reporting rare events of probe binding with its surface receptors. Invoking established principles of Brownian physics and statistical thermodynamics, we describe an off-line method of super resolution that improves precision of probe separations from a non-reactive steric boundary to ~1 nm.

  12. Site and bond-specific dynamics of reactions at the gas-liquid interface.

    Science.gov (United States)

    Tesa-Serrate, Maria A; King, Kerry L; Paterson, Grant; Costen, Matthew L; McKendrick, Kenneth G

    2014-01-01

    The dynamics of the interfacial reactions of O((3)P) with the hydrocarbon liquids squalane (C30H62, 2,6,10,15,19,23-hexamethyltetracosane) and squalene (C30H50, trans-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene) have been studied experimentally. Laser-induced fluorescence (LIF) was used to detect the nascent gas-phase OH products. The O((3)P) atoms are acutely sensitive to the chemical differences of the squalane and squalene surfaces. The larger exothermicity of abstraction from allylic C-H sites in squalene is reflected in markedly hotter OH rotational and vibrational distributions. There is a more modest increase in translational energy release. A larger fraction of the available energy is deposited in the liquid for squalene than for squalane, consistent with a more extensive geometry change on formation of the allylic radical co-product. Although the dominant reaction mechanism is direct, impulsive scattering, there is some evidence for OH being accommodated at both liquid surfaces, resulting in thermalised translation and rotational distributions. Despite the H-abstraction reaction being strongly favoured energetically for squalene, the yield of OH is substantially lower than for squalane. This is very likely due to competitive addition of O((3)P) to the unsaturated sites in squalene, implying that double bonds are extensively exposed at the liquid surface.

  13. Fluid dynamic interface between hull and hydrofoil; Sentai to suichuyoku no ryutai rikigakuteki kansho ni tsuite

    Energy Technology Data Exchange (ETDEWEB)

    Kataoka, K.; Ando, J.; Nakatake, K. [Kyushu University, Fukuoka (Japan). Faculty of Engineering

    1996-04-10

    For the high-speed ship with hydrofoil, it is important to grasp the mutual interference between its hydrofoil and hull. In this study, effects of the state of hydrofoils and velocity on the hull were fluid-dynamically investigated through the numerical calculation by means of Rankine source method using a Wigley model with two hydrofoils. Before considering the model with hydrofoils, the attitude change of a hull without hydrofoils during traveling in high-speed was examined. For the high-speed ship, various measuring systems have been conceived due to the large change in its attitude. The Wigley model has been used for the numerical calculation when considering the attitude change in the medium- and low-speed regions. In this study, resistance tests without constraining the sinkage and trim were conducted using a Wigley model in the high-speed region around Fn=1.0, which have not been usually conducted. The attitude changes were compared with the numerical calculation results by the Rankine source method. The wave making resistance and attitude change of the Wigley model with hydrofoils were also calculated. 12 refs., 10 figs.

  14. Achieving tunable surface tension in the pseudopotential lattice Boltzmann modeling of interface dynamics

    CERN Document Server

    Li, Q

    2013-01-01

    In this paper, we aim to address an important issue about the pseudopotential lattice Boltzmann (LB) model, which has attracted much attention as a mesoscopic model for simulating interfacial dynamics of complex fluids, but suffers from the problem that the surface tension cannot be tuned independently of the density ratio. In the literature, a multi-range potential was devised to adjust the surface tension [Sbragaglia et al., Phys. Rev. E, 2007, 75, 026702; Sbragaglia et al. Soft Matter, 2012, 8, 10773]. However, this approach was found to be unable to keep the density ratio unchanged when the surface tension is adjusted. An alternative approach is therefore proposed in the present work. The basic strategy is to add a new source term to the LB equation so as to tune the surface tension of the pseudopotential LB model. The proposed approach can guarantee that the adjustment of the surface tension does not affect the mechanical stability condition of the pseudopotential LB model, and thus provides a separate c...

  15. The origin, dynamics, and molecular evolution of transmissible cancers

    Directory of Open Access Journals (Sweden)

    Jones EA

    2015-09-01

    Full Text Available Elizabeth A Jones, Yuanyuan Cheng, Katherine BelovFaculty of Veterinary Science, University of Sydney, NSW, AustraliaAbstract: Three transmissible cancers are known to have emerged naturally in the wild: canine transmissible venereal tumor (CTVT; Tasmanian devil facial tumor disease (DFTD; and a recently discovered leukemia-like cancer in soft-shell clams (Mya arenaria. These cancers have all acquired the ability to pass between individuals. DFTD emerged approximately 20 years ago and has decimated the Tasmanian devil population. CTVT arose over 10,000 years ago in an ancient breed of dog. The clam cancer is believed to have evolved at least 40 years ago. In this manuscript, we review CTVT and DFTD, the two transmissible mammalian cancers, and provide an overview of the leukemia-like cancer of clams. We showcase how genetics and genomics have enhanced our understanding of the unique biology, origins, and evolutionary histories of these rare cancers.Keywords: transmissible cancer, devil facial tumor disease, DFTD, canine transmissible venereal tumor, origin, evolution

  16. Moving domain computational fluid dynamics to interface with an embryonic model of cardiac morphogenesis.

    Directory of Open Access Journals (Sweden)

    Juhyun Lee

    Full Text Available Peristaltic contraction of the embryonic heart tube produces time- and spatial-varying wall shear stress (WSS and pressure gradients (∇P across the atrioventricular (AV canal. Zebrafish (Danio rerio are a genetically tractable system to investigate cardiac morphogenesis. The use of Tg(fli1a:EGFP (y1 transgenic embryos allowed for delineation and two-dimensional reconstruction of the endocardium. This time-varying wall motion was then prescribed in a two-dimensional moving domain computational fluid dynamics (CFD model, providing new insights into spatial and temporal variations in WSS and ∇P during cardiac development. The CFD simulations were validated with particle image velocimetry (PIV across the atrioventricular (AV canal, revealing an increase in both velocities and heart rates, but a decrease in the duration of atrial systole from early to later stages. At 20-30 hours post fertilization (hpf, simulation results revealed bidirectional WSS across the AV canal in the heart tube in response to peristaltic motion of the wall. At 40-50 hpf, the tube structure undergoes cardiac looping, accompanied by a nearly 3-fold increase in WSS magnitude. At 110-120 hpf, distinct AV valve, atrium, ventricle, and bulbus arteriosus form, accompanied by incremental increases in both WSS magnitude and ∇P, but a decrease in bi-directional flow. Laminar flow develops across the AV canal at 20-30 hpf, and persists at 110-120 hpf. Reynolds numbers at the AV canal increase from 0.07±0.03 at 20-30 hpf to 0.23±0.07 at 110-120 hpf (p< 0.05, n=6, whereas Womersley numbers remain relatively unchanged from 0.11 to 0.13. Our moving domain simulations highlights hemodynamic changes in relation to cardiac morphogenesis; thereby, providing a 2-D quantitative approach to complement imaging analysis.

  17. Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics.

    Science.gov (United States)

    Skelton, A A; Wesolowski, D J; Cummings, P T

    2011-07-19

    Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.

  18. Moving domain computational fluid dynamics to interface with an embryonic model of cardiac morphogenesis.

    Science.gov (United States)

    Lee, Juhyun; Moghadam, Mahdi Esmaily; Kung, Ethan; Cao, Hung; Beebe, Tyler; Miller, Yury; Roman, Beth L; Lien, Ching-Ling; Chi, Neil C; Marsden, Alison L; Hsiai, Tzung K

    2013-01-01

    Peristaltic contraction of the embryonic heart tube produces time- and spatial-varying wall shear stress (WSS) and pressure gradients (∇P) across the atrioventricular (AV) canal. Zebrafish (Danio rerio) are a genetically tractable system to investigate cardiac morphogenesis. The use of Tg(fli1a:EGFP) (y1) transgenic embryos allowed for delineation and two-dimensional reconstruction of the endocardium. This time-varying wall motion was then prescribed in a two-dimensional moving domain computational fluid dynamics (CFD) model, providing new insights into spatial and temporal variations in WSS and ∇P during cardiac development. The CFD simulations were validated with particle image velocimetry (PIV) across the atrioventricular (AV) canal, revealing an increase in both velocities and heart rates, but a decrease in the duration of atrial systole from early to later stages. At 20-30 hours post fertilization (hpf), simulation results revealed bidirectional WSS across the AV canal in the heart tube in response to peristaltic motion of the wall. At 40-50 hpf, the tube structure undergoes cardiac looping, accompanied by a nearly 3-fold increase in WSS magnitude. At 110-120 hpf, distinct AV valve, atrium, ventricle, and bulbus arteriosus form, accompanied by incremental increases in both WSS magnitude and ∇P, but a decrease in bi-directional flow. Laminar flow develops across the AV canal at 20-30 hpf, and persists at 110-120 hpf. Reynolds numbers at the AV canal increase from 0.07±0.03 at 20-30 hpf to 0.23±0.07 at 110-120 hpf (p< 0.05, n=6), whereas Womersley numbers remain relatively unchanged from 0.11 to 0.13. Our moving domain simulations highlights hemodynamic changes in relation to cardiac morphogenesis; thereby, providing a 2-D quantitative approach to complement imaging analysis.

  19. Modelling coupled turbulence - dissolved oxygen dynamics near the sediment-water interface under wind waves and sea swell.

    Science.gov (United States)

    Chatelain, Mathieu; Guizien, Katell

    2010-03-01

    A one-dimensional vertical unsteady numerical model for diffusion-consumption of dissolved oxygen (DO) above and below the sediment-water interface was developed to investigate DO profile dynamics under wind waves and sea swell (high-frequency oscillatory flows with periods ranging from 2 to 30s). We tested a new approach to modelling DO profiles that coupled an oscillatory turbulent bottom boundary layer model with a Michaelis-Menten based consumption model. The flow regime controls both the mean value and the fluctuations of the oxygen mass transfer efficiency during a wave cycle, as expressed by the non-dimensional Sherwood number defined with the maximum shear velocity (Sh). The Sherwood number was found to be non-dependent on the sediment biogeochemical activity (mu). In the laminar regime, both cycle-averaged and variance of the Sherwood number are very low (Sh wave cycle fluctuations that increase with the wave Reynolds number (VAR(Sh) up to 30%). Our computations show that DO mass transfer efficiency under high-frequency oscillatory flows in the turbulent regime are water-side controlled by: (a) the diffusion time across the diffusive boundary layer and (b) diffusive boundary layer dynamics during a wave cycle. As a result of these two processes, when the wave period decreases, the Sh minimum increases and the Sh maximum decreases. Sh values vary little, ranging from 0.17 to 0.23. For periods up to 30s, oxygen penetration depth into the sediment did not show any intra-wave fluctuations. Values for the laminar regime are small (

  20. Freezing hot electrons. Electron transfer and solvation dynamics at D{sub 2}O and NH{sub 3}-metal interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Staehler, A.J.

    2007-05-15

    The present work investigates the electron transfer and solvation dynamics at the D{sub 2}O/Cu(111), D{sub 2}O/Ru(001), and NH{sub 3}/Cu(111) interfaces using femtosecond time-resolved two-photon photoelectron spectroscopy. Within this framework, the influence of the substrate, adsorbate structure and morphology, solvation site, coverage, temperature, and solvent on the electron dynamics are studied, yielding microscopic insight into the underlying fundamental processes. Transitions between different regimes of ET, substrate-dominated, barrier-determined, strong, and weak coupling are observed by systematic variation of the interfacial properties and development of empirical model descriptions. It is shown that the fundamental steps of the interfacial electron dynamics are similar for all investigated systems: Metal electrons are photoexcited to unoccupied metal states and transferred into the adlayer via the adsorbate's conduction band. The electrons localize at favorable sites and are stabilized by reorientations of the surrounding polar solvent molecules. Concurrently, they decay back two the metal substrate, as it offers a continuum of unoccupied states. However, the detailed characteristics vary for the different investigated interfaces: For amorphous ice-metal interfaces, the electron transfer is initially, right after photoinjection, dominated by the substrate's electronic surface band structure. With increasing solvation, a transient barrier evolves at the interface that increasingly screens the electrons from the substrate. Tunneling through this barrier becomes the rate-limiting step for ET. The competition of electron decay and solvation leads to lifetimes of the solvated electrons in the order of 100 fs. Furthermore, it is shown that the electrons bind in the bulk of the ice layers, but on the edges of adsorbed D{sub 2}O clusters and that the ice morphology strongly influences the electron dynamics. For the amorphous NH{sub 3}/Cu(111

  1. Application of biomarkers in cancer risk management: evaluation from stochastic clonal evolutionary and dynamic system optimization points of view.

    Directory of Open Access Journals (Sweden)

    Xiaohong Li

    2011-02-01

    Full Text Available Aside from primary prevention, early detection remains the most effective way to decrease mortality associated with the majority of solid cancers. Previous cancer screening models are largely based on classification of at-risk populations into three conceptually defined groups (normal, cancer without symptoms, and cancer with symptoms. Unfortunately, this approach has achieved limited successes in reducing cancer mortality. With advances in molecular biology and genomic technologies, many candidate somatic genetic and epigenetic "biomarkers" have been identified as potential predictors of cancer risk. However, none have yet been validated as robust predictors of progression to cancer or shown to reduce cancer mortality. In this Perspective, we first define the necessary and sufficient conditions for precise prediction of future cancer development and early cancer detection within a simple physical model framework. We then evaluate cancer risk prediction and early detection from a dynamic clonal evolution point of view, examining the implications of dynamic clonal evolution of biomarkers and the application of clonal evolution for cancer risk management in clinical practice. Finally, we propose a framework to guide future collaborative research between mathematical modelers and biomarker researchers to design studies to investigate and model dynamic clonal evolution. This approach will allow optimization of available resources for cancer control and intervention timing based on molecular biomarkers in predicting cancer among various risk subsets that dynamically evolve over time.

  2. Photo-modulated thin film transistor based on dynamic charge transfer within quantum-dots-InGaZnO interface

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xiang [Electronic Science and Engineering School, Southeast University, Nanjing (China); National Center for Nanoscience and Technology, Beijing (China); Yang, Xiaoxia; Liu, Mingju [National Center for Nanoscience and Technology, Beijing (China); Tao, Zhi; Wei, Lei, E-mail: lw@seu.edu.cn; Li, Chi, E-mail: lichi@seu.edu.cn; Zhang, Xiaobing; Wang, Baoping [Electronic Science and Engineering School, Southeast University, Nanjing (China); Dai, Qing, E-mail: daiq@nanoctr.cn [National Center for Nanoscience and Technology, Beijing (China); London Center for Nanotechnology, University College London, London WC1H 0AH (United Kingdom); Nathan, Arokia [Electronic Science and Engineering School, Southeast University, Nanjing (China); London Center for Nanotechnology, University College London, London WC1H 0AH (United Kingdom)

    2014-03-17

    The temporal development of next-generation photo-induced transistor across semiconductor quantum dots and Zn-related oxide thin film is reported in this paper. Through the dynamic charge transfer in the interface between these two key components, the responsibility of photocurrent can be amplified for scales of times (∼10{sup 4} A/W 450 nm) by the electron injection from excited quantum dots to InGaZnO thin film. And this photo-transistor has a broader waveband (from ultraviolet to visible light) optical sensitivity compared with other Zn-related oxide photoelectric device. Moreover, persistent photoconductivity effect can be diminished in visible waveband which lead to a significant improvement in the device's relaxation time from visible illuminated to dark state due to the ultrafast quenching of quantum dots. With other inherent properties such as integrated circuit compatible, low off-state current and high external quantum efficiency resolution, it has a great potential in the photoelectric device application, such as photodetector, phototransistor, and sensor array.

  3. Dynamics of the functional profile of the urban-rural interface of Târgovişte

    Directory of Open Access Journals (Sweden)

    Cristina Georgiana Petrea

    2013-12-01

    Full Text Available Economic restructuring of central places is a complex process, which has to take into account the emerging rural surroundings as well, in the sense that these have to assume a part of the economic activities pertaining to the secondary sector. The government policy of supporting the entrepreneurial sector, which is in force since the year 2000, has rapidly entailed desirable effects: a boost of the national business environment and a better dynamics of the small and medium-sized enterprises. In this context, we have selected, processed and analyzed the following statistical information: number of companies, number of employees, turnover and profit. This was done on spheres of activity (according to the National Classification of Economic Activities, but also at the level of Târgovişte and its first ring of settlements. By processing these primary indicators for the mentioned administrative units, we were able to compute and establish the distribution of the functional diversity index. This expresses, on the one hand, the diversity of the fields of activity and the economic profile of an area, and on the other hand, analyzed from a temporal perspective, it shows to what extent the urban-rural interface has taken over the ultra-specialized labor force of Târgovişte.

  4. Molecular dynamics simulation of the cooperative adsorption of barley lipid transfer protein and cis-isocohumulone at the vacuum-water interface.

    Science.gov (United States)

    Euston, S R; Hughes, P; Naser, Md A; Westacott, R E

    2008-11-01

    Molecular dynamic simulations have been carried out on systems containing a mixture of barley lipid transfer protein (LTP) and cis-isocohumulone (a hop derived iso-alpha-acid) in one of its enol forms, in bulk water and at the vacuum-water interface. In solution, the cis-isocohumulone molecules bind to the surface of the LTP molecule. The mechanism of binding appears to be purely hydrophobic in nature via desolvation of the protein surface. Binding of hop acids to the LTP leads to a small change in the 3-D conformation of the protein, but no change in the proportion of secondary structure present in helices, even though there is a significant degree of hop acid binding to the helical regions. At the vacuum-water interface, cis-isocohumulone shows a high surface activity and adsorbs rapidly at the interface. LTP then shows a preference to bind to the preadsorbed hop acid layer at the interface rather than to the bare water-vacuum interface. The free energy of adsorption of LTP at the hop-vacuum-water interface is more favorable than for adsorption at the vacuum-water interface. Our results support the view that hop iso-alpha-acids promote beer foam stability by forming bridges between separate adsorbed protein molecules, thus strengthening the adsorbed protein layer and reducing foam breakdown by lamellar phase drainage. The results also suggest a second mechanism may also occur, whereby the concentration of protein at the interface is increased via enhanced protein adsorption to adsorbed hop acid layers. This too would increase foam stability through its effect on the stabilizing protein layer around the foam bubbles.

  5. Interfacing with the WEB

    CERN Document Server

    Dönszelmann, M

    1995-01-01

    Interfacing to the Web or programming interfaces for the Web is used to provide dynamic information for Web users. Using the Web as a transport system of information poses three constraints: namespace, statelessness and performance. To build interfaces on either server or client side of the Web one has to meet these constraints. Several examples, currently in use in High Energy Physics Experiments are described. They range from an interface to show where buildings are located to an interface showing active values of the On-line System of the DELPHI (CERN)..

  6. Usefulness of dynamic CT in the evaluation of percutaneous microwave coagulation therapy for liver cancer

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Naoki [Tottori Univ., Yonago (Japan). Faculty of Medicine

    1999-07-01

    This paper is concerned with effects of percutaneous microwave coagulation therapy (PMCT) and evaluation of PMCT by dynamic computed tomography (CT). Between January 1996 and March 1998, 23 patients with liver cancer were selected for this study. In 5 patients in the series, the extent of heating with irradiation at 60 Watts for 60 seconds was measured. In remaining 18 patients, PMCT was repeated till the hyperechogenic areas extended the whole target area on ultrasonography (US). Dynamic CT obtained one week after PMCT was compared with histological findings of the resected specimen that had been obtained 8 days after PMCT. The temperature rose over 60degC within 7.5 mm-area from the electrode. Each area coagulated by PMCT was shown as low density one both in early and delayed phase of dynamic CT. Accurate diagnoses whether undestroyed cancerous tissue was left or not were obtained by dynamic CT in 6 of 8 patients whose tumor was incompletely destroyed, and in all of 10 patients whose tumor was completely destroyed after PMCT. PMCT as a local treatment for liver cancer was considered to be a highly effective technique, because a certain area around punctured electrode fell into necrosis without exception. And dynamic CT was revealed to be a useful method for the patients with liver cancer to evaluate the effect of PMCT. (author)

  7. Enhanced heat transfer through filler-polymer interface by surface-coupling agent in heat-dissipation material: A non-equilibrium molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, Kouichi [DENSO CORPORATION, Kariya, Aichi 448-8661 (Japan); Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Ogata, Shuji; Kobayashi, Ryo; Tamura, Tomoyuki [Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555 (Japan); Kitsunezuka, Masashi; Shinma, Atsushi [DENSO CORPORATION, Kariya, Aichi 448-8661 (Japan)

    2013-11-21

    Developing a composite material of polymers and micrometer-sized fillers with higher heat conductance is crucial to realize modular packaging of electronic components at higher densities. Enhancement mechanisms of the heat conductance of the polymer-filler interfaces by adding the surface-coupling agent in such a polymer composite material are investigated through the non-equilibrium molecular dynamics (MD) simulation. A simulation system is composed of α-alumina as the filler, bisphenol-A epoxy molecules as the polymers, and model molecules for the surface-coupling agent. The inter-atomic potential between the α-alumina and surface-coupling molecule, which is essential in the present MD simulation, is constructed to reproduce the calculated energies with the electronic density-functional theory. Through the non-equilibrium MD simulation runs, we find that the thermal resistance at the interface decreases significantly by increasing either number or lengths of the surface-coupling molecules and that the effective thermal conductivity of the system approaches to the theoretical value corresponding to zero thermal-resistance at the interface. Detailed analyses about the atomic configurations and local temperatures around the interface are performed to identify heat-transfer routes through the interface.

  8. Comparing an ionic liquid to a molecular solvent in the cesium cation extraction by a calixarene: a molecular dynamics study of the aqueous interfaces.

    Science.gov (United States)

    Sieffert, Nicolas; Wipff, Georges

    2006-10-01

    We report a molecular dynamics (MD) study of the interfacial behavior of key partners involved in the Cs(+) cation extraction by a calix[4]arene-crown-6 host (L), comparing an ionic liquid (IL) to a classical molecular solvent (chloroform) as receiving "oil" phase. The IL is composed of hydrophobic 1-butyl-3-methylimidazolium cations (BMI(+)) and bis(trifluoromethylsulfonyl)imide anions (Tf(2)N(-)) and forms a biphasic system with water. The simulations reveal similarities but also interesting differences between the two types of interfaces. Much longer times are needed to "equilibrate" IL systems, compared to classical liquid mixtures, and there is more intersolvent mixing with the IL than with chloroform, especially concerning the water-in-oil content. There is also some excess of the BMI(+) cations over the Tf(2)N(-) anions in the aqueous phase. Simulations on the Na(+)NO(3)(-) and Cs(+)NO(3)(-) ions show that they sometimes interact at the interface with the IL ions, forming hydrated intimate ion pairs, whereas they are "repelled" by the classical interface. The LCs(+) complex and L ligand also behave differently, depending on the "oil phase". They are better solvated by the IL than by chloroform and thus poorly attracted at the IL interface, whereas they adsorb at the chloroform interface, adopting well-defined amphiphilic orientations. The results are discussed in the context of assisted ion transfer and provide a number of arguments explaining the specificity and efficiency of IL based, compared to classical extraction systems.

  9. Molecular Dynamics Simulation of Atomic Force Microscopy at the Water-Muscovite Interface: Hydration Layer Structure and Force Analysis.

    Science.gov (United States)

    Kobayashi, Kazuya; Liang, Yunfeng; Amano, Ken-ichi; Murata, Sumihiko; Matsuoka, Toshifumi; Takahashi, Satoru; Nishi, Naoya; Sakka, Tetsuo

    2016-04-19

    With the development of atomic force microscopy (AFM), it is now possible to detect the buried liquid-solid interfacial structure in three dimensions at the atomic scale. One of the model surfaces used for AFM is the muscovite surface because it is atomically flat after cleavage along the basal plane. Although it is considered that force profiles obtained by AFM reflect the interfacial structures (e.g., muscovite surface and water structure), the force profiles are not straightforward because of the lack of a quantitative relationship between the force and the interfacial structure. In the present study, molecular dynamics simulations were performed to investigate the relationship between the muscovite-water interfacial structure and the measured AFM force using a capped carbon nanotube (CNT) AFM tip. We provide divided force profiles, where the force contributions from each water layer at the interface are shown. They reveal that the first hydration layer is dominant in the total force from water even after destruction of the layer. Moreover, the lateral structure of the first hydration layer transcribes the muscovite surface structure. It resembles the experimentally resolved surface structure of muscovite in previous AFM studies. The local density profile of water between the tip and the surface provides further insight into the relationship between the water structure and the detected force structure. The detected force structure reflects the basic features of the atomic structure for the local hydration layers. However, details including the peak-peak distance in the force profile (force-distance curve) differ from those in the density profile (density-distance curve) because of disturbance by the tip.

  10. Conformational dynamics is key to understanding loss-of-function of NQO1 cancer-associated polymorphisms and its correction by pharmacological ligands

    Science.gov (United States)

    Encarnación, Medina-Carmona; Palomino-Morales, Rogelio J.; Fuchs, Julian E.; Esperanza, Padín-Gonzalez; Noel, Mesa-Torres; Salido, Eduardo; Timson, David J.; Pey, Angel L.

    2016-02-01

    Protein dynamics is essential to understand protein function and stability, even though is rarely investigated as the origin of loss-of-function due to genetic variations. Here, we use biochemical, biophysical, cell and computational biology tools to study two loss-of-function and cancer-associated polymorphisms (p.R139W and p.P187S) in human NAD(P)H quinone oxidoreductase 1 (NQO1), a FAD-dependent enzyme which activates cancer pro-drugs and stabilizes several oncosuppressors. We show that p.P187S strongly destabilizes the NQO1 dimer in vitro and increases the flexibility of the C-terminal domain, while a combination of FAD and the inhibitor dicoumarol overcome these alterations. Additionally, changes in global stability due to polymorphisms and ligand binding are linked to the dynamics of the dimer interface, whereas the low activity and affinity for FAD in p.P187S is caused by increased fluctuations at the FAD binding site. Importantly, NQO1 steady-state protein levels in cell cultures correlate primarily with the dynamics of the C-terminal domain, supporting a directional preference in NQO1 proteasomal degradation and the use of ligands binding to this domain to stabilize p.P187S in vivo. In conclusion, protein dynamics are fundamental to understanding loss-of-function in p.P187S, and to develop new pharmacological therapies to rescue this function.

  11. A molecular dynamics simulation of the structure of ionic liquid (BMIM+/PF6-)/rutile (110) interface

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The interfacial structure between the room-temperature ionic liquid, 1-butyl-3-methyl-imidazolium hexafluorophosphate (BMIM+/PF6-) and rutile (110) surface is simulated by classical molecular dynam-ics simulation, aiming to model a crucial constituent of the electrolyte/semiconductor interface. The simulation results show several enhanced layers forming in the interfacial region, especially for the anions. A well ordered double layering structure of the ions is also observed in the interfacial region. The cations are found to organize themselves in a parallel alignment with respect to the TiO2 slab, with an obvious elongation of the side chains.

  12. Suicide Gene-Engineered Stromal Cells Reveal a Dynamic Regulation of Cancer Metastasis

    Science.gov (United States)

    Shen, Keyue; Luk, Samantha; Elman, Jessica; Murray, Ryan; Mukundan, Shilpaa; Parekkadan, Biju

    2016-02-01

    Cancer-associated fibroblasts (CAFs) are a major cancer-promoting component in the tumor microenvironment (TME). The dynamic role of human CAFs in cancer progression has been ill-defined because human CAFs lack a unique marker needed for a cell-specific, promoter-driven knockout model. Here, we developed an engineered human CAF cell line with an inducible suicide gene to enable selective in vivo elimination of human CAFs at different stages of xenograft tumor development, effectively circumventing the challenge of targeting a cell-specific marker. Suicide-engineered CAFs were highly sensitive to apoptosis induction in vitro and in vivo by the addition of a simple small molecule inducer. Selection of timepoints for targeted CAF apoptosis in vivo during the progression of a human breast cancer xenograft model was guided by a bi-phasic host cytokine response that peaked at early timepoints after tumor implantation. Remarkably, we observed that the selective apoptosis of CAFs at these early timepoints did not affect primary tumor growth, but instead increased the presence of tumor-associated macrophages and the metastatic spread of breast cancer cells to the lung and bone. The study revealed a dynamic relationship between CAFs and cancer metastasis that has counter-intuitive ramifications for CAF-targeted therapy.

  13. Dynamics and forecast of morbidity and mortality from prostate cancer in St. Petersburg

    Directory of Open Access Journals (Sweden)

    N. G. Petrova

    2015-01-01

    Full Text Available The paper presents the characteristics of primary disease incidence, prevalence and mortality from prostate cancer among men's population of St. Petersburg (normal and age-standardized rates; analyzed their dynamics for 20 years; shows the calculated trend of these indicators up to 2020.

  14. Integrated Multimodal Imaging of Dynamic Bone-Tumor Alterations Associated with Metastatic Prostate Cancer

    NARCIS (Netherlands)

    Brisset, Jean-Christophe; Hoff, Benjamin A.; Chenevert, Thomas L.; Jacobson, Jon A.; Boes, Jennifer L.; Galban, Stefanie; Rehemtulla, Alnawaz; Johnson, Timothy D.; Pienta, Kenneth J.; Galban, Craig J.; Meyer, Charles R.; Schakel, Timothy; Nicolay, Klaas; Alva, Ajjai S.; Hussain, Maha; Ross, Brian D.; Schakel, Tim

    2015-01-01

    Bone metastasis occurs for men with advanced prostate cancer which promotes osseous growth and destruction driven by alterations in osteoblast and osteoclast homeostasis. Patients can experience pain, spontaneous fractures and morbidity eroding overall quality of life. The complex and dynamic cellul

  15. LncRNA HOTAIR: a master regulator of chromatin dynamics and cancer

    Science.gov (United States)

    Bhan, Arunoday; Mandal, Subhrangsu S.

    2015-01-01

    Non-coding RNAs (ncRNAs) are emerging classes of regulatory RNA that play key roles in various cellular and physiological processes such as in gene regulation, chromatin dynamics, cell differentiation, development etc. NcRNAs are dysregulated in a variety of human disorders including cancers, neurological disorders, and immunological disorders. The mechanisms through which ncRNAs regulate various biological processes and human diseases still remain elusive. HOX antisense intergenic RNA (HOTAIR) is a recently discovered long non-coding RNA (lncRNA) that plays critical role in gene regulation and chromatin dynamics, appears to be misregulated in a variety of cancers. HOTAIR interacts with key epigenetic regulators such as histone methyltransferase PRC2 and histone demethylase LSD1 and regulates gene silencing. Here, we have reviewed recent advancements in understanding the functions and regulation of HOTAIR and its association with cancer and other diseases. PMID:26208723

  16. The role of telomere dynamics in aging and cancer

    Science.gov (United States)

    Blagoev, Krastan; Goodwin, Edwin

    2006-03-01

    Telomere length changes are far more dynamic than previously thought. In addition to a gradual loss of ˜100 base pairs per telomere in each cell division, losses as well as gains may occur within a single cell cycle. We are investigating how telomere exchange, extension, and deletion affect the proliferative potential of telomerase-negative somatic cells. Experimental techniques are being devised to detect dynamic telomere processes and quantify both the frequency and length changes of each. In parallel, a ``dynamic telomere model'' is being used that incorporates telomere dynamics to study how the telomere size distribution evolves with time. This is an essential step towards understanding the role that telomere dynamics play in the normal aging of tissues and organisms. The model casts light on relationships not otherwise easily explained by a deterministic ``mitotic clock,'' or to what extent the shortest initial telomere determines the onset of senescence. We also expect to identify biomarkers that will correlate with aging better than average telomere length and to shed light on the transition to unlimited growth found in telomerase-negative tumor cells having the ALT (alternative lengthening of telomeres) phenotype, and to evaluate strategies to suppress the growth of these tumors.

  17. The [BMI][Tf2N] ionic liquid/water binary system: a molecular dynamics study of phase separation and of the liquid-liquid interface.

    Science.gov (United States)

    Sieffert, N; Wipff, G

    2006-07-01

    We report molecular dynamics (MD) simulations of the aqueous interface of the hydrophobic [BMI][Tf2N] ionic liquid (IL), composed of 1-butyl-3-methylimidazolium cations (BMI+) and bis(trifluoromethylsulfonyl)imide anions (Tf2N-). The questions of water/IL phase separation and properties of the neat interface are addressed, comparing different liquid models (TIP3P vs TIP5P water and +1.0/-1.0 vs +0.9/-0.9 charged IL ions), the Ewald vs the reaction field treatments of the long range electrostatics, and different starting conditions. With the different models, the "randomly" mixed liquids separate much more slowly (in 20 to 40 ns) than classical water-oil mixtures do (typically, in less than 1 ns), finally leading to distinct nanoscopic phases separated by an interface, as in simulations which started with a preformed interface, but the IL phase is more humid. The final state of water in the IL thus depends on the protocol and relates to IL heterogeneities and viscosity. Water mainly fluctuates in hydrophilic basins (rich in O(Tf2N) and aromatic CH(BMI) groups), separated by more hydrophobic domains (rich in CF3(Tf2N) and alkyl(BMI) groups), in the form of monomers and dimers in the weakly humid IL phase, and as higher aggregates when the IL phase is more humid. There is more water in the IL than IL in water, to different extents, depending on the model. The interface is sharper and narrower (approximately 10 A) than with the less hydrophobic [BMI][PF6] IL and is overall neutral, with isotropically oriented molecules, as in the bulk phases. The results allow us to better understand the analogies and differences of aqueous interfaces with hydrophobic (but hygroscopic) ILs, compared to classical organic liquids.

  18. Hierarchic Theory of Condensed Matter Role of water in protein dynamics, function and cancer emergency

    CERN Document Server

    Kaivarainen, A

    2000-01-01

    1. Role of inter-domain water clusters in large-scale dynamics of proteins; 2. Description of large-scale dynamics of proteins based on generalized Stokes-Einstein and Eyring-Polany equation; 3. Dynamic model of protein-ligand complexes formation; 4. The life-time of quasiparticles and frequencies of their excitation; 5. Mesoscopic mechanism of enzyme catalysis; 6. The mechanism of ATP hydrolysis energy utilization in muscle contraction and protein polymerization; 7. Water activity as a regulative factor in the intra- and inter-cell processes; 8. Water and cancer.

  19. In-situ Study of Dynamic Phenomena at Metal Nanosolder Interfaces Using Aberration Corrected Scanning Transmission Electron Microcopy.

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Ping

    2014-10-01

    Controlling metallic nanoparticle (NP) interactions plays a vital role in the development of new joining techniques (nanosolder) that bond at lower processing temperatures but remain viable at higher temperatures. The pr imary objective of this project is t o develop a fundamental understanding of the actual reaction processes, associated atomic mechanisms, and the resulting microstructure that occur during thermally - driven bond formation concerning metal - metal nano - scale (%3C50nm) interfaces. In this LDRD pr oject, we have studied metallic NPs interaction at the elevated temperatures by combining in - situ transmission electron microscopy (TEM ) using an aberration - corrected scanning transmission electron microscope (AC - STEM) and atomic - scale modeling such as m olecular dynamic (MD) simulations. Various metallic NPs such as Ag, Cu and Au are synthesized by chemical routines. Numerous in - situ e xperiments were carried out with focus of the research on study of Ag - Cu system. For the first time, using in - situ STEM he ating experiments , we directly observed t he formation of a 3 - dimensional (3 - D) epitaxial Cu - Ag core - shell nanoparticle during the thermal interaction of Cu and Ag NPs at elevated temperatures (150 - 300 o C). The reaction takes place at temperatures as low as 150 o C and was only observed when care was taken to circumvent the effects of electron beam irradiation during STEM imaging. Atomic - scale modeling verified that the Cu - Ag core - shell structure is energetically favored, and indicated that this phenomenon is a nano - scale effect related to the large surface - to - volume ratio of the NPs. The observation potentially can be used for developing new nanosolder technology that uses Ag shell as the "glue" that stic ks the particles of Cu together. The LDRD has led to several journal publications and numerous conference presentations, and a TA. In addition, we have developed new TEM characterization techniques and phase

  20. Molecular dynamics simulation of the electrochemical interface between a graphite surface and the ionic liquid [BMIM][PF6].

    Science.gov (United States)

    Kislenko, Sergey A; Samoylov, Igor S; Amirov, Ravil H

    2009-07-21

    The structure of the electrical double layer in the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) near a basal plane of graphite was investigated by molecular dynamics simulation. The calculations were performed both for an uncharged graphite surface and for positively and negatively charged ones. It is found that near an uncharged surface the ionic liquid structure differs from its bulk structure and represents a well-ordered region, extending over approximately 20 A from the surface. Three dense layers of ca 5 A thick are clearly observed at the interface, composed of negative ions and positively charged rings. It is established that in the first adsorption layer the imidazolium ring in the [BMIM]+ cation tends to be arranged in parallel to the graphite surface at a distance of 3.5 A. The [PF6]- anion is oriented in such a way that the phosphorus atom is at a distance of 4.1 A from the surface and triplets of fluorine atoms form two planes parallel to the graphite surface. Ions adsorbed at the uncharged surface are arranged in a highly defective 2D hexagonal lattice and the corresponding lattice spacing is approximately four times larger than that of the graphene substrate. The influence of the electrode potential on the distribution of electrolyte ions and their orientation has also been investigated. Increase in the electrode potential induces broadening of the angle distribution of adsorbed rings and a shift of the most probable tilt angle towards bigger values. It was shown that there are no adsorbed anions on the negatively charged surface (sigma = -8.2 microC cm(-2)), but the surface concentration of adsorbed cations on the positively charged surface (sigma = +8.2 microC cm(-2)) has a nonzero value. In addition, the influence of the surface charge (+/- sigma) on the volume charge density and electric potential profiles in an electrolyte was studied. The differences in the cation and anion structure result in the fact that the

  1. Optimizing event-related potential based brain-computer interfaces: a systematic evaluation of dynamic stopping methods

    Science.gov (United States)

    Schreuder, Martijn; Höhne, Johannes; Blankertz, Benjamin; Haufe, Stefan; Dickhaus, Thorsten; Tangermann, Michael

    2013-06-01

    Objective. In brain-computer interface (BCI) research, systems based on event-related potentials (ERP) are considered particularly successful and robust. This stems in part from the repeated stimulation which counteracts the low signal-to-noise ratio in electroencephalograms. Repeated stimulation leads to an optimization problem, as more repetitions also cost more time. The optimal number of repetitions thus represents a data-dependent trade-off between the stimulation time and the obtained accuracy. Several methods for dealing with this have been proposed as ‘early stopping’, ‘dynamic stopping’ or ‘adaptive stimulation’. Despite their high potential for BCI systems at the patient's bedside, those methods are typically ignored in current BCI literature. The goal of the current study is to assess the benefit of these methods. Approach. This study assesses for the first time the existing methods on a common benchmark of both artificially generated data and real BCI data of 83 BCI sessions, allowing for a direct comparison between these methods in the context of text entry. Main results. The results clearly show the beneficial effect on the online performance of a BCI system, if the trade-off between the number of stimulus repetitions and accuracy is optimized. All assessed methods work very well for data of good subjects, and worse for data of low-performing subjects. Most methods, however, are robust in the sense that they do not reduce the performance below the baseline of a simple no stopping strategy. Significance. Since all methods can be realized as a module between the BCI and an application, minimal changes are needed to include these methods into existing BCI software architectures. Furthermore, the hyperparameters of most methods depend to a large extend on only a single variable—the discriminability of the training data. For the convenience of BCI practitioners, the present study proposes linear regression coefficients for directly estimating

  2. Molecular dynamics analysis of multiphase interfaces based on in situ extraction of the pressure distribution of a liquid droplet on a solid surface.

    Science.gov (United States)

    Nishida, S; Surblys, D; Yamaguchi, Y; Kuroda, K; Kagawa, M; Nakajima, T; Fujimura, H

    2014-02-21

    Molecular dynamics simulations of a nanoscale liquid droplet on a solid surface are carried out in order to examine the pressure tensor field around the multiphase interfaces, and to explore the validity of Young's equation. By applying the virial theorem to a hemicylindrical droplet consisting of argon molecules on a solid surface, two-dimensional distribution of the pressure tensor is obtained. Tensile principal pressure tangential to the interface is observed around the liquid-vapor transition layer, while both tensile and compressive principal pressure tangential to the interface exists around the solid-liquid transition layer due to the inhomogeneous density distribution. The two features intermix inside the overlap region between the transition layers at the contact line. The contact angle is evaluated by using a contour line of the maximum principal pressure difference. The interfacial tensions are calculated by using Bakker's equation and Young-Laplace equation to the pressure tensor distribution. The relation between measured contact angle and calculated interfacial tensions turns out to be consistent with Young's equation, which is known as the description of the force balance at the three-phase interface.

  3. Temperature-dependent phase transition and desorption free energy of sodium dodecyl sulfate at the water/vapor interface: approaches from molecular dynamics simulations.

    Science.gov (United States)

    Chen, Meng; Lu, Xiancai; Liu, Xiandong; Hou, Qingfeng; Zhu, Youyi; Zhou, Huiqun

    2014-09-09

    Adsorption of surfactants at the water/vapor interface depends upon their chemical potential at the interface, which is generally temperature-dependent. Molecular dynamics simulations have been performed to reveal temperature influences on the microstructure of sodium dodecyl sulfate (SDS) molecule adsorption layer. At room temperature, SDS molecules aggregate at the interface, being in a liquid-expanded phase, whereas they tend to spread out and probably transit to a gaseous phase as the temperature increases to above 318 K. This phase transition has been confirmed by the temperature-dependent changes in two-dimensional array, tilt angles, and immersion depths to the aqueous phase of SDS molecules. The aggregation of SDS molecules accompanies with larger immersion depths, more coordination of Na(+) ions, and less coordination of water. Desorption free energy profiles show that higher desorption free energy appears for SDS molecules at the aggregate state at low temperatures, but no energy barrier is observed. The shapes of desorption free energy profiles depend upon the distribution of SDS at the interface, which, in turn, is related to the phase state of SDS. Our study sheds light on the development of adsorption thermodynamics and kinetics theories.

  4. Dynamics of microalgal communities in the water-column/sediment interface of the inner shelf off Parana State, Southern Brazil

    Directory of Open Access Journals (Sweden)

    Ricardo Luiz Queiroz

    2004-12-01

    Full Text Available The composition and biomass of the microalgal community at the water-column/sediment interface on the continental shelf off Parana State (Brazil were studied every 2 months during 1999. Samples for cell identification and determination of chlorophyll a were taken from the interface layer and at discrete depths up to 4 m above the sediment. Results showed a community mainly formed by benthic and planktonic diatoms >30 µm, benthic diatoms 30 µm, which accounted for most of the pigment biomass, were resuspended from the interface after turbulent periods, and may take advantage of calm periods to stay and grow at the interface. Small benthic diatoms were more susceptible to wind-induced turbulence occurring in higher densities in the water column just above the water-sediment interface. A cyanobacterial bloom (Trichodesmiun was observed at these bottom layers in the spring-summer periods.A composição geral e a biomassa da comunidade microalgal da interface sedimento/água da plataforma do Estado do Paraná (Brasil foram estudadas em 1999 em relação ao regime de ventos. A cada dois meses foram coletadas amostras para a identificação de organismos e determinação de clorofila a, na interface água-sedimento e em profundidades discretas, ao longo da coluna d'água, até 4m acima do sedimento. Os resultados obtidos revelaram uma comunidade constituída principalmente por diatomáceas planctônicas e bentônicas maiores que 30 µm, diatomáceas bentônicas menores que 30 µm, e cianobactérias coloniais. As densidades celulares foram geralmente mais altas na interface. Eventos de mistura e sedimentação parecem ser determinantes na regulação da composição e biomassa de tais comunidades. Formas menores, mais susceptíveis à turbulência, dominaram a comunidade de água de fundo na maioria das ocasiões, e foram as mais abundantes na interface apenas em períodos de extrema estabilidade. Células maiores, aparentemente contendo a maior parte

  5. First-principles molecular dynamics simulations of NH4(+) and CH3COO(-) adsorption at the aqueous quartz interface.

    Science.gov (United States)

    Wright, Louise B; Walsh, Tiffany R

    2012-12-14

    The ability to exert molecular-level control at the aqueous interface between biomolecules and inorganic substrates is pivotal to advancing applications ranging from sustainable manufacturing to targeted therapeutics. Progress is hindered by a lack of structural information of these interfaces with atomic resolution. Molecular simulation is one approach to obtain such data, but can be limited by the reliability of the force-field used. First-principles simulations, in principle, can provide insights into such aqueous interfaces, but are resource-intensive, limiting previous first-principles studies to approximate the environment of liquid water. Here, we use Car-Parrinello simulations to investigate adsorption of two charged adsorbates that are functional groups common to all amino-acids--ethanoate and ammonium--at the interface between hydroxylated quartz and liquid water, directly incorporating full solvation effects at the interface. Our findings reveal the stable character of carboxylate-quartz binding, as well as the surprisingly indifferent nature of ammonium-quartz interactions, in liquid water.

  6. Dynamic modulation of thymidylate synthase gene expression and fluorouracil sensitivity in human colorectal cancer cells.

    Directory of Open Access Journals (Sweden)

    Kentaro Wakasa

    Full Text Available Biomarkers have revolutionized cancer chemotherapy. However, many biomarker candidates are still in debate. In addition to clinical studies, a priori experimental approaches are needed. Thymidylate synthase (TS expression is a long-standing candidate as a biomarker for 5-fluorouracil (5-FU treatment of cancer patients. Using the Tet-OFF system and a human colorectal cancer cell line, DLD-1, we first constructed an in vitro system in which TS expression is dynamically controllable. Quantitative assays have elucidated that TS expression in the transformant was widely modulated, and that the dynamic range covered 15-fold of the basal level. 5-FU sensitivity of the transformant cells significantly increased in response to downregulated TS expression, although being not examined in the full dynamic range because of the doxycycline toxicity. Intriguingly, our in vitro data suggest that there is a linear relationship between TS expression and the 5-FU sensitivity in cells. Data obtained in a mouse model using transformant xenografts were highly parallel to those obtained in vitro. Thus, our in vitro and in vivo observations suggest that TS expression is a determinant of 5-FU sensitivity in cells, at least in this specific genetic background, and, therefore, support the possibility of TS expression as a biomarker for 5-FU-based cancer chemotherapy.

  7. Aggregation behaviors of PEO-PPO-ph-PPO-PEO and PPO-PEO-ph-PEO-PPO at an air/water interface: experimental study and molecular dynamics simulation.

    Science.gov (United States)

    Gong, Houjian; Xu, Guiying; Liu, Teng; Xu, Long; Zhai, Xueru; Zhang, Jian; Lv, Xin

    2012-09-25

    The block polyethers PEO-PPO-ph-PPO-PEO (BPE) and PPO-PEO-ph-PEO-PPO (BEP) are synthesized by anionic polymerization using bisphenol A as initiator. Compared with Pluronic P123, the aggregation behaviors of BPE and BEP at an air/water interface are investigated by the surface tension and dilational viscoelasticity. The molecular construction can influence the efficiency and effectiveness of block polyethers in decreasing surface tension. BPE has the most efficient ability to decrease surface tension of water among the three block polyethers. The maximum surface excess concentration (Γ(max)) of BPE is larger than that of BEP or P123. Moreover, the dilational modulus of BPE is almost the same as that of P123, but much larger than that of BEP. The molecular dynamics simulation provides the conformational variations of block polyethers at the air/water interface.

  8. Kinetic Interface

    DEFF Research Database (Denmark)

    2009-01-01

    A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises.......A kinetic interface for orientation detection in a video training system is disclosed. The interface includes a balance platform instrumented with inertial motion sensors. The interface engages a participant's sense of balance in training exercises....

  9. Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution

    Science.gov (United States)

    Eirew, Peter; Steif, Adi; Khattra, Jaswinder; Ha, Gavin; Yap, Damian; Farahani, Hossein; Gelmon, Karen; Chia, Stephen; Mar, Colin; Wan, Adrian; Laks, Emma; Biele, Justina; Shumansky, Karey; Rosner, Jamie; McPherson, Andrew; Nielsen, Cydney; Roth, Andrew J. L.; Lefebvre, Calvin; Bashashati, Ali; de Souza, Camila; Siu, Celia; Aniba, Radhouane; Brimhall, Jazmine; Oloumi, Arusha; Osako, Tomo; Bruna, Alejandra; Sandoval, Jose; Algara, Teresa; Greenwood, Wendy; Leung, Kaston; Cheng, Hongwei; Xue, Hui; Wang, Yuzhuo; Lin, Dong; Mungall, Andrew J.; Moore, Richard; Zhao, Yongjun; Lorette, Julie; Nguyen, Long; Huntsman, David; Eaves, Connie J.; Hansen, Carl; Marra, Marco A.; Caldas, Carlos; Shah, Sohrab P.; Aparicio, Samuel

    2016-01-01

    Human cancers, including breast cancers, are comprised of clones differing in mutation content. Clones evolve dynamically in space and time following principles of Darwinian evolution1,2, underpinning important emergent features such as drug resistance and metastasis3–7. Human breast cancer xenoengraftment is used as a means of capturing and studying tumour biology, and breast tumour xenografts are generally assumed to be reasonable models of the originating tumours8–10. However the consequences and reproducibility of engraftment and propagation on the genomic clonal architecture of tumours has not been systematically examined at single cell resolution. Here we show by both deep genome and single cell sequencing methods, the clonal dynamics of initial engraftment and subsequent serial propagation of primary and metastatic human breast cancers in immunodeficient mice. In all 15 cases examined, clonal selection on engraftment was observed in both primary and metastatic breast tumours, varying in degree from extreme selective engraftment of minor (<5% of starting population) clones to moderate, polyclonal engraftment. Furthermore, ongoing clonal dynamics during serial passaging is a feature of tumours experiencing modest initial selection. Through single cell sequencing, we show that major mutation clusters estimated from tumour population sequencing relate predictably to the most abundant clonal genotypes, even in clonally complex and rapidly evolving cases. Finally, we show that similar clonal expansion patterns can emerge in independent grafts of the same starting tumour population, indicating that genomic aberrations can be reproducible determinants of evolutionary trajectories. Our results show that measurement of genomically defined clonal population dynamics will be highly informative for functional studies utilizing patient-derived breast cancer xenoengraftment. PMID:25470049

  10. Dynamics of the Innermost Accretion Flows Around Compact Objects: Magnetosphere-Disc Interface, Global Oscillations and Instabilities

    CERN Document Server

    Fu, Wen

    2012-01-01

    We study global non-axisymmetric oscillation modes and instabilities in magnetosphere- disc systems, as expected in neutron star X-ray binaries and possibly also in accreting black hole systems. Our two-dimensional magnetosphere-disc model consists of a Keplerian disc in contact with an uniformly rotating magnetosphere with low plasma density. Two types of global overstable modes exist in such systems, the interface modes and the disc inertial-acoustic modes. We examine various physical effects and parameters that influence the properties of these oscillation modes, particularly their growth rates, including the magnetosphere field configuration, the velocity and density contrasts across the magnetosphere-disc interface, the rotation profile (with Newtonian or General Relativistic potential), the sound speed and magnetic field of the disc. The interface modes are driven unstable by Rayleigh-Taylor and Kelvin-Helmholtz in- stabilities, but can be stabilized by the toroidal field (through magnetic tension) and ...

  11. The overshoot and phenotypic equilibrium in characterizing cancer dynamics of reversible phenotypic plasticity.

    Science.gov (United States)

    Chen, Xiufang; Wang, Yue; Feng, Tianquan; Yi, Ming; Zhang, Xingan; Zhou, Da

    2016-02-07

    The paradigm of phenotypic plasticity indicates reversible relations of different cancer cell phenotypes, which extends the cellular hierarchy proposed by the classical cancer stem cell (CSC) theory. Since it is still questionable if the phenotypic plasticity is a crucial improvement to the hierarchical model or just a minor extension to it, it is worthwhile to explore the dynamic behavior characterizing the reversible phenotypic plasticity. In this study we compare the hierarchical model and the reversible model in predicting the cell-state dynamics observed in biological experiments. Our results show that the hierarchical model shows significant disadvantages over the reversible model in describing both long-term stability (phenotypic equilibrium) and short-term transient dynamics (overshoot) in cancer cell populations. In a very specific case in which the total growth of population due to each cell type is identical, the hierarchical model predicts neither phenotypic equilibrium nor overshoot, whereas the reversible model succeeds in predicting both of them. Even though the performance of the hierarchical model can be improved by relaxing the specific assumption, its prediction to the phenotypic equilibrium strongly depends on a precondition that may be unrealistic in biological experiments. Moreover, it still does not show as rich dynamics as the reversible model in capturing the overshoots of both CSCs and non-CSCs. By comparison, it is more likely for the reversible model to correctly predict the stability of the phenotypic mixture and various types of overshoot behavior.

  12. Diagnositc value of 3D-gradient echo dynamic contrast enhanced MRI in breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Ik; Chung, Soo Young; Park, Hai Jung; Lee, Yul; Chung, Bong Wha; Shim, Jeong Won [Hallym Univ. College of Medicine, Seoul (Korea, Republic of)

    1997-10-01

    To assess the usefulness of 3D-gradient echo dynamic contrast enhanced MRI (3D-DMRI) in the diagnosis of breast cancer and to determine the most useful parameter for this diagnosis. Using a 1.0T MR unit, (Magnetom, Siemens, Erlaugen, Germany), 3D-DMRI (TR/TE=3D30/12) with Gd-DTPA was performed in 38 cases of breast cancer, 22 of fibroadenoma, and in three normal volunteers. We retrospectively evaluated the findings according to the speed on dynamic study and maximal amount of contrast enhancement during the delayed phase;we calculated the contrast index and morphology of the cancers and compared diagnostic accuracy among these three diagnostic parameters. On conventional spin-echo T1-and T2-weighted images, there was no significant difference of signal intensity between benign fibroadenoma and breast carcinoma. Rapid contrast enhancement (within one minute) was noted in 35 breast cancer lesions (92.1%), but relatively low and slow contrast enhancement (after five minutes) was noted in three such lesions (7.9%). Gradual contrast enhancement was noted in 21 lesions of fibroadenoma(95.5%), but a moderate degree of rapid contrast enhancement (from three to five minutes) was noted in the other case (7.9%). of On the delayed enhanced phase of 3D-DMRI, the maximal amount of contrast enhancement showed no significant difference between fibroadenoma and cancer. On 3D-DMRI, an irregular, spiculated border, with high contrast enhancement was noted in all cases of breast cancer, in particular, irregular thick peripheral contrast enhancement with central necrosis was noted 11cases(28.9%). For the diagnosis of breast cancer, 3D-DMRI is a useful technique. Among the diagnostic criteria of speed, maximal amount of contrast enhancement and morphology, morphologic change after contrast enhancement study was the most useful diagnostic parameter.=20.

  13. Telomere dynamics and homeostasis in a transmissible cancer.

    Directory of Open Access Journals (Sweden)

    Beata Ujvari

    Full Text Available BACKGROUND: Devil Facial Tumour Disease (DFTD is a unique clonal cancer that threatens the world's largest carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii with extinction. This transmissible cancer is passed between individual devils by cell implantation during social interactions. The tumour arose in a Schwann cell of a single devil over 15 years ago and since then has expanded clonally, without showing signs of replicative senescence; in stark contrast to a somatic cell that displays a finite capacity for replication, known as the "Hayflick limit". METHODOLOGY/PRINCIPAL FINDINGS: In the present study we investigate the role of telomere length, measured as Telomere Copy Number (TCN, and telomerase and shelterin gene expression, as well as telomerase activity in maintaining hyperproliferation of Devil Facial Tumour (DFT cells. Our results show that DFT cells have short telomeres. DFTD TCN does not differ between geographic regions or between strains. However, TCN has increased over time. Unlimited cell proliferation is likely to have been achieved through the observed up-regulation of the catalytic subunit of telomerase (TERT and concomitant activation of telomerase. Up-regulation of the central component of shelterin, the TRF1-intercating nuclear factor 2 (TINF2 provides DFT a mechanism for telomere length homeostasis. The higher expression of both TERT and TINF2 may also protect DFT cells from genomic instability and enhance tumour proliferation. CONCLUSIONS/SIGNIFICANCE: DFT cells appear to monitor and regulate the length of individual telomeres: i.e. shorter telomeres are elongated by up-regulation of telomerase-related genes; longer telomeres are protected from further elongation by members of the shelterin complex, which may explain the lack of spatial and strain variation in DFT telomere copy number. The observed longitudinal increase in gene expression in DFT tissue samples and telomerase activity in DFT cell lines might

  14. Dynamic Interactions between a Silica Sphere and Deformable Interfaces in Organic Solvents Studied by Atomic Force Microscopy.

    Science.gov (United States)

    Kuznicki, Natalie P; Harbottle, David; Masliyah, Jacob; Xu, Zhenghe

    2016-09-27

    Recent studies have successfully measured surface forces using atomic force microscope (AFM) and modeled surface deformations using the Stokes-Reynolds-Young-Laplace (SRYL) equations for particle-droplet, particle-bubble, droplet-droplet, and bubble-bubble systems in various solutions. The current work focuses on interactions between spherical silica particles and a viscoelastic interface of water droplets in crude oil. The self-assembly of surface active natural polyaromatic molecules (NPAMs) at the oil-water interface has previously been shown to change a viscous dominant oil-water interface to an elastic dominant interface upon aging, due to gradual formation of rigid interfacial networks. AFM was used to measure the interactions between a small silica sphere (D ≈ 8 μm) and a deformable water droplet (D ≈ 70 μm), which exhibits time-dependent interfacial viscoelasticity in NPAM solutions. Unlike the systems studied previously, the measured deformation shown as a repulsive force over the region of constant compliance could not be modeled adequately by the conventional SRYL equations which are applicable only to purely Laplacian interfaces. As the water droplet ages in NPAM solutions, a rigid "skin" forms at the oil-water interface, with the interface exhibiting increased elasticity. Over a short aging period (up to 15 min in NPAM-in-toluene solution), interfacial deformation is well predicted by the SRYL model. However, upon further exposure to the NPAM solution, droplet deformation is overpredicted by the model. Physical properties of this mechanical barrier as a function of interfacial aging were further investigated by measuring interfacial tension, dilatational rheology, and interfacial "crumpling" (non-smooth, non-Laplacian interface) upon droplet volume reduction. By introducing a viscoelasticity parameter to account for interfacial stiffening and using experimentally determined elasticity, we are able to correct this discrepancy and predict droplet

  15. Dynamic modularity in protein interaction networks predicts breast cancer outcome

    DEFF Research Database (Denmark)

    Taylor, Ian W; Linding, Rune; Warde-Farley, David

    2009-01-01

    Changes in the biochemical wiring of oncogenic cells drives phenotypic transformations that directly affect disease outcome. Here we examine the dynamic structure of the human protein interaction network (interactome) to determine whether changes in the organization of the interactome can be used...... to predict patient outcome. An analysis of hub proteins identified intermodular hub proteins that are co-expressed with their interacting partners in a tissue-restricted manner and intramodular hub proteins that are co-expressed with their interacting partners in all or most tissues. Substantial differences...

  16. Design and Development of a User Interface and User Manual for a System Dynamics Model of Software Management

    Science.gov (United States)

    1989-03-01

    Perceptual Mechanisms in the Search of Computer Command Menus," Proceedings on Human Factors in Computer Systems, March 1982. 4. Covington, Michael A...Dynamo interface \\IF or MA Press \\1D<ESC> \\lAto return to the Main Menu! \\IF 53 end DUCEY %I I if %1 = key0lb goto -topi PD PROJBCT.DYN retum -%0-4

  17. Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers.

    Directory of Open Access Journals (Sweden)

    Elena Pereira

    critical inflection point in precision medicine. This study suggests that the use of personalized ctDNA biomarkers in gynecologic cancers can identify the presence of residual tumor while also more dynamically predicting response to treatment relative to currently used serum and imaging studies. Of particular interest, ctDNA was an independent predictor of survival in patients with ovarian and endometrial cancers. Earlier recognition of disease persistence and/or recurrence and the ability to stratify into better and worse outcome groups through ctDNA surveillance may open the window for improved survival and quality and life in these cancers.

  18. Dynamic changes and surveillance function of prion protein expression in gastric cancer drug resistance

    Institute of Scientific and Technical Information of China (English)

    Ji-Heng Wang; Jing-Ping Du; Ying-Hai Zhang; Xiao-Jun Zhao; Ru-Ying Fan; Zhi-Hong Wang; Zi-Tao Wu; Ying Han

    2011-01-01

    AIM: To explore the dynamic changes of prion protein (PrPc) in the process of gastric cancer drug resistance and the role of PrPc expression in the prognosis of gastric cancer patients receiving chemotherapy. METHODS: A series of gastric cancer cell lines resistant to different concentrations of adriamycin was established,and the expression of PrPc, Bcl-2 and Bax was detected in these cells. Apoptosis was determined using Annexin V staining. Western blotting and immunohistochemistry were performed to detect the expression of PrPc in patients receiving chemotherapy and to explore the role of PrPc expression in predicting the chemosensitivity and the outcome of gastric cancer patients receiving chemotherapy. Follow-up was performed for 2 years. RESULTS: PrPc expression was increased with the increase in drug resistance. Bcl-2, together with PrPc, increased the level of anti-apoptosis of cancer cells. Increased PrPc expression predicted the enhanced level of anti-apoptosis and resistance to anticancer drugs. PrPc expression could be used as a marker for predicting the efficacy of chemotherapy and the prognosis of gastric cancer. Increased PrPc expression predicted both poor chemosensitivity and a low 2-year survival rate. Contrarily, low PrPc expression predicted favorable chemosensitivity and a relatively high 2-year survival rate.CONCLUSION: PrPc expression is associated with histological types and differentiation of gastric cancer cells; The PrPc expression level might be a valuable marker in predicting the efficacy of chemotherapy and the prognosis of gastric cancer patients receiving chemotherapy.

  19. Assessing Tumor Response to Treatment in Patients with Lung Cancer Using Dynamic Contrast-Enhanced CT

    DEFF Research Database (Denmark)

    Strauch, Louise S; Eriksen, Rie Ø; Sandgaard, Michael

    2016-01-01

    after treatment. Four out of five studies that measured blood flow post anti-angiogenic treatments found that blood flow was significantly decreased. DCE-CT may be a useful tool in assessing treatment response in patients with lung cancer. It seems that particularly permeability and blood flow......The aim of this study was to provide an overview of the literature available on dynamic contrast-enhanced computed tomography (DCE-CT) as a tool to evaluate treatment response in patients with lung cancer. This systematic review was compiled according to Preferred Reporting Items for Systematic...... Reviews and Meta-Analyses (PRISMA) guidelines. Only original research articles concerning treatment response in patients with lung cancer assessed with DCE-CT were included. To assess the validity of each study we implemented Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2). The initial search...

  20. Precise Photodynamic Therapy of Cancer via Subcellular Dynamic Tracing of Dual-loaded Upconversion Nanophotosensitizers

    Science.gov (United States)

    Chang, Yulei; Li, Xiaodan; Zhang, Li; Xia, Lu; Liu, Xiaomin; Li, Cuixia; Zhang, Youlin; Tu, Langping; Xue, Bin; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

    2017-01-01

    Recent advances in upconversion nanophotosensitizers (UCNPs-PS) excited by near-infrared (NIR) light have led to substantial progress in improving photodynamic therapy (PDT) of cancer. For a successful PDT, subcellular organelles are promising therapeutic targets for reaching a satisfactory efficacy. It is of vital importance for these nanophotosensitizers to reach specifically the organelles and to perform PDT with precise time control. To do so, we have in this work traced the dynamic subcellular distribution, especially in organelles such as lysosomes and mitochondria, of the poly(allylamine)-modified and dual-loaded nanophotosensitizers. The apoptosis of the cancer cells induced by PDT with the dependence of the distribution status of the nanophotosensitizers in organelles was obtained, which has provided an in-depth picture of intracellular trafficking of organelle-targeted nanophotosensitizers. Our results shall facilitate the improvement of nanotechnology assisted photodynamic therapy of cancers. PMID:28361967

  1. Protein complex formation and intranuclear dynamics of NAC1 in cancer cells.

    Science.gov (United States)

    Nakayama, Naomi; Kato, Hiroaki; Sakashita, Gyosuke; Nariai, Yuko; Nakayama, Kentaro; Kyo, Satoru; Urano, Takeshi

    2016-09-15

    Nucleus accumbens-associated protein 1 (NAC1) is a cancer-related transcription regulator protein that is also involved in the pluripotency and differentiation of embryonic stem cells. NAC1 is overexpressed in various carcinomas including ovarian, cervical, breast, and pancreatic carcinomas. NAC1 knock-down was previously shown to result in the apoptosis of ovarian cancer cell lines and to rescue their sensitivity to chemotherapy, suggesting that NAC1 may be a potential therapeutic target, but protein complex formation and the dynamics of intranuclear NAC1 in cancer cells remain poorly understood. In this study, analysis of HeLa cell lysates by fast protein liquid chromatography (FPLC) on a sizing column showed that the NAC1 peak corresponded to an apparent molecular mass of 300-500 kDa, which is larger than the estimated molecular mass (58 kDa) of the protein. Furthermore, live cell photobleaching analyses with green fluorescent protein (GFP)-fused NAC1 proteins revealed the intranuclear dynamics of NAC1. Collectively our results demonstrate that NAC1 forms a protein complex to function as a transcriptional regulator in cancer cells.

  2. Differentiation of early gastric cancer with ulceration and resectable advanced gastric cancer using multiphasic dynamic multidetector CT

    Energy Technology Data Exchange (ETDEWEB)

    Tsurumaru, Daisuke; Miyasaka, Mitsutoshi; Nishimuta, Yusuke; Asayama, Yoshiki; Nishie, Akihiro; Honda, Hiroshi [Kyushu University, Department of Clinical Radiology, Graduate School of Medical Sciences, Fukuoka (Japan); Kawanami, Satoshi [Kyushu University, Department of Molecular Imaging and Diagnosis, Graduate School of Medical Sciences, Fukuoka (Japan); Oki, Eiji [Kyushu University, Department of Surgery and Sciences, Graduate School of Medical Sciences, Fukuoka (Japan); Hirahashi, Minako [Kyushu University, Department of Anatomic Pathology and Pathological Sciences, Graduate School of Medical Sciences, Fukuoka (Japan)

    2016-05-15

    Early gastric cancer with ulceration (EGC-U) mimics advanced gastric cancer (AGC), as EGC-Us and ACGs often have similar endoscopic appearance to ulceration. The purpose of this retrospective study was to determine whether multiphasic dynamic multidetector CT (MDCT) can help differentiate EGC-Us from AGCs. Patients with EGC-Us with ulcer stages Ul-III or IV and AGCs with tumour stages T2 to T4a were enrolled. MDCT images were obtained 40 s (arterial phase), 70 s (portal phase) and 240 s (delayed phase) after injection of non-ionic contrast material. Two readers independently measured the attenuation values of the lesions by placing regions of interest. We compared the EGC-Us and AGCs using the mean attenuation values in each phase and peak enhancement phase. We analysed the diagnostic performance of CT for differentiating EGC-Us from AGCs. Forty cases (16 EGC-Us and 24 AGCs) were analysed. The mean attenuation values of the EGC-Us were significantly lower than those of the AGCs in both the arterial and portal phases (all p < 0.0001 for each reader). The peak enhancement was significantly different between the EGC-Us and AGCs for both readers (Reader 1, p = 0.0131; Reader 2, p = 0.0006). Multiphasic dynamic contrast-enhanced MDCT can help differentiate EGC-Us from AGCs. (orig.)

  3. Energy-resolved depth profiling of metal-polymer interfaces using dynamic quadrupole secondary ion mass spectrometry.

    Science.gov (United States)

    Téllez, Helena; Vadillo, José M; Laserna, J Javier

    2009-08-01

    Quadrupole secondary ion mass spectrometry (qSIMS) characterization of a metallized polypropylene film used in the manufacturing of capacitors has been performed. Ar(+) primary ions were used to preserve the oxidation state of the surface. The sample exhibits an incomplete metallization that made it difficult to determine the exact location of the metal-polymer interface due to the simultaneous contribution of ions with identical m/z values from the metallic and the polymer layers. Energy filtering by means of a 45 degrees electrostatic analyzer allowed resolution of the metal-polymer interface by selecting a suitable kinetic energy corresponding to the ions generated in the metallized layer but not from the polymer. Under these conditions, selective analyses of isobaric interferences such as (27)Al(+) and (27)C(2)H(3) (+) or (43)AlO(+) and (43)C(3)H(7) (+) have been successfully performed.

  4. Flexible, Robust and Dynamic Dialogue Modeling with a Speech Dialogue Interface for Controlling a Hi-Fi Audio System.

    OpenAIRE

    Fernández Martínez, Fernando; Ferreiros López, Javier; Lucas Cuesta, Juan Manuel; Echeverry Correa, Julian David; San Segundo Hernández, Rubén; Córdoba Herralde, Ricardo de

    2010-01-01

    This work is focused on the context of speech interfaces for controlling household electronic devices. In particular, we present an example of a spoken dialogue system for controlling a Hi-Fi audio system. This system demonstrates that a more natural, flexible and robust dialogue is possible. That is due to both the Bayesian Networks based solution that we propose for dialogue modeling, and also to carefully designed contextual information handling strategies.

  5. Molecular dynamics simulations of structure-property relationships of Tween 80 surfactants in water and at interfaces.

    Science.gov (United States)

    Tang, Xueming; Huston, Kyle J; Larson, Ronald G

    2014-11-13

    We build a united atom model for Tween 80 (polyoxyethylene sorbitan oleates), based on the GROMOS53A6(OXY+D) force field, and apply it to two stereoisomers, three constitutional isomers, and three structures with one, two, and three tails, to represent components in the Tween 80 commercial mixture. In a preassembled micelle containing 60 molecules, the distribution of Tween tail and ethylene oxide head groups is found to be insensitive to stereoisomerization but sensitive to changes in relative lengths of the four polyoxyethylene head groups. At the air-water and oil-water interfaces, the interfacial tension is significantly lower for the constitutional isomer with a shorter W headgroup, which attaches the tail to the sorbitan ring, and for Tween 80 isomers with more than one tail group. The results indicate the possible scope for improvement in the design of polyoxyethylene sorbitan oleates with improved surface tension reduction or better spreading at the oil-water interface. We also report surfactant component distribution profiles within preassembled micelles and at interfaces that can be used for validating coarse-grained surfactant models needed for simulation of self-assembly of Tween 80 surfactant mixtures.

  6. Liquid/liquid interface layering of 1-butanol and [bmim]PF6 ionic liquid: a nonlinear vibrational spectroscopy and molecular dynamics simulation study.

    Science.gov (United States)

    Iwahashi, Takashi; Ishiyama, Tatsuya; Sakai, Yasunari; Morita, Akihiro; Kim, Doseok; Ouchi, Yukio

    2015-10-14

    IR-visible sum-frequency generation (IV-SFG) vibrational spectroscopy and a molecular dynamics (MD) simulation were used to study the local layering order at the interface of 1-butanol-d9 and 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim]PF6), a room-temperature ionic liquid (RTIL). The presence of a local non-polar layer at the interface of the two polar liquids was successfully demonstrated. In the SFG spectra of 1-butanol-d9, we observed significant reduction and enhancement in the strength of the CD3 symmetric stretching (r(+)) mode and the antisymmetric stretching (r(-)) mode peaks, respectively. The results can be well explained by the presence of an oppositely oriented quasi-bilayer structure of butanol molecules, where the bottom layer is strongly bound by hydrogen-bonding with the PF6(-) anion. MD simulations reveal that the hydrogen-bonding of butanol with the PF6(-) anion causes the preferential orientation of the butanols; the restriction on the rotational distribution of the terminal methyl group along their C3 axis enhances the r(-) mode. As for the [bmim](+) cations, the SFG spectra taken within the CH stretch region indicate that the butyl chain of [bmim](+) points away from the bulk RTIL phase to the butanol phase at the interface. Combining the SFG spectroscopy and MD simulation results, we propose an interfacial model structure of layering, in which the butyl chains of the butanol molecules form a non-polar interfacial layer with the butyl chains of the [bmim](+) cations at the interface.

  7. Dynamics between cancer cell subpopulations reveals a model coordinating with both hierarchical and stochastic concepts.

    Directory of Open Access Journals (Sweden)

    Weikang Wang

    Full Text Available Tumors are often heterogeneous in which tumor cells of different phenotypes have distinct properties. For scientific and clinical interests, it is of fundamental importance to understand their properties and the dynamic variations among different phenotypes, specifically under radio- and/or chemo-therapy. Currently there are two controversial models describing tumor heterogeneity, the cancer stem cell (CSC model and the stochastic model. To clarify the controversy, we measured probabilities of different division types and transitions of cells via in situ immunofluorescence. Based on the experiment data, we constructed a model that combines the CSC with the stochastic concepts, showing the existence of both distinctive CSC subpopulations and the stochastic transitions from NSCCs to CSCs. The results showed that the dynamic variations between CSCs and non-stem cancer cells (NSCCs can be simulated with the model. Further studies also showed that the model can be used to describe the dynamics of the two subpopulations after radiation treatment. More importantly, analysis demonstrated that the experimental detectable equilibrium CSC proportion can be achieved only when the stochastic transitions from NSCCs to CSCs occur, indicating that tumor heterogeneity may exist in a model coordinating with both the CSC and the stochastic concepts. The mathematic model based on experimental parameters may contribute to a better understanding of the tumor heterogeneity, and provide references on the dynamics of CSC subpopulation during radiotherapy.

  8. Leukocyte population dynamics and detection of IL-9 as a major cytokine at the mouse fetal-maternal interface.

    Directory of Open Access Journals (Sweden)

    Mohamed Habbeddine

    Full Text Available Despite much interest in the mechanisms regulating fetal-maternal interactions, information on leukocyte populations and major cytokines present in uterus and placenta remains fragmentary. This report presents a detailed and quantitative study of leukocyte populations at the mouse fetal-maternal interface, including a comparison between pregnancies from syngeneic and allogeneic crosses. Our results provide evidence for drastic differences not only in the composition of leukocyte populations in the uterus during pregnancy, but also between uterine and placental tissues. Interestingly, we have observed a significant decrease in the number of myeloid Gr1+ cells including monocytes, and myeloid CD11c+ cells including DCs in placenta from an allogeneic pregnancy. In addition, we have compared the expression levels of a panel of cytokines in non-pregnant (NP or pregnant mouse uterus, in placenta, or in their isolated resident leukocytes. Qualitative and quantitative differences have emerged between NP, pregnant uterus and placenta. Unexpectedly, IL-9 was the major cytokine in NP uterus, and was maintained at high levels during pregnancy both in uterus and placenta. Moreover, we have found that pregnancy is associated with an increase in uterine IL-1a and a significant decrease in uterine G-CSF and GM-CSF. Comparing allogeneic versus syngeneic pregnancy, less allogeneic placental pro-inflammatory cytokines CCL2 (MCP-1, CXCL10 (IP-10 and more IL1-α in whole uterus was reproducibly observed. To our knowledge, this is the first report showing a detailed overview of the leukocyte and cytokine repertoire in the uterus of virgin females and at the fetal-maternal interface, including a comparison between syngeneic and allogeneic pregnancy. This is also the first evidence for the presence of IL-9 in NP uterus and at the maternal-fetal interface, suggesting a major role in the regulation of local inflammatory or immune responses potentially detrimental to the

  9. Integrated multimodal imaging of dynamic bone-tumor alterations associated with metastatic prostate cancer.

    Directory of Open Access Journals (Sweden)

    Jean-Christophe Brisset

    Full Text Available Bone metastasis occurs for men with advanced prostate cancer which promotes osseous growth and destruction driven by alterations in osteoblast and osteoclast homeostasis. Patients can experience pain, spontaneous fractures and morbidity eroding overall quality of life. The complex and dynamic cellular interactions within the bone microenvironment limit current treatment options thus prostate to bone metastases remains incurable. This study uses voxel-based analysis of diffusion-weighted MRI and CT scans to simultaneously evaluate temporal changes in normal bone homeostasis along with prostate bone metatastsis to deliver an improved understanding of the spatiotemporal local microenvironment. Dynamic tumor-stromal interactions were assessed during treatment in mouse models along with a pilot prospective clinical trial with metastatic hormone sensitive and castration resistant prostate cancer patients with bone metastases. Longitudinal changes in tumor and bone imaging metrics during delivery of therapy were quantified. Studies revealed that voxel-based parametric response maps (PRM of DW-MRI and CT scans could be used to quantify and spatially visualize dynamic changes during prostate tumor growth and in response to treatment thereby distinguishing patients with stable disease from those with progressive disease (p<0.05. These studies suggest that PRM imaging biomarkers are useful for detection of the impact of prostate tumor-stromal responses to therapies thus demonstrating the potential of multi-modal PRM image-based biomarkers as a novel means for assessing dynamic alterations associated with metastatic prostate cancer. These results establish an integrated and clinically translatable approach which can be readily implemented for improving the clinical management of patients with metastatic bone disease.

  10. Dynamic prediction of risk of death using history of cancer recurrences in joint frailty models.

    Science.gov (United States)

    Mauguen, Audrey; Rachet, Bernard; Mathoulin-Pélissier, Simone; MacGrogan, Gaetan; Laurent, Alexandre; Rondeau, Virginie

    2013-12-30

    Evaluating the prognosis of patients according to their demographic, biological, or disease characteristics is a major issue, as it may be used for guiding treatment decisions. In cancer studies, typically, more than one endpoint can be observed before death. Patients may undergo several types of events, such as local recurrences and distant metastases, with death as the terminal event. Accuracy of clinical decisions may be improved when the history of these different events is considered. Thus, it may be useful to dynamically predict patients' risk of death using recurrence history. As previously applied within the framework of joint models for longitudinal and time to event data, we propose a dynamic prediction tool based on joint frailty models. Joint modeling accounts for the dependence between recurrent events and death, by the introduction of a random effect shared by the two processes. We estimate the probability of death between the prediction time t and a horizon t + w, conditional on information available at time t. Prediction can be updated with the occurrence of a new event. We proposed and compared three prediction settings, taking into account three different information levels. The proposed tools are applied to patients diagnosed with a primary invasive breast cancer and treated with breast-conserving surgery, followed for more than 10 years in a French comprehensive cancer center.

  11. The evolving role of the dynamic thermal analysis in the early detection of breast cancer

    Science.gov (United States)

    Salhab, M; Al Sarakbi, W; Mokbel, K

    2005-01-01

    It is now recognised that the breast exhibits a circadian rhythm which reflects its physiology. There is increasing evidence that rhythms associated with malignant cells proliferation are largely non-circadian and that a circadian to ultradian shift may be a general correlation to neoplasia. Cancer development appears to generate its own thermal signatures and the complexity of these signatures may be a reflection of its degree of development. The limitations of mammography as a screening modality especially in young women with dense breasts necessitated the development of novel and more effective screening strategies with a high sensitivity and specificity. Dynamic thermal analysis of the breast is a safe, non invasive approach that seems to be sensitive for the early detection of breast cancer. This article focuses on dynamic thermal analysis as an evolving method in breast cancer detection in pre-menopausal women with dense breast tissue. Prospective multi-centre trials are required to validate this promising modality in screening. The issue of false positives require further investigation using molecular genetic markers of malignancy and novel techniques such as mammary ductoscopy. PMID:15819982

  12. A tale of two interfaces: Dynamic nitrate removal in the hyporheic zone of a tidal fresh river

    Science.gov (United States)

    Sawyer, A. H.; Knights, D. H.; Barnes, R. T.; Wallace, C.; Bray, S. N.; Musial, C.

    2015-12-01

    At the interface of rivers and oceans, tidal freshwater zones (TFZs) stretch for tens to hundreds of kilometers but are rarely monitored for nitrogen export due to their complex hydrodynamics. Field observations from the TFZ of White Clay Creek (Delaware, USA) show that river discharge and nitrate export rates decrease during rising tide, while hyporheic storage increases. During falling tide, river discharge and nitrate export rates increase, while stored hyporheic water is released to the river. We estimate that 11% of river water exchanges through the hyporheic zone of this TFZ due to tidal pumping alone. We developed a one-dimensional, coupled fluid flow and solute transport model to quantify the influence of tidal pumping on nitrate removal in the riverbed. Tidal pumping promotes a deep, oscillating zone of aerobic respiration that limits denitrification near the sediment-water interface. As tide rises, groundwater residence times in shallow riverbed sediments increase, which causes a doubling of denitrification rates relative to falling tide. Given a uniform substrate along TFZs, removal rates of groundwater-borne nitrate should decrease as tidal amplitude increases downstream. Denitrification hot spots should occur in less permeable, organic-rich sediment under low tidal ranges. Because TFZs connect lowland nitrogen sources to the ocean, it is imperative that we expand monitoring efforts and elucidate their role in nitrogen export to the coast.

  13. Advanced Simulation and Optimization Tools for Dynamic Aperture of Non-scaling FFAGs and Accelerators including Modern User Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Mills, F.; Makino, Kyoko; Berz, Martin; Johnstone, C.

    2010-09-01

    With the U.S. experimental effort in HEP largely located at laboratories supporting the operations of large, highly specialized accelerators, colliding beam facilities, and detector facilities, the understanding and prediction of high energy particle accelerators becomes critical to the success, overall, of the DOE HEP program. One area in which small businesses can contribute to the ongoing success of the U.S. program in HEP is through innovations in computer techniques and sophistication in the modeling of high-energy accelerators. Accelerator modeling at these facilities is performed by experts with the product generally highly specific and representative only of in-house accelerators or special-interest accelerator problems. Development of new types of accelerators like FFAGs with their wide choices of parameter modifications, complicated fields, and the simultaneous need to efficiently handle very large emittance beams requires the availability of new simulation environments to assure predictability in operation. In this, ease of use and interfaces are critical to realizing a successful model, or optimization of a new design or working parameters of machines. In Phase I, various core modules for the design and analysis of FFAGs were developed and Graphical User Interfaces (GUI) have been investigated instead of the more general yet less easily manageable console-type output COSY provides.

  14. Hydrological exchanges and Organic Matter dynamics in highly vulnerable tidal wetland ecosystems at the land-ocean interface

    Science.gov (United States)

    Tzortziou, M.; Neale, P.; Megonigal, P.; Loughner, C.

    2014-12-01

    Occupying a critical interface between the land and the sea, tidal wetlands are amongst the most ecologically valuable and economically important ecosystems on Earth, but also especially vulnerable to human pressures and climate change. These rich in biodiversity and highly productive ecosystems are hot spots of biogeochemical transformations, consistently exchanging Organic Matter with adjacent estuarine waters through tidal flushing. Here we discuss new results on the amount and directions of biogeochemical exchanges at the tidal wetland-estuary interface. Detailed microbial and photochemical degradation experiments and high resolution bio-optical observations in tidal freshwater and salt marsh systems of the Eastern US coast provide insights on the quality and fate of the organic compounds exported from tidal marshes and their influence on near-shore biological processes, biogeochemical cycles and optical variability. Impacts of anthropogenic activities and resulting air-pollution are also discussed. High resolution model runs were performed using the Community Multi-scale Air Quality (CMAQ) model, to examine atmospheric composition along the shoreline where processes such as sea and bay breeze circulations often favor the accumulation and air-deposition of atmospheric pollutants, impacting biogeochemical processes in sensitive tidal wetland ecosystems.

  15. Lectures on random interfaces

    CERN Document Server

    Funaki, Tadahisa

    2016-01-01

    Interfaces are created to separate two distinct phases in a situation in which phase coexistence occurs. This book discusses randomly fluctuating interfaces in several different settings and from several points of view: discrete/continuum, microscopic/macroscopic, and static/dynamic theories. The following four topics in particular are dealt with in the book. Assuming that the interface is represented as a height function measured from a fixed-reference discretized hyperplane, the system is governed by the Hamiltonian of gradient of the height functions. This is a kind of effective interface model called ∇φ-interface model. The scaling limits are studied for Gaussian (or non-Gaussian) random fields with a pinning effect under a situation in which the rate functional of the corresponding large deviation principle has non-unique minimizers. Young diagrams determine decreasing interfaces, and their dynamics are introduced. The large-scale behavior of such dynamics is studied from the points of view of the hyd...

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

    Science.gov (United States)

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

    2015-10-28

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

  17. The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer

    Science.gov (United States)

    Fernandez, Agustin F.; Rosales, Cecilia; Lopez-Nieva, Pilar; Graña, Osvaldo; Ballestar, Esteban; Ropero, Santiago; Espada, Jesus; Melo, Sonia A.; Lujambio, Amaia; Fraga, Mario F.; Pino, Irene; Javierre, Biola; Carmona, Francisco J.; Acquadro, Francesco; Steenbergen, Renske D.M.; Snijders, Peter J.F.; Meijer, Chris J.; Pineau, Pascal; Dejean, Anne; Lloveras, Belen; Capella, Gabriel; Quer, Josep; Buti, Maria; Esteban, Juan-Ignacio; Allende, Helena; Rodriguez-Frias, Francisco; Castellsague, Xavier; Minarovits, Janos; Ponce, Jordi; Capello, Daniela; Gaidano, Gianluca; Cigudosa, Juan Cruz; Gomez-Lopez, Gonzalo; Pisano, David G.; Valencia, Alfonso; Piris, Miguel Angel; Bosch, Francesc X.; Cahir-McFarland, Ellen; Kieff, Elliott; Esteller, Manel

    2009-01-01

    The natural history of cancers associated with virus exposure is intriguing, since only a minority of human tissues infected with these viruses inevitably progress to cancer. However, the molecular reasons why the infection is controlled or instead progresses to subsequent stages of tumorigenesis are largely unknown. In this article, we provide the first complete DNA methylomes of double-stranded DNA viruses associated with human cancer that might provide important clues to help us understand the described process. Using bisulfite genomic sequencing of multiple clones, we have obtained the DNA methylation status of every CpG dinucleotide in the genome of the Human Papilloma Viruses 16 and 18 and Human Hepatitis B Virus, and in all the transcription start sites of the Epstein-Barr Virus. These viruses are associated with infectious diseases (such as hepatitis B and infectious mononucleosis) and the development of human tumors (cervical, hepatic, and nasopharyngeal cancers, and lymphoma), and are responsible for 1 million deaths worldwide every year. The DNA methylomes presented provide evidence of the dynamic nature of the epigenome in contrast to the genome. We observed that the DNA methylome of these viruses evolves from an unmethylated to a highly methylated genome in association with the progression of the disease, from asymptomatic healthy carriers, through chronically infected tissues and pre-malignant lesions, to the full-blown invasive tumor. The observed DNA methylation changes have a major functional impact on the biological behavior of the viruses. PMID:19208682

  18. Nuclear Magnetic Resonance as a Probe of Meso-timescale Dynamics: Ion and H2O Behavior at Mineral-H2O Interfaces

    Science.gov (United States)

    Bowers, G. M.; Kirkpatrick, R. J.; Singer, J. W.

    2012-12-01

    One of the important meso-scales in geochemistry is the meso-timescale that is characteristic of processes too slow to probe with light spectroscopy but too fast to probe macroscopically. Nuclear magnetic resonance (NMR) spectroscopy is one of the only analytical methods with dynamic sensitivity to motions with correlation times on the 10-9 to 1 s timescales and is thus a uniquely powerful probe of meso-timescale dynamic behavior. Here, we describe the results of several studies exploring the meso-timescale motion of ions and H2O at the mineral-H2O interface of hectorite, a smectite clay mineral.1-3 2H, 23Na, 39K and 43Ca NMR results show that H2O molecules associated with the interface undergo anisotropic reorientation due to proximity to the surface and surface-associated cations. This motion can be described by rotational diffusion of the H2O molecule about its C2 symmetry axis at GHz frequencies combined with hopping of the H2O molecule about the normal to the smectite surface at ~>200 kHz. This model describes well the observed 2H NMR spectra of Na+, K+, and Ca2+ hectorites over a range temperatures between -80°C and 50°C, with the specific range dependent only on the total system H2O content. At temperatures above -20°C, systems with excess H2O with respect to a two-layer hydrate (low-H2O pastes through dilute aqueous suspensions) experience additional dynamic averaging due to H2O exchange between cation hydration shells, surface-sorbed species, and bulk inter-particle water. The extent of 2H averaging due to this exchange mechanism is strongly affected by the total H2O content in the system, the identity of the charge balancing cation, and the temperature. The dynamic averaging mechanisms affecting the cationic NMR resonances in these systems become dominated by diffusional processes at progressively lower temperatures as the hydration energy of the cation increases. These interfacial cation dynamics and binding sites are strongly affected by surface

  19. Quantitative mathematical modeling of PSA dynamics of prostate cancer patients treated with intermittent androgen suppression

    Institute of Scientific and Technical Information of China (English)

    Yoshito Hirata; Koichiro Akakura; Celestia S.Higano; Nicholas Bruchovsky; Kazuyuki Aihara

    2012-01-01

    If a mathematical model is to be used in the diagnosis,treatment,or prognosis of a disease,it must describe the inherent quantitative dynamics of the state.An ideal candidate disease is prostate cancer owing to the fact that it is characterized by an excellent biomarker,prostate-specific antigen (PSA),and also by a predictable response to treatment in the form of androgen suppression therapy.Despite a high initial response rate,the cancer will often relapse to a state of androgen independence which no longer responds to manipulations of the hormonal environment.In this paper,we present relevant background information and a quantitative mathematical model that potentially can be used in the optimal management of patients to cope with biochemical relapse as indicated by a rising PSA.

  20. Multi-purpose droop controllers incorporating a passivity-based stabilizer for unified control of electronically interfaced distributed generators including primary source dynamics.

    Science.gov (United States)

    Azimi, Seyed Mohammad; Afsharnia, Saeed

    2016-07-01

    This paper presents multi-purpose droop controllers for electronically-interfaced distributed generators (EI-DGs). These controllers allow the micro-grids to operate in grid-connected mode, islanded mode and mode transition transients with a unique control configuration. The active and reactive-power sharing among EI-DGs are satisfied by the proposed droop controllers in islanded mode. On the other hand, in the grid-connected mode, the droop controllers adjust the output active and reactive-powers of EI-DGs at the pre-programmed constant levels. The provision of sufficient damping capability and maintenance of the transient stability in all operational modes of EI-DGs are warranted by the suggested stabilizer. This stabilizer, which is designed using the passivity-based control (PBC) approach, is incorporated in the droop controllers to dampen power-angle, frequency and voltage deviations during large transients using solely local information. The primary source dynamics of EI-DGs are also considered. It is analytically proven that the presence of the primary source dynamics leads to attenuation of the damping capability of EI-DGs in transients. To compensate the adverse effect of the primary source dynamics during transients a novel compensator is inserted in the frequency-droop loop. Finally, time-domain simulations are performed on a multi-resources MG to verify the analytical results compared to those obtained, based on a recently-developed strategy.

  1. High resolution Dopplerimetry of correlated angular and quantum state-resolved CO(2) scattering dynamics at the gas-liquid interface.

    Science.gov (United States)

    Perkins, Bradford G; Nesbitt, David J

    2010-11-14

    Full three dimensional (3D) translational distributions for quantum state-resolved scattering dynamics at the gas-liquid interface are presented for experimental and theoretical studies of CO(2) + perfluorinated surfaces. Experimentally, high resolution absorption profiles are measured as a function of incident (θ(inc)) and scattering (θ(scat)) angles for CO(2) that has been scattered from a 300 K perfluorinated polyether surface (PFPE) with an incident energy of E(inc) = 10.6(8) kcal mol(-1). Line shape analysis of the absorption profiles reveals non-equilibrium dynamics that are characterized by trapping-desorption (TD) and impulsive scattering (IS) components, with each channel simply characterized by an effective "temperature" that compares very well with previous results from rotational state analysis [Perkins and Nesbitt, J. Phys. Chem. A, 2008, 112, 9324]. From a theoretical perspective, molecular dynamics (MD) simulations of CO(2) + fluorinated self-assembled monolayer surface (F-SAMs) yield translational probability distributions that are also compared with experimental results. Trajectories are parsed by θ(scat) and J, with the results rigorously corrected by flux-to-density transformation and providing comparisons in near quantitative agreement with experiment. 3D flux and velocity distributions obtained from MD simulations are also presented to illustrate the role of in- and out-of-plane scattering.

  2. Intercellular cancer collisions generate an ejected crystal comet tail effect with fractal interface embryoid body reassembly transformation

    Directory of Open Access Journals (Sweden)

    Díaz JA

    2011-05-01

    Full Text Available Jairo A Díaz, Mauricio F Murillo, Alvaro BarreroDepartment of Pathology, Hospital Departmental Villavicencio, Hospital Departmental Granada, Medicine School, University Cooperative of Colombia, Villavicencio, Meta, ColombiaAbstract: We have documented self-assembled geometric triangular chiral crystal complexes (GTCHC and a framework of collagen vascular invariant geometric attractors in cancer tissues. This article shows how this system evolves in time. These structures are incorporated together and evolve in different ways. When the geometric core is stable, and the tissue architecture collapses, fragmented components emerge, which reveal a hidden interior identifying how each molecule is reassembled into the original mold, using one common connection, ie, a fractal self-similarity that guided the system from the beginning. GTCHC complexes generate ejected crystal comet tail effects and produce strange helicity states that arise in the form of spin domain interactions. As the crystal growth vibration stage progresses, biofractal echo images converge in a master-built construction of embryoid bodies with enolase-selective immunopositivity in relation to clusters of triangular chiral cell organization. In our electro-optic collision model, we were able to predict and replicate all the characteristics of this complex geometry that connects a physical phenomenon with the signal patterns that generate biologic chaos. Intrinsically, fractal geometry makes spatial correction errors embrace the chaotic system in a way that permits new structures to emerge, and as a result, an ordered self-assembly of embryoid bodies with neural differentiation at the final stage of cancer development is a predictable process. We hope that further investigation of these structures will lead not only to a new way of thinking about physics and biology, but also to a rewarding area in cancer research.Keywords: embryoid bodies, cancer, electro-optic collision model

  3. Intercellular cancer collisions generate an ejected crystal comet tail effect with fractal interface embryoid body reassembly transformation

    OpenAIRE

    Díaz JA; Murillo MF; Barrero A

    2011-01-01

    Jairo A Díaz, Mauricio F Murillo, Alvaro BarreroDepartment of Pathology, Hospital Departmental Villavicencio, Hospital Departmental Granada, Medicine School, University Cooperative of Colombia, Villavicencio, Meta, ColombiaAbstract: We have documented self-assembled geometric triangular chiral crystal complexes (GTCHC) and a framework of collagen vascular invariant geometric attractors in cancer tissues. This article shows how this system evolves in time. These structures are incor...

  4. Mammography combined with breast dynamic contrast-enhanced-magnetic resonance imaging for the diagnosis of early breast cancer

    Institute of Scientific and Technical Information of China (English)

    Yakun He; Guohui Xu; Jin Ren; Bin Feng; Xiaolei Dong; Hao Lu; Changjiu He

    2016-01-01

    Objective The aim of this study was to investigate the application of mammography combined with breast dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) for the diagnosis of early breast cancer. Methods Mammography and DCE-MRI were performed for 120 patients with breast cancer (malignant, 102; benign; 18). Results The sensitivity of mammography for early diagnosis of breast cancer was 66.67%, specificity was 77.78%, and accuracy was 68.33%. The sensitivity of MRI for early diagnosis of breast cancer was 94.12%, specificity was 88.89%, and accuracy was 93.33%. However, the sensitivity of mammography combined with DCE-MRI volume imaging with enhanced water signal (VIEWS) scanning for early diagnosis of breast cancer was 97.06%, specificity was 94.44%, and accuracy was 96.67%. Conclusion Mammography combined with DCE-MRI increased the sensitivity, specificity, and accuracy of diagnosing early breast cancer.

  5. Direct observation of the dynamics of single metal ions at the interface with solids in aqueous solutions

    Science.gov (United States)

    Ricci, Maria; Trewby, William; Cafolla, Clodomiro; Voïtchovsky, Kislon

    2017-02-01

    The dynamics of ions adsorbed at the surface of immersed charged solids plays a central role in countless natural and industrial processes such as crystal growth, heterogeneous catalysis, electrochemistry, or biological function. Electrokinetic measurements typically distinguish between a so-called Stern layer of ions and water molecules directly adsorbed on to the solid’s surface, and a diffuse layer of ions further away from the surface. Dynamics within the Stern layer remain poorly understood, largely owing to a lack of in-situ atomic-level insights. Here we follow the dynamics of single Rb+ and H3O+ ions at the surface of mica in water using high-resolution atomic force microscopy with 25 ms resolution. Our results suggest that single hydrated Rb+ions reside τ1 = 104 ± 5 ms at a given location, but this is dependent on the hydration state of the surface which evolves on a slower timescale of τ2 = 610 ± 30 ms depending on H3O+ adsorption. Increasing the liquid’s temperature from 5 °C to 65 °C predictably decreases the apparent glassiness of the interfacial water, but no clear effect on the ions’ dynamics was observed, indicating a diffusion-dominated process. These timescales are remarkably slow for individual monovalent ions and could have important implications for interfacial processes in electrolytes.

  6. Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Sebbari, Karim [EDF-R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Ecuelles, 77818 Moret Sur Loing (France); Institut de Physique Nucleaire d' Orsay, Universite Paris-Sud, CNRS UMR 8608, 15 rue Georges Clemenceau, Batiment 100, 91406 Orsay Cedex (France); Roques, Jerome; Simoni, Eric [Institut de Physique Nucleaire d' Orsay, Universite Paris-Sud, CNRS UMR 8608, 15 rue Georges Clemenceau, Batiment 100, 91406 Orsay Cedex (France); Domain, Christophe [EDF-R and D, Departement Materiaux et Mecanique des Composants, Les Renardieres, Ecuelles, 77818 Moret Sur Loing (France)

    2012-10-28

    The behavior of the UO{sub 2}{sup 2+} uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT +U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 A above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d{sub U-O{sub a{sub d{sub s{sub o{sub r{sub p{sub t{sub i{sub o{sub n}}}}}}}}}}}=2.39 A. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

  7. Molecular dynamics study of the effect of calcium ions on the monolayer of SDC and SDSn surfactants at the vapor/liquid interface.

    Science.gov (United States)

    Yan, Hui; Guo, Xin-Li; Yuan, Shi-Ling; Liu, Cheng-Bu

    2011-05-17

    The effect of Ca(2+) ions on the hydration shell of sodium dodecyl carboxylate (SDC) and sodium dodecyl sulfonate (SDSn) monolayer at vapor/liquid interfaces was studied using molecular dynamics simulations. For each surfactant, two different surface concentrations were used to perform the simulations, and the aggregation morphologies and structural details have been reported. The results showed that the aggregation structures relate to both the surface coverage and the calcium ions. The divalent ions can screen the interaction between the polar head and Na(+) ions. Thus, Ca(2+) ions locate near the vapor/liquid interface to bind to the headgroup, making the aggregations much more compact via the salt bridge. The potential of mean force (PMF) between Ca(2+) and the headgroups shows that the interaction is decided by a stabilizing solvent-separated minimum in the PMF. To bind to the headgroup, Ca(2+) should overcome the energy barrier. Among contributions to the PMF, the major repulsive interaction was due to the rearrangement of the hydration shell after the calcium ions entered into the hydration shell of the headgroup. The PMFs between the headgroup and Ca(2+) in the SDSn systems showed higher energy barriers than those in the SDC systems. This result indicated that SDSn binds the divalent ions with more difficulty compared with SDC, so the ions have a strong effect on the hydration shell of SDC. That is why sulfonate surfactants have better efficiency in salt solutions with Ca(2+) ions for enhanced oil recovery.

  8. Vibrational Dynamics of Interfacial Water by Free Induction Decay Sum Frequency Generation (FID-SFG) at the Al2O3(1120)/H2O Interface.

    Science.gov (United States)

    Boulesbaa, Abdelaziz; Borguet, Eric

    2014-02-06

    The dephasing dynamics of a vibrational coherence may reveal the interactions of chemical functional groups with their environment. To investigate this process at a surface, we employ free induction decay sum frequency generation (FID-SFG) to measure the time that it takes for free OH stretch oscillators at the charged (pH ≈ 13, KOH) interface of alumina/water (Al2O3/H2O) to lose their collective coherence. By employing noncollinear optical parametric amplification (NOPA) technology and nonlinear vibrational spectroscopy, we showed that the single free OH peak actually corresponds to two distinct oscillators oriented opposite to each other and measured the total dephasing time, T2, of the free OH stretch modes at the Al2O3/H2O interface with a sub-40 fs temporal resolution. Our results suggested that the free OH oscillators associated with interfacial water dephase on the time scale of 89.4 ± 6.9 fs, whereas the homogeneous dephasing of interfacial alumina hydroxyls is an order of magnitude slower.

  9. Molecular dynamics simulations of the formation for NaCl cluster at the interface between the supersaturated solution and the substrate

    Energy Technology Data Exchange (ETDEWEB)

    Yamanaka, Shinya, E-mail: eth1503@mail4.doshisha.ac.jp; Shimosaka, Atsuko; Shirakawa, Yoshiyuki, E-mail: yshiraka@mail.doshisha.ac.jp; Hidaka, Jusuke [Doshisha University, Department of Chemical Engineering and Materials Science (Japan)

    2010-03-15

    Molecular dynamics simulations of supersaturated aqueous NaCl solution including the Pt(100) or NaCl(100) crystal surfaces have been performed at an average temperature of 298 K. The behavior of the NaCl cluster produced in the solution have been studied through the consideration of the water dielectric property near the crystalline surfaces for understanding the role of crystal growth on the surface. The surfaces in the solutions greatly influence heterogeneous nucleation in crystallization process. Density profile of the supersaturated solution and polarization of water molecules was calculated in order to describe the effect of the surfaces on the solution structure at the solid-liquid interfaces. The formation levels of NaCl clusters heavily depended on the water orientation at the interfaces. NaCl clusters were easily formed near the Pt(100) surface compared with the NaCl(100) surface owing to a different construction of water molecules between the platinum and NaCl surface.

  10. Modeling reactive scattering of F(2P) at a liquid squalane interface: a hybrid QM/MM molecular dynamics study.

    Science.gov (United States)

    Radak, Brian K; Yockel, Scott; Kim, Dongwook; Schatz, George C

    2009-07-01

    To better understand the reactivity of gases with liquid surfaces, experimentalists have recently probed the reactive scattering of atomic fluorine at the surface of liquid squalane (C(30)H(62)). In this paper we further this research by simulating this scattering process at collision energies of 0.5 and 1.0 eV using a hybrid QM/MM molecular dynamics scheme. To model the structure of the liquid surface, classical molecular dynamics calculations were performed utilizing the OPLS-AA force field. During the F + squalane molecular dynamics simulation, QM/MM calculations are performed at every trajectory step by combining the MSINDO semiempirical Hamiltonian with OPLS-AA and using a dynamic partitioning of the atoms in the QM or MM regions via a "seed atom" method. This computational model provides a type of "on-the-fly" direct dynamics applicable to larger scale chemical processes that include the making/breaking of chemical bonds not available in standard force field models. Our results show that H abstraction is the only reactive scattering pathway and that most trajectories result in reactive scattering. Reaction statistics at the squalane surface are discussed, including variation of the results with incident angle and collision energy, and the probability of reaction as a function of carbon atom type, collision depth, and residence time. Product states, including angular distributions and final translational and rovibrational energies, are also considered and found to be significantly affected by the exothermic reaction energy for H abstraction. The vibrational distributions are in good agreement with recent experiments, but the rotational distributions are dominated by a nonthermal component while the experiments, which involve thermal incident energies, show comparable thermal and nonthermal contributions. Results for O + squalane at 1.0 eV, which we also present, show analogous comparisons with experiment, with OH vibrational distributions which are cold and

  11. Quantum-state resolved reaction dynamics at the gas-liquid interface: Direct absorption detection of HF(v,J) product from F(2P)+squalane

    Science.gov (United States)

    Zolot, Alexander M.; Harper, Warren W.; Perkins, Bradford G.; Dagdigian, Paul J.; Nesbitt, David J.

    2006-07-01

    Exothermic reactive scattering of F atoms at the gas-liquid interface of a liquid hydrocarbon (squalane) surface has been studied under single collision conditions by shot noise limited high-resolution infrared absorption on the nascent HF (v,J) product. The nascent HF (v,J) vibrational distributions are inverted, indicating insufficient time for complete vibrational energy transfer into the surface liquid. The HF (v=2,J) rotational distributions are well fit with a two temperature Boltzmann analysis, with a near room temperature component (TTD≈290K) and a second much hotter scattering component (THDS≈1040K). These data provide quantum state level support for microscopic branching in the atom abstraction dynamics corresponding to escape of nascent HF from the liquid surface on time scales both slow and fast with respect to rotational relaxation.

  12. Exciton dynamics at the heteromolecular interface between N,N′-dioctyl-3,4,9,10-perylenedicarboximide and quaterrylene, studied using time-resolved photoluminescence

    Directory of Open Access Journals (Sweden)

    Nobuya Hiroshiba

    2014-06-01

    Full Text Available To elucidate the exciton dynamics at the heteromolecular interface, the temperature dependence of time-resolved photoluminescence (TRPL spectra of neat-N,N′-dioctyl-3,4,9,10-perylenedicarboximide (PTCDI-C8 and PTCDI-C8/Quaterrylene (QT heteromolecular thin films was investigated. The lifetimes of excitons were evaluated to identify the Frenkel (FE, high energy charge-transfer (CTEhigh, low energy charge-transfer (CTElow, and excimer exciton states. The thermal activation energy (Δact of CTElow in PTCDI-C8 thin film was evaluated as 25 meV, which is 1/5 of that of FE, indicating that CTElow is more thermally sensitive than FE in PTCDI-C8 thin film. We investigated the exciton transport length (l along the vertical direction against the substrate surface in PTCDI-C8/QT thin film at 30 K, and demonstrated that lFE = 9.9 nm, lCTElow = 4.2 nm, lCTEhigh = 4.3 nm, and lexcimer = 11.9 nm. To elucidate the difference in l among these excitons, the activation energies (Ea for quenching at the heteromolecular interface were investigated. Ea values were estimated to be 13.1 meV for CTElow and 18.6 meV for CTEhigh. These values agree with the thermal sensitivity of CTEs as reported in a previous static PL study. This latter situation is different from the case of FE and excimer excitons, which are transported via a resonant process and have no temperature dependence. The small Ea values of CTEs suggest that exciton transport takes place via a thermal hopping process in CTEs. The present experimental study provides information on nano-scaled exciton dynamics in a well-defined PTCDI-C8 (2 ML/QT (2 ML system.

  13. Alterations in ovarian cancer cell adhesion drive taxol resistance by increasing microtubule dynamics in a FAK-dependent manner.

    Science.gov (United States)

    McGrail, Daniel J; Khambhati, Niti N; Qi, Mark X; Patel, Krishan S; Ravikumar, Nithin; Brandenburg, Chandler P; Dawson, Michelle R

    2015-04-17

    Chemorefractory ovarian cancer patients show extremely poor prognosis. Microtubule-stabilizing Taxol (paclitaxel) is a first-line treatment against ovarian cancer. Despite the close interplay between microtubules and cell adhesion, it remains unknown if chemoresistance alters the way cells adhere to their extracellular environment, a process critical for cancer metastasis. To investigate this, we isolated Taxol-resistant populations of OVCAR3 and SKOV3 ovarian cancer cell lines. Though Taxol-resistant cells neither effluxed more drug nor gained resistance to other chemotherapeutics, they did display increased microtubule dynamics. These changes in microtubule dynamics coincided with faster attachment rates and decreased adhesion strength, which correlated with increased surface β1-integrin expression and decreased focal adhesion formation, respectively. Adhesion strength correlated best with Taxol-sensitivity, and was found to be independent of microtubule polymerization but dependent on focal adhesion kinase (FAK), which was up-regulated in Taxol-resistant cells. FAK inhibition also decreased microtubule dynamics to equal levels in both populations, indicating alterations in adhesive signaling are up-stream of microtubule dynamics. Taken together, this work demonstrates that Taxol-resistance dramatically alters how ovarian cancer cells adhere to their extracellular environment causing down-stream increases in microtubule dynamics, providing a therapeutic target that may improve prognosis by not only recovering drug sensitivity, but also decreasing metastasis.

  14. Static and Dynamic Mechanics Analysis on Artificial Hip Joints with Different Interface Designs by the Finite Element Method

    Institute of Scientific and Technical Information of China (English)

    Hai-bo Jiang

    2007-01-01

    Four different structural models of artificial joints were developed and the finite element method (FEM) was employed to investigate their mechanical characteristics under static and dynamic conditions. The materials used in the FEM calculation were ultra-high molecular weight polyethylene (UHMWPE), 316L stainless steel, CoCrMo alloy and Ti6A14V alloy. The stress distribution, strain, and elastic deformation under static and dynamic conditions were obtained. Analysis and comparison of the calculation results of different models were conducted. It is shown that with the same parameters the model of a metallic femur head covered with an artificial cartilage layer is more similar to the structure of the natural human joint and its mechanical characteristics are the best of the four models.

  15. Exploring the Altered Dynamics of Mammalian Central Carbon Metabolic Pathway in Cancer Cells: A Classical Control Theoretic Approach.

    Directory of Open Access Journals (Sweden)

    Debjyoti Paul

    Full Text Available In contrast with normal cells, most of the cancer cells depend on aerobic glycolysis for energy production in the form of adenosine triphosphate (ATP bypassing mitochondrial oxidative phosphorylation. Moreover, compared to normal cells, cancer cells exhibit higher consumption of glucose with higher production of lactate. Again, higher rate of glycolysis provides the necessary glycolytic intermediary precursors for DNA, protein and lipid synthesis to maintain high active proliferation of the tumor cells. In this scenario, classical control theory based approach may be useful to explore the altered dynamics of the cancer cells. Since the dynamics of the cancer cells is different from that of the normal cells, understanding their dynamics may lead to development of novel therapeutic strategies.We have developed a model based on the state space equations of classical control theory along with an order reduction technique to mimic the actual dynamic behavior of mammalian central carbon metabolic (CCM pathway in normal cells. Here, we have modified Michaelis Menten kinetic equation to incorporate feedback mechanism along with perturbations and cross talks associated with a metabolic pathway. Furthermore, we have perturbed the proposed model to reduce the mitochondrial oxidative phosphorylation. Thereafter, we have connected proportional-integral (PI controller(s with the model for tuning it to behave like the CCM pathway of a cancer cell. This methodology allows one to track the altered dynamics mediated by different enzymes.The proposed model successfully mimics all the probable dynamics of the CCM pathway in normal cells. Moreover, experimental results demonstrate that in cancer cells, a coordination among enzymes catalyzing pentose phosphate pathway and intermediate glycolytic enzymes along with switching of pyruvate kinase (M2 isoform plays an important role to maintain their altered dynamics.

  16. Development of in-situ observation system of dynamic contact interface between dies and materials during microforming operation

    Directory of Open Access Journals (Sweden)

    Shimizu Tetsuhide

    2015-01-01

    Full Text Available Application of diamond like carbon (DLC films are reported in several microforming processes, in view of its great tribological performance owe to the low friction and the high chemical stability. However, due to its high internal residual stress, the film properties with the low adhesion strength and the high wear rate under severe tribological conditions are still remain as technical issues. However, since the dynamic variation of the contact state cannot be observed during the forming operation, it is difficult to recognize the origin and the influential tribological factors of tool life for DLC coated microforming die. Therefore, the appropriate DLC film properties for the contact state in microforming operation have not been clarified. To observe the dynamic variation of the contact state during the microforming operation, present study developed a novel microforming die assembly installed the in-situ observation system with silica glass die and high speed recording camera. By using this system, the dynamic delamination behaviour of DLC films during the progressive micro-bending process was successfully demonstrated. The influential factors for the durability of DLC coated microdies were discussed.

  17. 3D quantification of dynamic fluid-fluid interfaces in porous media with fast x-ray microtomography: A comparison with quasi-equilibrium methods

    Science.gov (United States)

    Meisenheimer, D.; Brueck, C. L.; Wildenschild, D.

    2015-12-01

    X-ray microtomography imaging of fluid-fluid interfaces in three-dimensional porous media allows for the testing of thermodynamically derived predictions that seek a unique relationship between capillary pressure, fluid saturation, and specific interfacial area (Pc-Sw-Anw). Previous experimental studies sought to test this functional dependence under quasi-equilibrium conditions (assumed static on the imaging time-scale); however, applying predictive models developed under static conditions for dynamic scenarios can lead to substantial flaws in predicted outcomes. Theory and models developed using dynamic data can be verified using fast x-ray microtomography which allows for the unprecedented measurement of developing interfacial areas, curvatures, and trapping behaviors of fluid phases in three-dimensional systems. We will present results of drainage and imbibition experiments of air and water within a mixture of glass beads. The experiments were performed under both quasi-equilibrium and dynamic conditions at the Advanced Photon Source (APS) at Argonne National Laboratory. Fast x-ray microtomography was achieved by utilizing the high brilliance of the x-ray beam at the APS under pink-beam conditions where the white beam is modified with a 4 mm Al absorber and a 0.8 mrad Pt-coated mirror to eliminate low and high-energy photons, respectively. We present a comparison of the results from the quasi-equilibrium and dynamic experiments in an effort to determine if the Pc-Sw-Anw relationship is comparable under either experimental condition and to add to the discussion on whether the Pc-Sw-Anw relationship is unique as hypothesized by existing theory.

  18. Macroscopic coherent structures in a stochastic neural network: from interface dynamics to coarse-grained bifurcation analysis.

    Science.gov (United States)

    Avitable, Daniele; Wedgwood, Kyle C A

    2017-02-01

    We study coarse pattern formation in a cellular automaton modelling a spatially-extended stochastic neural network. The model, originally proposed by Gong and Robinson (Phys Rev E 85(5):055,101(R), 2012), is known to support stationary and travelling bumps of localised activity. We pose the model on a ring and study the existence and stability of these patterns in various limits using a combination of analytical and numerical techniques. In a purely deterministic version of the model, posed on a continuum, we construct bumps and travelling waves analytically using standard interface methods from neural field theory. In a stochastic version with Heaviside firing rate, we construct approximate analytical probability mass functions associated with bumps and travelling waves. In the full stochastic model posed on a discrete lattice, where a coarse analytic description is unavailable, we compute patterns and their linear stability using equation-free methods. The lifting procedure used in the coarse time-stepper is informed by the analysis in the deterministic and stochastic limits. In all settings, we identify the synaptic profile as a mesoscopic variable, and the width of the corresponding activity set as a macroscopic variable. Stationary and travelling bumps have similar meso- and macroscopic profiles, but different microscopic structure, hence we propose lifting operators which use microscopic motifs to disambiguate them. We provide numerical evidence that waves are supported by a combination of high synaptic gain and long refractory times, while meandering bumps are elicited by short refractory times.

  19. The impact of Au doping on the charge carrier dynamics at the interfaces between cationic porphyrin and silver nanoclusters

    KAUST Repository

    Almansaf, Abdulkhaleq A.

    2017-02-04

    We explore the impact of Au doping on the charge transfer dynamics between the positively charged porphyrin (TMPyP) and negatively charged silver nanoclusters (Ag29 NCs). Our transient absorption (TA) spectroscopic results demonstrate that the interfacial charge transfer, the intersystem crossing and the triplet state lifetime of porphyrin can be tuned by the doping of Au atoms in Ag29 NCs. Additionally, we found that the electrostatic interaction between the negative charge of the cluster and the positive charge on the TMPyP is the driving force that brings them close to each other for complex formation and subsequently facilitates the transfer process.

  20. Assessing Tumor Response to Treatment in Patients with Lung Cancer Using Dynamic Contrast-Enhanced CT

    Directory of Open Access Journals (Sweden)

    Louise S. Strauch

    2016-07-01

    Full Text Available The aim of this study was to provide an overview of the literature available on dynamic contrast-enhanced computed tomography (DCE-CT as a tool to evaluate treatment response in patients with lung cancer. This systematic review was compiled according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA guidelines. Only original research articles concerning treatment response in patients with lung cancer assessed with DCE-CT were included. To assess the validity of each study we implemented Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2. The initial search yielded 651 publications, and 16 articles were included in this study. The articles were divided into groups of treatment. In studies where patients were treated with systemic chemotherapy with or without anti-angiogenic drugs, four out of the seven studies found a significant decrease in permeability after treatment. Four out of five studies that measured blood flow post anti-angiogenic treatments found that blood flow was significantly decreased. DCE-CT may be a useful tool in assessing treatment response in patients with lung cancer. It seems that particularly permeability and blood flow are important perfusion values for predicting treatment outcome. However, the heterogeneity in scan protocols, scan parameters, and time between scans makes it difficult to compare the included studies.

  1. A dynamical perspective of CTL cross-priming and regulation: implications for cancer immunology.

    Science.gov (United States)

    Wodarz, Dominik; Jansen, Vincent A A

    2003-05-01

    Cytotoxic T lymphocytes (CTL) responses are required to fight many diseases such as viral infections and tumors. At the same time, they can cause disease when induced inappropriately. Which factors regulate CTL and decide whether they should remain silent or react is open to debate. The phenomenon called cross-priming has received attention in this respect. That is, CTL expansion occurs if antigen is recognized on the surface of professional antigen presenting cells (APCs). This is in contrast to direct presentation where antigen is seen on the surface of the target cells (e.g. infected cells or tumor cells). Here we introduce a mathematical model, which takes the phenomenon of cross-priming into account. We propose a new mechanism of regulation which is implicit in the dynamics of the CTL: According to the model, the ability of a CTL response to become established depends on the ratio of cross-presentation to direct presentation of the antigen. If this ratio is relatively high, CTL responses are likely to become established. If this ratio is relatively low, tolerance is the likely outcome. The behavior of the model includes a parameter region where the outcome depends on the initial conditions. We discuss our results with respect to the idea of self/non-self discrimination and the danger signal hypothesis. We apply the model to study the role of CTL in cancer initiation, cancer evolution/progression, and therapeutic vaccination against cancers.

  2. Interface dermatitis

    Directory of Open Access Journals (Sweden)

    Rajiv Joshi

    2013-01-01

    Full Text Available Interface dermatitis includes diseases in which the primary pathology involves the dermo-epidermal junction. The salient histological findings include basal cell vacuolization, apoptotic keratinocytes (colloid or Civatte bodies, and obscuring of the dermo-epidermal junction by inflammatory cells. Secondary changes of the epidermis and papillary dermis along with type, distribution and density of inflammatory cells are used for the differential diagnoses of the various diseases that exhibit interface changes. Lupus erythematosus, dermatomyositis, lichen planus, graft versus host disease, erythema multiforme, fixed drug eruptions, lichen striatus, and pityriasis lichenoides are considered major interface diseases. Several other diseases (inflammatory, infective, and neoplastic may show interface changes.

  3. Correlation of the depletion layer with the Helmholtz layer in the anatase TiO2-H2O interface via molecular dynamics simulations.

    Science.gov (United States)

    Sang, Lixia; Zhang, Yudong; Wang, Jun; Zhao, Yangbo; Chen, Yi-Tung

    2016-06-01

    Molecular dynamics simulations have been conducted to study the interaction between anatase TiO2(001), (100), and (101) surfaces and water at room temperature. The dynamic interfacial structure and properties of water on anatase TiO2 surfaces are obtained by analyzing the water density, the diffusion coefficient of water, the surface charge distribution, electric fields and the electrostatic potential distribution. The simulation results have revealed that a highly-ordered water layer structure can be formed near to the anatase TiO2 surface and have also given the Helmholtz layer width and potential drop at the water-TiO2 interface. By correlating the Helmholtz layer with the depletion layer, the depletion layer widths of three surfaces (001), (100), and (101) have been calculated as 474 Å, 237 Å and 99 Å, respectively. The resulting order of the photoelectrochemical activity of the anatase TiO2 surfaces is (001) > (100) > (101), which is consistent with the experimental results. This study may provide a useful correlation of the depletion layer with the Helmholtz layer based on simulations results for the prediction of the behavior and the control of photon-energy conversion devices.

  4. DYNAMICS OF ON-DISK PLUMES AS OBSERVED WITH THE INTERFACE REGION IMAGING SPECTROGRAPH, THE ATMOSPHERIC IMAGING ASSEMBLY, AND THE HELIOSEISMIC AND MAGNETIC IMAGER

    Energy Technology Data Exchange (ETDEWEB)

    Pant, Vaibhav; Mazumder, Rakesh; Banerjee, Dipankar; Panditi, Vemareddy [Indian Institute of Astrophysics, Koramangala, Bangalore 560034 (India); Dolla, Laurent [Solar-Terrestrial Center of Excellence, Royal Observatory of Belgium, Avenue Circulaire 3, B-1180 Brussels (Belgium); Prasad, S. Krishna, E-mail: vaibhav@iiap.res.in [Astrophysics Research Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN (United Kingdom)

    2015-07-01

    We examine the role of small-scale transients in the formation and evolution of solar coronal plumes. We study the dynamics of plume footpoints seen in the vicinity of a coronal hole using the Atmospheric Imaging Assembly (AIA) images, the Helioseismic and Magnetic Imager magnetogram on board the Solar Dynamics Observatory and spectroscopic data from the Interface Region Imaging Spectrograph (IRIS). Quasi-periodic brightenings are observed in the base of the plumes and are associated with magnetic flux changes. With the high spectral and spatial resolution of IRIS, we identify the sources of these oscillations and try to understand what role the transients at the footpoints can play in sustaining the coronal plumes. IRIS “sit-and-stare” observations provide a unique opportunity to study the evolution of footpoints of the plumes. We notice enhanced line width and intensity, and large deviation from the average Doppler shift in the line profiles at specific instances, which indicate the presence of flows at the footpoints of plumes. We propose that outflows (jet-like features) as a result of small-scale reconnections affect the line profiles. These jet-like features may also be responsible for the generation of propagating disturbances (PDs) within the plumes, which are observed to be propagating to larger distances as recorded from multiple AIA channels. These PDs can be explained in terms of slow magnetoacoustic waves.

  5. Supramolecular control of the spin-dependent dynamics of long-lived charge-separated states at the micellar interface as studied by magnetic field effect.

    Science.gov (United States)

    Miura, Tomoaki

    2013-05-30

    Spin selectivity in long-lived charge separation at the micellar interface is studied using the magnetic field effect (MFE). An amphiphilic viologen is complexed with a nonionic surfactant to form a supramolecular acceptor cage, of which the size is controlled by the acceptor concentration, as confirmed by dynamic light scattering measurement. Photoinduced electron transfer (ET) from a guest polyaromatic molecule to the viologen moiety is observed spin-dependently with time-resolved fluorescence (trFL) and transient absorption (TA). A negative MFE on the radical yield is successfully observed, which indicates generation of singlet-born long-lived radical pair that is realized by supramolecular control of the donor-acceptor (D-A) distances. The dominance of the singlet-precursor MFE is sensitive to the acceptor concentration, which presumably affects the D-A distance as well as the cage size. However, theoretical analysis of the MFE gives large recombination rates of ca. 10(8) s(-1), which indicate the contribution of spin-allowed recombination of the pseudocontact radical pair generated by still active in-cage diffusion. Dependence of the viologen concentration and alkyl chain length on the recombination and escape dynamics is discussed in terms of precursor spin states and the microenvironments in the cage.

  6. A qualitative analysis of changes in relationship dynamics and roles between people with cancer and their primary informal carer.

    Science.gov (United States)

    Ussher, Jane M; Tim Wong, W K; Perz, Janette

    2011-11-01

    It is widely accepted that cancer is an intersubjective experience that impacts upon the psychological well-being of people with cancer and informal carers, as well as on couple relationships. This qualitative study examined the nature and consequences of cancer on the relationship between informal carers and the person with cancer, from the perspective of Australian cancer carers. Sixty-two carers (42 women and 20 men), across a range of cancer types, stages and relationship dyads took part in semi-structured interviews. Participants reported that cancer had precipitated a change in roles and in the dynamics of the relationship, including having to take on quasi-medical tasks and decisions, neglecting self and other relationships, changes to the emotions or personality of the person with cancer, changed patterns of communication, and changes to sexuality and intimacy. The impact of the changed relationship included sadness, anger and frustration, as well as feelings of love and being closer together, resulting in relationship enhancement. Women were more likely to report changes in the person with cancer and to mourn the previous relationship, while more men reported relationship enhancement.

  7. The dynamics and prognostic potential of DNA methylation changes at stem cell gene loci in women's cancer.

    Directory of Open Access Journals (Sweden)

    Joanna Zhuang

    2012-02-01

    Full Text Available Aberrant DNA methylation is an important cancer hallmark, yet the dynamics of DNA methylation changes in human carcinogenesis remain largely unexplored. Moreover, the role of DNA methylation for prediction of clinical outcome is still uncertain and confined to specific cancers. Here we perform the most comprehensive study of DNA methylation changes throughout human carcinogenesis, analysing 27,578 CpGs in each of 1,475 samples, ranging from normal cells in advance of non-invasive neoplastic transformation to non-invasive and invasive cancers and metastatic tissue. We demonstrate that hypermethylation at stem cell PolyComb Group Target genes (PCGTs occurs in cytologically normal cells three years in advance of the first morphological neoplastic changes, while hypomethylation occurs preferentially at CpGs which are heavily Methylated in Embryonic Stem Cells (MESCs and increases significantly with cancer invasion in both the epithelial and stromal tumour compartments. In contrast to PCGT hypermethylation, MESC hypomethylation progresses significantly from primary to metastatic cancer and defines a poor prognostic signature in four different gynaecological cancers. Finally, we associate expression of TET enzymes, which are involved in active DNA demethylation, to MESC hypomethylation in cancer. These findings have major implications for cancer and embryonic stem cell biology and establish the importance of systemic DNA hypomethylation for predicting prognosis in a wide range of different cancers.

  8. Dynamic volume perfusion CT in patients with lung cancer: Baseline perfusion characteristics of different histological subtypes

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Jingyun, E-mail: shijingyun89179@126.com [Department of Radiology, Shanghai Pulmonary Hospital, Tongji University School of Medicine (China); Institute of Clinical Radiology and Nuclear Medicine, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim (Germany); Schmid-Bindert, Gerald, E-mail: gerald.schmid-bindert@medma.uni-heidelberg.de [Division of Surgical Oncology and Thoracic Surgery, Department of Surgery, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim (Germany); Fink, Christian, E-mail: Christian.Fink@akh-celle.de [Institute of Clinical Radiology and Nuclear Medicine, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim (Germany); Sudarski, Sonja, E-mail: sonja_sudarski@gmx.de [Institute of Clinical Radiology and Nuclear Medicine, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim (Germany); Apfaltrer, Paul, E-mail: Paul.Apfaltrer@medma.uni-heidelberg.de [Institute of Clinical Radiology and Nuclear Medicine, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim (Germany); Pilz, Lothar R., E-mail: Lothar.Pilz@medma.uni-heidelberg.de [Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1, 68167 Mannheim (Germany); Liu, Bo, E-mail: bo.liu@siemens.com [Siemens Healthcare, No. 278, Zhouzhu Road, Shanghai, 201318 (China); Haberland, Ulrike, E-mail: ulrike.haberland@siemens.com [Siemens Healthcare Sector, H IM CR R and D PA SC, Siemensstraße 1, 91301 Forchheim (Germany); Klotz, Ernst, E-mail: ernst.klotz@siemens.com [Siemens Healthcare Sector, H IM CR R and D PA SC, Siemensstraße 1, 91301 Forchheim (Germany); and others

    2013-12-01

    Objective: To evaluate dynamic volume perfusion CT (dVPCT) tumor baseline characteristics of three different subtypes of lung cancer in untreated patients. Materials and methods: 173 consecutive patients (131 men, 42 women; mean age 61 ± 10 years) with newly diagnosed lung cancer underwent dVPCT prior to biopsy. Tumor permeability, blood flow (BF), blood volume (BV) and mean transit time (MTT) were quantitatively assessed as well as tumor diameter and volume. Tumor subtypes were histologically determined and compared concerning their dVPCT results. dVPCT results were correlated to tumor diameter and volume. Results: Histology revealed adenocarcinoma in 88, squamous cell carcinoma in 54 and small cell lung cancer (SCLC) in 31 patients. Tumor permeability was significantly differing between adenocarcinoma, squamous cell carcinoma and SCLC (all p < 0.05). Tumor BF and BV were higher in adenocarcinomathan in SCLC (p = 0.001 and p = 0.0002 respectively). BV was also higher in squamous cell carcinoma compared to SCLC (p = 0.01). MTT was not differing between tumor subtypes. Regarding all tumors, tumor diameter did not correlate with any of the dVPCT parameters, whereas tumor volume was negatively associated with permeability, BF and BV (r = −0.22, −0.24, −0.24, all p < 0.05). In squamous cell carcinoma, tumor diameter und volume correlated with BV (r = 0.53 and r = −0.40, all p < 0.05). In SCLC, tumor diameter und volume correlated with MTT (r = 0.46 and r = 0.39, all p < 0.05). In adenocarcinoma, no association between morphological and functional tumor characteristics was observed. Conclusions: dVPCT parameters are only partially related to tumor diameter and volume and are significantly differing between lung cancer subtypes.

  9. Photochemistry at Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Eisenthal, Kenneth B [Columbia Univ., New York, NY (United States)

    2015-02-24

    We have advanced our capabilities to investigate ultrafast excited state dynamics at a liquid interface using a pump to excite molecules to higher electronic states and then probe the subsequent time evolution of the interfacial molecules with femtosecond time delayed vibrational SFG.

  10. The impact of different phytosterols on the molecular dynamics in the hydrophobic/hydrophilic interface phosphatidylcholine- liposomes

    DEFF Research Database (Denmark)

    Hellgren, Lars; Sandelius, A.S.

    2001-01-01

    Plant sterols differ from cholesterol in having an alkyl group at Delta -24, and, in the case of stigmasterol, also a Delta -22 double bond. The effects of 10 mol% of three plant sterols (campesterol, fl-sitosterol, stigmasterol) and cholesterol on the molecular dynamics and phase behavior...... of dipolar relaxation of water molecules close to the glycerol backbone of PC. Our results showed that the Delta -24 alkyl group of plant sterols did not affect their ability to reduce molecular mobility in this region of the PC membranes. However, the plant sterols had a decreased capacity compared...... to cholesterol to inhibit formation of co-existing domains of gel and liquid-crystalline phases in membranes composed of equimolar dilauroyl-PC and dipalmitoyl-PC. The Delta -22 double bond present in stigmasterol decreased the ability of this sterol, compared to the other phytosterols, to reduce the molecular...

  11. Dynamics of a morbillivirus at the domestic-wildlife interface: Canine distemper virus in domestic dogs and lions.

    Science.gov (United States)

    Viana, Mafalda; Cleaveland, Sarah; Matthiopoulos, Jason; Halliday, Jo; Packer, Craig; Craft, Meggan E; Hampson, Katie; Czupryna, Anna; Dobson, Andrew P; Dubovi, Edward J; Ernest, Eblate; Fyumagwa, Robert; Hoare, Richard; Hopcraft, J Grant C; Horton, Daniel L; Kaare, Magai T; Kanellos, Theo; Lankester, Felix; Mentzel, Christine; Mlengeya, Titus; Mzimbiri, Imam; Takahashi, Emi; Willett, Brian; Haydon, Daniel T; Lembo, Tiziana

    2015-02-03

    Morbilliviruses cause many diseases of medical and veterinary importance, and although some (e.g., measles and rinderpest) have been controlled successfully, others, such as canine distemper virus (CDV), are a growing concern. A propensity for host-switching has resulted in CDV emergence in new species, including endangered wildlife, posing challenges for controlling disease in multispecies communities. CDV is typically associated with domestic dogs, but little is known about its maintenance and transmission in species-rich areas or about the potential role of domestic dog vaccination as a means of reducing disease threats to wildlife. We address these questions by analyzing a long-term serological dataset of CDV in lions and domestic dogs from Tanzania's Serengeti ecosystem. Using a Bayesian state-space model, we show that dynamics of CDV have changed considerably over the past three decades. Initially, peaks of CDV infection in dogs preceded those in lions, suggesting that spill-over from dogs was the main driver of infection in wildlife. However, despite dog-to-lion transmission dominating cross-species transmission models, infection peaks in lions became more frequent and asynchronous from those in dogs, suggesting that other wildlife species may play a role in a potentially complex maintenance community. Widespread mass vaccination of domestic dogs reduced the probability of infection in dogs and the size of outbreaks but did not prevent transmission to or peaks of infection in lions. This study demonstrates the complexity of CDV dynamics in natural ecosystems and the value of long-term, large-scale datasets for investigating transmission patterns and evaluating disease control strategies.

  12. Investigation of the electron dynamics at the PTCDA/Ag(111)-interface; Untersuchung der Elektronendynamik an der PTCDA-Ag (111) - Grenzflaeche

    Energy Technology Data Exchange (ETDEWEB)

    Schwalb, Christian

    2008-12-17

    In this work the electron dynamics at the PTCDA/Ag(111) interface have been studied with time- and angleresolved Two-photon photoemission (2PPE) as well as time-resolved photoluminescence (PL). The first part of this work concentrates on the characterization of an unoccupied electronic state, that develops 0.6 eV above the Fermi level due to the adsorption of the PTCDA molecules, whereas the shockley surface state of the clean surface vanishes. The measurements clearly identify this state as an interface state that is located between the metal surface and the first layer of the molecules. Dispersion measurements yield an effective mass of this state of 0.39 m{sub e} at the Gamma-point and show backfolding at the zone boundaries of the rectangular PTCDA unit cell. Time-resolved measurements show a surprisingly short lifetime of t=54 fs, clearly indicating a strong coupling of the state with the metal. This behaviour can be explained by a shift of the shockley surface state. This for the clean Ag(111)-surface normally occupied state shifts above the Fermi level because of the highly polarizable PTCDA molecules. Calculations with a one dimensional model potential support this interpretation. Angleresolved lifetime measurements as a function of parallel momentum show a correlation of the decay dynamics of the interface state with the measured bandstructure. The observed drop of the lifetime for larger parallel momentum is significantly smaller as expected for the pure shockley state. This behaviour can be explained due to a hybridisation of the shockley state with the LUMO+1 of the first PTCDA monolayer for k parallel >>0. The second part of this work deals with the intramolecular excitation at the PTCDA/Ag(111) interface after excitation with laser pulses with 2.33 eV and 4.66 eV photon energy. Time-resolved photoluminescence measurements show a strong rise in the PL-lifetime as a function of PTCDA coverage, that can be explained by an increase in the crystallinity of

  13. Interface models

    DEFF Research Database (Denmark)

    Ravn, Anders P.; Staunstrup, Jørgen

    1994-01-01

    This paper proposes a model for specifying interfaces between concurrently executing modules of a computing system. The model does not prescribe a particular type of communication protocol and is aimed at describing interfaces between both software and hardware modules or a combination of the two...

  14. Fluid Interfaces

    DEFF Research Database (Denmark)

    Hansen, Klaus Marius

    2001-01-01

    Fluid interaction, interaction by the user with the system that causes few breakdowns, is essential to many user interfaces. We present two concrete software systems that try to support fluid interaction for different work practices. Furthermore, we present specificity, generality, and minimality...... as design goals for fluid interfaces....

  15. Testing Interfaces

    DEFF Research Database (Denmark)

    Holbøll, Joachim T.; Henriksen, Mogens; Nilson, Jesper K.;

    1999-01-01

    The wide use of solid insulating materials combinations in combinations has introduced problems in the interfaces between components. The most common insulating materials are cross-linked polyethylene (XLPE), silicone rubber (SIR) and ethylene-propylene rubbers (EPR). Assemblies of these materials...... have caused major failures. In the Netherlands, a major black out was caused by interface problems in 150kV cable terminations, causing a cascade of breakdowns. There is a need to investigate the reasons for this and other similar breakdowns.The major problem is expected to lie in the interface between...... two different materials. Environmental influence, surface treatment, defects in materials and interface, design, pressure and rubbing are believed to have an effect on interface degradation. These factors are believed to increase the possibility of partial discharges (PD). PD will, with time, destroy...

  16. Dynamic conformations of nucleophosmin (NPM1 at a key monomer-monomer interface affect oligomer stability and interactions with granzyme B.

    Directory of Open Access Journals (Sweden)

    Wei D Duan-Porter

    Full Text Available Nucleophosmin (NPM1 is an abundant, nucleolar tumor antigen with important roles in cell proliferation and putative contributions to oncogenesis. Wild-type NPM1 forms pentameric oligomers through interactions at the amino-terminal core domain. A truncated form of NPM1 found in some hepatocellular carcinoma tissue formed an unusually stable oligomer and showed increased susceptibility to cleavage by granzyme B. Initiation of translation at the seventh methionine generated a protein (M7-NPM that shared all these properties. We used deuterium exchange mass spectrometry (DXMS to perform a detailed structural analysis of wild-type NPM1 and M7-NPM, and found dynamic conformational shifts or local "unfolding" at a specific monomer-monomer interface which included the β-hairpin "latch." We tested the importance of interactions at the β-hairpin "latch" by replacing a conserved tyrosine in the middle of the β-hairpin loop with glutamic acid, generating Y67E-NPM. Y67E-NPM did not form stable oligomers and further, prevented wild-type NPM1 oligomerization in a dominant-negative fashion, supporting the critical role of the β-hairpin "latch" in monomer-monomer interactions. Also, we show preferential cleavage by granzyme B at one of two available aspartates (either D161 or D122 in M7-NPM and Y67E-NPM, whereas wild-type NPM1 was cleaved at both sites. Thus, we observed a correlation between the propensity to form oligomers and granzyme B cleavage site selection in nucleophosmin proteins, suggesting that a small change at an important monomer-monomer interface can affect conformational shifts and impact protein-protein interactions.

  17. Surface charge dynamics and OH and H number density distributions in near-surface nanosecond pulse discharges at a liquid / vapor interface

    Science.gov (United States)

    Winters, Caroline; Petrishchev, Vitaly; Yin, Zhiyao; Lempert, Walter R.; Adamovich, Igor V.

    2015-10-01

    The present work provides insight into surface charge dynamics and kinetics of radical species reactions in nanosecond pulse discharges sustained at a liquid-vapor interface, above a distilled water surface. The near-surface plasma is sustained using two different discharge configurations, a surface ionization wave discharge between two exposed metal electrodes and a double dielectric barrier discharge. At low discharge pulse repetition rates (~100 Hz), residual surface charge deposition after the discharge pulse is a minor effect. At high pulse repetition rates (~10 kHz), significant negative surface charge accumulation over multiple discharge pulses is detected, both during alternating polarity and negative polarity pulse trains. Laser induced fluorescence (LIF) and two-photon absorption LIF (TALIF) line imaging are used for in situ measurements of spatial distributions of absolute OH and H atom number densities in near-surface, repetitive nanosecond pulse discharge plasmas. Both in a surface ionization wave discharge and in a double dielectric barrier discharge, peak measured H atom number density, [H] is much higher compared to peak OH number density, due to more rapid OH decay in the afterglow between the discharge pulses. Higher OH number density was measured near the regions with higher plasma emission intensity. Both OH and especially H atoms diffuse out of the surface ionization wave plasma volume, up to several mm from the liquid surface. Kinetic modeling calculations using a quasi-zero-dimensional H2O vapor / Ar plasma model are in qualitative agreement with the experimental data. The results demonstrate the experimental capability of in situ radical species number density distribution measurements in liquid-vapor interface plasmas, in a simple canonical geometry that lends itself to the validation of kinetic models.

  18. Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models.

    Science.gov (United States)

    Bauer, Brad A; Zhong, Yang; Meninger, David J; Davis, Joseph E; Patel, Sandeep

    2011-04-01

    We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ɛ(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ɛ(||) for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13 and 198.7±0.01 mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for

  19. DMPD: Regulation of TLR4 signaling and the host interface with pathogens and danger:the role of RP105. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17470533 Regulation of TLR4 signaling and the host interface with pathogens and danger:the role...tion of TLR4 signaling and the host interface with pathogens and danger:the role ...of RP105. PubmedID 17470533 Title Regulation of TLR4 signaling and the host interface with pathogens and danger:the role

  20. Effects of oxygen and nitrogen gases on the dynamics between the interfaces of self-mated titanium pairs

    Directory of Open Access Journals (Sweden)

    Yuh-Ping Chang

    2016-04-01

    Full Text Available The chemical reactions of titanium in air include both TiO2 and TiN. The phenomena are quite complex, and the reaction mechanisms are still unclear. However, as titanium is in widespread use all over the world, it is important that the reaction mechanisms be thoroughly investigated. Therefore, in this study, the continuous variations in the electrical contact resistance and the friction coefficient are simultaneously measured to monitor the dynamics of self-mated titanium pairs in an air, O2 or N2 gas flow. When a large amount of TiO2 formed on the surface of the plate for Ti/Ti, the results showed the tribo-physical phenomena of higher electrical contact resistance, friction coefficient almost doubled and severe wear. When a large amount of TiN formed on the surface of the plate for Ti/Ti, the results showed the tribo-physical phenomena of lower electrical contact resistance, friction coefficient almost halved and mild wear with some lubrication. Therefore, variations in the electrical contact resistance can be applied to determine whether the chemical reaction on the surface was TiO2 or Ti with TiN. The unsymmetrical frictional models and wear mechanisms of the self-mated titanium pairs in the air, O2 or N2 gas flow were proposed.

  1. Molecular dynamics simulations of the structure of the graphene-ionic liquid/alkali salt mixtures interface.

    Science.gov (United States)

    Méndez-Morales, Trinidad; Carrete, Jesús; Pérez-Rodríguez, Martín; Cabeza, Óscar; Gallego, Luis J; Lynden-Bell, Ruth M; Varela, Luis M

    2014-07-14

    We performed molecular dynamics simulations of mixtures of 1-butyl-3-methylimidazolium tetrafluoroborate with lithium tetrafluoroborate and potassium tetrafluoroborate between two charged and uncharged graphene walls, in order to analyze the structure of the well-known formation of layers that takes place on liquids under confinement. For this purpose, we studied the molecular density profiles, free energy profiles for bringing lithium and potassium cations from the bulk mixture to the graphene wall and the orientational distributions of imidazolium rings within the first adsorbed layer as a function of salt concentration and electrode potential. The charge densities in the electrodes were chosen to be zero and ±1 e nm(-2), and the salt molar percentages were %salt = 0, 10 and 25. We found that the layered structure extends up to 1-2 nm, where the bulk behaviour is recovered. In addition, whereas for the neutral surface the layers are composed of both ionic species, increasing the electrode potential, the structure changes to alternating cationic and anionic layers leading to an overcompensation of the charge of the previous layer. We also calculated the distribution of angles of imidazolium rings near neutral and charged graphene walls, finding a limited influence of the added salt. In addition, the average tilt of the imidazolium ring within the first layer goes from 36° with respect to a normal vector to the uncharged graphene wall to 62° in the presence of charged walls. The free energy profiles revealed that lithium and potassium ions are adsorbed on the negative surface only for the highest amount of salt, since the free energy barriers for approaching this electrode are considerably higher than kBT.

  2. Microprocessor interfacing

    CERN Document Server

    Vears, R E

    2014-01-01

    Microprocessor Interfacing provides the coverage of the Business and Technician Education Council level NIII unit in Microprocessor Interfacing (syllabus U86/335). Composed of seven chapters, the book explains the foundation in microprocessor interfacing techniques in hardware and software that can be used for problem identification and solving. The book focuses on the 6502, Z80, and 6800/02 microprocessor families. The technique starts with signal conditioning, filtering, and cleaning before the signal can be processed. The signal conversion, from analog to digital or vice versa, is expl

  3. Dynamic transcription factor networks in epithelial-mesenchymal transition in breast cancer models.

    Science.gov (United States)

    Siletz, Anaar; Schnabel, Michael; Kniazeva, Ekaterina; Schumacher, Andrew J; Shin, Seungjin; Jeruss, Jacqueline S; Shea, Lonnie D

    2013-01-01

    The epithelial-mesenchymal transition (EMT) is a complex change in cell differentiation that allows breast carcinoma cells to acquire invasive properties. EMT involves a cascade of regulatory changes that destabilize the epithelial phenotype and allow mesenchymal features to manifest. As transcription factors (TFs) are upstream effectors of the genome-wide expression changes that result in phenotypic change, understanding the sequential changes in TF activity during EMT provides rich information on the mechanism of this process. Because molecular interactions will vary as cells progress from an epithelial to a mesenchymal differentiation program, dynamic networks are needed to capture the changing context of molecular processes. In this study we applied an emerging high-throughput, dynamic TF activity array to define TF activity network changes in three cell-based models of EMT in breast cancer based on HMLE Twist ER and MCF-7 mammary epithelial cells. The TF array distinguished conserved from model-specific TF activity changes in the three models. Time-dependent data was used to identify pairs of TF activities with significant positive or negative correlation, indicative of interdependent TF activity throughout the six-day study period. Dynamic TF activity patterns were clustered into groups of TFs that change along a time course of gene expression changes and acquisition of invasive capacity. Time-dependent TF activity data was combined with prior knowledge of TF interactions to construct dynamic models of TF activity networks as epithelial cells acquire invasive characteristics. These analyses show EMT from a unique and targetable vantage and may ultimately contribute to diagnosis and therapy.

  4. Dynamic transcription factor networks in epithelial-mesenchymal transition in breast cancer models.

    Directory of Open Access Journals (Sweden)

    Anaar Siletz

    Full Text Available The epithelial-mesenchymal transition (EMT is a complex change in cell differentiation that allows breast carcinoma cells to acquire invasive properties. EMT involves a cascade of regulatory changes that destabilize the epithelial phenotype and allow mesenchymal features to manifest. As transcription factors (TFs are upstream effectors of the genome-wide expression changes that result in phenotypic change, understanding the sequential changes in TF activity during EMT provides rich information on the mechanism of this process. Because molecular interactions will vary as cells progress from an epithelial to a mesenchymal differentiation program, dynamic networks are needed to capture the changing context of molecular processes. In this study we applied an emerging high-throughput, dynamic TF activity array to define TF activity network changes in three cell-based models of EMT in breast cancer based on HMLE Twist ER and MCF-7 mammary epithelial cells. The TF array distinguished conserved from model-specific TF activity changes in the three models. Time-dependent data was used to identify pairs of TF activities with significant positive or negative correlation, indicative of interdependent TF activity throughout the six-day study period. Dynamic TF activity patterns were clustered into groups of TFs that change along a time course of gene expression changes and acquisition of invasive capacity. Time-dependent TF activity data was combined with prior knowledge of TF interactions to construct dynamic models of TF activity networks as epithelial cells acquire invasive characteristics. These analyses show EMT from a unique and targetable vantage and may ultimately contribute to diagnosis and therapy.

  5. Subseafloor to Sea-Air Interface Characterization of Methane Dynamics in the northern US Atlantic Margin Seep Province

    Science.gov (United States)

    Ruppel, C. D.; Kluesner, J.; Danforth, W. W.; Casso, M.; Pohlman, J.

    2015-12-01

    Since the discovery of hundreds of northern US Atlantic margin (USAM) cold seeps in 2012 and 2013, the USGS Gas Hydrates Project has undertaken intensive studies of the along-margin gas hydrate/free gas distribution, the plumbing systems sustaining seeps, seafloor gas emissions, and sea-air methane flux. Interest in the USAM is motivated both by climate change (i.e., documented ocean warming may contribute to seepage) and energy resource (i.e., the amount of gas-in-place in hydrates on the USAM is about the same as that in the northern Gulf of Mexico) issues. USGS-led field efforts have included an April 2015 study to acquire high-resolution multichannel seismic data, coincident split-beam water column methane plume imaging data, and real-time sea-air methane flux measurements between Wilmington and Norfolk Canyons and a September 2015 cruise (with OSU, UCLA, and Geomar) to collect piston cores, multicores, heat flow data, subbottom imagery, CTDs, and coincident water column imagery from Block Canyon to the Currituck Slide. In April 2015, we discovered methane seeps not included in the previously-published database, but found that some known seeps were not active. New high-resolution multi-channel seismic data revealed clear differences between the deep gas distribution in mid-Atlantic upper slope zones that are replete with (up to 240 sites) and lacking in seeps. Based on sea-air flux measurements, even shallow-water outer shelf (~125 m water depth) seeps and a 900-m-high methane plume originating on the mid-slope do not contribute methane to the atmosphere. Using thermistors placed on piston core outriggers, we will in September 2015 acquire thermal data to identify zones of high fluid advection and to constrain background geotherms in areas where heat flow has never been measured. During that same cruise, we will collect a series of piston cores across the no-hydrate/hydrate transition on the upper slope to constrain fluid and gas dynamics in this zone.

  6. Pareto front analysis of 6 and 15 MV dynamic IMRT for lung cancer using pencil beam, AAA and Monte Carlo

    DEFF Research Database (Denmark)

    Ottosson, R O; Hauer, Anna Karlsson; Behrens, C.F.

    2010-01-01

    of motion on the dose distribution was investigated. Four non-small cell lung cancer cases were selected for this study. Inverse planning was conducted using Varian Eclipse. A total number of 31 dynamic IMRT plans, distributed amongst the four cases, were created ranging from PTV conformity weighted...

  7. Transforming growth factor-beta plasma dynamics and post-irradiation lung injury in lung cancer patients

    NARCIS (Netherlands)

    Novakova-Jiresova, A; van Gameren, MM; Coppes, RP; Kampinga, HH; Groen, HJM

    2004-01-01

    Purpose: To investigate the relevance of transforming growth factor-beta (TGF-beta) dynamics in plasma for identification of patients at low risk for developing pneumonitis as a complication of thoracic radiotherapy (RT). Patients and methods: Non-small cell lung cancer patients undergoing conventio

  8. Dynamic contrast-enhanced MRI for treatment response assessment in patients with oesophageal cancer receiving neoadjuvant chemoradiotherapy

    NARCIS (Netherlands)

    Heethuis, Sophie E.; van Rossum, Peter S N; Lips, IM; Goense, Lucas; Voncken, Francine E.; Reerink, Onne; van Hillegersberg, Richard; Ruurda, Jelle P.; Philippens, Marielle E.; van Vulpen, Marco; Meijer, Gert J.; Lagendijk, JJW; van Lier, A.L.H.M.W.

    2016-01-01

    Purpose To explore and evaluate the potential value of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) for the prediction of pathologic response to neoadjuvant chemoradiotherapy (nCRT) in oesophageal cancer. Material and methods Twenty-six patients underwent DCE-MRI before, during (

  9. The use of dynamic nuclear polarization 13C-pyruvate MRS in cancer

    DEFF Research Database (Denmark)

    Borgwardt, Henrik Gutte; Espe Hansen, Adam; Hjort Johannesen, Helle;

    2015-01-01

    In recent years there has been an immense development of new targeted anti-cancer drugs. For practicing precision medicine, a sensitive method imaging for non-invasive, assessment of early treatment response and for assisting in developing new drugs is warranted. Magnetic Resonance Spectroscopy...... (MRS) is a potent technique for non-invasive in vivo investigation of tissue chemistry and cellular metabolism. Hyperpolarization by Dynamic Nuclear Polarization (DNP) is capable of creating solutions of molecules with polarized nuclear spins in a range of biological molecules and has enabled the real......-time investigation of in vivo metabolism. The development of this new method has been demonstrated to enhance the nuclear polarization more than 10,000-fold, thereby significantly increasing the sensitivity of the MRS with a spatial resolution to the millimeters and a temporal resolution at the subsecond range...

  10. Clonal dynamics following p53 loss of heterozygosity in Kras-driven cancers

    Science.gov (United States)

    Muzumdar, Mandar Deepak; Dorans, Kimberly Judith; Chung, Katherine Minjee; Robbins, Rebecca; Tammela, Tuomas; Gocheva, Vasilena; Li, Carman Man-Chung; Jacks, Tyler

    2016-01-01

    Although it has become increasingly clear that cancers display extensive cellular heterogeneity, the spatial growth dynamics of genetically distinct clones within developing solid tumours remain poorly understood. Here we leverage mosaic analysis with double markers (MADM) to trace subclonal populations retaining or lacking p53 within oncogenic Kras-initiated lung and pancreatic tumours. In both models, p53 constrains progression to advanced adenocarcinomas. Comparison of lineage-related p53 knockout and wild-type clones reveals a minor role of p53 in suppressing cell expansion in lung adenomas. In contrast, p53 loss promotes both the initiation and expansion of low-grade pancreatic intraepithelial neoplasia (PanINs), likely through differential expression of the p53 regulator p19ARF. Strikingly, lineage-related cells are often dispersed in lung adenomas and PanINs, contrasting with more contiguous growth of advanced subclones. Together, these results support cancer type-specific suppressive roles of p53 in early tumour progression and offer insights into clonal growth patterns during tumour development. PMID:27585860

  11. Steroid hormone receptors and prostate cancer: role of structural dynamics in therapeutic targeting

    Directory of Open Access Journals (Sweden)

    Raj Kumar

    2016-01-01

    Full Text Available Steroid hormone receptors (SHRs act in cell type- and gene-specific manner through interactions with coregulatory proteins to regulate numerous physiological and pathological processes at the level of gene regulation. Binding of steroid receptor modulator (SRM ligand leads to allosteric changes in SHR to exert positive or negative effects on the expression of target genes. Due, in part, to the fact that current SRMs generally target ligand binding domain (LBD/AF2 and neglect intrinsically disordered (ID N-terminal domain (NTD/AF1, clinically relevant SRMs lack selectivity and are also prone to the development of resistance over time. Therefore, to maximize the efficacy of SHR-based therapeutics, the possibility of developing unique modulators that act to control AF1 activity must be considered. Recent studies targeting androgen receptor′s (AR′s ID AF1 domain for the castration-resistant prostate cancer has provided the possibility of therapeutically targeting ID NTD/AF1 surfaces by allosteric modulations to achieve desired effects. In this review article, we discuss how inter- and intra- molecular allosteric regulations controlled by AR′s structural flexibility and dynamics particularly the ID NTD/AF1 is an emerging area of investigation, which could be exploited for drug development and therapeutic targeting of prostate cancer.

  12. Direct observation of key photoinduced dynamics in a potential nano-delivery vehicle of cancer drugs.

    Science.gov (United States)

    Sardar, Samim; Chaudhuri, Siddhi; Kar, Prasenjit; Sarkar, Soumik; Lemmens, Peter; Pal, Samir Kumar

    2015-01-01

    In recent times, significant achievements in the use of zinc oxide (ZnO) nanoparticles (NPs) as delivery vehicles of cancer drugs have been made. The present study is an attempt to explore the key photoinduced dynamics in ZnO NPs upon complexation with a model cancer drug protoporphyrin IX (PP). The nanohybrid has been characterized by FTIR, Raman scattering and UV-Vis absorption spectroscopy. Picosecond-resolved Förster resonance energy transfer (FRET) from the defect mediated emission of ZnO NPs to PP has been used to study the formation of the nanohybrid at the molecular level. Picosecond-resolved fluorescence studies of PP-ZnO nanohybrids reveal efficient electron migration from photoexcited PP to ZnO, eventually enhancing the ROS activity. The dichlorofluorescin (DCFH) oxidation and no oxidation of luminol in PP/PP-ZnO nanohybrids upon green light illumination unravel that the nature of ROS is essentially singlet oxygen rather than superoxide anions. Surface mediated photocatalysis of methylene blue (MB) in an aqueous solution of the nanohybrid has also been investigated. Direct evidence of the role of electron transfer as a key player in enhanced ROS generation from the nanohybrid is also clear from the photocurrent measurement studies. We have also used the nanohybrid in a model photodynamic therapy application in a light sensitized bacteriological culture experiment.

  13. The complexity of cancer in multiple family members: dynamics of social work collaboration.

    Science.gov (United States)

    Snow, Alison; Gilbertson, Kristen

    2011-01-01

    This article presents a case study of one family affected by a cancer diagnosis in both the father and the daughter, who were diagnosed within the same time interval and who underwent treatment at the same time. The article examines the relationship between the caregivers and the oncology patient as well as with one another when the stress of diagnosis is compounded by multiple, simultaneous, and similar diagnoses in a highly condensed period of time. A thorough examination of the literature reveals that there are significant gaps regarding how multiple cancer diagnoses in one family affect the family dynamic, individual and collective coping styles, and caregiver burden. The diagnoses can also dramatically exacerbate economic stressors in a family. The coordination of psychosocial care from the perspectives of the adult and pediatric oncology social workers at an urban academic medical center will be discussed. The social work role, importance of collaboration, and family centered care perspective will be discussed as a method of easing the treatment experience for families in psychosocial distress.

  14. Steroid hormone receptors and prostate cancer: role of structural dynamics in therapeutic targeting

    Science.gov (United States)

    Kumar, Raj

    2016-01-01

    Steroid hormone receptors (SHRs) act in cell type- and gene-specific manner through interactions with coregulatory proteins to regulate numerous physiological and pathological processes at the level of gene regulation. Binding of steroid receptor modulator (SRM) ligand leads to allosteric changes in SHR to exert positive or negative effects on the expression of target genes. Due, in part, to the fact that current SRMs generally target ligand binding domain (LBD)/AF2 and neglect intrinsically disordered (ID) N-terminal domain (NTD)/AF1, clinically relevant SRMs lack selectivity and are also prone to the development of resistance over time. Therefore, to maximize the efficacy of SHR-based therapeutics, the possibility of developing unique modulators that act to control AF1 activity must be considered. Recent studies targeting androgen receptor's (AR's) ID AF1 domain for the castration-resistant prostate cancer has provided the possibility of therapeutically targeting ID NTD/AF1 surfaces by allosteric modulations to achieve desired effects. In this review article, we discuss how inter- and intra- molecular allosteric regulations controlled by AR's structural flexibility and dynamics particularly the ID NTD/AF1 is an emerging area of investigation, which could be exploited for drug development and therapeutic targeting of prostate cancer. PMID:27364545

  15. Interface Realisms

    DEFF Research Database (Denmark)

    Pold, Søren

    2005-01-01

    This article argues for seeing the interface as an important representational and aesthetic form with implications for postmodern culture and digital aesthetics. The interface emphasizes realism due in part to the desire for transparency in Human-Computer Interaction (HCI) and partly to the devel......This article argues for seeing the interface as an important representational and aesthetic form with implications for postmodern culture and digital aesthetics. The interface emphasizes realism due in part to the desire for transparency in Human-Computer Interaction (HCI) and partly...... to the development of illusionistic realism within computer graphics and games. The article compares the pragmatic realism of HCI with aesthetic notions of realism in the computer game Max Payne (illusionistic realism), the artist Jodi's game modifications (media realism), and Adrian Ward's software art work......, "Signwave Auto Illustrator" (functional realism)....

  16. Capillary flows with forming interfaces

    CERN Document Server

    Shikhmurzaev, Yulii D

    2007-01-01

    PREFACEINTRODUCTION Free-surface flows in nature and industryScope of the bookFUNDAMENTALS OF FLUID MECHANICS Main concepts Governing equations Elements of thermodynamics Classical boundary conditions Physically meaningful solutions and paradoxes of modelingMOVING CONTACT LINES: AN OVERVIEW Essence of the problem Experimental observations Molecular dynamics simulations Review of theoriesThe key to the moving contact-line problemBOUNDARY CONDITIONS ON FORMING INTERFACES Modeling of interfacesConservation lawsLiquid-gas and liquid-solid interfacesLiquid-liquid interfaces SummaryOpen questions an

  17. Wave operators, similarity and dynamics for a class of Schrödinger operators with generic non-mixed interface conditions in 1D

    Energy Technology Data Exchange (ETDEWEB)

    Mantile, Andrea [Laboratoire de Mathématiques, Université de Reims - FR3399 CNRS, Moulin de la Housse BP 1039, 51687 Reims (France)

    2013-08-15

    We consider a simple modification of the 1D-Laplacian where non-mixed interface conditions occur at the boundaries of a finite interval. It has recently been shown that Schrödinger operators having this form allow a new approach to the transverse quantum transport through resonant heterostructures. In this perspective, it is important to control the deformations effects introduced on the spectrum and on the time propagator by this class of non-selfadjoint perturbations. In order to obtain uniform-in-time estimates of the perturbed semigroup, our strategy consists in constructing stationary wave operators allowing to intertwine the modified non-selfadjoint Schrödinger operator with a “physical” Hamiltonian. For small values of a deformation parameter “θ,” this yields a dynamical comparison between the two models showing that the distance between the corresponding semigroups is dominated by ‖θ‖ uniformly in time in the L{sup 2}-operator norm.

  18. Dynamics of charge at water-to-semiconductor interface: Case study of wet [0 0 1] anatase TiO2 nanowire

    Science.gov (United States)

    Huang, Shuping; Balasanthiran, Choumini; Tretiak, Sergei; Hoefelmeyer, James D.; Kilina, Svetlana V.; Kilin, Dmitri S.

    2016-12-01

    The behavior of water molecules on the surfaces of the TiO2 nanowire grown in [0 0 1] direction has been investigated by combining theoretical calculations and experiments. Calculated UV-visible absorption spectra reproduce the main features of the experimental spectra. Computations predict that a photoexcitation followed by a sequence of relaxation events results in photoluminescence across the gap. TiO2 nanowires in vacuum and aqueous environment exhibit different dynamics of photo-excited charge carriers. In water, computed relaxation of electrons (holes) is approximately 2 (4) times faster compared with vacuum environment. Faster relaxation of holes vs. electrons and specific spatial localization of holes result to formation of long lived charge transfer excitation with positive charge at the surface of the nanowire. Comparison of relaxation process in TiO2/water interfaces focusing on different surfaces and nanostructures has potential in identifying structural characteristics of TiO2 materials important for efficient photo-electrochemical water splitting.

  19. Dynamic study of a sliding interface wear process of TiAlN and CrN multi-layers by X-ray absorption

    DEFF Research Database (Denmark)

    Rasmussen, Inge Lise; Guibert, M.; Belin, M.

    studies of hard coatings by SR are possible and that the tribological wear of a multi-layer system can be monitored with an embedded CrN marker layer. This was achieved by keeping the SR energy on the chromium K-edge energy (close to 6 keV), while a drop in absorption was monitored. The absorption drop...... in France. The contact under investigation (TiAlN/CrN/TiAlN (2000nm/1000nm/2000nm) multi-layer system) was exposed to a reciprocating sliding motion under a normal load. Simultaneously, the contact zone was submitted to a direct, focused and monochromatic SR photon beam. In this way we have studied...... indicates the marker layer is worn off and thus the wear process finished. The measurements of the wear during the sliding interface wear experiments were performed in-situ, with a special portable tribo-meter designed and build at Laboratory of Tribologi and System Dynamics, Ecole Centrale de Lyon...

  20. Utilizing multichannel electrical resistivity methods to examine the dynamics of the fresh water–seawater interface in two Hawaiian groundwater systems

    Science.gov (United States)

    Dimova, Natasha T.; Swarzenski, Peter W.; Dulaiova, Henrieta; Glenn, Craig R.

    2012-01-01

    Multichannel electrical resistivity (ER) measurements were conducted at two contrasting coastal sites in Hawaii to obtain new information on the spatial scales and dynamics of the fresh water–seawater interface and rates of coastal groundwater exchange. At Kiholo Bay (located on the dry, Kona side of the Big Island) and at a site in Maunalua Bay (Oahu), there is an evidence for abundant submarine groundwater discharge (SGD). However, the hydrologic and geologic controls on coastal groundwater discharge are likely to be different at these two sites. While at Kiholo Bay SGD is predominantly through lava tubes, at the Maunalua Bay site exchange occurs mostly through nearshore submarine springs. In order to calculate SGD fluxes, it is important to understand the spatial and temporal scales of coastal groundwater exchange. From ER time series data, subsurface salinity distributions were calculated using site-specific formation factors. A salinity mass balance box model was then used to calculate rates of point source (i.e., spatially discreet) and total fresh water discharge. From these data, mean SGD rates were calculated for Kiholo Bay (∼9,200 m3/d) and for the Maunalua Bay site (∼5,900 m3/d). While such results are on the same order of magnitude to geochemical tracer-derived SGD rates, the ER SGD rates provide enhanced details of coastal groundwater exchange that can enable a more cohesive whole watershed perspective.

  1. Influence of ester and ether linkage in phospholipids on the environment and dynamics of the membrane interface: a wavelength-selective fluorescence approach.

    Science.gov (United States)

    Mukherjee, Soumi; Chattopadhyay, Amitabha

    2005-01-04

    We have monitored the environment and dynamics of the membrane interface formed by the ester-linked phospholipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and the ether-linked phospholipid 1,2-dihexadecyl-sn-glycero-3-phosphocholine (DHPC) utilizing the wavelength-selective fluorescence approach and using the fluorescent membrane probe 2-(9-anthroyloxy)stearic acid (2-AS). This interfacially localized probe offers a number of advantages over those which lack a fixed location in the membrane. When incorporated in membranes formed by DPPC and DHPC, 2-AS exhibits red edge excitation shift (REES) of 14 and 8 nm, respectively. This implies that the rate of solvent reorientation, as sensed by the interfacial anthroyloxy probe, in ester-linked DPPC membranes is slow compared to the rate of solvent reorientation in ether-linked DHPC membranes. In addition, the fluorescence polarization values of 2-AS are found to be higher in DHPC membranes than in DPPC membranes. This is further supported by wavelength-dependent changes in fluorescence polarization and lifetime. Taken together, these results are useful in understanding the role of interfacial chemistry on membrane physical properties.

  2. The electric double layer at a rutile TiO₂ water interface modelled using density functional theory based molecular dynamics simulation.

    Science.gov (United States)

    Cheng, J; Sprik, M

    2014-06-18

    A fully atomistic model of a compact electric double layer at the rutile TiO2(1 1 0)-water interface is constructed by adding protons to bridging oxygens or removing them from H2O molecules adsorbed on terminal metal cation sites. The surface charge is compensated by F(-) or Na(+) counter ions in outer as well as inner sphere coordination. For each of the protonation states the energy of the TiO2 conduction band minimum is determined relative to the standard hydrogen electrode by computing the free energy for the combined insertion of an electron in the solid and a proton in solution away from the double layer using density functional theory based molecular dynamics methods. Interpreted as electrode potentials, this gives an estimate of the capacitance which is compared to the capacitance obtained from the difference in the average electrostatic potentials in the solid and aqueous phase. When aligned at the point of zero charge these two methods lead to almost identical potential-charge profiles. We find that inner sphere complexes have a slightly larger capacitance (0.4 F m(-2)) compared to outer sphere complexes (0.3 F m(-2)).

  3. Binding structure and kinetics of surfactin monolayer formed at the air/water interface to counterions: A molecular dynamics simulation study.

    Science.gov (United States)

    Gang, Hongze; Liu, Jinfeng; Mu, Bozhong

    2015-10-01

    The binding structure and kinetics of ionized surfactin monolayer formed at the air/water interface to five counterions, Li+, Na+, K+, Ca2+, and Ba2+ (molar ratios of surfactin to monovalent and divalent counterions are 1:2 and 1:1 respectively), have been studied using molecular dynamics simulation. The results show that surfactin exhibits higher binding affinity to divalent counterions, Ca2+, and Ba2+, and smaller monovalent counterion, Li+, than Na+ and K+. Both carboxyl groups in surfactin are accessible for counterions, but the carboxyl group in Glu1 is easier to access by counterions than Asp5. Salt bridges are widely built between carboxyl groups by counterions, and the probability of the formation of intermolecular salt bridge is markedly larger than that of intramolecular salt bridge. Divalent counterions perform well in forming salt bridges between carboxyl groups. The salt bridges mediated by Ca2+ are so rigid that the lifetimes are about 0.13 ns, and the break rates of these salt bridges are 1-2 orders of magnitude smaller than those mediated by K+ which is about 5 ps in duration. The positions of the hydration layer of carboxyl groups are independent of counterions, but the bound counterions induce the dehydration of carboxyl groups and disturb the hydrogen bonds built between carboxyl group and hydration water.

  4. Chemically-specific time-resolved surface photovoltage spectroscopy: Carrier dynamics at the interface of quantum dots attached to a metal oxide

    Science.gov (United States)

    Spencer, Ben F.; Cliffe, Matthew J.; Graham, Darren M.; Hardman, Samantha J. O.; Seddon, Elaine A.; Syres, Karen L.; Thomas, Andrew G.; Sirotti, Fausto; Silly, Mathieu G.; Akhtar, Javeed; O'Brien, Paul; Fairclough, Simon M.; Smith, Jason M.; Chattopadhyay, Swapan; Flavell, Wendy R.

    2015-11-01

    We describe a new experimental pump-probe methodology where a 2D delay-line detector enables fast (ns) monitoring of a narrow XPS spectrum in combination with a continuous pump laser. This has been developed at the TEMPO beamline at Synchrotron SOLEIL to enable the study of systems with intrinsically slow electron dynamics, and to complement faster measurements that use a fs laser as the pump. We demonstrate its use in a time-resolved study of the surface photovoltage of the m-plane ZnO (10 1 bar 0) surface which shows persistent photoconductivity, requiring monitoring periods on ms timescales and longer. We make measurements from this surface in the presence and absence of chemically-linked quantum dots (QDs), using type I PbS and type II CdSe/ZnSe (core/shell) QDs as examples. We monitor signals from both the ZnO substrate and the bound QDs during photoexcitation, yielding evidence for charge injection from the QDs into the ZnO. The chemical specificity of the technique allows us to observe differences in the extent to which the QD systems are influenced by the field of the surface depletion layer at the ZnO surface, which we attribute to differences in the band structure at the interface.

  5. Examining the pathogenesis of breast cancer using a novel agent-based model of mammary ductal epithelium dynamics.

    Directory of Open Access Journals (Sweden)

    Joaquin Chapa

    Full Text Available The study of the pathogenesis of breast cancer is challenged by the long time-course of the disease process and the multi-factorial nature of generating oncogenic insults. The characterization of the longitudinal pathogenesis of malignant transformation from baseline normal breast duct epithelial dynamics may provide vital insight into the cascading systems failure that leads to breast cancer. To this end, extensive information on the baseline behavior of normal mammary epithelium and breast cancer oncogenesis was integrated into a computational model termed the Ductal Epithelium Agent-Based Model (DEABM. The DEABM is composed of computational agents that behave according to rules established from published cellular and molecular mechanisms concerning breast duct epithelial dynamics and oncogenesis. The DEABM implements DNA damage and repair, cell division, genetic inheritance and simulates the local tissue environment with hormone excretion and receptor signaling. Unrepaired DNA damage impacts the integrity of the genome within individual cells, including a set of eight representative oncogenes and tumor suppressors previously implicated in breast cancer, with subsequent consequences on successive generations of cells. The DEABM reproduced cellular population dynamics seen during the menstrual cycle and pregnancy, and demonstrated the oncogenic effect of known genetic factors associated with breast cancer, namely TP53 and Myc, in simulations spanning ∼40 years of simulated time. Simulations comparing normal to BRCA1-mutant breast tissue demonstrated rates of invasive cancer development similar to published epidemiologic data with respect to both cumulative incidence over time and estrogen-receptor status. Investigation of the modeling of ERα-positive (ER+ tumorigenesis led to a novel hypothesis implicating the transcription factor and tumor suppressor RUNX3. These data suggest that the DEABM can serve as a potentially valuable framework to

  6. Examining the pathogenesis of breast cancer using a novel agent-based model of mammary ductal epithelium dynamics.

    Science.gov (United States)

    Chapa, Joaquin; Bourgo, Ryan J; Greene, Geoffrey L; Kulkarni, Swati; An, Gary

    2013-01-01

    The study of the pathogenesis of breast cancer is challenged by the long time-course of the disease process and the multi-factorial nature of generating oncogenic insults. The characterization of the longitudinal pathogenesis of malignant transformation from baseline normal breast duct epithelial dynamics may provide vital insight into the cascading systems failure that leads to breast cancer. To this end, extensive information on the baseline behavior of normal mammary epithelium and breast cancer oncogenesis was integrated into a computational model termed the Ductal Epithelium Agent-Based Model (DEABM). The DEABM is composed of computational agents that behave according to rules established from published cellular and molecular mechanisms concerning breast duct epithelial dynamics and oncogenesis. The DEABM implements DNA damage and repair, cell division, genetic inheritance and simulates the local tissue environment with hormone excretion and receptor signaling. Unrepaired DNA damage impacts the integrity of the genome within individual cells, including a set of eight representative oncogenes and tumor suppressors previously implicated in breast cancer, with subsequent consequences on successive generations of cells. The DEABM reproduced cellular population dynamics seen during the menstrual cycle and pregnancy, and demonstrated the oncogenic effect of known genetic factors associated with breast cancer, namely TP53 and Myc, in simulations spanning ∼40 years of simulated time. Simulations comparing normal to BRCA1-mutant breast tissue demonstrated rates of invasive cancer development similar to published epidemiologic data with respect to both cumulative incidence over time and estrogen-receptor status. Investigation of the modeling of ERα-positive (ER+) tumorigenesis led to a novel hypothesis implicating the transcription factor and tumor suppressor RUNX3. These data suggest that the DEABM can serve as a potentially valuable framework to augment the

  7. Radiogenomic analysis of breast cancer: dynamic contrast enhanced - magnetic resonance imaging based features are associated with molecular subtypes

    Science.gov (United States)

    Wang, Shijian; Fan, Ming; Zhang, Juan; Zheng, Bin; Wang, Xiaojia; Li, Lihua

    2016-03-01

    Breast cancer is one of the most common malignant tumor with upgrading incidence in females. The key to decrease the mortality is early diagnosis and reasonable treatment. Molecular classification could provide better insights into patient-directed therapy and prognosis prediction of breast cancer. It is known that different molecular subtypes have different characteristics in magnetic resonance imaging (MRI) examination. Therefore, we assumed that imaging features can reflect molecular information in breast cancer. In this study, we investigated associations between dynamic contrasts enhanced MRI (DCE-MRI) features and molecular subtypes in breast cancer. Sixty patients with breast cancer were enrolled and the MR images were pre-processed for noise reduction, registration and segmentation. Sixty-five dimensional imaging features including statistical characteristics, morphology, texture and dynamic enhancement in breast lesion and background regions were semiautomatically extracted. The associations between imaging features and molecular subtypes were assessed by using statistical analyses, including univariate logistic regression and multivariate logistic regression. The results of multivariate regression showed that imaging features are significantly associated with molecular subtypes of Luminal A (p=0.00473), HER2-enriched (p=0.00277) and Basal like (p=0.0117), respectively. The results indicated that three molecular subtypes are correlated with DCE-MRI features in breast cancer. Specifically, patients with a higher level of compactness or lower level of skewness in breast lesion are more likely to be Luminal A subtype. Besides, the higher value of the dynamic enhancement at T1 time in normal side reflect higher possibility of HER2-enriched subtype in breast cancer.

  8. Study on the Functional Dynamic Changes of Peri-Operative Cellular Immunity in Esophageal and Cardiac Cancer

    Institute of Scientific and Technical Information of China (English)

    Chen Sheng; Li Shiting; Fang Youping

    2014-01-01

    Objective: To explore the systemic and local cellular immune function of patients with esophageal carcinoma or cardiac cancer. Methods: The distribution of tumor-infiltrating lymphocyte (TIL) and cancer-associated macrophage (TAM) in local tumor tissues of 52 patients with esophageal cancer or cardiac cancer were observed by immunehistochemical method. The level of peripheral SIL-2R and TNF-α of preoperative and postoperative 1, 2, 3 weeks were detected by ELISA and ABC-ELISA methods respectively, then the acquired results were compared with 30 cases of normal control group. Results:The peritumor inifltration densities of TIL and TAM was greater than that of cancer nest stroma (P<0.05). Compared with the normal control group, the levels of sIL-2R and TNF-α increased signiifcantly (P<0.01). Immune function could be suppressed by operative wound in a short time of post-operation, whose damage severity was closely associated with tumor TNM stages. Conclusion: Patients with esophageal or cardiac cancer have cellular immune function disorders. Dynamic testing of peripheral sIL-2R and TNT-α level in patients with esophageal or cardiac cancer has positive clinical signiifcance in the evaluation of cellular immune function, tumor lesion degree and curative effect.

  9. Center of cancer systems biology second annual workshop--tumor metronomics: timing and dose level dynamics.

    Science.gov (United States)

    Hahnfeldt, Philip; Hlatky, Lynn; Klement, Giannoula Lakka

    2013-05-15

    Metronomic chemotherapy, the delivery of doses in a low, regular manner so as to avoid toxic side effects, was introduced over 12 years ago in the face of substantial clinical and preclinical evidence supporting its tumor-suppressive capability. It constituted a marked departure from the classic maximum-tolerated dose (MTD) strategy, which, given its goal of rapid eradication, uses dosing sufficiently intense to require rest periods between cycles to limit toxicity. Even so, upfront tumor eradication is frequently not achieved with MTD, whereupon a de facto goal of longer-term tumor control is often pursued. As metronomic dosing has shown tumor control capability, even for cancers that have become resistant to the same drug delivered under MTD, the question arises whether it may be a preferable alternative dosing approach from the outset. To date, however, our knowledge of the coupled dynamics underlying metronomic dosing is neither sufficiently well developed nor widely enough disseminated to establish its actual potential. Meeting organizers thus felt the time was right, armed with new quantitative approaches, to call a workshop on "Tumor Metronomics: Timing and Dose Level Dynamics" to explore prospects for gaining a deeper, systems-level appreciation of the metronomics concept. The workshop proved to be a forum in which experts from the clinical, biologic, mathematical, and computational realms could work together to clarify the principles and underpinnings of metronomics. Among other things, the need for significant shifts in thinking regarding endpoints to be used as clinical standards of therapeutic progress was recognized.

  10. Multi-color fluorescence imaging of sub-cellular dynamics of cancer cells in live mice

    Science.gov (United States)

    Hoffman, Robert M.

    2006-02-01

    We have genetically engineered dual-color fluorescent cells with one color in the nucleus and the other in the cytoplasm that enables real-time nuclear-cytoplasmic dynamics to be visualized in living cells in the cytoplasm in vivo as well as in vitro. To obtain the dual-color cells, red fluorescent protein (RFP) was expressed of the cancer cells, and green fluorescent protein (GFP) linked to histone H2B was expressed in the nucleus. Mitotic cells were visualized by whole-body imaging after injection in the mouse ear. Common carotid artery or heart injection of dual-color cells and a reversible skin flap enabled the external visualization of the dual-color cells in microvessels in the mouse where extreme elongation of the cell body as well as the nucleus occurred. The migration velocities of the dual-color cancer cells in the capillaries were measured by capturing individual images of the dual-color fluorescent cells over time. Human HCT-116-GFP-RFP colon cancer and mouse mammary tumor (MMT)-GFP-RFP cells were injected in the portal vein of nude mice. Extensive clasmocytosis (destruction of the cytoplasm) of the HCT-116-GFP-RFP cells occurred within 6 hours. The data suggest rapid death of HCT-116-GFP-RFP cells in the portal vein. In contrast, MMT-GFP-RFP cells injected into the portal vein mostly survived and formed colonies in the liver. However, when the host mice were pretreated with cyclophosphamide, the HCT-116-GFP-RFP cells also survived and formed colonies in the liver after portal vein injection. These results suggest that a cyclophosphamide-sensitive host cellular system attacked the HCT-116-GFP-RFP cells but could not effectively kill the MMT-GFP-RFP cells. With the ability to continuously image cancer cells at the subcellular level in the live animal, our understanding of the complex steps of metastasis will significantly increase. In addition, new drugs can be developed to target these newly visible steps of metastasis.

  11. Differentiation of breast cancer from fibroadenoma with dual-echo dynamic contrast-enhanced MRI.

    Directory of Open Access Journals (Sweden)

    Shiwei Wang

    Full Text Available Dynamic contrast-enhanced magnetic resonance imaging (DCE MRI of the breast is a routinely used imaging method which is highly sensitive for detecting breast malignancy. Specificity, though, remains suboptimal. Dynamic susceptibility contrast magnetic resonance imaging (DSC MRI, an alternative dynamic contrast imaging technique, evaluates perfusion-related parameters unique from DCE MRI. Previous work has shown that the combination of DSC MRI with DCE MRI can improve diagnostic specificity, though an additional administration of intravenous contrast is required. Dual-echo MRI can measure both T1W DCE MRI and T2*W DSC MRI parameters with a single contrast bolus, but has not been previously implemented in breast imaging. We have developed a dual-echo gradient-echo sequence to perform such simultaneous measurements in the breast, and use it to calculate the semi-quantitative T1W and T2*W related parameters such as peak enhancement ratio, time of maximal enhancement, regional blood flow, and regional blood volume in 20 malignant lesions and 10 benign fibroadenomas in 38 patients. Imaging parameters were compared to surgical or biopsy obtained tissue samples. Receiver operating characteristic (ROC curves and area under the ROC curves were calculated for each parameter and combination of parameters. The time of maximal enhancement derived from DCE MRI had a 90% sensitivity and 69% specificity for predicting malignancy. When combined with DSC MRI derived regional blood flow and volume parameters, sensitivity remained unchanged at 90% but specificity increased to 80%. In conclusion, we show that dual-echo MRI with a single administration of contrast agent can simultaneously measure both T1W and T2*W related perfusion and kinetic parameters in the breast and the combination of DCE MRI and DSC MRI parameters improves the diagnostic performance of breast MRI to differentiate breast cancer from benign fibroadenomas.

  12. Urban water interfaces

    Science.gov (United States)

    Gessner, M. O.; Hinkelmann, R.; Nützmann, G.; Jekel, M.; Singer, G.; Lewandowski, J.; Nehls, T.; Barjenbruch, M.

    2014-06-01

    Urban water systems consist of large-scale technical systems and both natural and man-made water bodies. The technical systems are essential components of urban infrastructure for water collection, treatment, storage and distribution, as well as for wastewater and runoff collection and subsequent treatment. Urban aquatic ecosystems are typically subject to strong human influences, which impair the quality of surface and ground waters, often with far-reaching impacts on downstream aquatic ecosystems and water users. The various surface and subsurface water bodies in urban environments can be viewed as interconnected compartments that are also extensively intertwined with a range of technical compartments of the urban water system. As a result, urban water systems are characterized by fluxes of water, solutes, gases and energy between contrasting compartments of a technical, natural or hybrid nature. Referred to as urban water interfaces, boundaries between and within these compartments are often specific to urban water systems. Urban water interfaces are generally characterized by steep physical and biogeochemical gradients, which promote high reaction rates. We hypothesize that they act as key sites of processes and fluxes with notable effects on overall system behaviour. By their very nature, urban water interfaces are heterogeneous and dynamic. Therefore, they increase spatial heterogeneity in urban areas and are also expected to contribute notably to the temporal dynamics of urban water systems, which often involve non-linear interactions and feedback mechanisms. Processes at and fluxes across urban water interfaces are complex and less well understood than within well-defined, homogeneous compartments, requiring both empirical investigations and new modelling approaches at both the process and system level. We advocate an integrative conceptual framework of the urban water system that considers interfaces as a key component to improve our fundamental

  13. Designing Interfaces

    CERN Document Server

    Tidwell, Jenifer

    2010-01-01

    Despite all of the UI toolkits available today, it's still not easy to design good application interfaces. This bestselling book is one of the few reliable sources to help you navigate through the maze of design options. By capturing UI best practices and reusable ideas as design patterns, Designing Interfaces provides solutions to common design problems that you can tailor to the situation at hand. This updated edition includes patterns for mobile apps and social media, as well as web applications and desktop software. Each pattern contains full-color examples and practical design advice th

  14. Polarizable Site Charge Model at Liquid/Solid Interfaces for Describing Surface Polarity: Application to Structure and Molecular Dynamics of Water/Rutile TiO2(110) Interface.

    Science.gov (United States)

    Nakamura, Hisao; Ohto, Tatsuhiko; Nagata, Yuki

    2013-02-12

    We present a novel scheme to construct a polarizable force field for liquid/solid interfaces, which takes into account the effect of the surface polarity induced by liquid-solid interactions explicitly. We extend the charge response kernel (CRK) method for molecules to solid surfaces by introducing the surface CRK. The CRK parameters are systematically determined by the first-principles calculations in the slab model with the dipole-correction method. Our methodology is applied to the water/clean rutile TiO2(110) interface. Structures and induced charges of a single water molecule attached to the TiO2 surface optimized by our polarizable force field show good agreement with those predicted by the first-principles calculations. Further, we carried out MD simulations for the liquid water/TiO2 interface and found three stable structures of water attached to the TiO2 surface. Two of them are predicted by both the polarizable and the nonpolarizable force fields, while the polarizable force field model predicts a structure of water with the hydrogen and oxygen atoms interacting with the oxygen atom of the surface TiO2 and the hydrogen atom of the other water molecule, respectively, which was reported by the previous first-principles MD simulation. This indicates that the dipole moments of water and TiO2 induced by the water-TiO2 interactions have significant impact on molecular conformations of the water/TiO2 interface.

  15. 基于 XML实时动态模型界面的研究与应用%RESEARCH AND APPLICATION OF XML-BASED REAL-TIME DYNAMIC MODEL INTERFACE

    Institute of Scientific and Technical Information of China (English)

    王雅光; 傅秀芬; 廖振云

    2013-01-01

    随着计算机网络的发展,Web门户应用已经在众多企业甚至政府机构中普遍存在,用户界面的设计变得至关重要,如何快速地开发灵活的、高效的图形用户界面是开发者一直面临的问题。讨论一种基于XML面向对象的图形用户界面,与以往图形界面不同的是,该图形界面在应用运行的过程中实时动态生成,具有较高的灵活性和可重用性。%With the development of computer network , Web portal applications are prevalent in a lot of enterprises , even in many governments , and the design of user interface becomes crucial .Developers are always confronted with the problem that how to rapidly develop the flexible and efficient graphics user interface .In this paper we discuss a kind of graphics user interface which is based on XML and object-oriented.In contrast to the previous graphics interfaces , the graphics interface in this paper is dynamically generated in the runtime timely and has higher flexibility and reusability .

  16. Bubble bursting as an aerosol generation mechanism during an oil spill in the deep-sea environment: molecular dynamics simulations of oil alkanes and dispersants in atmospheric air/salt water interfaces.

    Science.gov (United States)

    Liyana-Arachchi, Thilanga P; Zhang, Zenghui; Ehrenhauser, Franz S; Avij, Paria; Valsaraj, Kalliat T; Hung, Francisco R

    2014-01-01

    Potential of mean force (PMF) calculations and molecular dynamics (MD) simulations were performed to investigate the properties of oil n-alkanes [i.e., n-pentadecane (C15), n-icosane (C20) and n-triacontane (C30)], as well as several surfactant species [i.e., the standard anionic surfactant sodium dodecyl sulfate (SDS), and three model dispersants similar to the Tween and Span species present in Corexit 9500A] at air/salt water interfaces. This study was motivated by the 2010 Deepwater Horizon (DWH) oil spill, and our simulation results show that, from the thermodynamic point of view, the n-alkanes and the model dispersants have a strong preference to remain at the air/salt water interface, as indicated by the presence of deep free energy minima at these interfaces. The free energy minimum of these n-alkanes becomes deeper as their chain length increases, and as the concentration of surfactant species at the interface increases. The n-alkanes tend to adopt a flat orientation and form aggregates at the bare air/salt water interface. When this interface is coated with surfactants, the n-alkanes tend to adopt more tilted orientations with respect to the vector normal to the interface. These simulation results are consistent with the experimental findings reported in the accompanying paper [Ehrenhauser et al., Environ. Sci.: Processes Impacts 2013, in press, (DOI: 10.1039/c3em00390f)]. The fact that these long-chain n-alkanes show a strong thermodynamic preference to remain at the air/salt water interfaces, especially if these interfaces are coated with surfactants, makes these species very likely to adsorb at the surface of bubbles or droplets and be ejected to the atmosphere by sea surface processes such as whitecaps (breaking waves) and bubble bursting. Finally, the experimental finding that more oil hydrocarbons are ejected when Corexit 9500A is present in the system is consistent with the deeper free energy minima observed for the n-alkanes at the air/salt water

  17. Atomistic modeling of dislocation-interface interactions

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jian [Los Alamos National Laboratory; Valone, Steven M [Los Alamos National Laboratory; Beyerlein, Irene J [Los Alamos National Laboratory; Misra, Amit [Los Alamos National Laboratory; Germann, T. C. [Los Alamos National Laboratory

    2011-01-31

    Using atomic scale models and interface defect theory, we first classify interface structures into a few types with respect to geometrical factors, then study the interfacial shear response and further simulate the dislocation-interface interactions using molecular dynamics. The results show that the atomic scale structural characteristics of both heterophases and homophases interfaces play a crucial role in (i) their mechanical responses and (ii) the ability of incoming lattice dislocations to transmit across them.

  18. Testing Interfaces

    DEFF Research Database (Denmark)

    Holbøll, Joachim T.; Henriksen, Mogens; Nilson, Jesper K.;

    1999-01-01

    The wide use of solid insulating materials combinations in combinations has introduced problems in the interfaces between components. The most common insulating materials are cross-linked polyethylene (XLPE), silicone rubber (SIR) and ethylene-propylene rubbers (EPR). Assemblies of these materials...

  19. Gesture Interfaces

    NARCIS (Netherlands)

    Fikkert, F.W.

    2007-01-01

    Take away mouse and keyboard. Now, how do you interact with a computer? Especially one that has a display that is the size of an entire wall. One possibility is through gesture interfaces. Remember Minority Report? Cool stuff, but that was already five years ago.. So, what is already possible now an

  20. Manufacturing Interfaces

    NARCIS (Netherlands)

    Houten, van F.J.A.M.

    1992-01-01

    The paper identifies the changing needs and requirements with respect to the interfacing of manufacturing functions. It considers the manufacturing system, its components and their relationships from the technological and logistic point of view, against the background of concurrent engineering. Desi

  1. Proteomics reveals the importance of the dynamic redistribution of the subcellular location of proteins in breast cancer cells.

    Science.gov (United States)

    Pinto, Gabriella; Alhaiek, Abdulrab Ahmed M; Godovac-Zimmermann, Jasminka

    2015-02-01

    At the molecular level, living cells are enormously complicated complex adaptive systems in which intertwined genomic, transcriptomic, proteomic and metabolic networks all play a crucial role. At the same time, cells are spatially heterogeneous systems in which subcellular compartmentalization of different functions is ubiquitous and requires efficient cross-compartmental communication. Dynamic redistribution of multitudinous proteins to different subcellular locations in response to cellular functional state is increasingly recognized as a crucial characteristic of cellular function that seems to be at least as important as overall changes in protein abundance. Characterization of the subcellular spatial dynamics of protein distribution is a major challenge for proteomics and recent results with MCF7 breast cancer cells suggest that this may be of particular importance for cancer cells.

  2. Hydro-dynamic CT preoperative staging of gastric cancer: correlation with pathological findings. A prospective study of 107 cases

    Energy Technology Data Exchange (ETDEWEB)

    D' Elia, F.; Zingarelli, A.; Grani, M. [Dept. of Radiology, S. Donato Hospital, Arezzo (Italy); Palli, D. [Dept. of Epidemiology CSPO, Florence (Italy)

    2000-12-01

    The aim of this study was to evaluate the accuracy of dynamic CT in the preoperative staging of gastric cancer. One hundred seven patients affected by gastric cancer diagnosed by endoscopic biopsy were prospectively staged by dynamic CT prior to tumor resection. After an oral intake of 400-600 ml of tap water and an intravenous infusion of a hypotonic agent, 200 ml of non-ionic contrast agent were administered by power injector using a biphasic technique. The CT findings were prospectively analyzed and correlated with the pathological findings at surgery. The accuracy of dynamic CT for tumor detection was 80 and 99 % in early and advanced gastric cancer, respectively, with overall detection rate of 96 % (103 of 107). Three early (pT1) and one advanced (pT2) cancers were undetected. Tumor stage as determined by dynamic CT agreed with pathological findings in 83 of 107 patients with an overall accuracy of 78 %. The accuracy of CT in detecting increasing degrees of depth of tumor invasion when compared with pathological TNM staging was 20 % (3 of 15) and 87 % (80 of 92) in early and advanced cancer, respectively. The sensitivity, specificity, and accuracy of CT in the preoperative staging (pT3-pT4 vs pT1-pT2) was 93, 90, and 91.6 %, respectively. The sensitivity, specificity, and accuracy of CT in assessing metastasis to regional lymph nodes was 97.2, 65.7, and 87 %, respectively. Computed tomography correctly staged liver metastases in 105 of 107 patients with an overall sensitivity of 87.5 % and specificity of 99 %. The sensitivity of peritoneal involvement was 30 % when ascites or peritoneal nodules were absent. Our findings show that dynamic CT can play a role in the preoperative definition of gastric cancer stage. The results can be used to optimize the therapeutic strategy for each individual patient prior to surgery, thus avoiding unnecessary intervention and allowing careful planning of extended surgery in eligible patients. (orig.)

  3. [Population dynamics of ground carabid beetles and spiders in a wheat field along the wheat-alfalfa interface and their response to alfalfa mowing].

    Science.gov (United States)

    Liu, Wen-Hui; Hu, Yi-Jun; Hu, Wen-Chao; Hong, Bo; Guan, Xiao-Qing; Ma, Shi-Yu; He, Da-Han

    2014-09-01

    Taking the wheat-alfalfa and wheat-wheat interfaces as model systems, sampling points were set by the method of pitfall trapping in the wheat field at the distances of 3 m, 6 m, 9 m, 12 m, 15 m, 18 m, 21 m, 24 m, and 27 m from the interface. The species composition and abundance of ground carabid beetles and spiders captured in pitfalls were investigated. The results showed that, to some extent there was an edge effect on species diversity and abundance of ground carabid beetles and spiders along the two interfaces. A marked edge effect was observed between 15 m and 18 m along the alfalfa-wheat interface, while no edge effect was found at a distance over 20 m. The edge effect along the wheat-wheat interface was weaker in comparison to the alfalfa-wheat interface. Alfalfa mowing resulted in the migration of a large number of ground carabid beetles and spiders to the adjacent wheat filed. During ten days since mowing, both species and abundance of ground carabid beetles and spiders increased in wheat filed within the distance of 20 m along the alfalfa-wheat interface. The spatial distribution of species diversity of ground beetles and spiders, together with the population abundance of the dominant Chlaenius pallipes and Pardosa astrigera, were depicted, which could directly indicate the migrating process of natural enemy from alfalfa to wheat field.

  4. Ovarian Cancer Cell Adhesion/Migration Dynamics on Micro-Structured Laminin Gradients Fabricated by Multiphoton Excited Photochemistry

    Directory of Open Access Journals (Sweden)

    Ruei-Yu He

    2015-07-01

    Full Text Available Haptotaxis, i.e., cell migration in response to adhesive gradients, has been previously implicated in cancer metastasis. A better understanding of cell migration dynamics and their regulation could ultimately lead to new drug targets, especially for cancers with poor prognoses, such as ovarian cancer. Haptotaxis has not been well-studied due to the lack of biomimetic, biocompatible models, where, for example, microcontact printing and microfluidics approaches are primarily limited to 2D surfaces and cannot produce the 3D submicron features to which cells respond. Here we used multiphoton excited (MPE phototochemistry to fabricate nano/microstructured gradients of laminin (LN as 2.5D models of the ovarian basal lamina to study the haptotaxis dynamics of a series of ovarian cancer cells. Using these models, we found that increased LN concentration increased migration speed and also alignment of the overall cell morphology and their cytoskeleton along the linear axis of the gradients. Both these metrics were enhanced on LN compared to BSA gradients of the same design, demonstrating the importance of both topographic and ECM cues on the adhesion/migration dynamics. Using two different gradient designs, we addressed the question of the roles of local concentration and slope and found that the specific haptotactic response depends on the cell phenotype and not simply the gradient design. Moreover, small changes in concentration strongly affected the migration properties. This work is a necessary step in studying haptotaxis in more complete 3D models of the tumor microenvironment for ovarian and other cancers.

  5. Dynamic contrast-enhanced magnetic resonance imaging for prediction of response to neoadjuvant chemotherapy in breast cancer

    Science.gov (United States)

    Fu, Juzhong; Fan, Ming; Zheng, Bin; Shao, Guoliang; Zhang, Juan; Li, Lihua

    2016-03-01

    Breast cancer is the second leading cause of women death in the United States. Currently, Neoadjuvant Chemotherapy (NAC) has become standard treatment paradigms for breast cancer patients. Therefore, it is important to find a reliable non-invasive assessment and prediction method which can evaluate and predict the response of NAC on breast cancer. The Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) approach can reflect dynamic distribution of contrast agent in tumor vessels, providing important basis for clinical diagnosis. In this study, the efficacy of DCE-MRI on evaluation and prediction of response to NAC in breast cancer was investigated. To this end, fifty-seven cases of malignant breast cancers with MRI examination both before and after two cycle of NAC were analyzed. After pre-processing approach for segmenting breast lesions and background regions, 126-dimensional imaging features were extracted from DCE-MRI. Statistical analyses were then performed to evaluate the associations between the extracted DCE-MRI features and the response to NAC. Specifically, pairwise t test was used to calculate differences of imaging features between MRI examinations before-and-after NAC. Moreover, the associations of these image features with response to NAC were assessed using logistic regression. Significant association are found between response to NAC and the features of lesion morphology and background parenchymal enhancement, especially the feature of background enhancement in normal side of breast (P=0.011). Our study indicate that DCE-MRI features can provide candidate imaging markers to predict response of NAC in breast cancer.

  6. A systems biology approach to cancer: fractals, attractors, and nonlinear dynamics.

    Science.gov (United States)

    Dinicola, Simona; D'Anselmi, Fabrizio; Pasqualato, Alessia; Proietti, Sara; Lisi, Elisabetta; Cucina, Alessandra; Bizzarri, Mariano

    2011-03-01

    Cancer begins to be recognized as a highly complex disease, and advanced knowledge of the carcinogenic process claims to be acquired by means of supragenomic strategies. Experimental data evidence that tumor emerges from disruption of tissue architecture, and it is therefore consequential that the tissue level should be considered the proper level of observation for carcinogenic studies. This paradigm shift imposes to move from a reductionistic to a systems biology approach. Indeed, cell phenotypes are emergent modes arising through collective nonlinear interactions among different cellular and microenvironmental components, generally described by a phase space diagram, where stable states (attractors) are embedded into a landscape model. Within this framework cell states and cell transitions are generally conceived as mainly specified by the gene-regulatory network. However, the system's dynamics cannot be reduced to only the integrated functioning of the genome-proteome network, and the cell-stroma interacting system must be taken into consideration in order to give a more reliable picture. As cell form represents the spatial geometric configuration shaped by an integrated set of cellular and environmental cues participating in biological functions control, it is conceivable that fractal-shape parameters could be considered as "omics" descriptors of the cell-stroma system. Within this framework it seems that function follows form, and not the other way around.

  7. Cellular calcium dynamics in lactation and breast cancer: From physiology to pathology

    Science.gov (United States)

    Breast cancer is the second leading cause of cancer mortality in women, estimated at nearly 40,000 deaths and more than 230,000 new cases diagnosed in the U.S. this year alone. One of the defining characteristics of breast cancer is the radiographic presence of microcalcifications. These palpable mi...

  8. Interface learning

    DEFF Research Database (Denmark)

    Thorhauge, Sally

    2014-01-01

    for students. The research focuses on the learning that the students experience in the interface of the two learning environments: The formal learning environment of the upper secondary school and the informal learning environment of the museum. Focus is also on the learning that the teachers and museum......"Interface learning - New goals for museum and upper secondary school collaboration" investigates and analyzes the learning that takes place when museums and upper secondary schools in Denmark work together in local partnerships to develop and carry out school-related, museum-based coursework...... professionals experience as a result of their collaboration. The dissertation demonstrates how a given partnership’s collaboration affects the students’ learning experiences when they are doing the coursework. The dissertation presents findings that museum-school partnerships can use in order to develop...

  9. Dynamics of House Sparrows (Passer domesticus) in Newcastle disease virus transmission within the avifaunal-poultry interface: an epidemiological modeling approach

    Science.gov (United States)

    As emerging and persistent pathogens increase in prevalence, the agriculture-wildlife interface has been identified as a field requiring further research. Acceleration of wildlife urbanization, exotic species introductions, and habitat encroachment are disrupting barriers that once separated microb...

  10. Museets interface

    DEFF Research Database (Denmark)

    Pold, Søren

    2007-01-01

    Søren Pold gør sig overvejelser med udgangspunkt i museumsprojekterne Kongedragter.dk og Stigombord.dk. Han argumenterer for, at udviklingen af internettets interfaces skaber nye måder at se, forstå og interagere med kulturen på. Brugerne får nye medievaner og perceptionsmønstre, der må medtænkes i...

  11. Cancer

    Science.gov (United States)

    Cancer begins in your cells, which are the building blocks of your body. Normally, your body forms ... be benign or malignant. Benign tumors aren't cancer while malignant ones are. Cells from malignant tumors ...

  12. Prevalence of Prostate Cancer Clinical States and Mortality in the United States: Estimates Using a Dynamic Progression Model.

    Directory of Open Access Journals (Sweden)

    Howard I Scher

    Full Text Available To identify patient populations most in need of treatment across the prostate cancer disease continuum, we developed a novel dynamic transition model based on risk of disease progression and mortality.We modeled the flow of patient populations through eight prostate cancer clinical states (PCCS that are characterized by the status of the primary tumor, presence of metastases, prior and current treatment, and testosterone levels. Simulations used published US incidence rates for each year from 1990. Progression and mortality rates were derived from published clinical trials, meta-analyses, and observational studies. Model outputs included the incidence, prevalence, and mortality for each PCCS. The impact of novel treatments was modeled in three distinct scenarios: metastatic castration-resistant prostate cancer (mCRPC, non-metastatic CRPC (nmCRPC, or both.The model estimated the prevalence of prostate cancer as 2,219,280 in the US in 2009 and 3,072,480 in 2020, and incidence of mCRPC as 36,100 and 42,970, respectively. All-cause mortality in prostate cancer was estimated at 168,290 in 2009 and 219,360 in 2020, with 20.5% and 19.5% of these deaths, respectively, occurring in men with mCRPC. The majority (86% of incidence flow into mCRPC states was from the nmCRPC clinical state. In the scenario with novel interventions for nmCRPC states, the progression to mCRPC is reduced, thus decreasing mCRPC incidence by 12% in 2020, with a sustained decline in mCRPC mortality. A limitation of the model is that it does not estimate prostate cancer-specific mortality.The model informs clinical trial design for prostate cancer by quantifying outcomes in PCCS, and demonstrates the impact of an effective therapy applied in an earlier clinical state of nmCRPC on the incidence of mCRPC morbidity and subsequent mortality.

  13. Subendometrial enhancement and peritumoral enhancement for assessing endometrial cancer on dynamic contrast enhanced MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Fujii, Shinya [Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, Yonago (Japan); Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto (Japan); Kido, Aki, E-mail: akikido@kuhp.kyoto-u.ac.jp [Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto (Japan); Baba, Tsukasa [Departments of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto (Japan); Fujimoto, Koji; Daido, Sayaka [Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto (Japan); Matsumura, Noriomi; Konishi, Ikuo [Departments of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto (Japan); Togashi, Kaori [Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto (Japan)

    2015-04-15

    Highlights: •We have assessed the peritumoral enhancement (PTE), which mimics SEE on DCE. •We evaluated the diagnostic accuracy of SEE for the myometrial invasion and the frequency of PTE. •We assessed the relationship between these enhancements and important pathologic factors. •PTE Type 1 is the main factor causing the overestimation of myometrial invasion using SEE on DCE. •PTE Type 2 correlates the myometrial invasion and may play an important role in the diagnosis of LVSI. -- Abstract: Objectives: To evaluate the diagnostic accuracy of subendometrial enhancement (SEE) in assessing the myometrial invasion in endometrial cancer, the frequency and clinical significance of peritumoral enhancement (PTE) on dynamic contrast enhanced (DCE) imaging. Materials and methods: MR images of 147 patients with endometrial cancer were retrospectively analyzed for intact SEE and PTEs: Type 1, a focal early enhancement peritumorally, and Type 2, an irregular thin-layered early intense enhancement peritumorally. Two radiologists independently assessed intact SEE and PTEs on DCE imaging and compared the lesions by the presence and depth of myometrial invasion, grade, lymphovascular space involvement (LVSI), and lymph node metastasis. The relationship between SEE, PTEs, and each factor was analyzed using univariate and multivariate analyses. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy were calculated for SEE. Results: The sensitivity, specificity, PPV, NPV and diagnostic accuracy for myometrial invasion based on SEE disruption on DCE were 96.6%, 32.1–46.4%, 85.8–88.5%, 69.2–76.5%, and 84.4–87.1%. According to multivariate analysis, SEE significantly predicted myometrial invasion (p < 0.0001). PTE Type 2 significantly predicted myometrial invasion presence (p < 0.05) and depth (p < 0.01). Conclusion: Diagnosis of myometrial invasion only by using SEE might be difficult on DCE-MRI due to the

  14. Molecular dynamics simulations of hydrophobous ions at the liquid-liquid interfaces: case of dicarbollide anions as synergy agents and of ionic liquids as extracting medium; Simulations par dynamique moleculaire d'ions hydrophobes aux interfaces liquide - liquide: le cas des anions dicarbollides comme agents de synergie et celui des liquides ioniques comme milieu extractant

    Energy Technology Data Exchange (ETDEWEB)

    Chevrot, G

    2008-01-15

    Based on molecular dynamics simulations, we first describe the distribution of dicarbollide salts (CCD{sup -}, Mn{sup +}) in concentrated monophasic solutions (water, chloroform, octanol, nitrobenzene) and in the corresponding biphasic 'oil' - water solutions. We point to the importance of surface activity of the CCD{sup -}s and of their self-aggregation in water, with marked counterions effects, and we explain the synergistic effect of CCD{sup -}s in the Eu{sup 3+} extraction by BTP ligands. In the second part of the thesis we report exploratory simulations on the extraction of Sr{sup 2+} by 18-crown-6 to an hydrophobic ionic liquid ([BMI][PF6]), focusing on the liquid - liquid interface. Analogies and differences with a classical aqueous interface are outlined. (author)

  15. Somatostatin, somatostatin analogs and somatostatin receptor dynamics in the biology of cancer progression.

    Science.gov (United States)

    Ruscica, M; Arvigo, M; Steffani, L; Ferone, D; Magni, P

    2013-05-01

    The pharmacological effects (i.e., inhibition of endocrine secretion and cell proliferation) mediated by the hormone somatostatin (SRIF) are derived from its universal high-affinity binding to five different G proteincoupled receptors (GPCRs), named sst1-5. However, SRIF has a half-life of less than 3 min, whereas the available mono- and bi-specific SRIF preferential analogs show prolonged half-life and increased potency. These compounds may control tumor development, cell proliferation and metastatization by direct actions, including cell division arrest in G0/G1 phase (i.e., induction of cyclin-dependent kinase inhibitor p27(kip1) or p21(Cip1)), induction of apoptosis (i.e., induction of p53 and Bax) and suppression of cell invasion. Along with these direct actions on the biology of cancer progression, in vivo SRIF analogs may also regulate tumor growth through indirect actions, by suppressing the secretion of growth-promoting hormones and growth factors and angiogenesis. Interestingly, when ssts are co-expressed, they may interact forming homo- or heterodimers, also with other GPCRs such as type 2 dopamine receptor and the μ-opioid receptor 1, altering their original pharmacological and functional properties. Dimers can be not only constitutive, but perhaps also ligandpromoted: hence, compounds with high affinity for different ssts isoforms may be used to achieve effects elicited by specific dimers. Future developments in the knowledge of ssts dynamics upon SRIF and SRIF analogs binding in neoplastic tissues may allow the full elucidation of the pathophysiological role of this system and the exploitation of the therapeutic potential of its modulation.

  16. The Rutile (110)-Water Interface: A comment on "Structure and Dynamics of Liquid Water on Rutile TiO2(110)" by L.-M. Liu, C. Zhang, G. Thornton and A. Michaelides

    Energy Technology Data Exchange (ETDEWEB)

    Wesolowski, David J [ORNL; Sofo, Jorge O. [Pennsylvania State University; Bandura, Andrei V. [St. Petersburg State University, St. Petersburg, Russia; Zhang, Zhan [Argonne National Laboratory (ANL); Mamontov, Eugene [ORNL; Predota, M. [University of South Bohemia, Czech Republic; Kumar, Nitin [ORNL; Kubicki, James D. [Pennsylvania State University; Kent, Paul R [ORNL; Vlcek, Lukas [ORNL; Machesky, Michael L. [Illinois State Water Survey, Champaign, IL; Fenter, Paul [Argonne National Laboratory (ANL); Cummings, Peter T [ORNL; Anovitz, Lawrence {Larry} M [ORNL; Skelton, Adam [ORNL; Rosenqvist, Jorgen K [ORNL

    2010-01-01

    The (110) surface of rutile ( -TiO2) in contact with water is one of the most technologically-important and scientifically-investigated interfaces that exists. Liu and coworkers1 (hereafter Liu1) expanded on an excellent review of water-titania interfaces2, by conducting extensive static density functional theory (DFT) and DFT molecular dynamics (DFT-MD) investigations of rutile (110) using a range of cell configurations and DFT functionals. We agree with their DFT calculations of the influence of crystal slab thickness on water sorption energies, but find some of their major conclusions unwarranted or overstated, namely a.) that there is no dissociation of first-layer sorbed water at ~300K; b.) that translational diffusion of water molecules in contact with the surface approaches that of bulk liquid water ; and c.) that second layer water structuring and hydrogen bonding to surface oxygens are weak. We present published evidence not cited by Liu1 that challenge these assertions.

  17. Enhanced resting-state dynamics of the hemoglobin signal as a novel biomarker for detection of breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Graber, Harry L., E-mail: harry.graber@downstate.edu; Xu, Yong; Barbour, Randall L. [SUNY Downstate Medical Center, Brooklyn, New York 11203 (United States); NIRx Medical Technologies, LLC, Glen Head, New York 11545 (United States); Al abdi, Rabah [Department of Biomedical Engineering, Jordan University of Science and Technology, Irbid 22110 (Jordan); Asarian, Armand P.; Pappas, Peter J. [The Brooklyn Hospital Center, Brooklyn, New York 11201 (United States); Dresner, Lisa [SUNY Downstate Medical Center, Brooklyn, New York 11203 (United States); Patel, Naresh [Kaiser Permanente-Modesto Medical Center, Modesto, California 95356 (United States); Jagarlamundi, Kuppuswamy [Sarah Bush Lincoln Regional Cancer Center, 1000 Health Center Drive, Mattoon, Illinois 61938 (United States); Solomon, William B. [Maimonides Medical Center, Brooklyn, New York 11219 (United States)

    2015-11-15

    Purpose: The work presented here demonstrates an application of diffuse optical tomography (DOT) to the problem of breast-cancer diagnosis. The potential for using spatial and temporal variability measures of the hemoglobin signal to identify useful biomarkers was studied. Methods: DOT imaging data were collected using two instrumentation platforms the authors developed, which were suitable for exploring tissue dynamics while performing a simultaneous bilateral exam. For each component of the hemoglobin signal (e.g., total, oxygenated), the image time series was reduced to eight scalar metrics that were affected by one or more dynamic properties of the breast microvasculature (e.g., average amplitude, amplitude heterogeneity, strength of spatial coordination). Receiver-operator characteristic (ROC) analyses, comparing groups of subjects with breast cancer to various control groups (i.e., all noncancer subjects, only those with diagnosed benign breast pathology, and only those with no known breast pathology), were performed to evaluate the effect of cancer on the magnitudes of the metrics and of their interbreast differences and ratios. Results: For women with known breast cancer, simultaneous bilateral DOT breast measures reveal a marked increase in the resting-state amplitude of the vasomotor response in the hemoglobin signal for the affected breast, compared to the contralateral, noncancer breast. Reconstructed 3D spatial maps of observed dynamics also show that this behavior extends well beyond the tumor border. In an effort to identify biomarkers that have the potential to support clinical aims, a group of scalar quantities extracted from the time series measures was systematically examined. This analysis showed that many of the quantities obtained by computing paired responses from the bilateral scans (e.g., interbreast differences, ratios) reveal statistically significant differences between the cancer-positive and -negative subject groups, while the

  18. Interobserver and Intraobserver Reproducibility with Volume Dynamic Contrast Enhanced Computed Tomography (DCE-CT) in Gastroesophageal Junction Cancer

    DEFF Research Database (Denmark)

    Lundsgaard Hansen, Martin; Fallentin, Eva; Axelsen, Thomas;

    2016-01-01

    The purpose of this study was to assess inter- and intra-observer reproducibility of three different analytic methods to evaluate quantitative dynamic contrast-enhanced computed tomography (DCE-CT) measures from gastroesophageal junctional cancer. Twenty-five DCE-CT studies with gastroesophageal ...... were narrower for 3D analysis compared to 2D analysis. Three-dimensional volume DCE-CT analysis of gastroesophageal junction cancer provides higher inter- and intra-observer reproducibility with narrower limits of agreement between readers compared to 2D analysis.......The purpose of this study was to assess inter- and intra-observer reproducibility of three different analytic methods to evaluate quantitative dynamic contrast-enhanced computed tomography (DCE-CT) measures from gastroesophageal junctional cancer. Twenty-five DCE-CT studies with gastroesophageal...... for each observation. Inter- and intra-observer variability were assessed by Intraclass Correlation Coefficient (ICC) and Bland-Altman statistics. Interobserver ICC was excellent for arterial flow (0.88), for blood volume (0.89) and for permeability (0.91) with 3D-VOI analysis. The 95% limits of agreement...

  19. Cardiac Exposure in the Dynamic Conformal Arc Therapy, Intensity-Modulated Radiotherapy and Volumetric Modulated Arc Therapy of Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Xin Ming

    Full Text Available To retrospectively evaluate the cardiac exposure in three cohorts of lung cancer patients treated with dynamic conformal arc therapy (DCAT, intensity-modulated radiotherapy (IMRT, or volumetric modulated arc therapy (VMAT at our institution in the past seven years.A total of 140 lung cancer patients were included in this institutional review board approved study: 25 treated with DCAT, 70 with IMRT and 45 with VMAT. All plans were generated in a same commercial treatment planning system and have been clinically accepted and delivered. The dose distribution to the heart and the effects of tumor laterality, the irradiated heart volume and the beam-to-heart distance on the cardiac exposure were investigated.The mean dose to the heart among all 140 plans was 4.5 Gy. Specifically, the heart received on average 2.3, 5.2 and 4.6 Gy in the DCAT, IMRT and VMAT plans, respectively. The mean heart doses for the left and right lung tumors were 4.1 and 4.8 Gy, respectively. No patients died with evidence of cardiac disease. Three patients (2% with preexisting cardiac condition developed cardiac disease after treatment. Furthermore, the cardiac exposure was found to increase linearly with the irradiated heart volume while decreasing exponentially with the beam-to-heart distance.Compared to old technologies for lung cancer treatment, modern radiotherapy treatment modalities demonstrated better heart sparing. But the heart dose in lung cancer radiotherapy is still higher than that in the radiotherapy of breast cancer and Hodgkin's disease where cardiac complications have been extensively studied. With strong correlations of mean heart dose with beam-to-heart distance and irradiated heart volume, cautions should be exercised to avoid long-term cardiac toxicity in the lung cancer patients undergoing radiotherapy.

  20. Triple-negative invasive breast cancer on dynamic contrast-enhanced and diffusion-weighted MR imaging: comparison with other breast cancer subtypes

    Energy Technology Data Exchange (ETDEWEB)

    Youk, Ji Hyun; Son, Eun Ju; Chung, Jin; Kim, Jeong-Ah; Kim, Eun-kyung [Department of Radiology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)

    2012-08-15

    To determine the MRI features of triple-negative invasive breast cancer (TNBC) on dynamic contrast-enhanced MR imaging (DCE-MRI) and diffusion-weighted MR imaging (DWI) in comparison with ER-positive/HER2-negative (ER+) and HER2-positive cancer (HER2+). A total of 271 invasive cancers in 269 patients undergoing preoperative MRI and surgery were included. Two radiologists retrospectively assessed morphological and kinetic characteristics on DCE-MRI and tumour detectability on DWI. Apparent diffusion coefficient (ADC) values of lesions were measured. Clinical and MRI features of the three subtypes were compared. Compared with ER+ (n = 119) and HER2+ (n = 94), larger size, round/oval mass shape, smooth mass margin, and rim enhancement on DCE-MRI were significantly associated with TNBC (n = 58; P < 0.0001). On DWI, mean ADC value (x 10{sup -3} mm{sup 2}/s) of TNBC (1.03) was higher than the mean ADC values for ER+ and HER2+ (0.89 and 0.84; P < 0.0001). There was no difference in tumour detectability (P = 0.099). Tumour size (P = 0.009), mass margin (smooth, P < 0.0001; irregular, P = 0.020), and ADC values (P = 0.002) on DCE-MRI and DWI were independent features of TNBC. In addition to the morphological features, higher ADC values on DWI were independently associated with TNBC and could be useful in differentiating TNBC from ER+ and HER2+. (orig.)

  1. Bubble and drop interfaces

    CERN Document Server

    Miller

    2011-01-01

    The book aims at describing the most important experimental methods for characterizing liquid interfaces, such as drop profile analysis, bubble pressure and drop volume tensiometry, capillary pressure technique, and oscillating drops and bubbles. Besides the details of experimental set ups, also the underlying theoretical basis is presented in detail. In addition, a number of applications based on drops and bubbles is discussed, such as rising bubbles and the very complex process of flotation. Also wetting, characterized by the dynamics of advancing contact angles is discussed critically. Spec

  2. 2D self-assembly of phenylene-vinylene tectons at the liquid-highly oriented pyrolytic graphite interface: from chain length effects to anisotropic guest-host dynamics

    Science.gov (United States)

    Six, A.; Bocheux, A.; Charra, F.; Mathevet, F.; Kreher, D.; Attias, A.-J.

    2017-01-01

    Here we report the synthesis and characterization of a series of new phenylene-vinylene tectons. The study by scanning tunneling microscopy of their supramolecular self-assembly at the interface between a phenyloctane solution and highly oriented pyrolytic graphite demonstrates that variation of concentration and length of alkyl chains led to the formation of different networks, a compact one and a nanoporous one, with a fine control of the lattice parameters. The study of guest-host properties of the nanoporous network revealed a selectivity toward guest compounds according to their shape and size. Moreover, the statistical analysis of pore-to-pore guest dynamics evidences an anisotropic diffusion process.

  3. Area of Interest 1, CO2 at the Interface. Nature and Dynamics of the Reservoir/Caprock Contact and Implications for Carbon Storage Performance

    Energy Technology Data Exchange (ETDEWEB)

    Mozley, Peter [New Mexico Institute Of Mining And Technology, Socorro, NM (United States); Evans, James [New Mexico Institute Of Mining And Technology, Socorro, NM (United States); Dewers, Thomas [New Mexico Institute Of Mining And Technology, Socorro, NM (United States)

    2014-10-31

    We examined the influence of geologic features present at the reservoir/caprock interface on the transmission of supercritical CO2 into and through caprock. We focused on the case of deformation-band faults in reservoir lithologies that intersect the interface and transition to opening-mode fractures in caprock lithologies. Deformation-band faults are exceeding common in potential CO2 injection units and our fieldwork in Utah indicates that this sort of transition is common. To quantify the impact of these interface features on flow and transport we first described the sedimentology and permeability characteristics of selected sites along the Navajo Sandstone (reservoir lithology) and Carmel Formation (caprock lithology) interface, and along the Slickrock Member (reservoir lithology) and Earthy Member (caprock lithology) of the Entrada Sandstone interface, and used this information to construct conceptual permeability models for numerical analysis. We then examined the impact of these structures on flow using single-phase and multiphase numerical flow models for these study sites. Key findings include: (1) Deformation-band faults strongly compartmentalize the reservoir and largely block cross-fault flow of supercritical CO2. (2) Significant flow of CO2 through the fractures is possible, however, the magnitude is dependent on the small-scale geometry of the contact between the opening-mode fracture and the deformation band fault. (3) Due to the presence of permeable units in the caprock, caprock units are capable of storing significant volumes of CO2, particularly when the fracture network does not extend all the way through the caprock. The large-scale distribution of these deformation-bandfault-to-opening-mode-fractures is related to the curvature of the beds, with greater densities of fractures in high curvature regions. We also examined core and outcrops from the Mount Simon Sandstone and Eau Claire

  4. SU-E-T-381: Radio-Dynamic Therapy (RDT) for the Treatment of Late-Stage Cancers

    Energy Technology Data Exchange (ETDEWEB)

    Ma, C; Chen, L; Price, R [Fox Chase Cancer Center, Philadelphia, PA (United States); Zhang, Q [Wu Xi Yi Ren Tumor Hosiptal, Wuxi, Jiangsu (China); Zeng, J; Xu, K; Sun, Q [Wuxi Yiren Cancer Hospital, Wuxi, Jiangsu (China)

    2014-06-01

    Purpose: Photo-dynamic therapy (PDT) is an effective treatment modality because of the preferential absorption of photosensitizing agent in tumor cells than in surrounding normal tissues. A limitation of PDT for cancer therapy is the finite penetration of laser light to activate the targeting agent in deep-seated tumors. Radio-dynamic therapy (RDT) is designed to overcome this problem by the combination of high-energy (up to 45MV) photon beams and photo/radio-sensitizers. This work investigates the feasibility of PDT for late-stage cancer patients who are no longer respond to conventional therapies available. Methods: The high-energy photon beams are generated using a LA45 RaceTrack Microtron (Top Grade Medical, Beijing, China). The targeting agent investigated is 5- aminolevulinic acid (5-ALA). Both in vitro cell lines and in vivo animal models have been used to investigate the mechanisms of RDT and its therapeutic effects and normal tissue toxicities. Oral 5-ALA (30-60 mg/kg) was administered 4-6 hours before the radiation treatment and the total radiation dose varied between 0.1-4.0Gy in 1-4 fractions. Clinical trials are initiated in China for late-stage cancer patients targeting both primary tumors utilizing localized therapies such as 3DCRT/IMRT and metastases using TBI. Results: There is clear correlation between the cell death and the 5-ALA concentration/radiation dose. The therapeutic effect of RDT is demonstrated using an animal model where the volume of parotid tumors for the RT only group continued to grow after 3Gy irradiation while the RDT group showed a complete response with the same radiation dose. The preliminary clinical results showed encouraging clinical outcome. Conclusion: RDT is a novel treatment technique that may be developed into an effective cancer treatment modality. Further studies on the mechanisms of RDT and its potential clinical applications are warranted.

  5. Scale-free brain dynamics under physical and psychological distress: pre-treatment effects in women diagnosed with breast cancer.

    Science.gov (United States)

    Churchill, Nathan W; Cimprich, Bernadine; Askren, Mary K; Reuter-Lorenz, Patricia A; Jung, Mi Sook; Peltier, Scott; Berman, Marc G

    2015-03-01

    Stressful life events are related to negative outcomes, including physical and psychological manifestations of distress, and behavioral deficits. Patients diagnosed with breast cancer report impaired attention and working memory prior to adjuvant therapy, which may be induced by distress. In this article, we examine whether brain dynamics show systematic changes due to the distress associated with cancer diagnosis. We hypothesized that impaired working memory is associated with suppression of "long-memory" neuronal dynamics; we tested this by measuring scale-free ("fractal") brain dynamics, quantified by the Hurst exponent (H). Fractal scaling refers to signals that do not occur at a specific time-scale, possessing a spectral power curve P(f)∝ f(-β); they are "long-memory" processes, with significant autocorrelations. In a BOLD functional magnetic resonance imaging study, we scanned three groups during a working memory task: women scheduled to receive chemotherapy or radiotherapy and aged-matched controls. Surprisingly, patients' BOLD signal exhibited greater H with increasing intensity of anticipated treatment. However, an analysis of H and functional connectivity against self-reported measures of psychological distress (Worry, Anxiety, Depression) and physical distress (Fatigue, Sleep problems) revealed significant interactions. The modulation of (Worry, Anxiety) versus (Fatigue, Sleep Problems, Depression) showed the strongest effect, where higher worry and lower fatigue was related to reduced H in regions involved in visuospatial search, attention, and memory processing. This is also linked to decreased functional connectivity in these brain regions. Our results indicate that the distress associated with cancer diagnosis alters BOLD scaling, and H is a sensitive measure of the interaction between psychological versus physical distress.

  6. Nanoparticle Assemblies at Fluid Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Russell, Thomas P. [Univ. of Massachusetts, Amherst, MA (United States). Dept. of Polymer Science and Engineering

    2015-03-10

    A systematic study of the structure and dynamics of nanoparticles (NP) and NP-surfactants was performed. The ligands attached to both the NPs and NP-surfactants dictate the manner in which the nanoscopic materials assemble at fluid interfaces. Studies have shown that a single layer of the nanoscpic materials form at the interface to reduce the interactions between the two immiscible fluids. The shape of the NP is, also, important, where for spherical particles, a disordered, liquid-like monolayer forms, and, for nanorods, ordered domains at the interface is found and, if the monolayers are compressed, the orientation of the nanorods with respect to the interface can change. By associating end-functionalized polymers to the NPs assembled at the interface, NP-surfactants are formed that increase the energetic gain in segregating each NP at the interface which allows the NP-surfactants to jam at the interface when compressed. This has opened the possibility of structuring the two liquids by freezing in shape changes of the liquids.

  7. Analysis of the relationship between lung cancer drug response level and atom connectivity dynamics based on trimmed Delaunay triangulation

    Science.gov (United States)

    Zou, Bin; Wang, Debby D.; Ma, Lichun; Chen, Lijiang; Yan, Hong

    2016-05-01

    Epidermal growth factor receptor (EGFR) mutation is a pathogenic factor of non-small cell lung cancer (NSCLC). Tyrosine kinase inhibitors (TKIs), such as gefitinib, are widely used in NSCLC treatment. In this work, we investigated the relationship between the number of EGFR residues connected with gefitinib and the response level for each EGFR mutation type. Three-dimensional trimmed Delaunay triangulation was applied to construct connections between EGFR residues and gefitinib atoms. Through molecular dynamics (MD) simulations, we discovered that when the number of EGFR residues connected with gefitinib increases, the response level of the corresponding EGFR mutation tends to descend.

  8. Active matter clusters at interfaces.

    Science.gov (United States)

    Copenhagen, Katherine; Gopinathan, Ajay

    2016-03-01

    Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor formation and metastasis, colonies of bacteria in a biofilm, or even flocks of birds and schools of fish at the macro-scale. Such clusters typically encounter very heterogeneous environments. What happens when a cluster encounters an interface between two different environments has implications for its function and fate. Here we study this problem by using a mathematical model of a cluster that treats it as a single cohesive unit that moves in two dimensions by exerting a force/torque per unit area whose magnitude depends on the nature of the local environment. We find that low speed (overdamped) clusters encountering an interface with a moderate difference in properties can lead to refraction or even total internal reflection of the cluster. For large speeds (underdamped), where inertia dominates, the clusters show more complex behaviors crossing the interface multiple times and deviating from the predictable refraction and reflection for the low velocity clusters. We then present an extreme limit of the model in the absence of rotational damping where clusters can become stuck spiraling along the interface or move in large circular trajectories after leaving the interface. Our results show a wide range of behaviors that occur when collectively moving active biological matter moves across interfaces and these insights can be used to control motion by patterning environments.

  9. PREFACE: Water at interfaces Water at interfaces