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Sample records for models force interactions

  1. Interactions between internal forces, body stiffness, and fluid environment in a neuromechanical model of lamprey swimming.

    Science.gov (United States)

    Tytell, Eric D; Hsu, Chia-Yu; Williams, Thelma L; Cohen, Avis H; Fauci, Lisa J

    2010-11-16

    Animal movements result from a complex balance of many different forces. Muscles produce force to move the body; the body has inertial, elastic, and damping properties that may aid or oppose the muscle force; and the environment produces reaction forces back on the body. The actual motion is an emergent property of these interactions. To examine the roles of body stiffness, muscle activation, and fluid environment for swimming animals, a computational model of a lamprey was developed. The model uses an immersed boundary framework that fully couples the Navier-Stokes equations of fluid dynamics with an actuated, elastic body model. This is the first model at a Reynolds number appropriate for a swimming fish that captures the complete fluid-structure interaction, in which the body deforms according to both internal muscular forces and external fluid forces. Results indicate that identical muscle activation patterns can produce different kinematics depending on body stiffness, and the optimal value of stiffness for maximum acceleration is different from that for maximum steady swimming speed. Additionally, negative muscle work, observed in many fishes, emerges at higher tail beat frequencies without sensory input and may contribute to energy efficiency. Swimming fishes that can tune their body stiffness by appropriately timed muscle contractions may therefore be able to optimize the passive dynamics of their bodies to maximize peak acceleration or swimming speed.

  2. IM-UFF: Extending the universal force field for interactive molecular modeling.

    Science.gov (United States)

    Jaillet, Léonard; Artemova, Svetlana; Redon, Stephane

    2017-09-05

    The universal force field (UFF) is a broadly applicable classical force field that contains parameters for almost every atom type of the periodic table. This force field is non-reactive, i.e. the topology of the system under study is considered as fixed and no creation or breaking of covalent bonds is possible. This paper introduces interactive modeling-UFF (IM-UFF), an extension of UFF that combines the possibility to significantly modify molecular structures (as with reactive force fields) with a broad diversity of supported systems thanks to the universality of UFF. Such an extension lets the user easily build and edit molecular systems interactively while being guided by physics based inter-atomic forces. This approach introduces weighted atom types and weighted bonds, used to update topologies and atom parameterizations at every time step of a simulation. IM-UFF has been evaluated on a large set of benchmarks and is proposed as a self-contained implementation integrated in a new module for the SAMSON software platform for computational nanoscience available at http://www.samson-connect.net. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Atomic Force Microscopy Study of the Interactions of Indolicidin with Model Membranes and DNA.

    Science.gov (United States)

    Fojan, Peter; Gurevich, Leonid

    2017-01-01

    The cell membrane is the first barrier and quite often the primary target that antimicrobial peptides (AMPs) have to destroy or penetrate to fulfill their mission. Upon penetrating through the membrane, the peptides can further attack intracellular targets, in particular DNA. Studying the interaction of an antimicrobial peptide with a cell membrane and DNA holds keys to understanding its killing mechanisms. Commonly, these interactions are studied by using optical or scanning electron microscopy and appropriately labeled peptides. However, labeling can significantly affect the hydrophobicity, conformation, and size of the peptide, hence altering the interaction significantly. Here, we describe the use of atomic force microscopy (AFM) for a label-free study of the interactions of peptides with model membranes under physiological conditions and DNA as a possible intracellular target.

  4. Conformational mechanics, adsorption, and normal force interactions of lubricin and hyaluronic acid on model surfaces.

    Science.gov (United States)

    Chang, Debby P; Abu-Lail, Nehal I; Guilak, Farshid; Jay, Gregory D; Zauscher, Stefan

    2008-02-19

    Glycoproteins, such as lubricin, and hyaluronic acid (HA) play a prominent role in the boundary lubrication mechanism in diarthrodial joints. Although many studies have tried to elucidate the lubrication mechanisms of articular cartilage, the molecular details of how lubricin and HA interact with cartilage surfaces and mediate their interaction still remain poorly understood. Here we used model substrates, functionalized with self-assembled monolayers terminating in hydroxyl or methyl groups, (1) to determine the effect of surface chemistry on lubricin and HA adsorption using surface plasmon resonance (SPR) and (2) to study normal force interactions between these surfaces as a function of lubricin and HA concentration using colloidal probe microscopy. We found that lubricin is amphiphilic and adsorbed strongly onto both methyl- and hydroxyl-terminated surfaces. On hydrophobic surfaces, lubricin likely adopts a compact, looplike conformation in which its hydrophobic domains at the N and C termini serve as surface anchors. On hydrophilic surfaces, lubricin likely adsorbs anywhere along its hydrophilic central domain and adopts, with increasing solution concentration, an extended tail-like conformation. Overall, lubricin develops strong repulsive interactions when compressing two surfaces into contact. Furthermore, upon surface separation, adhesion occurs between the surfaces as a result of molecular bridging and chain disentanglement. This behavior is in contrast to that of HA, which does not adsorb appreciably on either of the model surfaces and does not develop significant repulsive interactions. Adhesive forces, particularly between the hydrophobic surfaces, are large and not appreciably affected by HA. For a mixture of lubricin and HA, we observed slightly larger adsorptions and repulsions than those found for lubricin alone. Our experiments suggest that this interaction depends on unspecific physical rather than chemical interactions between lubricin and HA. We

  5. Analysis of bit-rock interaction during stick-slip vibrations using PDC cutting force model

    Energy Technology Data Exchange (ETDEWEB)

    Patil, P.A.; Teodoriu, C. [Technische Univ. Clausthal, Clausthal-Zellerfeld (Germany). ITE

    2013-08-01

    Drillstring vibration is one of the limiting factors maximizing the drilling performance and also causes premature failure of drillstring components. Polycrystalline diamond compact (PDC) bit enhances the overall drilling performance giving the best rate of penetrations with less cost per foot but the PDC bits are more susceptible to the stick slip phenomena which results in high fluctuations of bit rotational speed. Based on the torsional drillstring model developed using Matlab/Simulink for analyzing the parametric influence on stick-slip vibrations due to drilling parameters and drillstring properties, the study of relations between weight on bit, torque on bit, bit speed, rate of penetration and friction coefficient have been analyzed. While drilling with the PDC bits, the bit-rock interaction has been characterized by cutting forces and the frictional forces. The torque on bit and the weight on bit have both the cutting component and the frictional component when resolved in horizontal and vertical direction. The paper considers that the bit is undergoing stick-slip vibrations while analyzing the bit-rock interaction of the PDC bit. The Matlab/Simulink bit-rock interaction model has been developed which gives the average cutting torque, T{sub c}, and friction torque, T{sub f}, values on cutters as well as corresponding average weight transferred by the cutting face, W{sub c}, and the wear flat face, W{sub f}, of the cutters value due to friction.

  6. Analytical Model of the Nonlinear Dynamics of Cantilever Tip-Sample Surface Interactions for Various Acoustic-Atomic Force Microscopies

    Science.gov (United States)

    Cantrell, John H., Jr.; Cantrell, Sean A.

    2008-01-01

    A comprehensive analytical model of the interaction of the cantilever tip of the atomic force microscope (AFM) with the sample surface is developed that accounts for the nonlinearity of the tip-surface interaction force. The interaction is modeled as a nonlinear spring coupled at opposite ends to linear springs representing cantilever and sample surface oscillators. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a standard iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and the commonly used intermittent contact mode (TappingMode) generally available on AFMs. The solutions are used to obtain a quantitative measure of image contrast resulting from variations in the Young modulus of the sample for the amplitude and phase images generated by the A-AFM techniques. Application of the model to RDF-AFUM and intermittent soft contact phase images of LaRC-cp2 polyimide polymer is discussed. The model predicts variations in the Young modulus of the material of 24 percent from the RDF-AFUM image and 18 percent from the intermittent soft contact image. Both predictions are in good agreement with the literature value of 21 percent obtained from independent, macroscopic measurements of sheet polymer material.

  7. A multi-scale continuum model of skeletal muscle mechanics predicting force enhancement based on actin-titin interaction.

    Science.gov (United States)

    Heidlauf, Thomas; Klotz, Thomas; Rode, Christian; Altan, Ekin; Bleiler, Christian; Siebert, Tobias; Röhrle, Oliver

    2016-12-01

    Although recent research emphasises the possible role of titin in skeletal muscle force enhancement, this property is commonly ignored in current computational models. This work presents the first biophysically based continuum-mechanical model of skeletal muscle that considers, in addition to actin-myosin interactions, force enhancement based on actin-titin interactions. During activation, titin attaches to actin filaments, which results in a significant reduction in titin's free molecular spring length and therefore results in increased titin forces during a subsequent stretch. The mechanical behaviour of titin is included on the microscopic half-sarcomere level of a multi-scale chemo-electro-mechanical muscle model, which is based on the classic sliding-filament and cross-bridge theories. In addition to titin stress contributions in the muscle fibre direction, the continuum-mechanical constitutive relation accounts for geometrically motivated, titin-induced stresses acting in the muscle's cross-fibre directions. Representative simulations of active stretches under maximal and submaximal activation levels predict realistic magnitudes of force enhancement in fibre direction. For example, stretching the model by 20 % from optimal length increased the isometric force at the target length by about 30 %. Predicted titin-induced stresses in the muscle's cross-fibre directions are rather insignificant. Including the presented development in future continuum-mechanical models of muscle function in dynamic situations will lead to more accurate model predictions during and after lengthening contractions.

  8. Lift force enhancement and fluid-structure interactions on a self-excited flapping wing model

    Science.gov (United States)

    Curet, Oscar; Swartz, Sharon; Breuer, Kenneth

    2011-11-01

    We present data from a mechanical model that we have used to explore a physical mechanism that may have aided transition from gliding to flapping flight over fifty million years ago. The model is composed of a cantilevered flat plate with a hinged trailing flap and is tested in a low-speed wind tunnel. For slow wind speeds the model is stationary, but above a critical wind speed the wing starts to oscillate due to an aeroelastic instability. A positive angle of attack on the wing results in a positive lift force. However, this lift force is significantly enhanced once the wing starts to oscillate. We used particle image velocimetry (PIV) to understand the unsteady aerodynamics of the self-excited flapping wing, and to identify and characterize the mechanisms that generate the enhanced lift force. We also discuss the implications of our results on the evolution of powered biological flight. This work was supported by AFOSR-MURI on bioinspired flight.

  9. Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues.

    Science.gov (United States)

    Li, Xinbi; Ponomarev, Sergei Y; Sa, Qina; Sigalovsky, Daniel L; Kaminski, George A

    2013-05-30

    A previously introduced polarizable simulations with second-order interaction model (POSSIM) force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies, and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being used in further development of the POSSIM fast polarizable force field for proteins.

  10. Quantitative modeling assesses the contribution of bond strengthening, rebinding and force sharing to the avidity of biomolecule interactions.

    Directory of Open Access Journals (Sweden)

    Valentina Lo Schiavo

    Full Text Available Cell adhesion is mediated by numerous membrane receptors. It is desirable to derive the outcome of a cell-surface encounter from the molecular properties of interacting receptors and ligands. However, conventional parameters such as affinity or kinetic constants are often insufficient to account for receptor efficiency. Avidity is a qualitative concept frequently used to describe biomolecule interactions: this includes incompletely defined properties such as the capacity to form multivalent attachments. The aim of this study is to produce a working description of monovalent attachments formed by a model system, then to measure and interpret the behavior of divalent attachments under force. We investigated attachments between antibody-coated microspheres and surfaces coated with sparse monomeric or dimeric ligands. When bonds were subjected to a pulling force, they exhibited both a force-dependent dissociation consistent with Bell's empirical formula and a force- and time-dependent strengthening well described by a single parameter. Divalent attachments were stronger and less dependent on forces than monovalent ones. The proportion of divalent attachments resisting a force of 30 piconewtons for at least 5 s was 3.7 fold higher than that of monovalent attachments. Quantitative modeling showed that this required rebinding, i.e. additional bond formation between surfaces linked by divalent receptors forming only one bond. Further, experimental data were compatible with but did not require stress sharing between bonds within divalent attachments. Thus many ligand-receptor interactions do not behave as single-step reactions in the millisecond to second timescale. Rather, they exhibit progressive stabilization. This explains the high efficiency of multimerized or clustered receptors even when bonds are only subjected to moderate forces. Our approach provides a quantitative way of relating binding avidity to measurable parameters including bond

  11. A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

    Science.gov (United States)

    Michalowsky, Julian; Schäfer, Lars V.; Holm, Christian; Smiatek, Jens

    2017-02-01

    We present a refined version of the polarizable Martini water model - coined refPOL - designed specifically for the use with long-range electrostatics. The refPOL model improves the agreement with the experimentally measured dielectric constant and the mass density of water at room temperature compared to the original polarizable Martini water force field when particle mesh Ewald electrostatics are employed. Our study reveals that the model remains applicable with various commonly used settings for the non-bonded interactions, including reaction field electrostatics. The oil/water partitioning behavior of uncharged Martini bead types is thoroughly investigated: Lennard-Jones interactions between the refPOL model and the remaining Martini beads are adjusted to reproduce the hydration free energies obtained with the original polarizable water model, while free energies of solvation in apolar media remain unchanged. The cross-interactions with charged bead types are parameterized to agree with the experimentally observed area per lipid of a fully solvated dipalmitoylphosphatidylcholine bilayer. We additionally verify the model by analyzing the potentials of mean force between different sample pairs in refPOL water and comparing the results to reference data obtained using the original polarizable Martini water model as well as fully atomistic simulations. Based on the results, we suggest to replace the original polarizable Martini water model with the new refPOL model for future applications.

  12. Modelling the effect of rail dampers on wheel-rail interaction forces and rail roughness growth rates

    Science.gov (United States)

    Croft, B. E.; Jones, C. J. C.; Thompson, D. J.

    2009-06-01

    Trains generate rolling noise because of the roughness of the wheel and rail running surfaces. Special acoustic grinding programmes have been introduced on some railways specifically to control rolling noise. Rail dampers are also used to reduce rolling noise; this paper studies rail damping as a possible mechanism to slow the rate of development of roughness on the surface of rails. This would reduce noise further over time or reduce the required frequency of grinding. High roughness growth on the rail occurs in situations with stiff vertical structural dynamics of the track. In particular the antiresonance above a sleeper at the pinned-pinned frequency has been identified as a wavelength fixing mechanism for short pitch corrugation. Rail dampers change the dynamic response of the rail, shifting the pinned-pinned frequency and smoothing the track receptance. Here, a simple time-stepping model is applied to calculate the interaction forces between wheel and rail for a track with and without rail dampers. The calculations show that rail dampers reduce dynamic interaction forces and shift the force spectrum to longer wavelengths. The interaction forces are used as input to an abrasive wear model to predict the roughness growth rate and the change in roughness after many wheel passages. Track without rail dampers is predicted to develop corrugation at the wavelength corresponding to the pinned-pinned frequency. With rail dampers the corrugation growth is reduced and shifted to a longer wavelength where its significance is diminished.

  13. The interaction of 2-mercaptobenzimidazole with human serum albumin as determined by spectroscopy, atomic force microscopy and molecular modeling.

    Science.gov (United States)

    Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua

    2013-04-01

    The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. Investigation of the Interaction between Patulin and Human Serum Albumin by a Spectroscopic Method, Atomic Force Microscopy, and Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Li Yuqin

    2014-01-01

    Full Text Available The interaction of patulin with human serum albumin (HSA was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis, circular dichroism (CD, atomic force microscopy (AFM, and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG0, ΔH0, and ΔS0 values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.

  15. Assessing the relative importance of parameter and forcing uncertainty and their interactions in conceptual hydrological model simulations

    Science.gov (United States)

    Mockler, E. M.; Chun, K. P.; Sapriza-Azuri, G.; Bruen, M.; Wheater, H. S.

    2016-11-01

    Predictions of river flow dynamics provide vital information for many aspects of water management including water resource planning, climate adaptation, and flood and drought assessments. Many of the subjective choices that modellers make including model and criteria selection can have a significant impact on the magnitude and distribution of the output uncertainty. Hydrological modellers are tasked with understanding and minimising the uncertainty surrounding streamflow predictions before communicating the overall uncertainty to decision makers. Parameter uncertainty in conceptual rainfall-runoff models has been widely investigated, and model structural uncertainty and forcing data have been receiving increasing attention. This study aimed to assess uncertainties in streamflow predictions due to forcing data and the identification of behavioural parameter sets in 31 Irish catchments. By combining stochastic rainfall ensembles and multiple parameter sets for three conceptual rainfall-runoff models, an analysis of variance model was used to decompose the total uncertainty in streamflow simulations into contributions from (i) forcing data, (ii) identification of model parameters and (iii) interactions between the two. The analysis illustrates that, for our subjective choices, hydrological model selection had a greater contribution to overall uncertainty, while performance criteria selection influenced the relative intra-annual uncertainties in streamflow predictions. Uncertainties in streamflow predictions due to the method of determining parameters were relatively lower for wetter catchments, and more evenly distributed throughout the year when the Nash-Sutcliffe Efficiency of logarithmic values of flow (lnNSE) was the evaluation criterion.

  16. Fluid–Structure Interaction Analysis of Papillary Muscle Forces Using a Comprehensive Mitral Valve Model with 3D Chordal Structure

    Energy Technology Data Exchange (ETDEWEB)

    Toma, Milan; Jensen, Morten Ø.; Einstein, Daniel R.; Yoganathan, Ajit P.; Cochran, Richard P.; Kunzelman, Karyn S.

    2015-07-17

    Numerical models of native heart valves are being used to study valve biomechanics to aid design and development of repair procedures and replacement devices. These models have evolved from simple two-dimensional approximations to complex three-dimensional, fully coupled fluid-structure interaction (FSI) systems. Such simulations are useful for predicting the mechanical and hemodynamic loading on implanted valve devices. A current challenge for improving the accuracy of these predictions is choosing and implementing modeling boundary conditions. In order to address this challenge, we are utilizing an advanced in-vitro system to validate FSI conditions for the mitral valve system. Explanted ovine mitral valves were mounted in an in vitro setup, and structural data for the mitral valve was acquired with *CT. Experimental data from the in-vitro ovine mitral valve system were used to validate the computational model. As the valve closes, the hemodynamic data, high speed lea et dynamics, and force vectors from the in-vitro system were compared to the results of the FSI simulation computational model. The total force of 2.6 N per papillary muscle is matched by the computational model. In vitro and in vivo force measurements are important in validating and adjusting material parameters in computational models. The simulations can then be used to answer questions that are otherwise not possible to investigate experimentally. This work is important to maximize the validity of computational models of not just the mitral valve, but any biomechanical aspect using computational simulation in designing medical devices.

  17. Forcings and Feedbacks on Convection in the 2010 Pakistan Flood: Modeling Extreme Precipitation with Interactive Large-Scale Ascent

    CERN Document Server

    Nie, Ji; Sobel, Adam H

    2016-01-01

    Extratropical extreme precipitation events are usually associated with large-scale flow disturbances, strong ascent and large latent heat release. The causal relationships between these factors are often not obvious, however, and the roles of different physical processes in producing the extreme precipitation event can be difficult to disentangle. Here, we examine the large-scale forcings and convective heating feedback in the precipitation events which caused the 2010 Pakistan flood within the Column Quasi-Geostrophic framework. A cloud-revolving model (CRM) is forced with the large-scale forcings (other than large-scale vertical motion) computed from the quasi-geostrophic omega equation with input data from a reanalysis data set, and the large-scale vertical motion is diagnosed interactively with the simulated convection. Numerical results show that the positive feedback of convective heating to large-scale dynamics is essential in amplifying the precipitation intensity to the observed values. Orographic li...

  18. Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone

    Science.gov (United States)

    Ponomarev, Sergei Y.; Kaminski, George A.

    2011-01-01

    A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06Å). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins. PMID:21743799

  19. Assessment of Some Density Functional Theory Methods and Force Field Models in Describing Various Interaction Modes of Benzene Dimer

    Institute of Scientific and Technical Information of China (English)

    Yu-wei Zhou; Igor Ying Zhang; Jian-ming Wu; An-an Wu; Xin Xu

    2011-01-01

    Benzene dimer (bz2) is the simplest prototype of the π-π interactions.Such interactions are ubiquitous in diverse areas of science and molecular engineering.In the present work,we have made assessment on some modern density functional methods including B97-D,BLYP-D3,M06-2X,XYG3,and force field models including CHARMM,AMBER,MM3,AMOEBA on six important interaction modes of bz2.Our results not only highlight the usefulness of these cost-effective methods,which can be used as economic substitutes of the expensive CCSD(T) for complex real-world systems,but also indicate their weakness in the description of the π-π interactions,which points to the future direction for further improvements.

  20. Intermolecular forces: a solution to dispersion interactions.

    Science.gov (United States)

    Shimizu, Ken D

    2013-12-01

    London dispersion forces have been cited as an important factor in protein folding, drug–receptor interactions, and catalyst selectivities. However, careful analysis of a model system finds that the dispersion interactions are only minor contributors to the formation of complexes in solution.

  1. Self-Assembly and Intermolecular Forces When Cellulose and Water Interact Using Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Ali Chami Khazraji

    2013-01-01

    Full Text Available Cellulose chains are linear and aggregation occurs via both intra- and intermolecular hydrogen bonds. Cellulose has a strong affinity to itself and toward materials containing hydroxyls groups. Based on the preponderance of hydroxyl functional groups, cellulose is very reactive with water. At room temperature, cellulose chains will have at least a monomolecular layer of water associated to it. The formation of hydrogen bonds at the cellulose/water interface is shown to depend essentially on the adsorption site, for example, the equatorial hydroxyls or OH moieties pointing outward from the cellulose chains. The vdW forces also contribute significantly to the adsorption energy. They are a considerable cohesive energy into the cellulose network. At the surface of the cellulose chains, many intermolecular hydrogen bonds of the cellulose chains are lost. However, they are compensated by hydrogen bonds with water molecules. Electronic clouds can be distorted and create electrostatic dipoles. The large antibonding electron cloud that exists around the glucosidic bonds produces an induced polarization at the approach of water molecules. The electron cloud can be distorted and create an electrostatic dipole. It applies to the total displacement of the atoms within the material. Orbitals play a special role in reaction mechanism. Hydrophilic/hydrophobic nature of cellulose is based on its structural anisotropy. Cellulose-water interactions are exothermic reactions. These interactions may occur spontaneously and result in higher randomness of the system. They are denoted by a negative heat flow (heat is lost to the surroundings. Energy does not need to be inputted in order for cellulose-water interactions to occur.

  2. Modelling of Nonlinear Dynamic of Mechanic Systems with the Force Tribological Interaction

    Directory of Open Access Journals (Sweden)

    K.A. Nuzhdin

    2015-09-01

    Full Text Available This paper considers the mechanisms with different structure: tribometric device and a mechanism for handling of optical glasses. In the first device, the movement of the upper platform is due to a reciprocating friction interaction. In the second device, the processing of the optical element or group of elements occurs due to the rotational motion. Modelling of the dynamic of these systems with Matlab/Simmechanic allowed carrying out the analysis of dynamic of mechanisms, considering nonlinearity tribological interactions for these systems. The article shows that using of the computer models can effectively carry out the selection of the control parameters to create the desired mode of operation, as well as to investigate the behaviour of systems with nonlinear parameters and processes of self-oscillations. The organization of the managed self-oscillation process is realized to create the relevant high-performance manufacturing, for example, for the processing of optical glasses.

  3. Forcings and feedbacks on convection in the 2010 Pakistan flood: Modeling extreme precipitation with interactive large-scale ascent

    Science.gov (United States)

    Nie, Ji; Shaevitz, Daniel A.; Sobel, Adam H.

    2016-09-01

    Extratropical extreme precipitation events are usually associated with large-scale flow disturbances, strong ascent, and large latent heat release. The causal relationships between these factors are often not obvious, however, the roles of different physical processes in producing the extreme precipitation event can be difficult to disentangle. Here we examine the large-scale forcings and convective heating feedback in the precipitation events, which caused the 2010 Pakistan flood within the Column Quasi-Geostrophic framework. A cloud-revolving model (CRM) is forced with large-scale forcings (other than large-scale vertical motion) computed from the quasi-geostrophic omega equation using input data from a reanalysis data set, and the large-scale vertical motion is diagnosed interactively with the simulated convection. Numerical results show that the positive feedback of convective heating to large-scale dynamics is essential in amplifying the precipitation intensity to the observed values. Orographic lifting is the most important dynamic forcing in both events, while differential potential vorticity advection also contributes to the triggering of the first event. Horizontal moisture advection modulates the extreme events mainly by setting the environmental humidity, which modulates the amplitude of the convection's response to the dynamic forcings. When the CRM is replaced by either a single-column model (SCM) with parameterized convection or a dry model with a reduced effective static stability, the model results show substantial discrepancies compared with reanalysis data. The reasons for these discrepancies are examined, and the implications for global models and theoretical models are discussed.

  4. Experimental and numerical modelling of surface water-groundwater flow and pollution interactions under tidal forcing

    Science.gov (United States)

    Spanoudaki, Katerina; Bockelmann-Evans, Bettina; Schaefer, Florian; Kampanis, Nikolaos; Nanou-Giannarou, Aikaterini; Stamou, Anastasios; Falconer, Roger

    2015-04-01

    Surface water and groundwater are integral components of the hydrologic continuum and the interaction between them affects both their quantity and quality. However, surface water and groundwater are often considered as two separate systems and are analysed independently. This separation is partly due to the different time scales, which apply in surface water and groundwater flows and partly due to the difficulties in measuring and modelling their interactions (Winter et al., 1998). Coastal areas in particular are a difficult hydrologic environment to represent with a mathematical model due to the large number of contributing hydrologic processes. Accurate prediction of interactions between coastal waters, groundwater and neighbouring wetlands, for example, requires the use of integrated surface water-groundwater models. In the past few decades a large number of mathematical models and field methods have been developed in order to quantify the interaction between groundwater and hydraulically connected surface water bodies. Field studies may provide the best data (Hughes, 1995) but are usually expensive and involve too many parameters. In addition, the interpretation of field measurements and linking with modelling tools often proves to be difficult. In contrast, experimental studies are less expensive and provide controlled data. However, experimental studies of surface water-groundwater interaction are less frequently encountered in the literature than filed studies (e.g. Ebrahimi et al., 2007; Kuan et al., 2012; Sparks et al., 2013). To this end, an experimental model has been constructed at the Hyder Hydraulics Laboratory at Cardiff University to enable measurements to be made of groundwater transport through a sand embankment between a tidal water body such as an estuary and a non-tidal water body such as a wetland. The transport behaviour of a conservative tracer was studied for a constant water level on the wetland side of the embankment, while running a

  5. Viewing dynamic interactions of proteins and a model lipid membrane with atomic force microscopy.

    Science.gov (United States)

    Quinn, Anthony S; Rand, Jacob H; Wu, Xiao-Xuan; Taatjes, Douglas J

    2013-01-01

    The information covered in this chapter will present a model homogenous membrane preparation technique and dynamic imaging procedure that can be successfully applied to more than one type of lipid study and atomic force microscope (AFM) instrument setup. The basic procedural steps have been used with an Asylum Research MFP-3D BIO and the Bruker (formerly, Veeco) BioScope. The AFM imaging protocol has been supplemented by procedures (not to be presented in this chapter) of ellipsometry, standardized western blotting, and dot-blots to verify appropriate purity and activity of all experimental molecular components; excellent purity and activity level of the lipids, proteins, and drug(s) greatly influence the success of imaging experiments in the scanning probe microscopy field. The major goal of the chapter is to provide detailed procedures for sample preparation and operation of the Asylum Research MFP-3D BIO AFM. In addition, one should be cognizant that our comprehensive description in the use of the MFP-3D BIO's functions for successful image acquisitions and analyses is greatly enhanced by Asylum Research's (AR's) accompanying extensive manual(s), technical notes, and AR's users forum. Ultimately, the stepwise protocol and information will allow novice personnel to begin acquiring quality images for processing and analysis with minimal supervision.

  6. Fluid-Structure Interaction Analysis of Papillary Muscle Forces Using a Comprehensive Mitral Valve Model with 3D Chordal Structure.

    Science.gov (United States)

    Toma, Milan; Jensen, Morten Ø; Einstein, Daniel R; Yoganathan, Ajit P; Cochran, Richard P; Kunzelman, Karyn S

    2016-04-01

    Numerical models of native heart valves are being used to study valve biomechanics to aid design and development of repair procedures and replacement devices. These models have evolved from simple two-dimensional approximations to complex three-dimensional, fully coupled fluid-structure interaction (FSI) systems. Such simulations are useful for predicting the mechanical and hemodynamic loading on implanted valve devices. A current challenge for improving the accuracy of these predictions is choosing and implementing modeling boundary conditions. In order to address this challenge, we are utilizing an advanced in vitro system to validate FSI conditions for the mitral valve system. Explanted ovine mitral valves were mounted in an in vitro setup, and structural data for the mitral valve was acquired with [Formula: see text]CT. Experimental data from the in vitro ovine mitral valve system were used to validate the computational model. As the valve closes, the hemodynamic data, high speed leaflet dynamics, and force vectors from the in vitro system were compared to the results of the FSI simulation computational model. The total force of 2.6 N per papillary muscle is matched by the computational model. In vitro and in vivo force measurements enable validating and adjusting material parameters to improve the accuracy of computational models. The simulations can then be used to answer questions that are otherwise not possible to investigate experimentally. This work is important to maximize the validity of computational models of not just the mitral valve, but any biomechanical aspect using computational simulation in designing medical devices.

  7. Simulation of Metal Flow During Friction Stir Welding Based on the Model of Interactive Force Between Tool and Material

    Science.gov (United States)

    Chen, G. Q.; Shi, Q. Y.; Fujiya, Y.; Horie, T.

    2014-04-01

    In this research, the three-dimensional flow of metal in friction stir welding (FSW) has been simulated based on computational fluid dynamics. Conservation equations of mass, momentum, and energy were solved in three dimensions. The interactive force was imposed as boundary conditions on the tool/material boundary in the model. The strain rate- and temperature-dependent non-Newtonian viscosity was adopted for the calculation of metal flow. The distribution of temperature, velocity, and strain rate were simulated based on the above models. The simulated temperature distribution agreed well with the experimental results. The simulation results showed that the velocity on the pin was much higher than that on the shoulder. From the comparison between the simulation results and the experiments results, contours line, corresponding to strain rate = 4 s-1, reflected reasonably well the shape of stir zone, especially at the ground portion.

  8. Interaction Force Estimation During Manipulation of Microparticles

    NARCIS (Netherlands)

    Khalil, I.S.M.; Metz, R.M.P.; Abelmann, L.; Misra, S.

    2012-01-01

    This work investigates the utilization of microparticles for the wireless sensing of interaction forces in magneticbased manipulation systems. The proposed force estimation approach allows for using microparticles in sensing the interaction forces at hard-to-reach regions to avoid the mechanical and

  9. Interaction Force Estimation During Manipulation of Microparticles

    NARCIS (Netherlands)

    Khalil, I.S.M.; Metz, R.M.P.; Abelmann, Leon; Misra, Sarthak

    2012-01-01

    This work investigates the utilization of microparticles for the wireless sensing of interaction forces in magneticbased manipulation systems. The proposed force estimation approach allows for using microparticles in sensing the interaction forces at hard-to-reach regions to avoid the mechanical and

  10. The unification of the fundamental interaction within Maxwell electromagnetism: Model of hydrogen atom. Gravity as the secondary electric force. Calculation of the unified inertia force

    CERN Document Server

    Neslusan, L

    2010-01-01

    Considering two static, electrically charged, elementary particles, we demonstrate a possible way of proving that all known fundamental forces in the nature are the manifestations of the single, unique interaction. We re-define the gauging of integration constants in the Schwarzschild solution of Einstein field equations. We consider the potential energy in this context regardless it is gravitational or electric potential energy. With the newly gauged constants, we sketch how the unique interaction can be described with the help of an appropriate solution of the well-known Maxwell equations. According the solution, there are two zones, in the system of two oppositely charged particles, where the force is oscillating. The first particle can be in a stable, constant distance from the second particle, between the neighbouring regions of repulsion and attraction. In an outer oscillation zone, the corresponding energy levels in the proton-electron systems are identical (on the level of accuracy of values calculate...

  11. Lateral and perpendicular interaction forces involved in mobile and immobile adhesion of microorganism on model solid surfaces

    NARCIS (Netherlands)

    Busscher, HJ; Poortinga, AT; Bos, R.R.M.

    1998-01-01

    Gliding and near-surface swimming of microorganisms are described as a mobile form of microbial adhesion that need not necessarily be reversible. It is argued that the reversibility of microbial adhesion depends on the depth of the secondary interaction minimum, calculated from the forces between an

  12. Continuous flow atomic force microscopy imaging reveals fluidity and time-dependent interactions of antimicrobial dendrimer with model lipid membranes.

    Science.gov (United States)

    Lind, Tania Kjellerup; Zielińska, Paulina; Wacklin, Hanna Pauliina; Urbańczyk-Lipkowska, Zofia; Cárdenas, Marité

    2014-01-28

    In this paper, an amphiphilic peptide dendrimer with potential applications against multi-resistant bacteria such as Staphylococcus aureus was synthesized and studied on model cell membranes. The combination of quartz crystal microbalance and atomic force microscopy imaging during continuous flow allowed for in situ monitoring of the very initial interaction processes and membrane transformations on longer time scales. We used three different membrane compositions of low and high melting temperature phospholipids to vary the membrane properties from a single fluid phase to a pure gel phase, while crossing the phase coexistence boundaries at room temperature. The interaction mechanism of the dendrimer was found to be time-dependent and to vary remarkably with the fluidity and coexistence of liquid-solid phases in the membrane. Spherical micelle-like dendrimer-lipid aggregates were formed in the fluid-phase bilayer and led to partial solubilization of the membrane, while in gel-phase membranes, the dendrimers caused areas of local depressions followed by redeposition of flexible lipid patches. Domain coexistence led to a sequence of events initiated by the formation of a ribbon-like network and followed by membrane solubilization via spherical aggregates from the edges of bilayer patches. Our results show that the dendrimer molecules were able to destroy the membrane integrity through different mechanisms depending on the lipid phase and morphology and shed light on their antimicrobial activity. These findings could have an impact on the efficacy of the dendrimers since lipid membranes in certain bacteria have transition temperatures very close to the host body temperature.

  13. Molecular dynamics study of force acting on a model nano particle immersed in fluid with temperature gradient: Effect of interaction potential

    Science.gov (United States)

    Tsuji, Tetsuro; Iseki, Hirotaka; Hanasaki, Itsuo; Kawano, Satoyuki

    2016-11-01

    Thermophoresis of a nano particle in a fluid is investigated using molecular dynamics simulation. In order to elucidate effective factors on the characteristics of thermophoresis, simple models for both the fluid and the nano particle are considered, namely, the surrounding fluid consists of Lennard-Jones (LJ) particles and the model nano particle is a cluster consisting of several tens of LJ particles. Interaction between the fluid particle and the model nano particle is described by the LJ interaction potential or repulsive interaction potential with the Lorentz-Berthelot mixing rule. As a preliminary result, the effect of mass on thermophoretic force acting on the model nano particle is investigated for both interaction potentials.

  14. Groundwater-soil moisture-climate interactions: lessons from idealized model experiments with forced water table depth

    Science.gov (United States)

    Ducharne, Agnès; Lo, Min-Hui; Decharme, Bertrand; Wang, Fuxing; Cheruy, Frédérique; Ghattas, Josefine; Chien, Rong-You; lan, Chia-Wei; Colin, Jeanne; Tyteca, Sophie

    2016-04-01

    Groundwater (GW) constitutes by far the largest volume of liquid freshwater on Earth. The most active part is soil moisture (SM), recognized as a key variable of land/atmosphere interactions, especially in so-called transition zones, where/when SM varies between wet and dry values. But GW can also be stored in deeper reservoirs than soils, in particular unconfined aquifer systems, in which the saturated part is called the water table (WT). The latter is characterized by slow and mostly horizontal water flows towards the river network, with well-known buffering effects on streamflow variability. Where/when the WT is shallow enough, it can also sustain SM by means of capillary rise, thus increase evapotranspiration (ET), with potential impact on the climate system (including temperatures and precipitation). The large residence time of GW may also increase the Earth system's memory, with consequences on the persistence of extreme events, hydro-climatic predictability, and anthropogenic climate change, particularly the magnitude of regional warming. Here, our main goal is to explore the potential impacts of the water table depth (WTD) on historical climate through idealized model analyses. To this end, we force three state-of-the art land surface models (LSMs), namely CLM, ORCHIDEE, and SURFEX, with prescribed WTDs ranging from 0.5 to 10 m. The LSMs are run either off-line or coupled to their parent climate model, following LMIP/AMIP-like protocols for intercomparability. Within this framework, we want to assess the sensitivity of ET and the simulated climate to the WTD in a systematic way. In particular, we will identify and compare the patterns of the critical WTD, defined as the deepest one to achieve a significant change in ET. To this end, we estimate derivatives of ET with respect to WTD, which tell how the sensitivity of ET to a unit change in WTD evolves with WTD. In each grid-point, these derivatives can be used to define the critical WTD, given a threshold ET

  15. Classical Gravitational Interactions and Gravitational Lorentz Force

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    In quantum gauge theory of gravity, the gravitational field is represented by gravitational gauge field.The field strength of gravitational gauge field has both gravitoelectric component and gravitomagnetic component. In classical level, gauge theory of gravity gives classical Newtonian gravitational interactions in a relativistic form. Besides,it gives gravitational Lorentz force, which is the gravitational force on a moving object in gravitomagnetic field The direction of gravitational Lorentz force is not the same as that of classical gravitational Newtonian force. Effects of gravitational Lorentz force should be detectable, and these effects can be used to discriminate gravitomagnetic field from ordinary electromagnetic magnetic field.

  16. Seasonal forcing and multi-year cycles in interacting populations: lessons from a predator-prey model.

    Science.gov (United States)

    Taylor, Rachel A; Sherratt, Jonathan A; White, Andrew

    2013-12-01

    Many natural systems are subject to seasonal environmental change. As a consequence many species exhibit seasonal changes in their life history parameters--such as a peak in the birth rate in spring. It is important to understand how this seasonal forcing affects the population dynamics. The main way in which seasonal models have been studied is through a two dimensional bifurcation approach. We augment this bifurcation approach with extensive simulation in order to understand the potential solution behaviours for a predator-prey system with a seasonally forced prey growth rate. We consider separately how forcing influences the system when the unforced dynamics have either monotonic decay to the coexistence steady state, or oscillatory decay, or stable limit cycles. The range of behaviour the system can exhibit includes multi-year cycles of different periodicities, parameter ranges with coexisting multi-year cycles of the same or different period as well as quasi-periodicity and chaos. We show that the level of oscillation in the unforced system has a large effect on the range of behaviour when the system is seasonally forced. We discuss how the methods could be extended to understand the dynamics of a wide range of ecological and epidemiological systems that are subject to seasonal changes.

  17. Comments on the paper "A comprehensive modeling and vibration analysis of AFM microcantilevers subjected to nonlinear tip-sample interaction forces" by Sohrab Eslami and Nader Jalili.

    Science.gov (United States)

    Passian, Ali; Tetard, Laurene; Thundat, Thomas

    2013-08-01

    This comment on the paper "A comprehensive modeling and vibration analysis of AFM microcantilevers subjected to nonlinear tip-sample interaction forces" by Sohrab Eslami and Jalili (2012) [1] aims to: (1) discuss and elucidate the concept of "virtual resonance" and thus (2) avert a misinterpretation of the experimental results and findings reported in the Tetard et al. Physical Review Letters 106, 180801 (2011) [2].

  18. Polarizable Simulations with Second order Interaction Modelforce field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations

    Science.gov (United States)

    Kaminski, George A.; Ponomarev, Sergei Y.; Liu, Aibing B.

    2009-01-01

    We are presenting POSSIM (POlarizable Simulations with Second order Interaction Model) – a software package and a set of parameters designed for molecular simulations. The key feature of POSSIM is that the electrostatic polarization is taken into account using a previously introduced fast formalism. This permits cutting computational cost of using the explicit polarization by about an order of magnitude. In this article, parameters for water, methane, ethane, propane, butane, methanol and NMA are introduced. These molecules are viewed as model systems for protein simulations. We have achieved our goal of ca. 0.5 kcal/mol accuracy for gas-phase dimerization energies and no more than 2% deviations in liquid state heats of vaporization and densities. Moreover, free energies of hydration of the polarizable methane, ethane and methanol have been calculated using the statistical perturbation theory. These calculations are a model for calculating protein pKa shifts and ligand binding affinities. The free energies of hydration were found to be 2.12 kcal/mol, 1.80 kcal/mol and −4.95 kcal/mol for methane, ethane and methanol, respectively. The experimentally determined literature values are 1.91 kcal/mol, 1.83 kcal/mol and −5.11 kcal/mol. The POSSIM average error in these absolute free energies of hydration is only about 0.13 kcal/mol. Using the statistical perturbation theory with polarizable force fields is not widespread, and we believe that this work opens road to further development of the POSSIM force field and its applications for obtaining accurate energies in protein-related computer modeling. PMID:20209038

  19. Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy.

    Science.gov (United States)

    Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

    2016-07-01

    In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers.

  20. Human-machine interaction force control:using a model-referenced adaptive impedance device to control an index finger exoskeleton

    Institute of Scientific and Technical Information of China (English)

    Qian BI; Can-jun YANG

    2014-01-01

    Exoskeleton robots and their control methods have been extensively developed to aid post-stroke rehabilitation. Most of the existing methods using linear controllers are designed for position control and are not suitable for human-machine interaction (HMI) force control, as the interaction system between the human body and exoskeleton is uncertain and nonlinear. We present an approach for HMI force control via model reference adaptive impedance control (MRAIC) to solve this problem in case of index finger exoskeleton control. First, a dynamic HMI model, which is based on a position control inner loop, is for-mulated. Second, the theoretical MRAC framework is implemented in the control system. Then, the adaptive controllers are designed according to the Lyapunov stability theory. To verify the performance of the proposed method, we compare it with a proportional-integral-derivative (PID) method in the time domain with real experiments and in the frequency domain with simu-lations. The results illustrate the effectiveness and robustness of the proposed method in solving the nonlinear HMI force control problem in hand exoskeleton.

  1. Image potential and stopping force in the interaction of fast ions with carbon nanotubes: The extended two-fluid hydrodynamic model

    Energy Technology Data Exchange (ETDEWEB)

    Karbunar, L., E-mail: ziloot@verat.net [School of Electrical Engineering, University of Belgrade, Bulevar kralja Aleksandra 73, 11120 Belgrade (Serbia); Borka, D., E-mail: dusborka@vin.bg.ac.rs [Vinča Institute of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade (Serbia); Radović, I., E-mail: iradovic@vin.bg.ac.rs [Vinča Institute of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade (Serbia)

    2016-01-01

    Highlights: • We study the interaction of protons with carbon nanotubes under channeling conditions. • We use the linearized, 2D, two-fluid extended hydrodynamic model. • We analyze the influence of the angular mode for different types of nanotubes. • The image potential and stopping are calculated inside and outside the nanotube. • The angular and spatial distributions of channeled protons are computed. - Abstract: We study the interaction of charged particles with a (6, 4) single-walled carbon nanotube (SWNT) under channeling conditions by means of the linearized, two dimensional (2D), two-fluid extended hydrodynamic model. We use the model to calculate analytically and numerically the image potential and the stopping force for a proton moving parallel to the axis of the SWNT, both inside and outside the nanotube at the speeds from 0.5 a.u. to 15 a.u. The effects of different angular modes on the velocity dependence of the image potential are compared for a proton moving in different types of SWNTs. We also compute the spatial and angular distributions of protons in the 2D two-fluid extended hydrodynamic model and compare them with the 2D two-fluid hydrodynamic model with zero damping.

  2. Biotic interactions as a structuring force in soil communities: evidence from the micro-arthropods of an Antarctic moss model system.

    Science.gov (United States)

    Caruso, Tancredi; Trokhymets, Vladlen; Bargagli, Roberto; Convey, Peter

    2013-06-01

    Current meta-community theories postulate that the structure of local communities depends on dispersal, environmental filtering, and biotic interactions. However, disentangling the relative effects of these factors in the field and for diverse assemblages is a major challenge. A solution is to address natural but simple communities (i.e. with low numbers of species in few trophic levels), wherein one of these factors is predominant. Here, we analyse the micro-arthropod community of a moss-turf habitat typical of the Antarctic Peninsula region, and test the widely accepted hypothesis that this system is abiotically driven. In the austral summers 2006/7 and 2007/8, we sampled nearly 80 units of moss from four islands in the Argentine Islands. Using variance partitioning, we quantified the relative contribution of: (1) multiple scale spatio-temporal autocorrelation; (2) environmental effects; (3) the island effect. Little variance (1 %) was accounted for by sources 1 (1 %, significant) and 2 (structured environmental variation (7 %). Null models demonstrated that species co-occurred less frequently than expected by chance, suggesting the prevalence of negative interactions. Our data support the novel hypothesis that negative biotic interactions are the most important structuring force of this micro-arthropod community. The analysed system is a good proxy for more complex communities in terms of taxonomic composition and the functional groups present. Thus, biotic interaction might be a predominant factor in soil meta-community dynamics.

  3. Comparison of two electro-hydrodynamic force models for the interaction between helium jet flow and an atmospheric-pressure "plasma jet"

    Science.gov (United States)

    Logothetis, D.; Papadopoulos, P. K.; Svarnas, P.; Vafeas, P.

    2016-12-01

    In this work, two simple phenomenological models of the electro-hydrodynamic force that arises in an atmospheric-pressure "plasma jet" are presented. The models are distinguished by the different boundary conditions applied for the consideration of the plasma propagation length. The comparison is based on numerical simulations, which are combined with experimental data, in order to determine the magnitude of the electro-hydrodynamic force and assess the ability of the two models to evaluate the visible plasma length. The results reveal that the gas flow characteristics depend on the spatial range of the force action and the force magnitude, and vice versa.

  4. Shape regulation generates elastic interaction between active force dipoles

    CERN Document Server

    Golkov, Roman

    2016-01-01

    The organization of live cells to tissues is associated with the mechanical interaction between cells, which is mediated through their mechanical environment. We model live cells as spherical active force dipoles surrounded by an infinite elastic matrix, and analytically evaluate their elastic interaction energy for different scenarios of their regulatory behavior. For purely dilational eigenstrains the elastic interaction energy between any two bodies vanishes. We identify mechanical interactions between active cells applying non isotropic displacements with a regulation mechanism designed so that they will preserve their spherical shape. We express the resultant non-isotropic deformation field by a multipole expansion in terms of spherical harmonics. Mechanical self-regulation of live cells is not fully understood, and we compare homeostatic (set point) force applied by the cells on their environment versus homeostatic displacements on their surface. By including or excluding the first term of the expansion...

  5. Chemical Force Microscopy of Chemical and Biological Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Noy, A

    2006-01-02

    Interactions between chemical functionalities define outcomes of the vast majority of important events in chemistry, biology and materials science. Chemical Force Microscopy (CFM)--a technique that uses direct chemical functionalization of AFM probes with specific functionalities--allows researchers to investigate these important interactions directly. We review the basic principles of CFM, some examples of its application, and theoretical models that provide the basis for understanding the experimental results. We also emphasize application of modern kinetic theory of non-covalent interactions strength to the analysis of CFM data.

  6. Evaluation of Polymer-Filler Interaction Characteristics by Force Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ratto, T; Saab, A

    2007-04-23

    Silicone polymers are frequently used as cushions and inserts between load bearing parts. In this capacity, they must act to position their associated parts and distribute mechanical force as appropriate. One type of failure is specific to silicones that are filled with high surface area particulates for purposes of tailoring the polymer compressive properties. Additives such as fumed silicon oxide are presumed to have a high degree of surface interaction with the polymer matrix, thus causing the polymer to stiffen and to display greater dimensional stability as a function of temperature. However, it has been observed that the compressive behavior of these materials is not always invariant over long times. There is evidence that suggests changes in humidity and temperature can irreversibly alter the silicone-filler interaction, thereby changing the overall characteristics of parts made from such materials. As before, changes in compressive or shear stability can have serious effects on the ability of these materials to effectively position precision parts or distribute high mechanical loads. We approach the analysis of the filled systems by creating controlled layers of silicone polymers attached to silicon oxide substrates. Straight chain vinyl-silicone polymers identical to those used in the formulation of pads for stockpile systems are chemically appended to a substrate surface, and cross-linked to form a three dimensional network. This type of structure serves as a model of silicone polymer coating a silicon oxide filler particle. We study these model systems first by using Atomic Force Microscopy (AFM) to image the samples with nanometer resolution, and then by measuring the forces of interactions between single model silica filler particles and polymer-coated surfaces. We use normal longitudinal force AFM to measure adhesion, and a relatively newly developed technique, lateral force AFM, to determine the frictional forces between the silica particles and the

  7. Long-term ice sheet-climate interactions under anthropogenic greenhouse forcing simulated with a complex Earth System Model

    Energy Technology Data Exchange (ETDEWEB)

    Vizcaino, Miren [Max-Planck-Institut fuer Meteorologie, Hamburg (Germany); University of California, Department of Geography, Berkeley, CA (United States); Mikolajewicz, Uwe; Maier-Reimer, Ernst [Max-Planck-Institut fuer Meteorologie, Hamburg (Germany); Groeger, Matthias [Max-Planck-Institut fuer Meteorologie, Hamburg (Germany); IFM-GEOMAR, Kiel (Germany); Schurgers, Guy [Max-Planck-Institut fuer Meteorologie, Hamburg (Germany); Lund University, Department of Physical Geography and Ecosystems Analysis, Lund (Sweden); Winguth, Arne M.E. [Center for Climatic Research, Department of Atmospheric and Oceanic Sciences, Madison (United States)

    2008-11-15

    Several multi-century and multi-millennia simulations have been performed with a complex Earth System Model (ESM) for different anthropogenic climate change scenarios in order to study the long-term evolution of sea level and the impact of ice sheet changes on the climate system. The core of the ESM is a coupled coarse-resolution Atmosphere-Ocean General Circulation Model (AOGCM). Ocean biogeochemistry, land vegetation and ice sheets are included as components of the ESM. The Greenland Ice Sheet (GrIS) decays in all simulations, while the Antarctic ice sheet contributes negatively to sea level rise, due to enhanced storage of water caused by larger snowfall rates. Freshwater flux increases from Greenland are one order of magnitude smaller than total freshwater flux increases into the North Atlantic basin (the sum of the contribution from changes in precipitation, evaporation, run-off and Greenland meltwater) and do not play an important role in changes in the strength of the North Atlantic Meridional Overturning Circulation (NAMOC). The regional climate change associated with weakening/collapse of the NAMOC drastically reduces the decay rate of the GrIS. The dynamical changes due to GrIS topography modification driven by mass balance changes act first as a negative feedback for the decay of the ice sheet, but accelerate the decay at a later stage. The increase of surface temperature due to reduced topographic heights causes a strong acceleration of the decay of the ice sheet in the long term. Other feedbacks between ice sheet and atmosphere are not important for the mass balance of the GrIS until it is reduced to 3/4 of the original size. From then, the reduction in the albedo of Greenland strongly accelerates the decay of the ice sheet. (orig.)

  8. On the Transition from Bulk to Ordered Form of Water: A Theoretical Model to Calculate Adhesion Force Due to Capillary and van der Waals Interaction

    NARCIS (Netherlands)

    Yaqoob, M.A.; Rooij, de M.B.; Schipper, D.J.

    2013-01-01

    The adhesion force due to capillary interaction between two hydrophilic surfaces is strongly dependent on the partial pressure of water and is often calculated using the Kelvin equation. The validity of the Kelvin equation is questionable at low relative humidity (RH) of water, like in high vacuum a

  9. Critical Casimir Interactions: New fluctuation forces in colloidal science

    Science.gov (United States)

    Schall, Peter

    2012-02-01

    Casimir forces arise from the confinement of fluctuations between two walls. Critical Casimir forces provide thermodynamic analogues of quantum-mechanical Casimir forces and arise from the confinement of concentration fluctuations of a critical solvent. These forces act also between colloidal particles that are suspended in this solvent, giving rise to temperature-dependent attractive interactions between the particles. We use these temperature-dependent forces to control colloidal phase transitions. In this talk, I will present a new index and density-matched model system that allows direct observation of these phase transitions with confocal microscopy. In three dimensions and real time, we follow how a colloidal gas freezes into a colloidal liquid, and the colloidal liquid freezes into a solid, all driven by critical Casimir forces. We measure the critical Casimir particle pair potential directly from the pair correlation function, and use Monte Carlo simulations to map the complete gas-liquid-solid phase diagram. Excellent agreement with the experimental observations is obtained. Our measurements include microgravity experiments on board the International Space Station (ISS) to elucidate non-equilibrium assembly of the particles achieved by controlled temperature quench.

  10. Influence of biosurfactant on interactive forces between mutans streptococci and enamel measured by atomic force microscopy

    NARCIS (Netherlands)

    van Hoogmoed, CG; Dijkstra, RJB; van der Mei, HC; Busscher, HJ

    Although interactive forces, influenced by environmental conditions, between oral bacteria and tooth surfaces are important for the development of plaque, they have never been estimated. It is hypothesized that interactive forces, as measured by atomic force microscopy, between enamel with or

  11. Force sensor free teleoperated robotic surgery : Interaction force estimation for realistic force feedback without force sensors

    OpenAIRE

    Nærum, Edvard

    2012-01-01

    List of papers. The papers are removed from the thesis due to copyright restrictions. Paper I E. Naerum, J. Cornellà and O.J. Elle. Wavelet networks for estimation of coupled friction in robotic manipulators Proc. IEEE Conference on Robotics and Automation, Pasadena, CA, USA, May 2008, pp. 862-867. doi:10.1109/ROBOT.2008.4543313 Paper II E. Naerum, J. Cornellà and O.J. Elle. Contact force estimation for backdrivable robotic manipulators with coupled friction IE...

  12. StringForce: A Forced Collaborative Interaction Game for Special Education

    DEFF Research Database (Denmark)

    Barendregt, Wolmet; Börjesson, Peter; Eriksson, Eva

    2017-01-01

    In this paper, we present the forced collaborative interaction game StringForce. StringForce is developed for a special education context to support training of collaboration skills, using readily available technologies and avoiding the creation of a "mobile bubble". In order to play String......Force to be an interesting demo for the IDC community, as it intertwines several relevant research fields, such as mobile interaction and collaborative gaming in the special education context....

  13. Vascular endothelium-leukocyte interaction; sticking shear force in venules.

    Science.gov (United States)

    Schmid-Schoenbein, G W; Fung, Y C; Zweifach, B W

    1975-01-01

    To determine the shear force acting on a white blood cell sticking to the endothelium of a blood vessel, the flow field about a single white blood cell in a venule was determined by hign-speed motion picture photomicrography. The force acting on the white blood cell was then calculated according to the principles of fluid mechanics. In this paper, the calculation was made using an experimentally determined dimensionless shear force coefficient obtained from a kinematically and dynamically similar model. The large physical model of the hemodynamic system could be easily instrumented, and the shear force acting on the model cell and the flow field around it were measured. The data were then used to calculate a shear force coefficient. On the basis of dynamic similarity, this shear force coefficient was applied to the white blood cell in the venule. The shear force coefficient was strongly influenced by the hematocrit, so in vivo hematocrits were measured from electron micrographs. It was found that in the venules of the rabbit omentum a white blood cell sticking to the endothelial wall was subjected to a shear force in the range of 4 times 10--5 dynes to 234 times 10--5 dynes; the exact value depended on the size and motion of the white blood cell, the size of the blood vessel, the velocity of the blood flow, and the local hematocrit, which varied between 20% and 40% in venules of about 40 mum in diameter. The contact area between the white blood cell and the endothelial cell was estimated, and the shear stress was found to range between 50 dynes/cm-2 and 1060 dynes/cm-2. The normal stress of interaction between the white blood cell and the endothelium had a maximum value that was of the same order of magnitude as the shear stress. The accumulated relative error of the experimental procedure was about 49%. The instantaneous shear force was a random function of time because of random fluctuations of the hematocrit.

  14. Bio-Molecular Interactions Measured by Atomic Force Microscopy

    NARCIS (Netherlands)

    Willemsen, O.H.; Snel, M.M.E.; Cambi, A.; Cambi, Alessandra; Greve, Jan; de Grooth, B.G.; Figdor, Carl

    2000-01-01

    Atomic force microscopy (AFM) is nowadays frequently applied to determine interaction forces between biological molecules. Starting with the detection of the first discrete unbinding forces between ligands and receptors by AFM only several years ago, measurements have become more and more

  15. Physics-Based Visual Characterization of Molecular Interaction Forces.

    Science.gov (United States)

    Hermosilla, Pedro; Estrada, Jorge; Guallar, Victor; Ropinski, Timo; Vinacua, Alvar; Vazquez, Pere-Pau

    2017-01-01

    Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.

  16. Acoustic interaction forces between small particles in an ideal fluid

    CERN Document Server

    Silva, Glauber T

    2014-01-01

    We present a theoretical expression for the acoustic interaction force between small spherical particles suspended in an ideal fluid exposed to an external acoustic wave. The acoustic interaction force is the part of the acoustic radiation force on one given particle involving the scattered waves from the other particles. The particles, either compressible liquid droplets or elastic microspheres, are considered to be much smaller than the acoustic wavelength. In this so-called Rayleigh limit, the acoustic interaction forces between the particles are well approximated by gradients of pair-interaction potentials with no restriction on the inter-particle distance. The theory is applied to studies of the acoustic interaction force on a particle suspension in either standing or traveling plane waves. The results show aggregation regions along the wave propagation direction, while particles may attract or repel each other in the transverse direction. In addition, a mean-field approximation is developed to describe ...

  17. Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

    OpenAIRE

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and...

  18. Nanoscale effects in the characterization of viscoelastic materials with atomic force microscopy: coupling of a quasi-three-dimensional standard linear solid model with in-plane surface interactions

    Science.gov (United States)

    2016-01-01

    Summary Significant progress has been accomplished in the development of experimental contact-mode and dynamic-mode atomic force microscopy (AFM) methods designed to measure surface material properties. However, current methods are based on one-dimensional (1D) descriptions of the tip–sample interaction forces, thus neglecting the intricacies involved in the material behavior of complex samples (such as soft viscoelastic materials) as well as the differences in material response between the surface and the bulk. In order to begin to address this gap, a computational study is presented where the sample is simulated using an enhanced version of a recently introduced model that treats the surface as a collection of standard-linear-solid viscoelastic elements. The enhanced model introduces in-plane surface elastic forces that can be approximately related to a two-dimensional (2D) Young’s modulus. Relevant cases are discussed for single- and multifrequency intermittent-contact AFM imaging, with focus on the calculated surface indentation profiles and tip–sample interaction force curves, as well as their implications with regards to experimental interpretation. A variety of phenomena are examined in detail, which highlight the need for further development of more physically accurate sample models that are specifically designed for AFM simulation. A multifrequency AFM simulation tool based on the above sample model is provided as supporting information. PMID:27335746

  19. Nanoscale effects in the characterization of viscoelastic materials with atomic force microscopy: coupling of a quasi-three-dimensional standard linear solid model with in-plane surface interactions.

    Science.gov (United States)

    Solares, Santiago D

    2016-01-01

    Significant progress has been accomplished in the development of experimental contact-mode and dynamic-mode atomic force microscopy (AFM) methods designed to measure surface material properties. However, current methods are based on one-dimensional (1D) descriptions of the tip-sample interaction forces, thus neglecting the intricacies involved in the material behavior of complex samples (such as soft viscoelastic materials) as well as the differences in material response between the surface and the bulk. In order to begin to address this gap, a computational study is presented where the sample is simulated using an enhanced version of a recently introduced model that treats the surface as a collection of standard-linear-solid viscoelastic elements. The enhanced model introduces in-plane surface elastic forces that can be approximately related to a two-dimensional (2D) Young's modulus. Relevant cases are discussed for single- and multifrequency intermittent-contact AFM imaging, with focus on the calculated surface indentation profiles and tip-sample interaction force curves, as well as their implications with regards to experimental interpretation. A variety of phenomena are examined in detail, which highlight the need for further development of more physically accurate sample models that are specifically designed for AFM simulation. A multifrequency AFM simulation tool based on the above sample model is provided as supporting information.

  20. Linear Latent Force Models using Gaussian Processes

    CERN Document Server

    Álvarez, Mauricio A; Lawrence, Neil D

    2011-01-01

    Purely data driven approaches for machine learning present difficulties when data is scarce relative to the complexity of the model or when the model is forced to extrapolate. On the other hand, purely mechanistic approaches need to identify and specify all the interactions in the problem at hand (which may not be feasible) and still leave the issue of how to parameterize the system. In this paper, we present a hybrid approach using Gaussian processes and differential equations to combine data driven modelling with a physical model of the system. We show how different, physically-inspired, kernel functions can be developed through sensible, simple, mechanistic assumptions about the underlying system. The versatility of our approach is illustrated with three case studies from motion capture, computational biology and geostatistics.

  1. Atomic force microscopy study of cellulose surface interaction controlled by cellulose binding domains

    OpenAIRE

    Nigmatullin, R.; Lovitt, R.; Wright, C; Linder, M.; Nakari-Setälä, T; Gama, F. M.

    2004-01-01

    Colloidal probe microscopy has been used to study the interaction between model cellulose surfaces and the role of cellulose binding domain (CBD), peptides specifically binding to cellulose, in interfacial interaction of cellulose surfaces modified with CBDs. The interaction between pure cellulose surfaces in aqueous electrolyte solution is dominated by double layer repulsive forces with the range and magnitude of the net force dependent on electrolyte concentration. AFM imaging reve...

  2. Probing anisotropic surface properties and interaction forces of chrysotile rods by atomic force microscopy and rheology.

    Science.gov (United States)

    Yang, Dingzheng; Xie, Lei; Bobicki, Erin; Xu, Zhenghe; Liu, Qingxia; Zeng, Hongbo

    2014-09-16

    Understanding the surface properties and interactions of nonspherical particles is of both fundamental and practical importance in the rheology of complex fluids in various engineering applications. In this work, natural chrysotile, a phyllosilicate composed of 1:1 stacked silica and brucite layers which coil into cylindrical structure, was chosen as a model rod-shaped particle. The interactions of chrysotile brucite-like basal or bilayered edge planes and a silicon nitride tip were measured using an atomic force microscope (AFM). The force-distance profiles were fitted using the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, which demonstrates anisotropic and pH-dependent surface charge properties of brucite-like basal plane and bilayered edge surface. The points of zero charge (PZC) of the basal and edge planes were estimated to be around pH 10-11 and 6-7, respectively. Rheology measurements of 7 vol % chrysotile (with an aspect ratio of 14.5) in 10 mM NaCl solution showed pH-dependent yield stress with a local maximum around pH 7-9, which falls between the two PZC values of the edge and basal planes of the rod particles. On the basis of the surface potentials of the edge and basal planes obtained from AFM measurements, theoretical analysis of the surface interactions of edge-edge, basal-edge, and basal-basal planes of the chrysotile rods suggests the yield stress maximum observed could be mainly attributed to the basal-edge attractions. Our results indicate that the anisotropic surface properties (e.g., charges) of chrysotile rods play an important role in the particle-particle interaction and rheological behavior, which also provides insight into the basic understanding of the colloidal interactions and rheology of nonspherical particles.

  3. Interaction forces between waterborne bacteria and activated carbon particles

    NARCIS (Netherlands)

    Busscher, Henk J.; Dijkstra, Rene J. B.; Langworthy, Don E.; Collias, Dimitris I.; Bjorkquist, David W.; Mitchell, Michael D.; Van der Mei, Henny C.

    2008-01-01

    Activated carbons remove waterborne bacteria from potable water systems through attractive Lifshitz-van der Waals forces despite electrostatic repulsion between negatively charged cells and carbon surfaces. In this paper we quantify the interaction forces between bacteria with negatively and positiv

  4. Automated boundary interaction force control of micromanipulators with in situ applications to microsurgery

    Science.gov (United States)

    Eslami, Sohrab; Jalili, Nader

    2012-12-01

    Most recent works on miniature tasks are concentrated on developing tools to take advantage of the visual servoing feedback to control the ultra-small interaction forces. This paper spans an extensive platform for automatic controlling of boundary interaction forces with high precision in the level of micro/nano-Newton with extensive micro/nanoengineering applications such as the microsurgery. To this end, a comprehensive piezoresistive microcantilever (PMC) model considering the shear deformation and rotary inertia effects treating as the distributed-parameters model along with the Hertzian contact force is presented. The purpose of considering the Hertzian contact force model is to investigate the dynamic response of the interaction force between the microcantilever's tip and the specimen. Afterward, a control platform is introduced to automatically manipulate the PMC to follow an ideal micro/nano-interaction force. By using the integrated PMC with the micromanipulator and a digital signal processor, an intuitive programming code is written to incorporate the micromanipulator and the controller in a real-time framework. To calibrate and verify the induced voltage in the PMC, a self-sensing experiment on the piezoelectric microcantilever is carried out to warrant the calibration procedure. Some experiments are established to affirm the validity of the proposed control for the autonomous real-time tasks on the boundary interaction force control. Unlike the conventional research studies, the measured force here contributes as the feedback source in contrast to the vision feedback while force sensors possess more precision, productivity and small size. This technique has several potential applications listed but not limited to the micro/nanomanipulation, developing artificial biological systems (e.g., fabricating hydrogel for the scaffold), and medicine such as microsurgery. As a result, using the proposed platform, we are able to manipulate and control the boundary

  5. Interaction of Rate of Force Development and Duration of Rate in Isometric Force.

    Science.gov (United States)

    Siegel, Donald

    A study attempted to determine whether force and duration parameters are programmed in an interactive or independent fashion prior to executing ballistic type isometric contractions of graded intensities. Four adult females each performed 360 trials of producing ballistic type forces representing 25, 40, 55, and 75 percent of their maximal…

  6. Predicting wind farm wake interaction with RANS: an investigation of the Coriolis force

    DEFF Research Database (Denmark)

    van der Laan, Paul; Hansen, Kurt Schaldemose; Sørensen, Niels N.;

    2015-01-01

    A Reynolds-averaged Navier-Stokes code is used to simulate the interaction of two neighboring wind farms. The influence of the Coriolis force is investigated by modeling the atmospheric surface/boundary layer with three different methodologies. The results show that the Coriolis force is negligible...

  7. Experimental study on the control interaction force coefficient; Soju ryutairyoku kansho keisu ni kansuru jikkenteki kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    Nakatake, K.; Oda, K.; Yoshitake, A.; Fujita, K.; Nakajima, A. [Kyushu University, Fukuoka (Japan). Faculty of Engineering

    1996-04-10

    The interaction force induced to hull by steering is important for prediction of control performance of ships. The control interaction force coefficient dependent on the steering has been investigated through the rudder angle tests using three small model ships with a length of 2.5 m, i.e., mathematical type of ship, cargo type of ship, and tanker type of ship. The interaction forces acting on the hull, propeller, and rudder were determined by measuring the lateral force as well as the forward force of the hydrodynamic forces acting on the rudder. These forces were compared with the theoretically calculated values. Prior to the rudder angle tests, the self propulsion factor and the number of revolution of propeller were determined from the results of the open water tests, resistance tests, and self propulsion tests by the changing load method. The rudder angle tests were conducted under this number of revolution of propeller as a standard condition, and under those increasing and decreasing by 15%. Consequently, the interaction forces determined from the rudder angle tests agreed well with those determined from the other tests. When comparing the control hydrodynamic forces determined from the tests with those theoretically calculated, a similar trend was observed. Effectiveness of the theoretical model was confirmed. 4 refs., 14 figs., 3 tabs.

  8. Model Checking Feature Interactions

    DEFF Research Database (Denmark)

    Le Guilly, Thibaut; Olsen, Petur; Pedersen, Thomas;

    2015-01-01

    This paper presents an offline approach to analyzing feature interactions in embedded systems. The approach consists of a systematic process to gather the necessary information about system components and their models. The model is first specified in terms of predicates, before being refined to t...... to timed automata. The consistency of the model is verified at different development stages, and the correct linkage between the predicates and their semantic model is checked. The approach is illustrated on a use case from home automation....

  9. Interaction English Teaching Model

    Institute of Scientific and Technical Information of China (English)

    穆宇娜

    2013-01-01

      Malash—Thomas pointed out“Interaction is a process in which people and things act upon each other through their ac⁃tions.”According to different subjects, interaction can be divided into human-computer interaction, people-people interaction and learner-content interaction. According to different forms, interactions can be divided into one-one interaction, one-more interac⁃tion and more-more interaction.“Interaction Education”means that teachers are leading parts and students are the center of class. During teaching process, teachers must lead students to discover. Demands from students can encourage teachers to inspire con⁃versely.Thus it can form a close communication between teachers and students. Teaching and learning are realized in a happy and harmonious atmosphere. Successful English teaching must take new bilateral teaching as the first part, which should let the func⁃tion of the two most important elements develop fully. Teachers should grasp opportunities to guide. Teaching methods need to be flexible, and contents of teaching need to be vivid;students should be keen to think, to participate actively, and can break the tradi⁃tion to produce fresh ideas, and in that situation the capability of students can develop fully. The educational model refers to the simplified description of detailed teaching activities. Possessing dual functions of theory and practice, the educational model is the manifestation of theoretical teaching method. The combination of interaction and educational model which are mentioned above form the“interactive teaching”model. With the coming of economic globalization and integration of science and technology, now communications are increasing with each passing day. If you want to take part in or to get in touch with others, you must use lan⁃guage. English has been learnt for 10 years in Middle school and in college, but it can’t be spoken very fluently. That is a realistic picture as the result of an

  10. Interaction forces in bitumen extraction from oil sands.

    Science.gov (United States)

    Liu, Jianjun; Xu, Zhenghe; Masliyah, Jacob

    2005-07-15

    Water-based extraction process (WBEP) has been successfully applied to bitumen recovery from Athabasca oil sand ore deposits in Alberta. In this process, two essential steps are involved. The bitumen first needs to be "liberated" from sand grains, followed by "aeration" with air bubbles. Bitumen "liberation" from the sand grains is controlled by the interaction between the bitumen and sand grains. Bitumen "aeration" is dependent, among other mechanical and hydrodynamic variables, on the hydrophobicity of the bitumen surface, which is controlled by water chemistry and interactions between bitumen and fine solids. In this paper, the interaction force measured with an atomic force microscope (AFM) between bitumen-bitumen, bitumen-silica, bitumen-clays and bitumen-fines is summarized. The measured interaction force barrier coupled with the contacted adhesion force allows us to predict the coagulative state of colloidal systems. Zeta potential distribution measurements, in terms of heterocoagulation, confirmed the prediction of the measured force profiles using AFM. The results show that solution pH and calcium addition can significantly affect the colloidal interactions of various components in oil sand extraction systems. The strong attachment of fines from a poor processing ore on bitumen is responsible for the corresponding low bitumen flotation recovery. The identification of the dominant non-contact forces by fitting with the classical DLVO or extended DLVO theory provides guidance for controlling the interaction behavior of the oil sand components through monitoring the factors that could affect the non-contact forces. The findings provide insights into megascale industrial operations of oil sand extraction.

  11. Mathematical Model of Gravitational and Electrostatic Forces

    OpenAIRE

    Krouglov, Alexei

    2006-01-01

    Author presents mathematical model for acting-on-a-distance attractive and repulsive forces based on propagation of energy waves that produces Newton expression for gravitational and Coulomb expression for electrostatic forces. Model uses mathematical observation that difference between two inverse exponential functions of the distance asymptotically converges to function proportional to reciprocal of distance squared.

  12. Monitoring ligand-receptor interactions by photonic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Jeney, Sylvia [M E Mueller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, Basel, 4056 (Switzerland); Mor, Flavio; Forro, Laszlo [Laboratory of Complex Matter Physics (LPMC), Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Koszali, Roland [Institute for Information and Communication Technologies (IICT), University of Applied Sciences of Western Switzerland (HEIG-VD), Rue Galilee 15, CH 1401 Yverdon-les-bains (Switzerland); Moy, Vincent T, E-mail: sylvia.jeney@unibas.ch, E-mail: vmoy@miami.edu [Department of Physiology and Biophysics, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136 (United States)

    2010-06-25

    We introduce a method for the acquisition of single molecule force measurements of ligand-receptor interactions using the photonic force microscope (PFM). Biotin-functionalized beads, manipulated with an optical trap, and a streptavidin-functionalized coverslip were used to measure the effect of different pulling forces on the lifetime of individual streptavidin-biotin complexes. By optimizing the design of the optical trap and selection of the appropriate bead size, pulling forces in excess of 50 pN were achieved. Based on the amplitude of three-dimensional (3D) thermal position fluctuations of the attached bead, we were able to select for a bead-coverslip interaction that was mediated by a single streptavidin-biotin complex. Moreover, the developed experimental system was greatly accelerated by automation of data acquisition and analysis. In force-dependent kinetic measurements carried out between streptavidin and biotin, we observed that the streptavidin-biotin complex exhibited properties of a catch bond, with the lifetime increasing tenfold when the pulling force increased from 10 to 20 pN. We also show that silica beads were more appropriate than polystyrene beads for the force measurements, as tethers, longer than 200 nm, could be extracted from polystyrene beads.

  13. Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.

    Science.gov (United States)

    Iakovou, Georgios; Hayward, Steven; Laycock, Stephen D

    2015-09-01

    Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500Hz to 1kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates.

  14. Ripping RNA by Force using Gaussian Network Models

    CERN Document Server

    Hyeon, Changbong

    2016-01-01

    Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in the context of proteins have shown that topology plays is the major determinant of the unfolding landscapes. By building on this finding we study the responses of RNA molecules to force by adapting Gaussian network model (GNM) that represents RNAs using a bead-spring network with isotropic interactions. Cross-correlation matrices of residue fluctuations, which are analytically calculated using GNM even upon application of mechanical force, show distinct allosteric communication as RNAs rupture. The model is used to calculate the force-extension curves at full thermodynamic equilibrium, and the corresponding unfolding pathways of four RNA molecules subject to a quasi-statically increased force.Our study finds that the analysis using GNM captures qualitatively the unfolding p...

  15. Quantitative evaluation of interaction force between functional groups in protein and polymer brush surfaces.

    Science.gov (United States)

    Sakata, Sho; Inoue, Yuuki; Ishihara, Kazuhiko

    2014-03-18

    To understand interactions between polymer surfaces and different functional groups in proteins, interaction forces were quantitatively evaluated by force-versus-distance curve measurements using atomic force microscopy with a functional-group-functionalized cantilever. Various polymer brush surfaces were systematically prepared by surface-initiated atom transfer radical polymerization as well-defined model surfaces to understand protein adsorption behavior. The polymer brush layers consisted of phosphorylcholine groups (zwitterionic/hydrophilic), trimethylammonium groups (cationic/hydrophilic), sulfonate groups (anionic/hydrophilic), hydroxyl groups (nonionic/hydrophilic), and n-butyl groups (nonionic/hydrophobic) in their side chains. The interaction forces between these polymer brush surfaces and different functional groups (carboxyl groups, amino groups, and methyl groups, which are typical functional groups existing in proteins) were quantitatively evaluated by force-versus-distance curve measurements using atomic force microscopy with a functional-group-functionalized cantilever. Furthermore, the amount of adsorbed protein on the polymer brush surfaces was quantified by surface plasmon resonance using albumin with a negative net charge and lysozyme with a positive net charge under physiological conditions. The amount of proteins adsorbed on the polymer brush surfaces corresponded to the interaction forces generated between the functional groups on the cantilever and the polymer brush surfaces. The weakest interaction force and least amount of protein adsorbed were observed in the case of the polymer brush surface with phosphorylcholine groups in the side chain. On the other hand, positive and negative surfaces generated strong forces against the oppositely charged functional groups. In addition, they showed significant adsorption with albumin and lysozyme, respectively. These results indicated that the interaction force at the functional group level might be

  16. Single-molecule force spectroscopy studies of fibrin 'A-a' polymerization interactions via the atomic force microscope

    Science.gov (United States)

    Averett, Laurel E.

    Fibrin, the polymerized form of the soluble plasma protein fibrinogen, plays a critical role in hemostasis as the structural scaffold of blood clots. The primary functions of fibrin are to withstand the shear forces of blood flow and provide mechanical stability to the clot, protecting the wound. While studies have investigated the mechanical properties of fibrin constructs, the response to force of critical polymerization interactions such as the 'A--a' knob--hole interaction remains unclear. Herein, the response of the 'A--a' bond to force was examined at the single-molecule level using the atomic force microscope. Force spectroscopy methodology was developed to examine the 'A--a' interaction while reducing the incidence of both nonspecific and multiple molecule interactions. The rupture of this interaction resulted in a previously unreported characteristic force profile comprised of up to four events. We hypothesized that the first event represented reorientation of the fibrinogen molecule, the second and third represented unfolding of structures in the D region of fibrinogen, and the last event was the rupture of the 'A--a' bond weakened by prior structural unfolding. The configuration, molecular extension, and kinetic parameters of each event in the characteristic pattern were examined to compare the unfolding of fibrin to other proteins unfolded by force. Fitting the pattern with polymer models showed that the D region of fibrinogen could lengthen by ˜50% of the length of a fibrin monomer before rupture of the 'A--a' bond. Analysis showed that the second and third events had kinetic parameters similar to other protein structures unfolded by force. Studies of the dependence of the characteristic pattern on calcium, concentration of sodium chloride, pH, and temperature demonstrated that the incidence of the last event was affected by solution conditions. However, only low pH and high temperatures reduced the probability that an interaction was characteristic

  17. Atomic Force Microscopy of dynamic protein DNA interactions

    NARCIS (Netherlands)

    Noort, van Simon Johannes Theodorus

    1999-01-01

    In this thesis a dedicated Atomic Force Microscopy (AFM) setup is used for imaging biochemical reactions with molecular resolution. The basis for the high resolution of AFM is the combination of a small probe, close proximity to the sample and a short-range interaction between the probe and the samp

  18. Acoustic interaction forces between small particles in an ideal fluid

    DEFF Research Database (Denmark)

    Silva, Glauber T.; Bruus, Henrik

    2014-01-01

    from the other particles. The particles, either compressible liquid droplets or elastic microspheres, are considered to be much smaller than the acoustic wavelength. In this so-called Rayleigh limit, the acoustic interaction forces between the particles are well approximated by gradients of pair...

  19. Weibull analyses of bacterial interaction forces measured using AFM

    NARCIS (Netherlands)

    van der Mei, Henderina; de Vries, Jacob; Busscher, Hendrik

    2010-01-01

    Statistically significant conclusions from interaction forces obtained by AFM are difficult to draw because of large data spreads. Weibull analysis, common in macroscopic bond-strength analyses, takes advantage of this spread to derive a Weibull distribution, yielding the probability of occurrence o

  20. How Student Teachers Understand Distance Force Interactions in Different Contexts

    Science.gov (United States)

    Kariotoglou, Petros; Spyrtou, Anna; Tselfes, Vassilis

    2009-01-01

    In this paper, we describe empirical research on the recording of primary school and preschool student teacher conceptions of the concept of distant force interactions in different contexts related to the school curriculum for this subject. For this objective to be achieved, we undertook ten semi-structured interviews with student teachers. Based…

  1. Interaction between polystyrene spheres by atomic force microscopy

    CERN Document Server

    Looi, L

    2002-01-01

    The interaction between a single polystyrene particle and a polystyrene substrate has been previously reported by a number of investigators. However, the effects of relative humidity, applied load and contact time on the adhesion of polystyrene surfaces have not been investigated and these effects are poorly understood. It is the primary aim of the current work to characterise the effect of the aforementioned parameters on the adhesion of polystyrene surfaces using atomic force microscopy. The polystyrene used in this study contained 1% of di-vinyl benzene as a cross-linking agent. From the work conducted using the custom-built instrument, the dependency of adhesion forces on the relative humidity is greatest at relative humidities above 60% where capillary forces cause a sharp increase in adhesion with increasing relative humidity. Hysteresis was observed in the solid-solid contact gradient of the accompanying force curves, suggesting non-elastic behaviour at the contact area of the surfaces

  2. A Heuristic Molecular Model of Hydrophobic Interactions

    OpenAIRE

    Hummer, G; Garde, S; Garcia, A.E.; Pohorille, A; Pratt, L.R.

    1995-01-01

    Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple heuristic model of hydrophobic effects in terms of density fluctuations is developed. This model accounts quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes; it therefore clarifies the underlying physics...

  3. Validation of Multibody Program to Optimize Simulated Trajectories II Parachute Simulation with Interacting Forces

    Science.gov (United States)

    Raiszadeh, Behzad; Queen, Eric M.; Hotchko, Nathaniel J.

    2009-01-01

    A capability to simulate trajectories of multiple interacting rigid bodies has been developed, tested and validated. This capability uses the Program to Optimize Simulated Trajectories II (POST 2). The standard version of POST 2 allows trajectory simulation of multiple bodies without force interaction. In the current implementation, the force interaction between the parachute and the suspended bodies has been modeled using flexible lines, allowing accurate trajectory simulation of the individual bodies in flight. The POST 2 multibody capability is intended to be general purpose and applicable to any parachute entry trajectory simulation. This research paper explains the motivation for multibody parachute simulation, discusses implementation methods, and presents validation of this capability.

  4. Active-Reserve Force Cost Model

    Science.gov (United States)

    2015-01-01

    of either the Department of Defense or the sponsoring organization. Acknowledgments Thank you to Daniel L. Cuda and Michael C. Frieders for performing...policy, 4 Ronald E. Porten, Daniel L. Cuda , and Arthur C. Yengling, “DoD Force & Infrastructure Categories: A FYDP-Based Conceptual Model of...Daniel L. Cuda , and Arthur C. Yengling. “DoD Force & Infrastructure Categories: A FYDP-Based Conceptual Model of Department of Defense Programs and

  5. Interaction forces drive the environmental transmission of pathogenic protozoa.

    Science.gov (United States)

    Dumètre, Aurélien; Aubert, Dominique; Puech, Pierre-Henri; Hohweyer, Jeanne; Azas, Nadine; Villena, Isabelle

    2012-02-01

    The protozoan parasites Giardia duodenalis, Cryptosporidium spp., and Toxoplasma gondii are pathogens that are resistant to a number of environmental factors and pose significant risks to public health worldwide. Their environmental transmission is closely governed by the physicochemical properties of their cysts (Giardia) and oocysts (Cryptosporidium and Toxoplasma), allowing their transport, retention, and survival for months in water, soil, vegetables, and mollusks, which are the main reservoirs for human infection. Importantly, the cyst/oocyst wall plays a key role in that regard by exhibiting a complex polymeric coverage that determines the charge and hydrophobic characteristics of parasites' surfaces. Interaction forces between parasites and other environmental particles may be, in a first approximation, evaluated following the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloidal stability. However, due to the molecular topography and nano- to microstructure of the cyst/oocyst surface, non-DVLO hydrophobic forces together with additional steric attractive and/or repulsive forces may play a pivotal role in controlling the parasite behavior when the organism is subjected to various external conditions. Here, we review several parameters that enhance or hinder the adhesion of parasites to other particles and surfaces and address the role of fast-emerging techniques for mapping the cyst/oocyst surface, e.g., by measuring its topology and the generated interaction forces at the nano- to microscale. We discuss why characterizing these interactions could be a crucial step for managing the environmental matrices at risk of microbial pollution.

  6. Which forcing data errors matter most when modeling seasonal snowpacks?

    Science.gov (United States)

    Raleigh, M. S.; Lundquist, J. D.; Clark, M. P.

    2014-12-01

    High quality forcing data are critical when modeling seasonal snowpacks and snowmelt, but their quality is often compromised due to measurement errors or deficiencies in gridded data products (e.g., spatio-temporal interpolation, empirical parameterizations, or numerical weather model outputs). To assess the relative impact of errors in different meteorological forcings, many studies have conducted sensitivity analyses where errors (e.g., bias) are imposed on one forcing at a time and changes in model output are compared. Although straightforward, this approach only considers simplistic error structures and cannot quantify interactions in different meteorological forcing errors (i.e., it assumes a linear system). Here we employ the Sobol' method of global sensitivity analysis, which allows us to test how co-existing errors in six meteorological forcings (i.e., air temperature, precipitation, wind speed, humidity, incoming shortwave and longwave radiation) impact specific modeled snow variables (i.e., peak snow water equivalent, snowmelt rates, and snow disappearance timing). Using the Sobol' framework across a large number of realizations (>100000 simulations annually at each site), we test how (1) the type (e.g., bias vs. random errors), (2) distribution (e.g., uniform vs. normal), and (3) magnitude (e.g., instrument uncertainty vs. field uncertainty) of forcing errors impact key outputs from a physically based snow model (the Utah Energy Balance). We also assess the role of climate by conducting the analysis at sites in maritime, intermountain, continental, and tundra snow zones. For all outputs considered, results show that (1) biases in forcing data are more important than random errors, (2) the choice of error distribution can enhance the importance of specific forcings, and (3) the level of uncertainty considered dictates the relative importance of forcings. While the relative importance of forcings varied with snow variable and climate, the results broadly

  7. Modeling and experimentation of bone drilling forces.

    Science.gov (United States)

    Lee, JuEun; Gozen, B Arda; Ozdoganlar, O Burak

    2012-04-05

    Prediction and control of bone drilling forces are critical to the success of many orthopaedic operations. Uncontrolled and large forces can cause drill-bit breakage, drill breakthrough, excessive heat generation, and mechanical damage to the bone. This paper presents a mechanistic model for prediction of thrust forces and torques experienced during bone drilling. The model incorporates the radially varying drill-bit geometry and cutting conditions analytically, while capturing the material and friction properties empirically through a specific energy formulation. The forces from the chisel edge are modeled by considering the indentation process that occurs in the vicinity of the drill-bit axis. A procedure is outlined to calibrate the specific energies, where only a small number of calibration experiments are required for a wide range of drilling conditions and drill-bit geometry. The calibration parameters for the cortical portions of bovine tibia are identified through drilling tests. Subsequently, a series of validation tests are conducted under different feed rates and spindle speeds. The thrust forces and torques were observed to vary considerably between bones from different animals. The forces from the model were seen to match well with those from the experimentation within the inherent variations from the bone characteristics. The model can be used to select favorable drilling conditions, to assist in robotic surgeries, and to design optimal orthopaedic drill bits. Copyright © 2012 Elsevier Ltd. All rights reserved.

  8. Gamma globulins-induced interaction between two red blood cells: forces measurement with optical tweezers

    Science.gov (United States)

    Lee, Kisung; Muravyov, Alexei; Semenov, Alexei; Wagner, Christian; Priezzhev, Alexander; Lyubin, Eugeny; Fedyanin, Andrey

    2017-03-01

    The protein contribution to the red blood cell (RBC) aggregation is studied using the in-house made two-channeled optical tweezers. The cells interaction was characterized using two forces: the force required for separating two cells (FD - disaggregating force) and the force required for holding them from their spontaneous aggregation (FA - aggregating force). The gamma globulin solutions with/without albumin were used to induce the RBC aggregation. The strong interaction (3-10 pN) between the cells was measured within the contact formed using optical tweezers. We found that FD becomes stronger as the gamma globulin concentration increases, while the addition of albumin to the solution led to the significant (few fold) enhancement of the cells interaction forces. However, despite of the strong interaction between the cells their spontaneous overlapping was not observed, unlike the case in plasma, where the cells did increase their overlapping surface, when attached with small interacting surface and released from optical traps. This work in addition to our previous work with model solutions of fibrinogen allows us to conclude that the synergy of blood components is one of the most important features that contribute to the reversible RBC aggregation.

  9. Direct force measurement of single DNA-peptide interactions using atomic force microscopy.

    Science.gov (United States)

    Chung, Ji W; Shin, Dongjin; Kwak, June M; Seog, Joonil

    2013-06-01

    The selective interactions between DNA and miniature (39 residues) engineered peptide were directly measured at the single-molecule level by using atomic force microscopy. This peptide (p007) contains an α-helical recognition site similar to leucine zipper GCN4 and specifically recognizes the ATGAC sequence in the DNA with nanomolar affinity. The average rupture force was 42.1 pN, which is similar to the unbinding forces of the digoxigenin-antidigoxigenin complex, one of the strongest interactions in biological systems. The single linear fit of the rupture forces versus the logarithm of pulling rates showed a single energy barrier with a transition state located at 0.74 nm from the bound state. The smaller koff compared with that of other similar systems was presumably due to the increased stability of the helical structure by putative folding residues in p007. This strong sequence-specific DNA-peptide interaction has a potential to be utilized to prepare well-defined mechanically stable DNA-protein hybrid nanostructures.

  10. Modeling Robot Flexibility for Endpoint Force Control.

    Science.gov (United States)

    1988-05-01

    SIDM 19. KE9Y WORDS fCntknu. OnPVOO&O 0401 It 00041000111O ed 0000#uF 6P 1111411 amA.w) robot force control * robot control / robot dynamics flexible...no. 3, pp. 62-75. [2] Eppinger, S.D. and Seering, W.P. On Dynamic Models of Robot Force Control . In Proceedings of International Conference on...W.P. Understanding Bandwidth Limitations in Robot Force Control . In Proceedings of International Conference on Robotics and Automation. IEEE, April 1987

  11. Contact force models for multibody dynamics

    CERN Document Server

    Flores, Paulo

    2016-01-01

    This book analyzes several compliant contact force models within the context of multibody dynamics, while also revisiting the main issues associated with fundamental contact mechanics. In particular, it presents various contact force models, from linear to nonlinear, from purely elastic to dissipative, and describes their parameters. Addressing the different numerical methods and algorithms for contact problems in multibody systems, the book describes the gross motion of multibody systems by using a two-dimensional formulation based on the absolute coordinates and employs different contact models to represent contact-impact events. Results for selected planar multibody mechanical systems are presented and utilized to discuss the main assumptions and procedures adopted throughout this work. The material provided here indicates that the prediction of the dynamic behavior of mechanical systems involving contact-impact strongly depends on the choice of contact force model. In short, the book provides a comprehens...

  12. A Force Structure Design Model

    Science.gov (United States)

    1991-09-01

    199) WRITE(20,*)’ MODEL FAR10 /ALL/’ WRITE(20, 159) 159 FORMAT(’*------------- LOOP--------------- WRITE(20,*) ’SOLVE FAR10 USING RMIP MINIMIZING...SOLVE FARIO USING RMIP MINIMIZING MAXDEV OPTION X:4:0:1 DISPLAY X.L OPTION FAR:4:O:1; DISPLAY FAR OPTION R:4:0:1 OPTION R1:4:Q:1 OPTION R2:4:0:1...LOOP ------------------------ 102 SOLVE FAR10 USING RMIP MINIMIZING MAXDEV 103 OPTION X:4:0:1 104 DISPLAY X.L 105 OPTION FAR

  13. TOOL FORCE MODEL FOR DIAMOND TURNING

    Institute of Scientific and Technical Information of China (English)

    Wang Hongxiang; Sun Tao; Li Dan; Dong Shen

    2004-01-01

    A new tool force model to be presented is based upon process geometry and the characteristics of the force system,in which the forces acting on the tool rake face,the cutting edge rounding and the clearance face have been considered,and the size effect is accountable for the new model.It is desired that the model can be well applicable to conventional diamond turning and the model may be employed as a tool in the design of diamond tools.This approach is quite different from traditional investigations primarily based on empirical studies.As the depth of cut becomes the same order as the rounded cutting edge radius,sliding along the clearance face due to elastic recovery of workpiece material and plowing due to the rounded cutting edge may become important in micro-machining,the forces acting on the cutting edge rounding and the clearance face can not be neglected.For this reason,it is very important to understand the influence of some parameters on tool forces and develop a model of the relationship between them.

  14. Estimating needle-tissue interaction forces for hollow needles using fiber Bragg grating sensors

    Science.gov (United States)

    Kumar, Saurabh; Shrikanth, V.; Bharadwaj, Amrutur; Asokan, Sundarrajan; Bobji, M. S.

    2016-03-01

    Brachytherapy and neurological procedures can benefit from real-time estimation of needle-tissue interaction forces, specifically for robotic or robot-assisted procedures. Fiber Bragg Grating Sensors provide advantages of very small size and electromagnetic immunity for use in measurement of the forces directly at the needle tip. This has advantages compared to measurements at the needle shaft which require extensive models of the friction between needle and tissues with varying depth. This paper presents the measurement of tip forces for a hollow needle and compensation for bending when encountering regions of varying stiffness in phantoms with multiple layers prepared using Polydimethylsiloxane.

  15. A novel three-filament model of force generation in eccentric contraction of skeletal muscles.

    Directory of Open Access Journals (Sweden)

    Gudrun Schappacher-Tilp

    Full Text Available We propose and examine a three filament model of skeletal muscle force generation, thereby extending classical cross-bridge models by involving titin-actin interaction upon active force production. In regions with optimal actin-myosin overlap, the model does not alter energy and force predictions of cross-bridge models for isometric contractions. However, in contrast to cross-bridge models, the three filament model accurately predicts history-dependent force generation in half sarcomeres for eccentric and concentric contractions, and predicts the activation-dependent forces for stretches beyond actin-myosin filament overlap.

  16. A cutting force model for micromilling applications

    DEFF Research Database (Denmark)

    Bissacco, Giuliano; Hansen, Hans Nørgaard; De Chiffre, Leonardo

    2006-01-01

    In micro milling the maximum uncut chip thickness is often smaller than the cutting edge radius. This paper introduces a new cutting force model for ball nose micro milling that is capable of taking into account the effect of the edge radius.......In micro milling the maximum uncut chip thickness is often smaller than the cutting edge radius. This paper introduces a new cutting force model for ball nose micro milling that is capable of taking into account the effect of the edge radius....

  17. Ridge Regression for Interactive Models.

    Science.gov (United States)

    Tate, Richard L.

    1988-01-01

    An exploratory study of the value of ridge regression for interactive models is reported. Assuming that the linear terms in a simple interactive model are centered to eliminate non-essential multicollinearity, a variety of common models, representing both ordinal and disordinal interactions, are shown to have "orientations" that are favorable to…

  18. Modeling noncontact atomic force microscopy resolution on corrugated surfaces

    Directory of Open Access Journals (Sweden)

    Kristen M. Burson

    2012-03-01

    Full Text Available Key developments in NC-AFM have generally involved atomically flat crystalline surfaces. However, many surfaces of technological interest are not atomically flat. We discuss the experimental difficulties in obtaining high-resolution images of rough surfaces, with amorphous SiO2 as a specific case. We develop a quasi-1-D minimal model for noncontact atomic force microscopy, based on van der Waals interactions between a spherical tip and the surface, explicitly accounting for the corrugated substrate (modeled as a sinusoid. The model results show an attenuation of the topographic contours by ~30% for tip distances within 5 Å of the surface. Results also indicate a deviation from the Hamaker force law for a sphere interacting with a flat surface.

  19. Atoms and Forces of Interaction Between Elementary Particles in the Expanding Universe

    CERN Document Server

    Gorbatenko, M V

    2011-01-01

    The earlier developed algorithm for constructing a self-conjugate Hamiltonian in the representation for Dirac particles interacting with a general gravitational field is extended to the case of electromagnetic fields. This Hamiltonian is applied to the case when the gravitational field describes the spatially flat Friedmann model, and the electromagnetic field is the Coulomb potential extended to the case of this model. The analysis of atomic systems and electromagnetic forces of interaction under the conditions of spatially flat expansion of the universe has demonstrated that the system of atomic levels does not change with cosmological time. Spectral lines of atoms in the spatially flat Friedmann model are identical at different points of cosmological time. In this case the redshift is stipulated entirely by the growth of wavelength of photons at movement in the expending universe. At the same time force of interaction between elementary particles can change with expansion of the universe.

  20. Shock Wave-Boundary Layer Interaction in Forced Shock Oscillations

    Institute of Scientific and Technical Information of China (English)

    Piotr Doerffer; Oskar Szulc; Franco Magagnato

    2003-01-01

    The flow in transonic diffusers as well as in supersonic air intakes becomes often unsteady due to shock wave boundary layer interaction. The oscillations may be induced by natural separation unsteadiness or may be forced by boundary conditions. Significant improvement of CFD tools, increase of computer resources as well as development of experimental methods have again.drawn the attention of researchers to this topic.To investigate the problem forced oscillations of transonic turbulent flow in asymmetric two-dimensional Laval nozzle were considered. A viscous, perfect gas flow, was numerically simulated using the Reynolds-averaged compressible Navier-Stokes solver SPARC, employing a two-equation, eddy viscosity, turbulence closure in the URANS approach.For time-dependent and stationary flow simulations, Mach numbers upstream of the shock between 1.2 and 1.4 were considered. Comparison of computed and experimental data for steady states generally gave acceptable agreement. In the case of forced oscillations, a harmonic pressure variation was prescribed at the exit plane resulting in shock wave motion. Excitation frequencies between 0 Hz and 1024 Hz were investigated at the same pressure amplitude.The main result of the work carried out is the relation between the amplitude of the shock wave motion and the excitation frequency in the investigated range. Increasing excitation frequency resulted in decreasing amplitude of the shock movement. At high frequencies a natural mode of shock oscillation (of small amplitude) was observed which is not sensitive to forced excitement.

  1. Forces between permanent magnets: experiments and model

    Science.gov (United States)

    González, Manuel I.

    2017-03-01

    This work describes a very simple, low-cost experimental setup designed for measuring the force between permanent magnets. The experiment consists of placing one of the magnets on a balance, attaching the other magnet to a vertical height gauge, aligning carefully both magnets and measuring the load on the balance as a function of the gauge reading. A theoretical model is proposed to compute the force, assuming uniform magnetisation and based on laws and techniques accessible to undergraduate students. A comparison between the model and the experimental results is made, and good agreement is found at all distances investigated. In particular, it is also found that the force behaves as r -4 at large distances, as expected.

  2. Nanobiosensors exploiting specific interactions between an enzyme and herbicides in atomic force spectroscopy.

    Science.gov (United States)

    da Silva, Aline C N; Deda, Daiana K; Bueno, Carolina C; Moraes, Ariana S; Da Roz, Alessandra L; Yamaji, Fabio M; Prado, Rogilene A; Viviani, Vadim; Oliveira, Osvaldo N; Leite, Fábio L

    2014-09-01

    The development of sensitive methodologies for detecting agrochemicals has become important in recent years due to the increasingly indiscriminate use of these substances. In this context, nanosensors based on atomic force microscopy (AFM) tips are useful because they provide higher sensitivity with operation at the nanometer scale. In this paper we exploit specific interactions between AFM tips functionalized with the enzyme acetolactate synthase (ALS) to detect the ALS-inhibitor herbicides metsulfuron-methyl and imazaquin. Using atomic force spectroscopy (AFS) we could measure the adhesion force between tip and substrate, which was considerably higher when the ALS-functionalized tip (nanobiosensor) was employed. The increase was approximately 250% and 160% for metsulfuron-methyl and imazaquin, respectively, in comparison to unfunctionalized probes. We estimated the specific enzyme-herbicide force by assuming that the measured force comprises an adhesion force according to the Johnson-Kendall-Roberts (JKR) model, the capillary force and the specific force. We show that the specific, biorecognition force plays a crucial role in the higher sensitivity of the nanobiosensor, thus opening the way for the design of similarly engineered tips for detecting herbicides and other analytes.

  3. Interactive Modelling of Molecular Structures

    Science.gov (United States)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  4. On Oscillations in the Social Force Model

    CERN Document Server

    Kretz, Tobias

    2015-01-01

    The Social Force Model is one of the most prominent models of pedestrian dynamics. As such naturally much discussion and criticism has spawned around it, some of which concerns the existence of oscillations in the movement of pedestrians. This contribution is investigating under which circumstances, parameter choices, and model variants oscillations do occur and how this can be prevented. It is shown that oscillations can be excluded if the model parameters fulfill certain relations. The fact that with some parameter choices oscillations occur and with some not is exploited to verify a specific computer implementation of the model.

  5. Modeling the Forced Extension of Nicked DNA

    Science.gov (United States)

    Balaeff, Alexander; Craig, Stephen; Beratan, David

    2007-03-01

    The design and study of DNA-based nanodevices has been a topic of considerable interest in the last decade. While the applications of classical continuous DNA structures have been thoroughly studied, nicked DNA structures, i.e., ones that contains breaks (``nicks'') in one or both DNA backbone chains, have received much less attention. Recently, Kersey et al. (JACS, 2004) reported the force spectroscopy of long DNA chains with periodic nicks, self-assembled from short DNA oligomers. We attempt to model the experimental force-extension profiles in a series of steered molecular dynamics simulations. The simulated all-atom model of a basic unit of the long self-assembled chain, a 16bp-long DNA segment with a nick in the middle of one strand, is extended by applying either a constant force or a moving harmonic potential to the DNA ends. The computed force-extension profiles are compared to those for a non-nicked DNA; the dynamics of structural changes in the nicked DNA during the forced extension is discussed. A theoretical framework is established to link the extension and rupture in the simulated basic unit to the corresponding events in the long self-assembled chain.

  6. Modeling capillary forces for large displacements

    NARCIS (Netherlands)

    Mastrangeli, M.; Arutinov, G.; Smits, E.C.P.; Lambert, P.

    2014-01-01

    Originally applied to the accurate, passive positioning of submillimetric devices, recent works proved capillary self-alignment as effective also for larger components and relatively large initial offsets. In this paper, we describe an analytic quasi-static model of 1D capillary restoring forces tha

  7. Hand-tool-tissue interaction forces in neurosurgery for haptic rendering.

    Science.gov (United States)

    Aggravi, Marco; De Momi, Elena; DiMeco, Francesco; Cardinale, Francesco; Casaceli, Giuseppe; Riva, Marco; Ferrigno, Giancarlo; Prattichizzo, Domenico

    2016-08-01

    Haptics provides sensory stimuli that represent the interaction with a virtual or tele-manipulated object, and it is considered a valuable navigation and manipulation tool during tele-operated surgical procedures. Haptic feedback can be provided to the user via cutaneous information and kinesthetic feedback. Sensory subtraction removes the kinesthetic component of the haptic feedback, having only the cutaneous component provided to the user. Such a technique guarantees a stable haptic feedback loop, while it keeps the transparency of the tele-operation system high, which means that the system faithfully replicates and render back the user's directives. This work focuses on checking whether the interaction forces during a bench model neurosurgery operation can lie in the solely cutaneous perception of the human finger pads. If this assumption is found true, it would be possible to exploit sensory subtraction techniques for providing surgeons with feedback from neurosurgery. We measured the forces exerted to surgical tools by three neurosurgeons performing typical actions on a brain phantom, using contact force sensors, while the forces exerted by the tools to the phantom tissue were recorded using a load cell placed under the brain phantom box. The measured surgeon-tool contact forces were 0.01-3.49 N for the thumb and 0.01-6.6 N for index and middle finger, whereas the measured tool-tissue interaction forces were from six to 11 times smaller than the contact forces, i.e., 0.01-0.59 N. The measurements for the contact forces fit the range of the cutaneous sensitivity for the human finger pad; thus, we can say that, in a tele-operated robotic neurosurgery scenario, it would possible to render forces at the fingertip level by conveying haptic cues solely through the cutaneous channel of the surgeon's finger pads. This approach would allow high transparency and high stability of the haptic feedback loop in a tele-operation system.

  8. A New Model for Ice Forces on A Conical Structure

    Institute of Scientific and Technical Information of China (English)

    FENG Wei; SHI Zhong-min; LIU Li-ming

    2005-01-01

    The ice force is an important factor to be taken into account for offshore structures in cold regions, and the calculation method of the ice force is meaningful for the offshore structure design. The cone is now used as an optimal ice-resistant structure because it can cause bending failure of the ice sheet. The interaction between an ice sheet and a conical structure is studied in this paper and Croasdale's model is modified based on field observations. The newly built model separates the ice sheet into the emersed part and the floating part, and the equilibrium analyses are carried out respectively. The bending moment distribution of the ice sheet is analyzed for the determination of the position of bending failure, which serves as a supplementary restraint. The analytic solution of the ice force on a conical structure is obtained and it is verified with the experimental data of previous researches.

  9. Numerical modelling of iceberg calving force responsible for glacial earthquakes

    Science.gov (United States)

    Sergeant, Amandine; Yastrebov, Vladislav; Castelnau, Olivier; Mangeney, Anne; Stutzmann, Eleonore; Montagner, Jean-Paul

    2016-04-01

    Glacial earthquakes is a class of seismic events of magnitude up to 5, occurring primarily in Greenland, in the margins of large marine-terminated glaciers with near-grounded termini. They are caused by calving of cubic-kilometer scale unstable icebergs which penetrate the full-glacier thickness and, driven by the buoyancy forces, capsize against the calving front. These phenomena produce seismic energy including surface waves with dominant energy between 10-150 s of period whose seismogenic source is compatible with the contact force exerted on the terminus by the iceberg while it capsizes. A reverse motion and posterior rebound of the terminus have also been measured and associated with the fluctuation of this contact force. Using a finite element model of iceberg and glacier terminus coupled with simplified fluid-structure interaction model, we simulate calving and capsize of icebergs. Contact and frictional forces are measured on the terminus and compared with laboratory experiments. We also study the influence of geometric factors on the force history, amplitude and duration at the laboratory and field scales. We show first insights into the force and the generated seismic waves exploring different scenarios for iceberg capsizing.

  10. Interacting Stochastic Processes: From Viciousness to Caging to Force Chains

    Science.gov (United States)

    Xu, Shiliyang

    the heterogeneous force network present in amorphous solids near the onset of rigidity, or jamming. The onset of rigidity can, in some sense, be viewed an interacting stochastic process with added constraints to enforce force-balance on each particle, for example. Our analysis yields string-like correlations in the locally-large forces in the system. Such correlations are reminiscent of force chains. While force chains have been readily observed in experiments, it is the first time these correlations have been observed in conjugate gradient simulations of repulsive soft spheres. We also study the contact geometry of the force network and explore a link with spin systems, namely spin glasses, to search for signatures of chaos due to marginal stability, for instance. Connections between jamming systems and spin glass systems will hopefully open up new avenues of theoretical investigation for both systems. Finally, we explore the quantum version of an individual stochastic process, namely the fractional Schrodinger equation. We prove that previously claimed exact solutions for certain potentials are incorrect and determine a new exact solution for a Levy index of unity and the harmonic oscillator potential. While our results contribute to the realm of mathematical physics, a physical realization of the fractional Schrodinger equation will indeed launch a new subfield of quantum mechanics.

  11. Modeling traction forces in collective cell migration

    Science.gov (United States)

    Zimmermann, Juliane; Basan, Markus; Hayes, Ryan L.; Rappel, Wouter-Jan; Levine, Herbert

    2015-03-01

    Collective cell migration is an important process in embryonic development, wound healing, and cancer metastasis. We have developed a particle-based simulation for collective cell migration that describes flow patterns and finger formation at the tissue edge observed in wound healing experiments. We can apply methods for calculating intercellular stress to our simulation model, and have thereby provided evidence for the validity of a stress reconstitution method from traction forces used in experiments. To accurately capture experimentally measured traction forces and stresses in the tissue, which are mostly tensile, we have to include intracellular acto-myosin contraction into our simulation. We can then reproduce the experimentally observed behavior of cells moving around a circular obstacle, and suggest underlying mechanisms for cell-cell alignment and generation of traction force patterns.

  12. Motivating forces of human actions. Neuroimaging reward and social interaction.

    Science.gov (United States)

    Walter, Henrik; Abler, Birgit; Ciaramidaro, Angela; Erk, Susanne

    2005-11-15

    In neuroeconomics, reward and social interaction are central concepts to understand what motivates human behaviour. Both concepts are investigated in humans using neuroimaging methods. In this paper, we provide an overview about these results and discuss their relevance for economic behaviour. For reward it has been shown that a system exists in humans that is involved in predicting rewards and thus guides behaviour, involving a circuit including the striatum, the orbitofrontal cortex and the amygdala. Recent studies on social interaction revealed a mentalizing system representing the mental states of others. A central part of this system is the medial prefrontal cortex, in particular the anterior paracingulate cortex. The reward as well as the mentalizing system is engaged in economic decision-making. We will discuss implications of this study for neuromarketing as well as general implications of these results that may help to provide deeper insights into the motivating forces of human behaviour.

  13. Asymmetric electrostatic and hydrophobic-hydrophilic interaction forces between mica surfaces and silicone polymer thin films.

    Science.gov (United States)

    Donaldson, Stephen H; Das, Saurabh; Gebbie, Matthew A; Rapp, Michael; Jones, Louis C; Roiter, Yuri; Koenig, Peter H; Gizaw, Yonas; Israelachvili, Jacob N

    2013-11-26

    We have synthesized model hydrophobic silicone thin films on gold surfaces by a two-step covalent grafting procedure. An amino-functionalized gold surface reacts with monoepoxy-terminated polydimethylsiloxane (PDMS) via a click reaction, resulting in a covalently attached nanoscale thin film of PDMS, and the click chemistry synthesis route provides great selectivity, reproducibility, and stability in the resulting model hydrophobic silicone thin films. The asymmetric interaction forces between the PDMS thin films and mica surfaces were measured with the surface forces apparatus in aqueous sodium chloride solutions. At an acidic pH of 3, attractive interactions are measured, resulting in instabilities during both approach (jump-in) and separation (jump-out from adhesive contact). Quantitative analysis of the results indicates that the Derjaguin-Landau-Verwey-Overbeek theory alone, i.e., the combination of electrostatic repulsion and van der Waals attraction, cannot fully describe the measured forces and that the additional measured adhesion is likely due to hydrophobic interactions. The surface interactions are highly pH-dependent, and a basic pH of 10 results in fully repulsive interactions at all distances, due to repulsive electrostatic and steric-hydration interactions, indicating that the PDMS is negatively charged at high pH. We describe an interaction potential with a parameter, known as the Hydra parameter, that can account for the extra attraction (low pH) due to hydrophobicity as well as the extra repulsion (high pH) due to hydrophilic (steric-hydration) interactions. The interaction potential is general and provides a quantitative measure of interfacial hydrophobicity/hydrophilicity for any set of interacting surfaces in aqueous solution.

  14. A Heuristic Molecular Model of Hydrophobic Interactions

    CERN Document Server

    Hummer, G; García, A E; Pohorille, A; Pratt, L R

    1995-01-01

    Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple heuristic model of hydrophobic effects in terms of density fluctuations is developed. This model accounts quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes; it therefore clarifies the underlying physics of hydrophobic effects and permits important applications to conformational equilibria of nonpolar solutes and hydrophobic residues in biopolymers.

  15. Protein Adsorption into Mesopores: A Combination of Electrostatic Interaction, Counterion Release and van der Waals Forces

    CERN Document Server

    Moerz, Sebastian T

    2015-01-01

    Bovine heart cytochrome c has been immobilized into the mesoporous silica host material SBA-15 in both its native folded and urea-unfolded state. The comparison of the two folding states' behavior casts doubt on the commonly used explanation of cytochrome c adsorption, i.e. the electrostatic interaction model. A detailed investigation of the protein binding as a function of pH and ionic strength of the buffer solution reveals the complex nature of the protein-silica interaction. Electrostatic interaction, van der Waals forces and entropic contributions by counterion release each contribute to adsorption on the silica pore walls.

  16. Profile of the intermolecular forces governing the interaction of drugs with mucin.

    Science.gov (United States)

    Caron, Giulia; Visentin, Sonja; Pontremoli, Carlotta; Ermondi, Giuseppe

    2015-07-05

    The study highlights the balance of the intermolecular forces governing the interaction between drugs and mucin. The interaction strength is expressed as a retention factor k (data retrieved from the literature (Gargano et al., 2014)) obtained by a new bio-affinity chromatographic method in which the stationary phase is based on covalently immobilized mucin (porcine gastric mucin, PGM). A quantitative structure-property relationship (QSPR) between logk and 82 VolSurf+ descriptors was established and mechanistically interpreted. Results evidence that all blocks contribute similarly to the model; moreover, hydrogen bonding donor (HBD) properties of solutes favor the interaction with mucin; and thus, support their detrimental role on drug permeability.

  17. Stall force of a cargo driven by N interacting motor proteins

    Science.gov (United States)

    Bhat, Deepak; Gopalakrishnan, Manoj

    2017-01-01

    We study a generic one-dimensional model for an intracellular cargo driven by N motor proteins against an external applied force. The model includes motor-cargo and motor-motor interactions. The cargo motion is described by an over-damped Langevin equation, while motor dynamics is specified by hopping rates which follow a local detailed balance condition with respect to the change in energy per hopping event. Based on this model, we show that the stall force, the mean external force corresponding to zero mean cargo velocity, is completely independent of the details of the interactions and is, therefore, always equal to the sum of the stall forces of the individual motors. This exact result is arrived on the basis of a simple assumption: the (macroscopic) state of stall of the cargo is analogous to a state of thermodynamic equilibrium, and is characterized by vanishing net probability current between any two microstates, with the latter specified by motor positions relative to the cargo. The corresponding probability distribution of the microstates under stall is also determined. These predictions are in complete agreement with numerical simulations, carried out using specific forms of interaction potentials.

  18. Modelling Fluidelastic Instability Forces in Tube Arrays

    Science.gov (United States)

    Anderson, J. Burns

    Historically, heat exchangers have been among the most failure prone components in nuclear power plants. Most of these failures are due to tube failures as a result of corrosion, fatigue and fretting wear. Fatigue and fretting wear are a result of flow induced vibration through turbulent buffeting and fluidelastic instability mechanisms. Fluidelastic instability is by far the most important and complex mechanism. This research deals with modelling fluidelastic instability and the resulting tube response. The proposed time domain model uses the concept of a flow cell (Hassan & Hayder [16]) to represent the complex flow field inside a shell and tube heat exchanger and accounts for temporal variations in the flow separation points as a result of tube motion. The fluidelastic forces are determined by predicting the attachment lengths. The predicted forces are used to simulate the response of a single flexible tube inside a shell and tube heat exchanger. It was found that accounting for temporal variations in the separation points predicted lower critical flow velocities, than that of fixed attachment and separation points. Once unstable a phase lag is predicted between the fluidelastic forces and tube response. It was determined that the predicted critical flow velocities agreed well with available experimental data. The developed model represents an important step towards a realistic fluidelastic instability model which can be used to design the new generation nuclear steam generators.

  19. Drilling forces model for lunar regolith exploration and experimental validation

    Science.gov (United States)

    Zhang, Tao; Ding, Xilun

    2017-02-01

    China's Chang'e lunar exploration project aims to sample and return lunar regolith samples at a minimum penetration depth of 2 m in 2017. Unlike such tasks on the Earth, automated drilling and sampling missions on the Moon are more complicated. Therefore, a delicately designed drill tool is required to minimize operational cost and enhance reliability. Penetration force and rotational torque are two critical parameters in designing the drill tool. In this paper, a novel numerical model for predicting penetration force and rotational torque in the drilling of lunar regolith is proposed. The model is based on quasi-static Mohr-Coulomb soil mechanics and explicitly describes the interaction between drill tool and lunar regolith. Geometric features of drill tool, mechanical properties of lunar regolith, and drilling parameters are taken into consideration in the model. Consequently, a drilling test bed was developed, and experimental penetration force and rotational torque were obtained in penetrating a lunar regolith simulant with different drilling parameters. Finally, theoretical and experimental results were compared to validate the proposed model. Experimental results indicated that the numerical model had good accuracy and was effective in predicting the penetration force and rotational torque in drilling the lunar regolith simulant.

  20. The effect of force feedback delay on stiffness perception and grip force modulation during tool-mediated interaction with elastic force fields.

    Science.gov (United States)

    Leib, Raz; Karniel, Amir; Nisky, Ilana

    2015-05-01

    During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain.

  1. Modeling Forces on the Human Body.

    Science.gov (United States)

    Pagonis, Vasilis; Drake, Russel; Morgan, Michael; Peters, Todd; Riddle, Chris; Rollins, Karen

    1999-01-01

    Presents five models of the human body as a mechanical system which can be used in introductory physics courses: human arms as levers, humans falling from small heights, a model of the human back, collisions during football, and the rotating gymnast. Gives ideas for discussions and activities, including Interactive Physics (TM) simulations. (WRM)

  2. Nonlinear Dynamics of Cantilever-Sample Interactions in Atomic Force Microscopy

    Science.gov (United States)

    Cantrell, John H.; Cantrell, Sean A.

    2010-01-01

    The interaction of the cantilever tip of an atomic force microscope (AFM) with the sample surface is obtained by treating the cantilever and sample as independent systems coupled by a nonlinear force acting between the cantilever tip and a volume element of the sample surface. The volume element is subjected to a restoring force from the remainder of the sample that provides dynamical equilibrium for the combined systems. The model accounts for the positions on the cantilever of the cantilever tip, laser probe, and excitation force (if any) via a basis set of set of orthogonal functions that may be generalized to account for arbitrary cantilever shapes. The basis set is extended to include nonlinear cantilever modes. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a matrix iteration procedure. The effects of oscillatory excitation forces applied either to the cantilever or to the sample surface (or to both) are obtained from the solution set and applied to the to the assessment of phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) modalities. The influence of bistable cantilever modes of on AFM signal generation is discussed. The effects on the cantilever-sample surface dynamics of subsurface features embedded in the sample that are perturbed by surface-generated oscillatory excitation forces and carried to the cantilever via wave propagation are accounted by the Bolef-Miller propagating wave model. Expressions pertaining to signal generation and image contrast in A-AFM are obtained and applied to amplitude modulation (intermittent contact) atomic force microscopy and resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM). The influence of phase accumulation in A-AFM on image contrast is discussed, as is the effect of hard contact and maximum nonlinearity regimes of A-AFM operation.

  3. Canonical Force Distributions in Pairwise Interatomic Interactions from the Perspective of the Hellmann-Feynman Theorem.

    Science.gov (United States)

    Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

    2016-05-26

    Force-based canonical approaches have recently given a unified but different viewpoint on the nature of bonding in pairwise interatomic interactions. Differing molecular categories (covalent, ionic, van der Waals, hydrogen, and halogen bonding) of representative interatomic interactions with binding energies ranging from 1.01 to 1072.03 kJ/mol have been modeled canonically giving a rigorous semiempirical verification to high accuracy. However, the fundamental physical basis expected to provide the inherent characteristics of these canonical transformations has not yet been elucidated. Subsequently, it was shown through direct numerical differentiation of these potentials that their associated force curves have canonical shapes. However, this approach to analyzing force results in inherent loss of accuracy coming from numerical differentiation of the potentials. We now show that this serious obstruction can be avoided by directly demonstrating the canonical nature of force distributions from the perspective of the Hellmann-Feynman theorem. This requires only differentiation of explicitly known Coulombic potentials, and we discuss how this approach to canonical forces can be used to further explain the nature of chemical bonding in pairwise interatomic interactions. All parameter values used in the canonical transformation are determined through explicit physical based algorithms, and it does not require direct consideration of electron correlation effects.

  4. Hemodynamic forces in a model left ventricle

    Science.gov (United States)

    Domenichini, Federico; Pedrizzetti, Gianni

    2016-12-01

    Intraventricular pressure gradients were clinically demonstrated to represent one useful indicator of the left ventricle (LV) function during the development of heart failure. We analyze the fluid dynamics inside a model LV to improve the understanding of the development of hemodynamic forces (i.e., mean pressure gradient) in normal conditions and their modification in the presence of alterations of LV tissue motion. To this aim, the problem is solved numerically and the global force exchanged between blood flow and LV boundaries is computed by volume integration. We also introduce a simplified analytical model, based on global conservation laws, to estimate hemodynamic forces from the knowledge of LV tissue information commonly available in cardiac imaging. Numerical results show that the normal intraventricular gradients feature a deep brief suction at early diastolic filling and a persistent thrust during systolic ejection. In presence of abnormalities of the wall motion, the loss of time synchrony is more relevant than the loss of spatial uniformity in modifying the normal pressure gradient spatiotemporal pattern. The main findings are reproduced in the integral model, which represents a possible easy approach for integrating fluid dynamics evaluations in the clinical examination.

  5. Interactions between synaptic vesicle fusion proteins explored by atomic force microscopy.

    Science.gov (United States)

    Yersin, A; Hirling, H; Steiner, P; Magnin, S; Regazzi, R; Hüni, B; Huguenot, P; De los Rios, P; Dietler, G; Catsicas, S; Kasas, S

    2003-07-22

    Measuring the biophysical properties of macromolecular complexes at work is a major challenge of modern biology. The protein complex composed of vesicle-associated membrane protein 2, synaptosomal-associated protein of 25 kDa, and syntaxin 1 [soluble N-ethyl-maleimide-sensitive factor attachment protein receptor (SNARE) complex] is essential for docking and fusion of neurotransmitter-filled synaptic vesicles with the presynaptic membrane. To better understand the fusion mechanisms, we reconstituted the synaptic SNARE complex in the imaging chamber of an atomic force microscope and measured the interaction forces between its components. Each protein was tested against the two others, taken either individually or as binary complexes. This approach allowed us to determine specific interaction forces and dissociation kinetics of the SNAREs and led us to propose a sequence of interactions. A theoretical model based on our measurements suggests that a minimum of four complexes is probably necessary for fusion to occur. We also showed that the regulatory protein neuronal Sec1 injected into the atomic force microscope chamber prevented the complex formation. Finally, we measured the effect of tetanus toxin protease on the SNARE complex and its activity by on-line registration during tetanus toxin injection. These experiments provide a basis for the functional study of protein microdomains and also suggest opportunities for sensitive screening of drugs that can modulate protein-protein interactions.

  6. What causes periodic beating in sperm flagella: synchronized internal forcing or fluid-structure interaction?

    Science.gov (United States)

    Prabhakar, Ranganathan; Nandagiri, Ashwin; Jadhav, Sameer

    2016-11-01

    Eucaryotic cells such as sperm propel themselves using internally driven flagella. Two different models for the origin of the whip-like beating observed in such flagella are compared. The first model assumes that internal protein motors actuate synchronously to cause a traveling active-force wave within the filament. The forcing wave is chosen such that its resultant and the total torque on the filament are zero. In contrast, the second model assumes that forces and torques exerted by the motors locally sum to zero across the scale of the filament diameter. The only effect of the motor activity is to give rise to a stresslet distribution across the filament length. In either model, the slender filament is modeled as a bead-spring chain with hydrodynamic interactions. Flagellar waveforms and trajectory patterns obtained are compared systematically while keeping the dissipation rates the same for the two models. Periodic beating emerges in freely swimming filaments with the second model without any imposed periodicity in the stresslet distribution. This suggests that periodic waveforms in eucaryotic flagella can emerge by fluid-structure interactions alone without significant internal synchronization of protein motor activity.

  7. Theoretical Models for Surface Forces and Adhesion and Their Measurement Using Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Osvaldo N. Oliveira

    2012-10-01

    Full Text Available The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS, it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of afs, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution.

  8. Theoretical models for surface forces and adhesion and their measurement using atomic force microscopy.

    Science.gov (United States)

    Leite, Fabio L; Bueno, Carolina C; Da Róz, Alessandra L; Ziemath, Ervino C; Oliveira, Osvaldo N

    2012-10-08

    The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS), it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of afs, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution.

  9. Parallel Processing Based on Ship Maneuvering in Identification of Interaction Force Coefficients

    Institute of Scientific and Technical Information of China (English)

    LIU Xiao-jian; HUANG Guo-liang; DENG De-heng

    2008-01-01

    The parallel processing based on the free running model test was adopted to predict the interac-tion force coefficients (flow straightening coefficient and wake fraction) of ship maneuvering. And the multi-population genetic algorithm (MPGA) based on real coding that can contemporarily process the data of freerunning model and simulation of ship maneuvering was applied to solve the problem. Accordingly the optimalindividual was obtained using the method of genetic algorithm. The parallel processing of multi-populationsolved the prematurity in the identification for single population, meanwhile, the parallel processing of the dataof ship maneuvering (turning motion and zigzag motion) is an attempt to solve the coefficient drift problem.In order to validate the method, the interaction force coefficients were verified by the procedure and thesecoefficients measured were compared with those ones identified. The maximum error is less than 5%, and theidentification is an effective method.

  10. Modeling cell-matrix traction forces in Keratinocyte colonies

    Science.gov (United States)

    Banerjee, Shiladitya

    2013-03-01

    Crosstalk between cell-cell and cell-matrix adhesions plays an essential role in the mechanical function of tissues. The traction forces exerted by cohesive keratinocyte colonies with strong cell-cell adhesions are mostly concentrated at the colony periphery. In contrast, for weak cadherin-based intercellular adhesions, individual cells in a colony interact with their matrix independently, with a disorganized distribution of traction forces extending throughout the colony. In this talk I will present a minimal physical model of the colony as contractile elastic media linked by springs and coupled to an elastic substrate. The model captures the spatial distribution of traction forces seen in experiments. For cell colonies with strong cell-cell adhesions, the total traction force of the colony measured in experiments is found to scale with the colony's geometrical size. This scaling suggests the emergence of an effective surface tension of magnitude comparable to that measured for non-adherent, three-dimensional cell aggregates. The physical model supports the scaling and indicates that the surface tension may be controlled by acto-myosin contractility. Supported by the NSF through grant DMR-1004789. This work was done in collaboration with Aaron F. Mertz, Eric R. Dufresne and Valerie Horsley (Yale University) and M. Cristina Marchetti (Syracuse University).

  11. Modeling meteorological forcing of snowcover in forests

    Science.gov (United States)

    Hellstrom, Robert Ake

    2000-11-01

    The architectural properties of a forest are known to modify significantly meteorological forcing of snowcover. Current numerical snow models utilize a wide range of vegetation representations that limit their application to particular biomes or for basic research on specialized problems. Most do not explicitly represent the combined effects of the canopy on processes of mass and energy transfer beneath the canopy. This project develops forest canopy sub-models that estimate the below-canopy solar and longwave irradiance, wind speed, and accumulation of precipitation, based on meteorological measurements above the canopy and parameters of forest architecture. The wind and solar radiation sub-model predictions were independently compared with meteorological observations at deciduous and coniferous sites in the snowbelt region of northern Michigan. The solar radiation and wind models required adjustments to match sub-canopy measurements. The primary experiment compared the simulations and measurements of snow depth for eight modified versions of the Utah Energy Balance (UEB) snow model during the 1998-99 snowcover season at the two forest sites and a near-by open site. Independent inclusion of each sub-model and a new stability scheme in the UEB model revealed significant sensitivity of modeled snow depth to stability and each of the four processes estimated by the sub-models. The original UEB model uses a simple forest canopy parameterization that does not consider precipitation interception. Comparison of the original and modified UEB models significantly improved simulations of snow depth at the open and coniferous sites, but performance was slightly worse for a leafless deciduous site. Unlike the modified model, the analysis suggests that the original model produces inconsistent results, which reduces its potential for application to different biomes. Results suggest that opposing processes of energy and mass exchange tend to moderate meteorological forcing

  12. Probing nanoscale graphene-liquid interfacial interactions via ultrasonic force spectroscopy.

    Science.gov (United States)

    Robinson, Benjamin J; Kolosov, Oleg V

    2014-09-21

    We probe the interfacial forces in graphene-air and graphene-liquid environments with nanoscale resolution. Experimentally, probe 'snap-in' to contact, in scanning probe microscopy, is overcome by combining the ultrasonic force spectroscopy (UFS) approach and MHz frequency range harmonic oscillation of the sample thereby sweeping the tip-surface dynamically from separated to indented state across the region of intimate interface contact. We measured the force interaction between nanoscale probe tip and graphene, graphite and reference SiO₂ surface in ambient, polar and non-polar liquid environments. Via modelling we estimated the decay length of the force interaction in water to be 0.25-0.75 nm, equivalent to 1-3 monolayers, and interfacial effective stiffness at these distances associated with the liquid layer was an order of magnitude greater for non-polar than for polar liquid environment. During the elastic indentation at increased forces, the effective Young's modulus of graphene was shown only to be slightly reduced in ambient environment while experiencing significant reduction by a factor of 3 in non-polar dodecane environment.

  13. Avoiding numerical pitfalls in social force models

    Science.gov (United States)

    Köster, Gerta; Treml, Franz; Gödel, Marion

    2013-06-01

    The social force model of Helbing and Molnár is one of the best known approaches to simulate pedestrian motion, a collective phenomenon with nonlinear dynamics. It is based on the idea that the Newtonian laws of motion mostly carry over to pedestrian motion so that human trajectories can be computed by solving a set of ordinary differential equations for velocity and acceleration. The beauty and simplicity of this ansatz are strong reasons for its wide spread. However, the numerical implementation is not without pitfalls. Oscillations, collisions, and instabilities occur even for very small step sizes. Classic solution ideas from molecular dynamics do not apply to the problem because the system is not Hamiltonian despite its source of inspiration. Looking at the model through the eyes of a mathematician, however, we realize that the right hand side of the differential equation is nondifferentiable and even discontinuous at critical locations. This produces undesirable behavior in the exact solution and, at best, severe loss of accuracy in efficient numerical schemes even in short range simulations. We suggest a very simple mollified version of the social force model that conserves the desired dynamic properties of the original many-body system but elegantly and cost efficiently resolves several of the issues concerning stability and numerical resolution.

  14. Analysis and Modeling of the Arctic Oscillation Using a Simple Barotropic Model with Baroclinic Eddy Forcing.

    Science.gov (United States)

    Tanaka, H. L.

    2003-06-01

    In this study, a numerical simulation of the Arctic Oscillation (AO) is conducted using a simple barotropic model that considers the barotropic-baroclinic interactions as the external forcing. The model is referred to as a barotropic S model since the external forcing is obtained statistically from the long-term historical data, solving an inverse problem. The barotropic S model has been integrated for 51 years under a perpetual January condition and the dominant empirical orthogonal function (EOF) modes in the model have been analyzed. The results are compared with the EOF analysis of the barotropic component of the real atmosphere based on the daily NCEP-NCAR reanalysis for 50 yr from 1950 to 1999.According to the result, the first EOF of the model atmosphere appears to be the AO similar to the observation. The annular structure of the AO and the two centers of action at Pacific and Atlantic are simulated nicely by the barotropic S model. Therefore, the atmospheric low-frequency variabilities have been captured satisfactorily even by the simple barotropic model.The EOF analysis is further conducted to the external forcing of the barotropic S model. The structure of the dominant forcing shows the characteristics of synoptic-scale disturbances of zonal wavenumber 6 along the Pacific storm track. The forcing is induced by the barotropic-baroclinic interactions associated with baroclinic instability.The result suggests that the AO can be understood as the natural variability of the barotropic component of the atmosphere induced by the inherent barotropic dynamics, which is forced by the barotropic-baroclinic interactions. The fluctuating upscale energy cascade from planetary waves and synoptic disturbances to the zonal motion plays the key role for the excitation of the AO.

  15. Intermittent gear rattle due to interactions between forcing and manufacturing errors

    Science.gov (United States)

    Ottewill, James R.; Neild, Simon A.; Wilson, R. Eddie

    2009-04-01

    The interaction between eccentricity and an external forcing fluctuation in gear rattle response is investigated experimentally. The experimental rig consists of a 1:1 ratio steel spur gear pair, the input gear being controlled in displacement and the output gear being under no load. Gear transmission errors recorded using high accuracy encoders are presented. Large variations in backlash oscillation amplitude are observed as the relative phase of the input forcing and the sinusoidal static transmission error due to eccentricity is varied. A simplified mathematical model incorporating eccentricity is developed. It is compared with experimental findings for three different gear eccentricity alignments by way of plots relating backlash oscillation amplitude to forcing amplitude and phase relative to eccentricity sinusoid. It is shown that eccentricity does not fully account for the experimentally observed large variations in amplitude. Through analysis of the experimental data, it is suggested that further tooth profiling errors may explain the discrepancies.

  16. Soliton interactions of integrable models

    Energy Technology Data Exchange (ETDEWEB)

    Ruan Hangyu E-mail: hyruan@mail.nbip.net; Chen Yixin

    2003-08-01

    The solution of integrable (n+1)-dimensional KdV system in bilinear form yields a dromion solution that is localized in all directions. The interactions between two dromions are studied both in analytical and in numerical for three (n+1)-dimensional KdV-type equations (n=1, 2, 3). The same interactive properties between two dromions (solitons) are revealed for these models. The interactions between two dromions (solitons) may be elastic or inelastic for different form of solutions.

  17. Soliton interactions of integrable models

    CERN Document Server

    Ruan Hang Yu

    2003-01-01

    The solution of integrable (n+1)-dimensional KdV system in bilinear form yields a dromion solution that is localized in all directions. The interactions between two dromions are studied both in analytical and in numerical for three (n+1)-dimensional KdV-type equations (n=1, 2, 3). The same interactive properties between two dromions (solitons) are revealed for these models. The interactions between two dromions (solitons) may be elastic or inelastic for different form of solutions.

  18. Force 2025 and Beyond Strategic Force Design Analytic Model

    Science.gov (United States)

    2017-01-12

    list and start and end times of each task. Table 1 shows the basic data needed for our example model in the AMD unit and mission space. Table 1... basically two parts; an objective (or functional) hierarchy linking the overall objective through sub-objectives (or tasks) to attributes (or required...used with any popular algebraic modeling and solver software, including packages such as pyomo in Python or lpSolve in R using the lp_solve solver

  19. Atomic force microscopy of model lipid membranes.

    Science.gov (United States)

    Morandat, Sandrine; Azouzi, Slim; Beauvais, Estelle; Mastouri, Amira; El Kirat, Karim

    2013-02-01

    Supported lipid bilayers (SLBs) are biomimetic model systems that are now widely used to address the biophysical and biochemical properties of biological membranes. Two main methods are usually employed to form SLBs: the transfer of two successive monolayers by Langmuir-Blodgett or Langmuir-Schaefer techniques, and the fusion of preformed lipid vesicles. The transfer of lipid films on flat solid substrates offers the possibility to apply a wide range of surface analytical techniques that are very sensitive. Among them, atomic force microscopy (AFM) has opened new opportunities for determining the nanoscale organization of SLBs under physiological conditions. In this review, we first focus on the different protocols generally employed to prepare SLBs. Then, we describe AFM studies on the nanoscale lateral organization and mechanical properties of SLBs. Lastly, we survey recent developments in the AFM monitoring of bilayer alteration, remodeling, or digestion, by incubation with exogenous agents such as drugs, proteins, peptides, and nanoparticles.

  20. A Unified Theory of Interaction: Gravitation, Electrodynamics and the Strong Force

    Directory of Open Access Journals (Sweden)

    Wagener P.

    2009-01-01

    Full Text Available A unified model of gravitation and electromagnetism is extended to derive the Yukawa potential for the strong force. The model satisfies the fundamental characteristics of the strong force and calculates the mass of the pion.

  1. Resonance in Interacting Induced-Dipole Polarizing Force Fields: Application to Force-Field Derivatives

    Directory of Open Access Journals (Sweden)

    Francisco Torrens

    2009-03-01

    Full Text Available The Silberstein model of the molecular polarizability of diatomic molecules, generalized by Applequist et al. for polyatomic molecules, is analyzed. The atoms are regarded as isotropically polarizable points located at their nuclei, interacting via the fields of their induced dipoles. The use of additive values for atom polarizabilities gives poor results, in some cases leading to artificial predictions of absorption bands. The molecular polarizability of methane and its derivative are computed. The agreement with experimental mean molecular polarizabilities is within 1–5%. A hypothesis is indispensable for a suitable representation of polarizability derivative.

  2. Structures and orientation-dependent interaction forces of titania nanowires using molecular dynamics simulations

    Science.gov (United States)

    Okeke, George; Antony, S. Joseph; Hammond, Robert B.; Ahmed, Kamran

    2017-07-01

    Engineering nanowires to develop new products and processes is highly topical due to their ability to provide highly enhanced physical, chemical, mechanical, thermal and electrical properties. In this work, using molecular dynamics simulations, we report fundamental information, about the structural and thermodynamic properties of individual anatase titania (TiO2) nanowires with cross-sectional diameters between 2 and 6 nm, and aspect ratio (length to diameter) of 6:1 at temperatures ranging from 300 to 3000 K. Estimates of the melting transition temperature of the nanowires are between 2000 and 2500 K. The melting transition temperature predicted from the radial distribution functions (RDFs) shows strong agreement with those predicted from the total energy profiles. Overall, the transition temperature is in reasonable agreement with melting points predicted from experiments and simulations reported in the literature for spherical nanoparticles of similar sizes. Hence, the melting transition temperature of TiO2 nanowires modelled here can be considered as shape independent. Furthermore, for the first time based on MD simulations, interaction forces between two nanowires are reported at ambient temperature (300 K) for different orientations: parallel, perpendicular and end-to-end. It is observed that end-to-end orientations manifested the strongest attraction forces, while the parallel and perpendicular orientations displayed weaker attractions. The results reported here could form a foundation in future multiscale modelling studies of the structured titania nanowire assemblies, depending on the inter-wire interaction forces.

  3. Modeling of the intermolecular Force-Induced Adhesion in Freestanding Nanostructures Made of Nano-beams

    Directory of Open Access Journals (Sweden)

    Alireza Yekrangi

    2015-11-01

    Full Text Available Among the intermolecular interactions, the Casimir and van der Waals forces are the most important forces that highly affect the behavior of nanostructures. This paper studies the effect of such forces on the adhesion of cantilever freestanding nanostructures. The nanostructures are made of a freestanding nano-beam which is suspended between two upper and lower conductive surfaces. The linear spring model is applied to derive the elastic force. The Lumped Parameter Model (LPM is used to obtain constitutive equations of the systems. The maximum length of the nano-beam which prevents the adhesion is computed. Results of this study are useful for design and development of miniature devices.

  4. EMG-to-force estimation with full-scale physiology based muscle model

    OpenAIRE

    Hayashibe, Mitsuhiro; Guiraud, David; Poignet, Philippe

    2009-01-01

    International audience; EMG-to-force estimation for voluntary muscle contraction has many applications in human-machine interaction, motion analysis, and rehabilitation robotics for prosthetic limbs or exoskeletons. EMG-based model can account for a subject's individual activation patterns to estimate muscle force. For the estimation, so-called Hill-type model has been used in most of the cases. It already has shown its promising performance, but it is still known as a phenomenological model ...

  5. PORTER S FIVE FORCES MODEL SCOTT MORTON S FIVE FORCES MODEL BAKOS TREACY MODEL ANALYZES STRATEGIC INFORMATION SYSTEMS MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Indra Gamayanto

    2004-01-01

    Full Text Available Wollongong City Council (WCC is one of the most progressive and innovative local government organizations in Australia. Wollongong City Council use Information Technology to gain the competitive advantage and to face a global economy in the future. Porter's Five Force model is one of the models that can be using at Wollongong City Council because porter's five Forces model has strength in relationship between buyer and suppliers (Bargaining power of suppliers and bargaining power of buyers. Other model such as Scott Morton's Five Forces model has strength to analyze the social impact factor, so to gain competitive advantage in the future and have a good IT/IS strategic planning; this model can be use also. Bakos & Treacy model almost the same as Porter's model but Bakos & Treacy model can also be applying into Wollongong City Council to improve the capability in Transforming organization, efficiency, and effectiveness.

  6. Numerical calculation of interaction forces between paramagnetic colloids in two-dimensional systems.

    Science.gov (United States)

    Du, Di; Toffoletto, Frank; Biswal, Sibani Lisa

    2014-04-01

    Typically the force between paramagnetic particles in a uniform magnetic field is described using the dipolar model, which is inaccurate when particles are in close proximity to each other. Instead, the exact force between paramagnetic particles can be determined by solving a three-dimensional Laplace's equation for magnetostatics under specified boundary conditions and calculating the Maxwell stress tensor. The analytical solution to this multi-boundary-condition Laplace's equation can be obtained by using a solid harmonics expansion in conjunction with the Hobson formula. However, for a multibody system, finite truncation of the Hobson formula does not lead to convergence of the expansion at all points, which makes the approximation physically unrealistic. Here we present a numerical method for solving this Laplace's equation for magnetostatics. This method uses a smoothed representation to replace all the boundary conditions. A two-step propagation is used to dramatically accelerate the calculation without losing accuracy. Using this method, we calculate the force between two paramagnetic particles in a uniform and a rotational external field and compare our results with other models. Furthermore, the many-body effects for three-particle, ten-particle, and 24-particle systems are examined using the same method. We also calculate the interaction between particles with different magnetic susceptibilities and particle diameters. The Laplace's equation solver method described in this article that is used to determine the force between paramagnetic particles is shown to be very useful for dynamic simulations for both two-particle systems and a large cluster of particles.

  7. Foot force models of crowd dynamics on a wobbly bridge

    CERN Document Server

    Belykh, Igor; Belykh, Vladamir

    2016-01-01

    Modern pedestrian and suspension bridges are designed using industry-standard packages, yet disastrous resonant vibrations are observed, necessitating multi-million dollar repairs. Recent examples include pedestrian induced vibrations during the openings of the Solf\\'erino Bridge in Paris in 1999 and the increased bouncing of the Squibb Park Bridge in Brooklyn in 2014. The most prominent example of an unstable lively bridge is the London Millennium Bridge which started wobbling as a result of pedestrian-bridge interactions. Pedestrian phase-locking due to footstep phase adjustment, is suspected to be the main cause of its large lateral vibrations; however, its role in the initiation of wobbling was debated. In this paper, we develop foot force models of pedestrians' response to bridge motion and detailed, yet analytically tractable models of crowd phase-locking. We use bio-mechanically inspired models of crowd lateral movement to investigate to what degree pedestrian synchrony must be present for a bridge to ...

  8. Interactive Dimensioning of Parametric Models

    KAUST Repository

    Kelly, T.

    2015-05-01

    We propose a solution for the dimensioning of parametric and procedural models. Dimensioning has long been a staple of technical drawings, and we present the first solution for interactive dimensioning: A dimension line positioning system that adapts to the view direction, given behavioral properties. After proposing a set of design principles for interactive dimensioning, we describe our solution consisting of the following major components. First, we describe how an author can specify the desired interactive behavior of a dimension line. Second, we propose a novel algorithm to place dimension lines at interactive speeds. Third, we introduce multiple extensions, including chained dimension lines, controls for different parameter types (e.g. discrete choices, angles), and the use of dimension lines for interactive editing. Our results show the use of dimension lines in an interactive parametric modeling environment for architectural, botanical, and mechanical models. © 2015 The Author(s) Computer Graphics Forum © 2015 The Eurographics Association and John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd.

  9. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

    Science.gov (United States)

    Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

    2014-12-12

    Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations.

  10. Modelling land surface - atmosphere interactions

    DEFF Research Database (Denmark)

    Rasmussen, Søren Højmark

    related to inaccurate land surface modelling, e.g. enhanced warm bias in warm dry summer months. Coupling the regional climate model to a hydrological model shows the potential of improving the surface flux simulations in dry periods and the 2 m air temperature in general. In the dry periods......The study is investigates modelling of land surface – atmosphere interactions in context of fully coupled climatehydrological model. With a special focus of under what condition a fully coupled model system is needed. Regional climate model inter-comparison projects as ENSEMBLES have shown bias...... representation of groundwater in the hydrological model is found to important and this imply resolving the small river valleys. Because, the important shallow groundwater is found in the river valleys. If the model does not represent the shallow groundwater then the area mean surface flux calculation...

  11. Magnetostatic interactions and forces between cylindrical permanent magnets

    Energy Technology Data Exchange (ETDEWEB)

    Vokoun, David [Institute of Physics ASCR, v.v.i., Prague (Czech Republic)], E-mail: vokoun@fzu.cz; Beleggia, Marco [Institute for Materials Research, University of Leeds, Leeds LS2 9JT (United Kingdom); Heller, Ludek; Sittner, Petr [Institute of Physics ASCR, v.v.i., Prague (Czech Republic)

    2009-11-15

    Permanent magnets of various shapes are often utilized in magnetic actuators, sensors or releasable magnetic fasteners. Knowledge of the magnetic force is required to control devices reliably. Here, we introduce an analytical expression for calculating the attraction force between two cylindrical permanent magnets on the assumption of uniform magnetization. Although the assumption is not fulfilled exactly in cylindrical magnets, we obtain a very good agreement between the calculated and measured forces between two identical cylindrical magnets and within an array of NdFeB cylindrical magnets.

  12. Magnetostatic interactions and forces between cylindrical permanent magnets

    Science.gov (United States)

    Vokoun, David; Beleggia, Marco; Heller, Luděk; Šittner, Petr

    2009-11-01

    Permanent magnets of various shapes are often utilized in magnetic actuators, sensors or releasable magnetic fasteners. Knowledge of the magnetic force is required to control devices reliably. Here, we introduce an analytical expression for calculating the attraction force between two cylindrical permanent magnets on the assumption of uniform magnetization. Although the assumption is not fulfilled exactly in cylindrical magnets, we obtain a very good agreement between the calculated and measured forces between two identical cylindrical magnets and within an array of NdFeB cylindrical magnets.

  13. Interactive modeling of storm impact

    Science.gov (United States)

    van Rooijen, A.; Baart, F.; Roelvink, J. A.; Donchyts, G.; Scheel, F.; de Boer, W.

    2014-12-01

    In the past decades the impact of storms on the coastal zone has increasingly drawn the attention of policy makers and coastal planners, engineers and researchers. The mean reason for this interest is the high density of the world's population living near the ocean, in combination with climate change. Due to sea level rise and extremer weather conditions, many of the world's coastlines are becoming more vulnerable to the potential of flooding. Currently it is common practice to predict storm impact using physics-based numerical models. The numerical model utilizes several inputs (e.g. bathymetry, waves, surge) to calculate the impact on the coastline. Traditionally, the numerical modeller takes the following three steps: schematization/model setup, running and post-processing. This process generally has a total feedback time in the order of hours to days, and is suitable for so-called confirmatory modelling.However, often models are applied as an exploratory tool, in which the effect of e.g. different hydraulic conditions, or measures is investigated. The above described traditional work flow is not the most efficient method for exploratory modelling. Interactive modelling lets users adjust a simulation while running. For models typically used for storm impact studies (e.g. XBeach, Delft3D, D-Flow FM), the user can for instance change the storm surge level, wave conditions, or add a measure such as a nourishment or a seawall. The model will take the adjustments into account immediately, and will directly compute the effect. Using this method, tools can be developed in which stakeholders (e.g. coastal planners, policy makers) are in control and together evaluate ideas by interacting with the model. Here we will show initial results for interactive modelling with a storm impact model.

  14. Acoustic interaction forces and torques acting on suspended spheres in an ideal fluid

    CERN Document Server

    Lopes, J Henrique; Silva, G T

    2014-01-01

    In this paper, the acoustic interaction forces and torques exerted by an arbitrary time-harmonic wave on a set of N spheres suspended in an inviscid fluid are theoretically analyzed. In so doing, we utilize the partial-wave expansion method to solve the related multiple scattering problem. The acoustic interaction force and torque are computed for a sphere using the farfield radiation force and torque formulas. To exemplify the method, we calculate the interaction forces exerted by an external traveling and standing plane wave on an arrangement of two and three olive-oil droplets in water. The droplets radii are comparable to the wavelength (i.e. Mie scattering regime). The results show that the radiation force may considerably deviates from that exerted solely by the external incident wave. In addition, we find that acoustic interaction torques arise on the droplets when a nonsymmetric effective incident wave interacts with the droplets.

  15. Interaction forces for symmetric hydrophilic and hydrophobic systems in aqueous isopropanol solutions.

    Science.gov (United States)

    Hupka, Lukasz; Nalaskowski, Jakub; Miller, Jan D

    2010-02-16

    Interaction force measurements were performed for a silica-silica hydrophilic system and for a silanated silica-silanated silica hydrophobic system using the atomic force microscopy colloidal probe technique. The influence of the solution composition on interaction forces was investigated. The hydrophilic silica-silica interactions were found to be described as a typical Derjaguin-Landau-Verwey-Overbeek (DLVO) system in solutions of various compositions, whereas silanated silica-silanated silica interactions were dominated by a long-range hydrophobic force. An increase in the isopropyl alcohol content of the solution diminishes both the repulsive forces in the case of the hydrophilic system and the attractive interactions in the case of the hydrophobic system.

  16. Based on the Force Deployment Model of Unascertained Expectation

    Directory of Open Access Journals (Sweden)

    Jianli Chen

    2013-05-01

    Full Text Available In this study, we utilize the unascertained mathematics method to give the unascertained number of countermeasure of anti-terrorism strategic force deployment and unknown event. It has been defined the situation sets of force deployment, condition density and mathematical expectation of density model. It has been given the unascertained parameters Cij which decide and direct the force deployment. Find out the condition density matrix of force deployment, further get the conditional density of single target force deployment, using the maximum density mathematical expectation in order to get the optimal mathematical model of multiple target force deployment. Analyzing the coefficient of model and provide two kinds of discussed computing method. The model overcomes the limitation of past deterministic thinking method which study the force deployment and provide the decision maker a relative substantial theory evidence.

  17. Pore-polymer interaction reveals non-universality in forced polymer translocation

    CERN Document Server

    Lehtola, V V; Linna, R P

    2010-01-01

    We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced translocation characteristics significantly in the biologically relevant pore force, i.e. driving force, range. Details of the model are shown to change even the obtained scaling relations, which is a strong indication of strongly out-of-equilibrium dynamics in the computational studies which have not yet succeeded in addressing the characteristics of the forced translocation for biopolymers at realistic length scale.

  18. Muscular activity and physical interaction forces during lower limb exoskeleton use.

    Science.gov (United States)

    Wilcox, Matthew; Rathore, Ashish; Morgado Ramirez, Dafne Zuleima; Loureiro, Rui C V; Carlson, Tom

    2016-12-01

    Spinal cord injury (SCI) typically manifests with a loss of sensorimotor control of the lower limbs. In order to overcome some of the disadvantages of chronic wheelchair use by such patients, robotic exoskeletons are an emerging technology that has the potential to transform the lives of patients. However, there are a number of points of contact between the robot and the user, which lead to interaction forces. In a recent study, the authors have shown that peak interaction forces are particularly prominent at the anterior aspect of the right leg. This study uses a similar experimental protocol with additional electromyography (EMG) analysis to examine whether such interaction forces are due to the muscular activity of the participant or the movement of the exoskeleton itself. Interestingly, the authors found that peak forces preceded peak EMG activity. This study did not find a significant correlation between EMG activity and force data, which would indicate that the interaction forces can largely be attributed to the movement of the exoskeleton itself. However, we also report significantly higher correlation coefficients in muscle/force pairs located at the anterior aspect of the right leg. In their previous research, the authors have shown peak interaction forces at the same locations, which suggests that muscular activity of the participant makes a more significant contribution to the interaction forces at these locations. The findings of this study are of significance for incomplete SCI patients, for whom EMG activity may provide an important input to an intuitive control schema.

  19. Modeling of Dynamic Fluid Forces in Fast Switching Valves

    DEFF Research Database (Denmark)

    Roemer, Daniel Beck; Johansen, Per; Pedersen, Henrik Clemmensen;

    2015-01-01

    force, but these models are computationally expensive and are not suitable for evaluating large numbers of different operation conditions or even design optimization. In the present paper, an effort is done to describe these fluid forces and their origin. An example of the total opposing fluid force...

  20. The interaction of two collinear cracks in a rectangular superconductor slab under an electromagnetic force

    Energy Technology Data Exchange (ETDEWEB)

    Gao Zhiwen, E-mail: gaozhw@lzu.edu.c [Key Laboratory of Mechanics on Western Disaster and Environment, Ministry of Education (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); School of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Zhou Youhe [Key Laboratory of Mechanics on Western Disaster and Environment, Ministry of Education (China); Department of Mechanics and Engineering Science, College of Civil Engineering and Mechanics, Lanzhou University, Lanzhou, Gansu 730000 (China); Lee, Kang Yong, E-mail: KYL2813@yonsei.ac.k [School of Mechanical Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2010-08-01

    The interaction of two collinear cracks is obtained for a type-II superconducting under electromagnetic force. Fracture analysis is performed by means of finite element method and the magnetic behavior of superconductor is described by the critical-state Bean model. The stress intensity factors at the crack tips can be obtained and discussed for decreasing field after zero-field cooling. It is revealed that the stress intensity factor decreases as applied field increases. The crack-tip stress intensity factors decrease when the distance between the two collinear cracks increases and the superconductors with smaller crack has more remarkable shielding effect than those with larger cracks.

  1. Switched Dynamical Latent Force Models for Modelling Transcriptional Regulation

    CERN Document Server

    López-Lopera, Andrés F

    2015-01-01

    In order to develop statistical approaches for transcription networks, statistical community has proposed several methods to infer activity levels of proteins, from time-series measurements of targets' expression levels. A few number of approaches have been proposed in order to outperform the representation of fast switching time instants, but computational overheads are significant due to complex inference algorithms. Using the theory related to latent force models (LFM), the development of this project provide a switched dynamical hybrid model based on Gaussian processes (GPs). To deal with discontinuities in dynamical systems (or latent driving force), an extension of the single input motif approach is introduced, that switches between different protein concentrations, and different dynamical systems. This creates a versatile representation for transcription networks that can capture discrete changes and non-linearities in the dynamics. The proposed method is evaluated on both simulated data and real data,...

  2. Cosmological Constraints on the Modified Entropic Force Model

    OpenAIRE

    Wei, Hao

    2010-01-01

    Very recently, Verlinde considered a theory in which space is emergent through a holographic scenario, and proposed that gravity can be explained as an entropic force caused by changes in the information associated with the positions of material bodies. Then, motivated by the Debye model in thermodynamics which is very successful in very low temperatures, Gao modified the entropic force scenario. The modified entropic force (MEF) model is in fact a modified gravity model, and the universe can...

  3. Interactive graphics for geometry modeling

    Science.gov (United States)

    Wozny, M. J.

    1984-01-01

    An interactive vector capability to create geometry and a raster color shaded rendering capability to sample and verify interim geometric design steps through color snapshots is described. The development is outlined of the underlying methodology which facilitates computer aided engineering and design. At present, raster systems cannot match the interactivity and line-drawing capability of refresh vector systems. Consequently, an intermediate step in mechanical design is used to create objects interactively on the vector display and then scan convert the wireframe model to render it as a color shaded object on a raster display. Several algorithms are presented for rendering such objects. Superquadric solid primitive extend the class of primitives normally used in solid modelers.

  4. Propagation of the state change induced by external forces in local interactions

    Science.gov (United States)

    Lu, Jianjun; Tokinaga, Shozo

    2016-10-01

    This paper analyses the propagation of the state changes of agents that are induced by external forces applied to a plane. In addition, we propose two models for the behavior of the agents placed on a lattice plane, both of which are affected by local interactions. We first assume that agents are allowed to move to another site to maximise their satisfaction. Second, we utilise a model in which the agents choose activities on each site. The results show that the migration (activity) patterns of agents in both models achieve stability without any external forces. However, when we apply an impulsive external force to the state of the agents, we then observe the propagation of the changes in the agents' states. Using simulation studies, we show the conditions for the propagation of the state changes of the agents. We also show the propagation of the state changes of the agents allocated in scale-free networks and discuss the estimation of the agents' decisions in real state changes. Finally, we discuss the estimation of the agents' decisions in real state temporal changes using economic and social data from Japan and the United States.

  5. Model Checking Interactive Markov Chains

    NARCIS (Netherlands)

    Neuhausser, M.; Zhang, Lijun; Esparza, J.; Majumdar, R.

    2010-01-01

    Hermanns has introduced interactive Markov chains (IMCs) which arise as an orthogonal extension of labelled transition systems and continuous-time Markov chains (CTMCs). IMCs enjoy nice compositional aggregation properties which help to minimize the state space incrementally. However, the model chec

  6. Modeling Interactions in Small Groups

    Science.gov (United States)

    Heise, David R.

    2013-01-01

    A new theory of interaction within small groups posits that group members initiate actions when tension mounts between the affective meanings of their situational identities and impressions produced by recent events. Actors choose partners and behaviors so as to reduce the tensions. A computer model based on this theory, incorporating reciprocal…

  7. Sedimentation of concentrated monodisperse colloidal suspensions: role of collective particle interaction forces.

    Science.gov (United States)

    Vesaratchanon, Jan S; Nikolov, Alex; Wasan, Darsh T

    2008-06-01

    The sedimentation velocities and concentration profiles of low-charge, monodisperse hydroxylate latex particle suspensions were investigated experimentally as a function of the particle concentration to study the effects of the collective particle interactions on suspension stability. We used the Kossel diffraction technique to measure the particle concentration profile and sedimentation rate. We conducted the sedimentation experiments using three different particle sizes. Collective hydrodynamic interactions dominate the particle-particle interactions at particle concentrations up to 6.5 vol%. However, at higher particle concentrations, additional collective particle-particle interactions resulting from the self-depletion attraction cause particle aggregation inside the suspension. The collective particle-particle interaction forces play a much more important role when relatively small particles (500 nm in diameter or less) are used. We developed a theoretical model based on the statistical particle dynamics simulation method to examine the role of the collective particle interactions in concentrated suspensions in the colloidal microstructure formation and sedimentation rates. The theoretical results agree with the experimentally-measured values of the settling velocities and concentration profiles.

  8. (Im)precise nuclear forces: From experiment to model

    Science.gov (United States)

    Navarro Perez, Rodrigo

    2017-01-01

    The nuclear force is the most fundamental building block in nuclear science. It is the cornerstone of every nuclear application from nuclear reactors to the production of heavy elements in supernovae. Despite being rigorously derived from the Standard Model, the actual determination of the nuclear force requires adjusting a set of parameters to reproduce experimental data. This introduces uncertainties that need to be quantified and propagated into all nuclear applications. I'll review a series of works on the determination of the Nucleon-Nucleon interaction from a collection of over 8000 elastic scattering data. Statistical tools used on the selection of data and the propagation of statistical uncertainties will be presented. The implications for charge independence of the pion-nucleon coupling constant and the predictive power of chiral interactions will be discussed. Although this is not the final word on theoretical nuclear uncertainties, as other sources of errors should be explored, this series of works allow to set the foundations for a new era for uncertainty quantification in nuclear applications. This work was performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344. Funding was also provided by the U.S. Department of Energy, Office of Science, Award DE-SC0008511 (NUCLEI SciDAC Collaboration)

  9. Reduced-order models for vertical human-structure interaction

    Science.gov (United States)

    Van Nimmen, Katrien; Lombaert, Geert; De Roeck, Guido; Van den Broeck, Peter

    2016-09-01

    For slender and lightweight structures, the vibration serviceability under crowd- induced loading is often critical in design. Currently, designers rely on equivalent load models, upscaled from single-person force measurements. Furthermore, it is important to consider the mechanical interaction with the human body as this can significantly reduce the structural response. To account for these interaction effects, the contact force between the pedestrian and the structure can be modelled as the superposition of the force induced by the pedestrian on a rigid floor and the force resulting from the mechanical interaction between the structure and the human body. For the case of large crowds, however, this approach leads to models with a very high system order. In the present contribution, two equivalent reduced-order models are proposed to approximate the dynamic behaviour of the full-order coupled crowd-structure system. A numerical study is performed to evaluate the impact of the modelling assumptions on the structural response to pedestrian excitation. The results show that the full-order moving crowd model can be well approximated by a reduced-order model whereby the interaction with the pedestrians in the crowd is modelled using a single (equivalent) SDOF system.

  10. Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

    Science.gov (United States)

    Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

    2008-02-19

    Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

  11. Exploring the properties of valence electron based potential functions for the nonbonded interactions in atomistic force fields

    CERN Document Server

    Plattner, Nuria

    2016-01-01

    The possibility to construct and parametrize the nonbonded interactions in atomistic force fields based on the valence electron structure of molecules is explored in this paper. Three different charge distribution models using simple valence electron based potential functions are introduced and compared. It is shown that the three models can be constructed such that they only require one adjustable parameter for the electrostatic potential of a molecule. The accuracy of the electrostatic potential is evaluated for the three models and compared to population-derived charges and higher order multipole moments for a set of 12 small molecules. Furthermore the accuracy and parametrization of the interaction energies of the three models is evaluated based on {\\it ab initio} intermolecular interaction energies. It is shown that the valence electron potential models provide systematic advantages over conventional point charge models for the calculation of intermolecular interaction energies even with the very simple ...

  12. Interaction Forces Between Microfluidic Droplets in a Hele-Shaw Cell

    CERN Document Server

    Sarig, Itai; Gat, Amir D

    2015-01-01

    Various microfluidic systems, such as chemical and biological lab-on-a-chip devices, involve motion of multiple droplets within an immersing fluid in shallow micro-channels. Modeling the dynamics of such systems requires calculation of the forces of interaction between the moving droplets. These forces are commonly approximated by superposition of dipoles solutions, which requires an assumption of sufficiently large distance between the droplets. In this work we obtain exact solutions (in the Hele-Shaw limit) for two moving droplets, and a droplet within a droplet, located within a moving immersing fluid, without limitation on the distance between the droplets. This is achieved by solution of the pressure field in a bi-polar coordinate system and calculation of the force in a Cartesian coordinate system. Our results are compared with numerical computations, experimental data and the existing dipole-based models. We utilize the results to calculate the dynamics of a droplet within a droplet, and of two close d...

  13. Interaction forces between microfluidic droplets in a Hele-Shaw cell

    Science.gov (United States)

    Sarig, I.; Starosvetsky, Y.; Gat, A. D.

    2016-08-01

    Various microfluidic systems, such as chemical and biological lab-on-a-chip devices, involve motion of multiple droplets within an immersing fluid in shallow micro-channels. Modeling the dynamics of such systems requires calculation of the forces of interaction between the moving droplets. These forces are commonly approximated by superposition of dipoles solutions, which requires an assumption of sufficiently large distance between the droplets. In this work we obtain exact solutions (in the Hele-Shaw limit) for two moving droplets, and a droplet within a droplet, located within a moving immersing fluid, without limitation on the distance between the droplets. This is achieved by solution of the pressure field in a bi-polar coordinate system and calculation of the force in a Cartesian coordinate system. Our results are compared with numerical computations, experimental data and the existing dipole-based models. We utilize the results to calculate the dynamics of a droplet within a droplet, and of two close droplets, located within an immersing fluid with oscillating speed. The obtained results may be used to study the dynamics of dense droplet lattices, common to many microfluidic systems.

  14. Interaction between force production and cognitive performance in humans

    NARCIS (Netherlands)

    Zijdewind, Inge; van Duinen, Hiske; Zielman, R; Lorist, MM

    2006-01-01

    Objective: A dual task paradigm was used to examine the effects of the generation of force on cognitive performance. Methods: Subjects (n = 22) were asked to respond to auditory stimuli with their left middle or index finger and concurrently maintain a sub-maximal contraction with their right index

  15. Anisotropic exchange-interaction model: From the Potts model to the exchange-interaction model

    Science.gov (United States)

    King, T. C.; Chen, H. H.

    1995-04-01

    A spin model called the anisotropic exchange-interaction model is proposed. The Potts model, the exchange-interaction model, and the spin-1/2 anisotropic Heisenberg model are special cases of the proposed model. Thermodynamic properties of the model on the bcc and the fcc lattices are determined by the constant-coupling approximation.

  16. Study of the Interaction Model of PDC Cutters with Rock

    Directory of Open Access Journals (Sweden)

    Wang Jiajun

    2014-06-01

    Full Text Available The existing PDC cutters with rock interaction models does not match the actual drilling condition, because WOB can’t be loaded on their equipment, the influence of the cutting velocity on the force of cutters doesn’t be considered. A drilling experiment was carried out in the experimental device in which cutters can be loaded WOB. The relationship of cutting area, cutting speed, back dip angle of PDC cutter and rock performance with the force of PDC cutter were considered. The multiple nonlinear regression analysis were done on the basis of the experimental data, a new cutter-rock interaction model was established. The cutter area is the principal component influencing the force of cutters though the cluster analysis and principal component analysis. It is a logarithmic relationship between cutting velocity and the force of cutter, the theory of particle dynamics confirms this relationship.

  17. Research on Key Factors and Their Interaction Effects of Electromagnetic Force of High-Speed Solenoid Valve

    Science.gov (United States)

    Fan, Liyun; Xu, De; Ma, Xiuzhen; Song, Enzhe

    2014-01-01

    Analysis consisting of numerical simulations along with lab experiments of interaction effects between key parameters on the electromagnetic force based on response surface methodology (RSM) has been also proposed to optimize the design of high-speed solenoid valve (HSV) and improve its performance. Numerical simulation model of HSV has been developed in Ansoft Maxwell environment and its accuracy has been validated through lab experiments. Effect of change of core structure, coil structure, armature structure, working air gap, and drive current on the electromagnetic force of HSV has been analyzed through simulation model and influence rules of various parameters on the electromagnetic force have been established. The response surface model of the electromagnetic force has been utilized to analyze the interaction effect between major parameters. It has been concluded that six interaction factors including working air gap with armature radius, drive current with armature thickness, coil turns with side pole radius, armature thickness with its radius, armature thickness with side pole radius, and armature radius with side pole radius have significant influence on the electromagnetic force. Optimal match values between coil turns and side pole radius; armature thickness and side pole radius; and armature radius and side pole radius have also been determined. PMID:25243217

  18. A New Method of Comparing Forcing Agents in Climate Models

    Energy Technology Data Exchange (ETDEWEB)

    Kravitz, Benjamin S.; MacMartin, Douglas; Rasch, Philip J.; Jarvis, Andrew

    2015-10-14

    We describe a new method of comparing different climate forcing agents (e.g., CO2, CH4, and solar irradiance) that avoids many of the ambiguities introduced by temperature-related climate feedbacks. This is achieved by introducing an explicit feedback loop external to the climate model that adjusts one forcing agent to balance another while keeping global mean surface temperature constant. Compared to current approaches, this method has two main advantages: (i) the need to define radiative forcing is bypassed and (ii) by maintaining roughly constant global mean temperature, the effects of state dependence on internal feedback strengths are minimized. We demonstrate this approach for several different forcing agents and derive the relationships between these forcing agents in two climate models; comparisons between forcing agents are highly linear in concordance with predicted functional forms. Transitivity of the relationships between the forcing agents appears to hold within a wide range of forcing. The relationships between the forcing agents obtained from this method are consistent across both models but differ from relationships that would be obtained from calculations of radiative forcing, highlighting the importance of controlling for surface temperature feedback effects when separating radiative forcing and climate response.

  19. Robot Physical Interaction through the combination of Vision, Tactile and Force Feedback Applications to Assistive Robotics

    CERN Document Server

    Prats, Mario; Sanz, Pedro J

    2013-01-01

    Robot manipulation is a great challenge; it encompasses versatility -adaptation to different situations-, autonomy -independent robot operation-, and dependability -for success under modeling or sensing errors. A complete manipulation task involves, first, a suitable grasp or contact configuration, and the subsequent motion required by the task. This monograph presents a unified framework by introducing task-related aspects into the knowledge-based grasp concept, leading to task-oriented grasps. Similarly, grasp-related issues are also considered during the execution of a task, leading to grasp-oriented tasks which is called framework for physical interaction (FPI). The book presents the theoretical framework for the versatile specification of physical interaction tasks, as well as the problem of autonomous planning of these tasks. A further focus is on sensor-based dependable execution combining three different types of sensors: force, vision and tactile. The FPI approach allows to perform a wide range of ro...

  20. Investigating the Effects of Non-Gravitational Force Modelling on GPS Satellite Orbits

    Science.gov (United States)

    Petrie, E. J.; King, R. W.; Herring, T.; Ziebart, M. K.

    2011-12-01

    Non-gravitational forces such as solar radiation pressure, earth radiation pressure, antenna thrust and thermal re-radiation are relatively small contributors to the overall GPS satellite orbital force budget. However, if neglected, these small non-gravitationally induced accelerations produce significant errors in satellite positions and velocities when integrated over time. For applications where centimetre level orbital accuracy is required (i.e. ppb accuracy ground positioning), these forces must be accounted for either through realistic a priori physical models and/or appropriate parameter estimation. Current GPS processing approaches typically use an approximate solar radiation pressure force, together with estimated parameters that are meant to account for non-modeled forces. These parameters often fall into the categories of scaling and sinusoidal once-per-revolution parameters. Here we investigate the effects of using more detailed physically based models of radiation forces and interaction between these models and the parameterisation of the non-modeled forces. Ideally, with a complete physical model, additional parameters are not required. Reduction of the number of empirical parameters estimated can result in large effects on the stability of the terrestrial reference frame determined with GPS. These analyses are done using an adapted version of the GAMIT processing software which includes a Fourier series model for radiation forces developed at University College London.

  1. Fuzzy logic algorithm to extract specific interaction forces from atomic force microscopy data

    Science.gov (United States)

    Kasas, Sandor; Riederer, Beat M.; Catsicas, Stefan; Cappella, Brunero; Dietler, Giovanni

    2000-05-01

    The atomic force microscope is not only a very convenient tool for studying the topography of different samples, but it can also be used to measure specific binding forces between molecules. For this purpose, one type of molecule is attached to the tip and the other one to the substrate. Approaching the tip to the substrate allows the molecules to bind together. Retracting the tip breaks the newly formed bond. The rupture of a specific bond appears in the force-distance curves as a spike from which the binding force can be deduced. In this article we present an algorithm to automatically process force-distance curves in order to obtain bond strength histograms. The algorithm is based on a fuzzy logic approach that permits an evaluation of "quality" for every event and makes the detection procedure much faster compared to a manual selection. In this article, the software has been applied to measure the binding strength between tubuline and microtubuline associated proteins.

  2. A mathematical model of muscle containing heterogeneous half-sarcomeres exhibits residual force enhancement.

    Science.gov (United States)

    Campbell, Stuart G; Hatfield, P Chris; Campbell, Kenneth S

    2011-09-01

    A skeletal muscle fiber that is stimulated to contract and then stretched from L₁ to L₂ produces more force after the initial transient decays than if it is stimulated at L₂. This behavior has been well studied experimentally, and is known as residual force enhancement. The underlying mechanism remains controversial. We hypothesized that residual force enhancement could reflect mechanical interactions between heterogeneous half-sarcomeres. To test this hypothesis, we subjected a computational model of interacting heterogeneous half-sarcomeres to the same activation and stretch protocols that produce residual force enhancement in real preparations. Following a transient period of elevated force associated with active stretching, the model predicted a slowly decaying force enhancement lasting >30 seconds after stretch. Enhancement was on the order of 13% above isometric tension at the post-stretch muscle length, which agrees well with experimental measurements. Force enhancement in the model was proportional to stretch magnitude but did not depend strongly on the velocity of stretch, also in agreement with experiments. Even small variability in the strength of half-sarcomeres (2.1% standard deviation, normally distributed) was sufficient to produce a 5% force enhancement over isometric tension. Analysis of the model suggests that heterogeneity in half-sarcomeres leads to residual force enhancement by storing strain energy introduced during active stretch in distributions of bound cross-bridges. Complex interactions between the heterogeneous half-sarcomeres then dissipate this stored energy at a rate much slower than isolated cross-bridges would cycle. Given the variations in half-sarcomere length that have been observed in real muscle preparations and the stochastic variability inherent in all biological systems, half-sarcomere heterogeneity cannot be excluded as a contributing source of residual force enhancement.

  3. Direct measurement of interaction forces between a platinum dichloride complex and DNA molecules.

    Science.gov (United States)

    Muramatsu, Hiroshi; Shimada, Shogo; Okada, Tomoko

    2017-06-29

    The interaction forces between a platinum dichloride complex and DNA molecules have been studied using atomic force microscopy (AFM). The platinum dichloride complex, di-dimethylsulfoxide-dichloroplatinum (II) (Pt(DMSO)2Cl2), was immobilized on an AFM probe by coordinating the platinum to two amino groups to form a complex similar to Pt(en)Cl2, which is structurally similar to cisplatin. The retraction forces were measured between the platinum complex and DNA molecules immobilized on mica plates using force curve measurements. The histogram of the retraction force for λ-DNA showed several peaks; the unit retraction force was estimated to be 130 pN for a pulling rate of 60 nm/s. The retraction forces were also measured separately for four single-base DNA oligomers (adenine, guanine, thymine, and cytosine). Retraction forces were frequently observed in the force curves for the DNA oligomers of guanine and adenine. For the guanine DNA oligomer, the most frequent retraction force was slightly lower than but very similar to the retraction force for λ-DNA. A higher retraction force was obtained for the adenine DNA oligomer than for the guanine oligomer. This result is consistent with a higher retraction activation energy of adenine with the Pt complex being than that of guanine because the kinetic rate constant for retraction correlates to exp(FΔx - ΔE) where ΔE is an activation energy, F is an applied force, and Δx is a displacement of distance.

  4. Interdependence between Army Conventional Forces and Special Operations Forces: Changing Institutional Mental Models

    Science.gov (United States)

    2013-03-23

    JCO Joint Commission Observer JCOA Joint and Coalition Operational Analysis JP Joint Publication JTF Joint Task Force GCC Geographic...inherited from British predecessors, the Joint Commission Observer teams ( JCOs ) provided liaison, information exchange, and expedient communications...integration, the operational SOF JCOs were omnipresent throughout the area of responsibility. Their frequent interaction with CF units and leaders

  5. Normal and friction stabilization techniques for interactive rigid body constraint-based contact force computations

    DEFF Research Database (Denmark)

    2010-01-01

    We present a novel, yet simple, method for stabilization of normal forces. A normal stabilization term, carefully designed from hypotheses about interactive usability, is added to the contact force problem. Further, we propose friction stabilization as a completely new stabilization paradigm in i...

  6. Effect of particle-particle interactions on the acoustic radiation force in an ultrasonic standing wave

    Energy Technology Data Exchange (ETDEWEB)

    Lipkens, Bart, E-mail: blipkens@wne.edu [Mechanical Engineering, Western New England University, Springfield, Massachusetts, 01119 (United States); Ilinskii, Yurii A., E-mail: ilinskii@gmail.com; Zabolotskaya, Evgenia A., E-mail: zheniazabolotskaya@gmail.com [Applied Research Laboratories, The University of Texas at Austin, Austin, Texas 78713–8029 (United States)

    2015-10-28

    Ultrasonic standing waves are widely used for separation applications. In MEMS applications, a half wavelength standing wave field is generated perpendicular to a laminar flow. The acoustic radiation force exerted on the particle drives the particle to the center of the MEMS channel, where concentrated particles are harvested. In macro-scale applications, the ultrasonic standing wave spans multiple wavelengths. Examples of such applications are oil/water emulsion splitting [1], and blood/lipid separation [2]. In macro-scale applications, particles are typically trapped in the standing wave, resulting in clumping or coalescence of particles/droplets. Subsequent gravitational settling results in separation of the secondary phase. An often used expression for the radiation force on a particle is that derived by Gorkov [3]. The assumptions are that the particle size is small relative to the wavelength, and therefore, only monopole and dipole scattering contributions are used to calculate the radiation force. This framework seems satisfactory for MEMS scale applications where each particle is treated separately by the standing wave, and concentrations are typically low. In macro-scale applications, particle concentration is high, and particle clumping or droplet coalescence results in particle sizes not necessarily small relative to the wavelength. Ilinskii et al. developed a framework for calculation of the acoustic radiation force valid for any size particle [4]. However, this model does not take into account particle to particle effects, which can become important as particle concentration increases. It is known that an acoustic radiation force on a particle or a droplet is determined by the local field. An acoustic radiation force expression is developed that includes the effect of particle to particle interaction. The case of two neighboring particles is considered. The approach is based on sound scattering by the particles. The acoustic field at the location of

  7. Evaluation of Chemical Interactions between Small Molecules in the Gas Phase Using Chemical Force Microscopy.

    Science.gov (United States)

    Lee, Jieun; Ju, Soomi; Kim, In Tae; Jung, Sun-Hwa; Min, Sun-Joon; Kim, Chulki; Sim, Sang Jun; Kim, Sang Kyung

    2015-12-04

    Chemical force microscopy analyzes the interactions between various chemical/biochemical moieties in situ. In this work we examined force-distance curves and lateral force to measure the interaction between modified AFM tips and differently functionalized molecular monolayers. Especially for the measurements in gas phase, we investigated the effect of humidity on the analysis of force-distance curves and the images in lateral force mode. Flat chemical patterns composed of different functional groups were made through micro-contact printing and lateral force mode provided more resolved analysis of the chemical patterns. From the images of 1-octadecanethiol/11-mercapto-1-undecanoic acid patterns, the amine group functionalized tip brought out higher contrast of the patterns than an intact silicon nitride tip owing to the additional chemical interaction between carboxyl and amine groups. For more complex chemical interactions, relative chemical affinities toward specific peptides were assessed on the pattern of 1-octadecanethiol/phenyl-terminated alkanethiol. The lateral image of chemical force microscopy reflected specific preference of a peptide to phenyl group as well as the hydrophobic interaction.

  8. G-mode magnetic force microscopy: Separating magnetic and electrostatic interactions using big data analytics

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Liam; Belianinov, Alex; Kalinin, Sergei V.; Jesse, Stephen [Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Proksch, Roger [Asylum Research, An Oxford Instruments Company, Santa Barbara, California 93117 (United States); Zuo, Tingting [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Deptarment of Materials Science and Engineering, The University of Tennessee, Knoxville, Tennessee 37996-2200 (United States); Zhang, Yong [State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Liaw, Peter K. [Deptarment of Materials Science and Engineering, The University of Tennessee, Knoxville, Tennessee 37996-2200 (United States)

    2016-05-09

    In this work, we develop a full information capture approach for Magnetic Force Microscopy (MFM), referred to as generalized mode (G-Mode) MFM. G-Mode MFM acquires and stores the full data stream from the photodetector, captured at sampling rates approaching the intrinsic photodiode limit. The data can be subsequently compressed, denoised, and analyzed, without information loss. Here, G-Mode MFM is implemented and compared to the traditional heterodyne-based MFM on model systems, including domain structures in ferromagnetic Yttrium Iron Garnet and the electronically and magnetically inhomogeneous high entropy alloy, CoFeMnNiSn. We investigate the use of information theory to mine the G-Mode MFM data and demonstrate its usefulness for extracting information which may be hidden in traditional MFM modes, including signatures of nonlinearities and mode-coupling phenomena. Finally, we demonstrate detection and separation of magnetic and electrostatic tip-sample interactions from a single G-Mode image, by analyzing the entire frequency response of the cantilever. G-Mode MFM is immediately implementable on any atomic force microscopy platform and as such is expected to be a useful technique for probing spatiotemporal cantilever dynamics and mapping material properties, as well as their mutual interactions.

  9. G-mode magnetic force microscopy: Separating magnetic and electrostatic interactions using big data analytics

    Science.gov (United States)

    Collins, Liam; Belianinov, Alex; Proksch, Roger; Zuo, Tingting; Zhang, Yong; Liaw, Peter K.; Kalinin, Sergei V.; Jesse, Stephen

    2016-05-01

    In this work, we develop a full information capture approach for Magnetic Force Microscopy (MFM), referred to as generalized mode (G-Mode) MFM. G-Mode MFM acquires and stores the full data stream from the photodetector, captured at sampling rates approaching the intrinsic photodiode limit. The data can be subsequently compressed, denoised, and analyzed, without information loss. Here, G-Mode MFM is implemented and compared to the traditional heterodyne-based MFM on model systems, including domain structures in ferromagnetic Yttrium Iron Garnet and the electronically and magnetically inhomogeneous high entropy alloy, CoFeMnNiSn. We investigate the use of information theory to mine the G-Mode MFM data and demonstrate its usefulness for extracting information which may be hidden in traditional MFM modes, including signatures of nonlinearities and mode-coupling phenomena. Finally, we demonstrate detection and separation of magnetic and electrostatic tip-sample interactions from a single G-Mode image, by analyzing the entire frequency response of the cantilever. G-Mode MFM is immediately implementable on any atomic force microscopy platform and as such is expected to be a useful technique for probing spatiotemporal cantilever dynamics and mapping material properties, as well as their mutual interactions.

  10. Visual information gain and task asymmetry interact in bimanual force coordination and control.

    Science.gov (United States)

    Hu, Xiaogang; Newell, Karl M

    2011-08-01

    This study examined the question of whether and how the influence of visual information on force coordination patterns is dependent on the settings of a task asymmetry constraint. In a bimanual isometric force experiment, the task asymmetry was manipulated via imposing different coefficients on the index finger forces such that the weighted sum of the finger forces matched the target force. The environmental constraint was quantified by the visual performance error and was manipulated through the change of visual gain (number of pixels on the screen representing the unit of force). The constraint arising from the individual was quantified by the bilateral coupling effect (i.e., symmetric force production) between hands. The results revealed improved performance in terms of lower variability and performance error and more complex total force structure with higher visual gain. The influence of visual gain on the force coordination pattern, however, was found to be dependent on the task coefficients imposed on the finger forces. Namely, the force sharing between hands became more symmetric with high visual gain only when the right finger force had the higher coefficient, and an error-compensatory strategy was evident with high gain only when symmetric coefficients were imposed on the two fingers. The findings support the proposition that the motor coordination and control patterns are organized by the interactive influence of different categories of constraints where the functional influence of the information provided is dependent on the motor output.

  11. EU Integrated Tokamak Modelling (ITM) Task Force

    Institute of Scientific and Technical Information of China (English)

    A Becoulet

    2007-01-01

    @@ At the end of 2003, the European Fusion Development Agreement (EFDA) structure set-up a long-term European task force (TF) in charge of "co-ordinating the development of a coherent set of validated simulation tools for the purpose of benchmarking on existing tokamak experiments, with the ultimate aim of providing a comprehensive simulation package for ITER plasmas" [http://www.efda-taskforce-itm.org/].

  12. Surface mediated cooperative interactions of drugs enhance mechanical forces for antibiotic action

    Science.gov (United States)

    Ndieyira, Joseph W.; Bailey, Joe; Patil, Samadhan B.; Vögtli, Manuel; Cooper, Matthew A.; Abell, Chris; McKendry, Rachel A.; Aeppli, Gabriel

    2017-02-01

    The alarming increase of pathogenic bacteria that are resistant to multiple antibiotics is now recognized as a major health issue fuelling demand for new drugs. Bacterial resistance is often caused by molecular changes at the bacterial surface, which alter the nature of specific drug-target interactions. Here, we identify a novel mechanism by which drug-target interactions in resistant bacteria can be enhanced. We examined the surface forces generated by four antibiotics; vancomycin, ristomycin, chloroeremomycin and oritavancin against drug-susceptible and drug-resistant targets on a cantilever and demonstrated significant differences in mechanical response when drug-resistant targets are challenged with different antibiotics although no significant differences were observed when using susceptible targets. Remarkably, the binding affinity for oritavancin against drug-resistant targets (70 nM) was found to be 11,000 times stronger than for vancomycin (800 μM), a powerful antibiotic used as the last resort treatment for streptococcal and staphylococcal bacteria including methicillin-resistant Staphylococcus aureus (MRSA). Using an exactly solvable model, which takes into account the solvent and membrane effects, we demonstrate that drug-target interactions are strengthened by pronounced polyvalent interactions catalyzed by the surface itself. These findings further enhance our understanding of antibiotic mode of action and will enable development of more effective therapies.

  13. Surface mediated cooperative interactions of drugs enhance mechanical forces for antibiotic action

    Science.gov (United States)

    Ndieyira, Joseph W.; Bailey, Joe; Patil, Samadhan B.; Vögtli, Manuel; Cooper, Matthew A.; Abell, Chris; McKendry, Rachel A.; Aeppli, Gabriel

    2017-01-01

    The alarming increase of pathogenic bacteria that are resistant to multiple antibiotics is now recognized as a major health issue fuelling demand for new drugs. Bacterial resistance is often caused by molecular changes at the bacterial surface, which alter the nature of specific drug-target interactions. Here, we identify a novel mechanism by which drug-target interactions in resistant bacteria can be enhanced. We examined the surface forces generated by four antibiotics; vancomycin, ristomycin, chloroeremomycin and oritavancin against drug-susceptible and drug-resistant targets on a cantilever and demonstrated significant differences in mechanical response when drug-resistant targets are challenged with different antibiotics although no significant differences were observed when using susceptible targets. Remarkably, the binding affinity for oritavancin against drug-resistant targets (70 nM) was found to be 11,000 times stronger than for vancomycin (800 μM), a powerful antibiotic used as the last resort treatment for streptococcal and staphylococcal bacteria including methicillin-resistant Staphylococcus aureus (MRSA). Using an exactly solvable model, which takes into account the solvent and membrane effects, we demonstrate that drug-target interactions are strengthened by pronounced polyvalent interactions catalyzed by the surface itself. These findings further enhance our understanding of antibiotic mode of action and will enable development of more effective therapies. PMID:28155918

  14. A Force-Sensing System on Legs for Biomimetic Hexapod Robots Interacting with Unstructured Terrain.

    Science.gov (United States)

    Zhang, He; Wu, Rui; Li, Changle; Zang, Xizhe; Zhang, Xuehe; Jin, Hongzhe; Zhao, Jie

    2017-06-27

    The tiger beetle can maintain its stability by controlling the interaction force between its legs and an unstructured terrain while it runs. The biomimetic hexapod robot mimics a tiger beetle, and a comprehensive force sensing system combined with certain algorithms can provide force information that can help the robot understand the unstructured terrain that it interacts with. This study introduces a complicated leg force sensing system for a hexapod robot that is the same for all six legs. First, the layout and configuration of sensing system are designed according to the structure and sizes of legs. Second, the joint toque sensors, 3-DOF foot-end force sensor and force information processing module are designed, and the force sensor performance parameters are tested by simulations and experiments. Moreover, a force sensing system is implemented within the robot control architecture. Finally, the experimental evaluation of the leg force sensor system on the hexapod robot is discussed and the performance of the leg force sensor system is verified.

  15. Comparison of atomic force microscopy interaction forces between bacteria and silicon nitride substrata for three commonly used immobilization methods.

    Science.gov (United States)

    Vadillo-Rodríguez, Virginia; Busscher, Henk J; Norde, Willem; De Vries, Joop; Dijkstra, René J B; Stokroos, Ietse; Van Der Mei, Henny C

    2004-09-01

    Atomic force microscopy (AFM) has emerged as a powerful technique for mapping the surface morphology of biological specimens, including bacterial cells. Besides creating topographic images, AFM enables us to probe both physicochemical and mechanical properties of bacterial cell surfaces on a nanometer scale. For AFM, bacterial cells need to be firmly anchored to a substratum surface in order to withstand the friction forces from the silicon nitride tip. Different strategies for the immobilization of bacteria have been described in the literature. This paper compares AFM interaction forces obtained between Klebsiella terrigena and silicon nitride for three commonly used immobilization methods, i.e., mechanical trapping of bacteria in membrane filters, physical adsorption of negatively charged bacteria to a positively charged surface, and glutaraldehyde fixation of bacteria to the tip of the microscope. We have shown that different sample preparation techniques give rise to dissimilar interaction forces. Indeed, the physical adsorption of bacterial cells on modified substrata may promote structural rearrangements in bacterial cell surface structures, while glutaraldehyde treatment was shown to induce physicochemical and mechanical changes on bacterial cell surface properties. In general, mechanical trapping of single bacterial cells in filters appears to be the most reliable method for immobilization.

  16. A contoured continuum surface force model for particle methods

    Science.gov (United States)

    Duan, Guangtao; Koshizuka, Seiichi; Chen, Bin

    2015-10-01

    A surface tension model is essential to simulate multiphase flows with deformed interfaces. This study develops a contoured continuum surface force (CCSF) model for particle methods. A color function that varies sharply across the interface to mark different fluid phases is smoothed in the transition region, where the local contour curvature can be regarded as the interface curvature. The local contour passing through each reference particle in the transition region is extracted from the local profile of the smoothed color function. The local contour curvature is calculated based on the Taylor series expansion of the smoothed color function, whose derivatives are calculated accurately according to the definition of the smoothed color function. Two schemes are proposed to specify the smooth radius: fixed scheme, where 2 ×re (re = particle interaction radius) is assigned to all particles in the transition region; and varied scheme, where re and 2 ×re are assigned to the central and edged particles in the transition region respectively. Numerical examples, including curvature calculation for static circle and ellipse interfaces, deformation of square droplet to a circle (2D and 3D), droplet deformation in shear flow, and droplet coalescence, are simulated to verify the CCSF model and compare its performance with those of other methods. The CCSF model with the fixed scheme is proven to produce the most accurate curvature and lowest parasitic currents among the tested methods.

  17. Modeling the interaction of DNA with alternating fields

    CERN Document Server

    Bergues-Pupo, Ana Elisa; Falo, Fernando; 10.1103/PhysRevE.87.022703

    2013-01-01

    We study the influence of a THz field on thermal properties of DNA molecules. A Peyrard- Bishop-Dauxois model with the inclusion of a solvent interaction term is considered. The THz field is included as a sinusoidal driven force in the equation of mo tion. We show how under certain field and system parameters, melting transition and bubble formation are modified.

  18. Interaction of two walkers: wave-mediated energy and force.

    Science.gov (United States)

    Borghesi, Christian; Moukhtar, Julien; Labousse, Matthieu; Eddi, Antonin; Fort, Emmanuel; Couder, Yves

    2014-12-01

    A bouncing droplet, self-propelled by its interaction with the waves it generates, forms a classical wave-particle association called a "walker." Previous works have demonstrated that the dynamics of a single walker is driven by its global surface wave field that retains information on its past trajectory. Here we investigate the energy stored in this wave field for two coupled walkers and how it conveys an interaction between them. For this purpose, we characterize experimentally the "promenade modes" where two walkers are bound and propagate together. Their possible binding distances take discrete values, and the velocity of the pair depends on their mutual binding. The mean parallel motion can be either rectilinear or oscillating. The experimental results are recovered analytically with a simple theoretical framework. A relation between the kinetic energy of the droplets and the total energy of the standing waves is established.

  19. Force

    CERN Document Server

    Graybill, George

    2007-01-01

    Forces are at work all around us. Discover what a force is, and different kinds of forces that work on contact and at a distance. We use simple language and vocabulary to make this invisible world easy for students to ""see"" and understand. Examine how forces ""add up"" to create the total force on an object, and reinforce concepts and extend learning with sample problems.

  20. A Heuristic Force Model for Haptic Simulation of Nasogastric Tube Insertion Using Fuzzy Logic.

    Science.gov (United States)

    Choi, Kup-Sze; He, Xue-Jian; Chiang, Vico C L; Deng, Zhaohong; Qin, Jing

    2016-01-01

    Nasogastric tube (NGT) placement is an essential clinical skill. The training is conventionally performed on rubber mannequins albeit practical limitations. Computer simulation with haptic feedback can potentially offer a more realistic and accessible training method. However, the complex interactions between the tube and the nasogastric passage make it difficult to model the haptic feedback during NGT placement. In this paper, a fuzzy-logic-based approach is proposed to directly transfer the experience of clinicians in NGT placement into the simulation system. Based on their perception of the varying tactile sensation and the conditions during NGT placement, the membership functions and fuzzy rules are defined to develop the force model. Forces created using the model are then combined with friction forces to drive the haptic device and render the insertion forces in real time. A prototype simulator is developed based on the proposed force model and the implementation details are presented. The usability of the prototype is also evaluated by clinical teachers. The proposed methodology has the potential for developing computerized NGT placement training methods for clinical education. It is also applicable for simulation systems involving complicated force interactions or computation-expensive models.

  1. Particle-fluid interaction forces as the source of acceleration PDF invariance in particle size

    CERN Document Server

    Meller, Yosef

    2014-01-01

    The conditions allowing particle suspension in turbulent flow are of interest in many applications, but understanding them is complicated both by the nature of turbulence and by the interaction of flow with particles. Observations on small particles indicate an invariance of acceleration PDFs of small particles independent of size. We show to be true the postulated role of particle/fluid interaction forces in maintaining suspension. The 3D-PTV method, applied for two particle phases (tracers and inertial particles) simultaneously, was used to obtain velocity and acceleration data, and through the use of the particle's equation of motion the magnitude of forces representing either the flow or the particle interaction were derived and compared. The invariance of PDFs is shown to extend to the component forces, and lift forces are shown to be significant.

  2. Students' Understanding on Newton's Third Law in Identifying the Reaction Force in Gravity Interactions

    Science.gov (United States)

    Zhou, Shaona; Zhang, Chunbin; Xiao, Hua

    2015-01-01

    In the past three decades, previous researches showed that students had various misconceptions of Newton's Third Law. The present study focused on students' difficulties in identifying the third-law force pair in gravity interaction situations. An instrument involving contexts with gravity and non-gravity associated interactions was designed and…

  3. Students' Understanding on Newton's Third Law in Identifying the Reaction Force in Gravity Interactions

    Science.gov (United States)

    Zhou, Shaona; Zhang, Chunbin; Xiao, Hua

    2015-01-01

    In the past three decades, previous researches showed that students had various misconceptions of Newton's Third Law. The present study focused on students' difficulties in identifying the third-law force pair in gravity interaction situations. An instrument involving contexts with gravity and non-gravity associated interactions was designed and…

  4. Adhesion forces in interactive mixtures for dry powder inhalers--evaluation of a new measuring method.

    Science.gov (United States)

    Lohrmann, Maike; Kappl, Michael; Butt, Hans-Juergen; Urbanetz, Nora Anne; Lippold, Bernhard Christian

    2007-09-01

    Dry powder inhalers mostly contain carrier based formulations where micronized drug particles are adhered to coarse carrier particles. The performance of the dry powder inhaler depends on the inhaler device, the inhalation manoeuvre and the formulation. The most important factor influencing the behaviour of the formulation is the adhesion force acting between the active ingredient and the carrier particles, which can be measured using different methods, for example the centrifuge technique or atomic force microscopy. In this study the tensile strength method, usually applied to determine cohesion forces between powder particles of one material, is optimized for adhesion force measurements between powder particles of unlike materials. Adhesion force measurements between the carrier materials lactose or mannitol and the drug substance salbutamol sulphate using the tensile strength method and the atomic force microscopy show higher values with increasing relative humidity. Consequently, the fine particle fraction determined using the Next Generation Impactor decreases with increasing relative humidity as a result of the enhanced interparticle interactions.

  5. Stability of GOY Model Under Modulation of Periodic External Force

    Institute of Scientific and Technical Information of China (English)

    ZHAO Ying-Kui; CHEN Shi-Gang; WANG Guang-Rui

    2008-01-01

    There is a phase transition between quasi-periodic state and intermittent chaos in GOY model with a critical value δ0. When we add a modulated periodic external force to the system, the phase transition can also be found with a critical value δe. Due to coupling between the force and the intrinsic fluctuation of the velocity on shells in GOY model, the stability of the system has been changed, which results in the variation of the critical value. For proper intensity and period of the force, δe is unequal to δ0. The critical value is a nonlinear function of amplitude of the force, and the fluctuation of the velocity can resonate with the external force for certain period Te.

  6. Dependency of micro particle adhesion of dispersive and nondispersive interactions analyzed by atomic force microscopy

    CERN Document Server

    Kawal, A; Andoh, E

    1999-01-01

    The adhesion behaviour of a micro semi-sphere tip (radius of curvature of 18 nm) after making contact with various inorganic solid surfaces is analyzed. Measurement force by the AFM tip corresponds to the interactive force estimated $9 using surface energy components, dispersion and nondispersion, based on van der Waal's interaction. These components can be obtained by measuring the contact angle of standard liquids on a material surface. By using two kinds of tip $9 with different component values, analysis of the interactive mechanism and prediction of macro tip (particle) adhesion can be made. (6 refs).

  7. Deciphering the energy landscape of the interaction uranyl-DCP with antibodies using dynamic force spectroscopy.

    Science.gov (United States)

    Teulon, Jean-Marie; Parot, Pierre; Odorico, Michael; Pellequer, Jean-Luc

    2008-11-15

    Previous studies on molecular recognition of uranyl-DCP (dicarboxy-phenanthroline chelator) compound by two distinct monoclonal antibodies (Mabs U04S and U08S) clearly showed the presence of a biphasic shape in Bell-Evans' plots and an accentuated difference in slopes at the high loading rates. To further explore the basis in the slope difference, we have performed complementary experiments using antibody PHE03S, raised against uranyl-DCP but, presenting a strong cross-reactivity toward the DCP chelator. This work allowed us to obtain a reallocation of the respective contributions of the metal ion itself and that of the chelator. Results led us to propose a 2D schematic model representing two energy barriers observed in the systems Mabs U04S- and U08S-[UO(2)-DCP] where the outer barrier characterizes the interaction between UO(2) and Mab whereas the inner barrier characterizes the interaction between DCP and Mab. Using dynamic force spectroscopy, it is thus possible to dissect molecular interactions during the unbinding between proteins and ligands.

  8. The Experience of Force: The Role of Haptic Experience of Forces in Visual Perception of Object Motion and Interactions, Mental Simulation, and Motion-Related Judgments

    Science.gov (United States)

    White, Peter A.

    2012-01-01

    Forces are experienced in actions on objects. The mechanoreceptor system is stimulated by proximal forces in interactions with objects, and experiences of force occur in a context of information yielded by other sensory modalities, principally vision. These experiences are registered and stored as episodic traces in the brain. These stored…

  9. Consideration of nonlinear wheel-rail contact forces for dynamic vehicle-bridge interaction in high-speed railways

    Science.gov (United States)

    Antolín, Pablo; Zhang, Nan; Goicolea, José M.; Xia, He; Astiz, Miguel Á.; Oliva, Javier

    2013-03-01

    In this work models with nonlinear wheel-rail contact forces are considered for analysing the dynamic interaction between high speed trains and bridges, in order to study dynamic effects both in the bridge and in the vehicles resulting from the coupling. Nonlinear contact models may be necessary for evaluating the stability and the safety of running traffic in situations such as vehicle overturn when the train is crossing a bridge under strong lateral winds or when an earthquake occurs. For studying the coupled dynamic response of trains and bridges, models of multibody dynamics are used for vehicles and the finite element method for structures. Special relevance is given here to the consideration of contact interaction forces between railway vehicles and the track. Four different interaction models are compared in this work: (1) a model where the vehicle wheelset is considered to be rigidly coupled to the track; (2) a staggered uncoupled method in which vehicle and structure are analysed separately; (3) a linear contact model in which lateral relative displacements between rails and train wheels are allowed, assuming biconic wheel and rail profiles and linear Kalker theory for tangential contact; (4) a nonlinear model in which realistic wheel and rail profiles, Hertz's nonlinear theory for normal contact and Kalker's nonlinear theory for tangential contact are used. The different models are applied and compared to experimental measurements for a test case of a high-speed train in China.

  10. Molecular model for force production and transmission during vertebrate gastrulation.

    Science.gov (United States)

    Pfister, Katherine; Shook, David R; Chang, Chenbei; Keller, Ray; Skoglund, Paul

    2016-02-15

    Vertebrate embryos undergo dramatic shape changes at gastrulation that require locally produced and anisotropically applied forces, yet how these forces are produced and transmitted across tissues remains unclear. We show that depletion of myosin regulatory light chain (RLC) levels in the embryo blocks force generation at gastrulation through two distinct mechanisms: destabilizing the myosin II (MII) hexameric complex and inhibiting MII contractility. Molecular dissection of these two mechanisms demonstrates that normal convergence force generation requires MII contractility and we identify a set of molecular phenotypes correlated with both this failure of convergence force generation in explants and of blastopore closure in whole embryos. These include reduced rates of actin movement, alterations in C-cadherin dynamics and a reduction in the number of polarized lamellipodia on intercalating cells. By examining the spatial relationship between C-cadherin and actomyosin we also find evidence for formation of transcellular linear arrays incorporating these proteins that could transmit mediolaterally oriented tensional forces. These data combine to suggest a multistep model to explain how cell intercalation can occur against a force gradient to generate axial extension forces. First, polarized lamellipodia extend mediolaterally and make new C-cadherin-based contacts with neighboring mesodermal cell bodies. Second, lamellipodial flow of actin coalesces into a tension-bearing, MII-contractility-dependent node-and-cable actin network in the cell body cortex. And third, this actomyosin network contracts to generate mediolateral convergence forces in the context of these transcellular arrays.

  11. Numerical derivation of the drag force coefficient in bubble swarms using a Front Tracking model

    NARCIS (Netherlands)

    Dijkhuizen, W.; Roghair, I.; van Sint Annaland, M.; Kuipers, J.A.M.

    2008-01-01

    Dispersed gas-liquid flows are often encountered in the chemical process industry. Large scale models which describe the overall behavior of these flows use closure relations to account for the interactions between the phases, such as the drag, lift and virtual mass forces. The closure relations for

  12. Jamming transitions in force-based models for pedestrian dynamics

    CERN Document Server

    Chraibi, Mohcine; Tordeux, Antoine; Nishinari, Katsuhiro; Schadschneider, Andreas; Seyfried, Armin

    2015-01-01

    Force-based models describe pedestrian dynamics in analogy to classical mechanics by a system of second order ordinary differential equations. By investigating the linear stability of two main classes of forces, parameter regions with unstable homogeneous states are identified. In this unstable regime it is then checked whether phase transitions or stop-and-go waves occur. Results based on numerical simulations show, however, that the investigated models lead to unrealistic behavior in form of backwards moving pedestrians and overlapping. This is one reason why stop-and-go waves have not been observed in these models. The unrealistic behavior is not related to the numerical treatment of the dynamic equations but rather indicates an intrinsic problem of this model class. Identifying the underlying generic problems gives indications how to define models that do not show such unrealistic behavior. As an example we introduce a new force-based model which produces realistic jam dynamics without the appearance of u...

  13. Mapping the distribution of specific antibody interaction forces on individual red blood cells

    Science.gov (United States)

    Yeow, Natasha; Tabor, Rico F.; Garnier, Gil

    2017-01-01

    Current blood typing methods rely on the agglutination of red blood cells (RBCs) to macroscopically indicate a positive result. An indirect agglutination mechanism is required when blood typing with IgG forms of antibodies. To date, the interaction forces between anti-IgG and IgG antibodies have been poorly quantified, and blood group related antigens have never been quantified with the atomic force microscope (AFM). Instead, the total intensity resulting from fluorescent-tagged antibodies adsorbed on RBC has been measured to calculate an average antigen density on a series of RBCs. In this study we mapped specific antibody interaction forces on the RBC surface. AFM cantilever tips functionalized with anti-IgG were used to probe RBCs incubated with specific IgG antibodies. This work provides unique insight into antibody-antigen interactions in their native cell-bound location, and crucially, on a per-cell basis rather than an ensemble average set of properties. Force profiles obtained from the AFM directly provide not only the anti-IgG – IgG antibody interaction force, but also the spatial distribution and density of antigens over a single cell. This new understanding might be translated into the development of very selective and quantitative interactions that underpin the action of drugs in the treatment of frontier illnesses. PMID:28157207

  14. Mapping the distribution of specific antibody interaction forces on individual red blood cells

    Science.gov (United States)

    Yeow, Natasha; Tabor, Rico F.; Garnier, Gil

    2017-02-01

    Current blood typing methods rely on the agglutination of red blood cells (RBCs) to macroscopically indicate a positive result. An indirect agglutination mechanism is required when blood typing with IgG forms of antibodies. To date, the interaction forces between anti-IgG and IgG antibodies have been poorly quantified, and blood group related antigens have never been quantified with the atomic force microscope (AFM). Instead, the total intensity resulting from fluorescent-tagged antibodies adsorbed on RBC has been measured to calculate an average antigen density on a series of RBCs. In this study we mapped specific antibody interaction forces on the RBC surface. AFM cantilever tips functionalized with anti-IgG were used to probe RBCs incubated with specific IgG antibodies. This work provides unique insight into antibody-antigen interactions in their native cell-bound location, and crucially, on a per-cell basis rather than an ensemble average set of properties. Force profiles obtained from the AFM directly provide not only the anti-IgG – IgG antibody interaction force, but also the spatial distribution and density of antigens over a single cell. This new understanding might be translated into the development of very selective and quantitative interactions that underpin the action of drugs in the treatment of frontier illnesses.

  15. Acoustic Interaction Forces and Torques Acting on Suspended Spheres in an Ideal Fluid.

    Science.gov (United States)

    Lopes, J Henrique; Azarpeyvand, Mahdi; Silva, Glauber T

    2016-01-01

    In this paper, the acoustic interaction forces and torques exerted by an arbitrary time-harmonic wave on a set of N objects suspended in an inviscid fluid are theoretically analyzed. We utilize the partial-wave expansion method with translational addition theorem and re-expansion of multipole series to solve the related multiple scattering problem. We show that the acoustic interaction force and torque can be obtained using the farfield radiation force and torque formulas. To exemplify the method, we calculate the interaction forces exerted by an external traveling and standing plane wave on an arrangement of two and three olive-oil droplets in water. The droplets' radii are comparable to the wavelength (i.e., Mie scattering regime). The results show that the acoustic interaction forces present an oscillatory spatial distribution which follows the pattern formed by interference between the external and rescattered waves. In addition, acoustic interaction torques arise on the absorbing droplets whenever a nonsymmetric wavefront is formed by the external and rescattered waves' interference.

  16. Hydroacoustic forcing function modeling using DNS database

    Science.gov (United States)

    Zawadzki, I.; Gershfield, J. L.; Na, Y.; Wang, M.

    1996-01-01

    A wall pressure frequency spectrum model (Blake 1971 ) has been evaluated using databases from Direct Numerical Simulations (DNS) of a turbulent boundary layer (Na & Moin 1996). Good agreement is found for moderate to strong adverse pressure gradient flows in the absence of separation. In the separated flow region, the model underpredicts the directly calculated spectra by an order of magnitude. The discrepancy is attributed to the violation of the model assumptions in that part of the flow domain. DNS computed coherence length scales and the normalized wall pressure cross-spectra are compared with experimental data. The DNS results are consistent with experimental observations.

  17. Kinetics of the multistep rupture of fibrin 'A-a' polymerization interactions measured using atomic force microscopy.

    Science.gov (United States)

    Averett, Laurel E; Schoenfisch, Mark H; Akhremitchev, Boris B; Gorkun, Oleg V

    2009-11-18

    Fibrin, the structural scaffold of blood clots, spontaneously polymerizes through the formation of 'A-a' knob-hole bonds. When subjected to external force, the dissociation of this bond is accompanied by two to four abrupt changes in molecular dimension observable as rupture events in a force curve. Herein, the configuration, molecular extension, and kinetic parameters of each rupture event are examined. The increases in contour length indicate that the D region of fibrinogen can lengthen by approximately 50% of the length of a fibrin monomer before rupture of the 'A-a' interaction. The dependence of the dissociation rate on applied force was obtained using probability distributions of rupture forces collected at different pull-off velocities. These distributions were fit using a model in which the effects of the shape of the binding potential are used to quantify the kinetic parameters of forced dissociation. We found that the weak initial rupture (i.e., event 1) was not well approximated by these models. The ruptured bonds comprising the strongest ruptures, events 2 and 3, had kinetic parameters similar to those commonly found for the mechanical unfolding of globular proteins. The bonds ruptured in event 4 were well described by these analyses, but were more loosely bound than the bonds in events 2 and 3. We propose that the first event represents the rupture of an unknown interaction parallel to the 'A-a' bond, events 2 and 3 represent unfolding of structures in the D region of fibrinogen, and event 4 is the rupture of the 'A-a' knob-hole bond weakened by prior structural unfolding. Comparison of the activation energy obtained via force spectroscopy measurements with the thermodynamic free energy of 'A-a' bond dissociation indicates that the 'A-a' bond may be more resistant to rupture by applied force than to rupture by thermal dissociation.

  18. Evaluation of medicine effects on the interaction of myoglobin and its aptamer or antibody using atomic force microscopy.

    Science.gov (United States)

    Wang, Qing; Liu, Lin; Yang, Xiaohai; Wang, Kemin; Chen, Nandi; Zhou, Chenchen; Luo, Bianxia; Du, Shasha

    2015-02-17

    The effects of medicine on the biomolecular interaction have been given increasing attention in biochemistry and affinity-based analytics since the environment in vivo is complex especially for the patients. Herein, myoglobin, a biomarker of acute myocardial infarction, was used as a model, and the medicine effects on the interactions of myoglobin/aptamer and myoglobin/antibody were systematically investigated using atomic force microscopy (AFM) for the first time. The results showed that the average binding force and the binding probability of myoglobin/aptamer almost remained unchanged after myoglobin-modified gold substrate was incubated with promazine, amoxicillin, aspirin, and sodium penicillin, respectively. These parameters were changed for myoglobin/antibody after the myoglobin-modified gold substrate was treated with these medicines. For promazine and amoxicillin, they resulted in the change of binding force distribution of myoglobin/antibody (i.e., from unimodal distribution to bimodal distribution) and the increase of binding probability; for aspirin, it only resulted in the change of the binding force distribution, and for sodium penicillin, it resulted in the increase of the average binding force and the binding probability. These results may be attributed to the different interaction modes and binding sites between myoglobin/aptamer and myoglobin/antibody, the different structures between aptamer and antibody, and the effects of medicines on the conformations of myoglobin. These findings could enrich our understanding of medicine effects on the interactions of aptamer and antibody to their target proteins. Moreover, this work will lay a good foundation for better research and extensive applications of biomolecular interaction, especially in the design of biosensors in complex systems.

  19. Measurement of interaction force between RGD-peptide and Hela cell surface by optical tweezers

    Institute of Scientific and Technical Information of China (English)

    Mincheng Zhong; Guosheng Xue; Jinhua Zhou; Ziqiang Wang; Yinmei Li

    2012-01-01

    Since RGD peptides (R:arginine; G:glycine; D:aspartic acid) are found to promote cell adhesion,they are modified at numerous materials surface for medical applications such as drug delivery and regenerative medicine.Peptide-cell surface interactions play a key role in the above applications.In this letter,we study the adhesion force between the RGD-coated bead and Hela cell surface by optical tweezes.The adhesion is dominated by the binding of α5β1 and RGD-peptide with higher adhesion probability and stronger adhesion strength compared with the adhesion of bare bead and cell surface.The binding force for a single α5β1-GRGDSP pair is determined to be 16.8 pN at a loading rate of 1.5 nN/s.The unstressed off-rate is 1.65 × 10-2 s-1 and the distance of transition state for the rigid binding model is 3.0 nm.

  20. New Cutting Force Modeling Approach for Flat End Mill

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A new mechanistic cutting force model for flat end milling using the instantaneous cutting force coefficients is proposed. An in-depth analysis shows that the total cutting forces can be separated into two terms: a nominal component independent of the runout and a perturbation component induced by the runout. The instantaneous value of the nominal component is used to calibrate the cutting force coefficients. With the help of the perturbation component and the cutting force coeffcients obtained above, the cutter runout is identified.Based on simulation and experimental results, the validity of the identification approach is demonstrated. The advantage of the proposed method lies in that the calibration performed with data of one cutting test under a specific regime can be applied for a great range of cutting conditions.

  1. Needle-Tissue Interaction Forces for Bevel-Tip Steerable Needles

    Science.gov (United States)

    Misra, Sarthak; Reed, Kyle B.; Douglas, Andrew S.; Ramesh, K. T.; Okamura, Allison M.

    2010-01-01

    The asymmetry of a bevel-tip needle results in the needle naturally bending when it is inserted into soft tissue. As a first step toward modeling the mechanics of deflection of the needle, we determine the forces at the bevel tip. In order to find the forces acting at the needle tip, we measure rupture toughness and nonlinear material elasticity parameters of several soft tissue simulant gels and chicken tissue. We incorporate these physical parameters into a finite element model that includes both contact and cohesive zone models to simulate tissue cleavage. We investigate the sensitivity of the tip forces to tissue rupture toughness, linear and nonlinear tissue elasticity, and needle tip bevel angle. The model shows that the tip forces are sensitive to the rupture toughness. The results from these studies contribute to a mechanics-based model of bevel-tip needle steering, extending previous work on kinematic models. PMID:22020139

  2. Needle-Tissue Interaction Forces for Bevel-Tip Steerable Needles.

    Science.gov (United States)

    Misra, Sarthak; Reed, Kyle B; Douglas, Andrew S; Ramesh, K T; Okamura, Allison M

    2008-10-19

    The asymmetry of a bevel-tip needle results in the needle naturally bending when it is inserted into soft tissue. As a first step toward modeling the mechanics of deflection of the needle, we determine the forces at the bevel tip. In order to find the forces acting at the needle tip, we measure rupture toughness and nonlinear material elasticity parameters of several soft tissue simulant gels and chicken tissue. We incorporate these physical parameters into a finite element model that includes both contact and cohesive zone models to simulate tissue cleavage. We investigate the sensitivity of the tip forces to tissue rupture toughness, linear and nonlinear tissue elasticity, and needle tip bevel angle. The model shows that the tip forces are sensitive to the rupture toughness. The results from these studies contribute to a mechanics-based model of bevel-tip needle steering, extending previous work on kinematic models.

  3. Interacting trophic forcing and the population dynamics of herring

    DEFF Research Database (Denmark)

    Lindegren, Martin; Ostman, Orjan; Gardmark, Anna

    2011-01-01

    Small pelagic fish occupy a central position in marine ecosystems worldwide, largely by determining the energy transfer from lower trophic levels to predators at the top of the food web, including humans. Population dynamics of small pelagic fish may therefore be regulated neither strictly bottom......-up nor top-down, but rather through multiple external and internal drivers. While in many studies single drivers have been identified, potential synergies of multiple factors, as well as their relative importance in regulating population dynamics of small pelagic fish, is a largely unresolved issue....... Using a statistical, age-structured modeling approach, we demonstrate the relative importance and influence of bottom-up (e.g., climate, zooplankton availability) and top-down (i.e., fishing and predation) factors on the population dynamics of Bothnian Sea herring (Clupea harengus) throughout its life...

  4. The role of the ion-molecule and molecule-molecule interactions in the formation of the two-ion average force interaction potential

    CERN Document Server

    Ajrian, E A; Sidorenko, S N

    2002-01-01

    The effect of the ion-molecule and intermolecular interactions on the formation of inter-ion average force potentials is investigated within the framework of a classical ion-dipole model of electrolyte solutions. These potentials are shown to possess the Coulomb asymptotics at large distances while in the region of mean distances they reveal creation and disintegration of solvent-shared ion pairs. The calculation results provide a qualitatively authentic physical picture which is experimentally observed in strong electrolytes solutions. In particular, an increased interaction between an ion and a molecule enhances formation of ion pairs in which the ions are separated by one solvent molecule

  5. Probing the interaction of individual amino acids with inorganic surfaces using atomic force spectroscopy.

    Science.gov (United States)

    Razvag, Yair; Gutkin, Vitaly; Reches, Meital

    2013-08-13

    This article describes single-molecule force spectroscopy measurements of the interaction between individual amino acid residues and inorganic surfaces in an aqueous solution. In each measurement, there is an amino acid residue, lysine, glutamate, phenylalanine, leucine, or glutamine, and each represents a class of amino acids (positively or negatively charged, aromatic, nonpolar, and polar). Force-distance curves measured the interaction of the individual amino acid bound to a silicon atomic force microscope (AFM) tip with a silcon substrate, cut from a single-crystal wafer, or mica. Using this method, we were able to measure low adhesion forces (below 300 pN) and could clearly determine the strength of interactions between the individual amino acid residues and the inorganic substrate. In addition, we observed how changes in the pH and ionic strength of the solution affected the adsorption of the residues to the substrates. Our results pinpoint the important role of hydrophobic interactions among the amino acids and the substrate, where hydrophobic phenylalanine exhibited the strongest adhesion to a silicon substrate. Additionally, electrostatic interactions also contributed to the adsorption of amino acid residues to inorganic substrates. A change in the pH or ionic strength values of the buffer altered the strength of interactions among the amino acids and the substrate. We concluded that the interplay between the hydrophobic forces and electrostatic interactions will determine the strength of adsorption among the amino acids and the surface. Overall, these results contribute to our understanding of the interaction at the organic-inorganic interface. These results may have implications for our perception of the specificity of peptide binding to inorganic surfaces. Consequently, it would possibly lead to a better design of composite materials and devices.

  6. Evolution of Neogene Mammals in Eurasia: Environmental Forcing and Biotic Interactions

    Science.gov (United States)

    Fortelius, Mikael; Eronen, Jussi T.; Kaya, Ferhat; Tang, Hui; Raia, Pasquale; Puolamäki, Kai

    2014-05-01

    The relative weights of physical forcing and biotic interaction as drivers of evolutionary change have been debated in evolutionary theory. The recent finding that species, genera, clades, and chronofaunas all appear to exhibit a symmetrical pattern of waxing and waning lends support to the view that biotic interactions shape the history of life. Yet, there is similarly abundant evidence that these primary units of biological evolution arise and wane in coincidence with major climatic change. We review these patterns and the process-level explanations offered for them. We also propose a tentative synthesis, characterized by interdependence between physical forcing and biotic interactions. We suggest that species with evolutionary novelties arise predominantly in "species factories" that develop under harsh environmental conditions, under dominant physical forcing, whereas exceptionally mild environments give rise to "oases in the desert," characterized by strong competition and survival of relics.

  7. Measurement of interaction force between small distances sandwiched with magnetic fluid under magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    Miyazaki, T.; Shibayama, A.; Sato, T.; Fujita, T. E-mail: fujita@ipc.akita-u.ac.jp

    2002-11-01

    In this contribution, the interactive force measurement between 10 nm distance under magnetic field is carried out. Previous measurement of the interactive force is reported by Israelachivili et al. However, its measurement under magnetic field has not been performed. The methodology described in this paper is easier as the distance between two surfaces is not measured optically but dynamically. Therefore, it is different from the previous reported studies. Based on the results of the measurement of the interactive force, the diameter of the particle suspended in a solution under magnetic field is also estimated. Moreover, it may be predictable how the clusters have been formed. The method described will be very useful for new productions based on magnetic fluid.

  8. Probing the interactions between lignin and inorganic oxides using atomic force microscopy

    Science.gov (United States)

    Wang, Jingyu; Qian, Yong; Deng, Yonghong; Liu, Di; Li, Hao; Qiu, Xueqing

    2016-12-01

    Understanding the interactions between lignin and inorganic oxides has both fundamental and practical importance in industrial and energy fields. In this work, the specific interactions between alkali lignin (AL) and three inorganic oxide substrates in aqueous environment are quantitatively measured using atomic force microscopy (AFM). The results show that the average adhesion force between AL and metal oxide such as Al2O3 or MgO is nearly two times bigger than that between AL and nonmetal oxide such as SiO2 due to the electrostatic difference and cation-π interaction. When 83% hydroxyl groups of AL is blocked by acetylation, the adhesion forces between AL and Al2O3, MgO and SiO2 decrease 43, 35 and 75% respectively, which indicate hydrogen bonds play an important role between AL and inorganic oxides, especially in AL-silica system.

  9. The short range anion-H interaction is the driving force for crystal formation of ions in water.

    Science.gov (United States)

    Alejandre, José; Chapela, Gustavo A; Bresme, Fernando; Hansen, Jean-Pierre

    2009-05-07

    The crystal formation of NaCl in water is studied by extensive molecular dynamics simulations. Ionic solutions at room temperature and various concentrations are studied using the SPC/E and TIP4P/2005 water models and seven force fields of NaCl. Most force fields of pure NaCl fail to reproduce the experimental density of the crystal, and in solution some favor dissociation at saturated conditions, while others favor crystal formation at low concentration. A new force field of NaCl is proposed, which reproduces the experimental phase diagram in the solid, liquid, and vapor regions. This force field overestimates the solubility of NaCl in water at saturation conditions when used with standard Lorentz-Berthelot combining rules for the ion-water pair potentials. It is shown that precipitation of ions is driven by the short range interaction between Cl-H pairs, a term which is generally missing in the simulation of ionic solutions. The effects of intramolecular flexibility of water on the solubility of NaCl ions are analyzed and is found to be small compared to rigid models. A flexible water model, extending the rigid SPC/E, is proposed, which incorporates Lennard-Jones interactions centered on the hydrogen atoms. This force field gives liquid-vapor coexisting densities and surface tensions in better agreement with experimental data than the rigid SPC/E model. The Cl-H, Na-O, and Cl-O pair distribution functions of the rigid and flexible models agree well with experiment. The predicted concentration dependence of the electric conductivity is in fair agreement with available experimental data.

  10. Double diffusivity model under stochastic forcing

    Science.gov (United States)

    Chattopadhyay, Amit K.; Aifantis, Elias C.

    2017-05-01

    The "double diffusivity" model was proposed in the late 1970s, and reworked in the early 1980s, as a continuum counterpart to existing discrete models of diffusion corresponding to high diffusivity paths, such as grain boundaries and dislocation lines. It was later rejuvenated in the 1990s to interpret experimental results on diffusion in polycrystalline and nanocrystalline specimens where grain boundaries and triple grain boundary junctions act as high diffusivity paths. Technically, the model pans out as a system of coupled Fick-type diffusion equations to represent "regular" and "high" diffusivity paths with "source terms" accounting for the mass exchange between the two paths. The model remit was extended by analogy to describe flow in porous media with double porosity, as well as to model heat conduction in media with two nonequilibrium local temperature baths, e.g., ion and electron baths. Uncoupling of the two partial differential equations leads to a higher-ordered diffusion equation, solutions of which could be obtained in terms of classical diffusion equation solutions. Similar equations could also be derived within an "internal length" gradient (ILG) mechanics formulation applied to diffusion problems, i.e., by introducing nonlocal effects, together with inertia and viscosity, in a mechanics based formulation of diffusion theory. While being remarkably successful in studies related to various aspects of transport in inhomogeneous media with deterministic microstructures and nanostructures, its implications in the presence of stochasticity have not yet been considered. This issue becomes particularly important in the case of diffusion in nanopolycrystals whose deterministic ILG-based theoretical calculations predict a relaxation time that is only about one-tenth of the actual experimentally verified time scale. This article provides the "missing link" in this estimation by adding a vital element in the ILG structure, that of stochasticity, that takes into

  11. Force/position control of a robot manipulator for human-robot interaction

    Directory of Open Access Journals (Sweden)

    Neranon Paramin

    2016-01-01

    Full Text Available With regard to both human and robot capabilities, human-robot interaction provides several benefits, and this will be significantly developed and implemented. This work focuses on the development of real-time external force/position control used for human-robot interaction. The force-controlled robotic system integrated with proportional integral control was performed and evaluated to ensure its reliably and timely operational characteristics, in which appropriate proportional integral gains were experimentally adopted using a set of virtual crank-turning tests. The designed robotic system is made up of a robot manipulator arm, an ATI Gamma multi-axis force/torque sensor and a real-time external PC based control system. A proportional integral controller has been developed to provide stable and robust force control on unknown environmental stiffness and motion. To quantify its effectiveness, the robotic system has been verified through a comprehensive set of experiments, in which force measurement and ALTER real-time path control systems were evaluated. In summary, the results indicated satisfactorily stable performance of the robot force/position control system. The gain tuning for proportional plus integral control algorithm was successfully implemented. It can be reported that the best performance as specified by the error root mean square method of the radial force is observed with proportional and integral gains of 0.10 and 0.005 respectively.

  12. Dynamic force spectroscopy on multiple bonds: experiments and model

    CERN Document Server

    Erdmann, T; Nassoy, P; Schwarz, U S

    2007-01-01

    We probe the dynamic strength of multiple biotin-streptavidin adhesion bonds under linear loading using the biomembrane force probe setup for dynamic force spectroscopy. Measured rupture force histograms are compared to results from a master equation model for the stochastic dynamics of bond rupture under load. This allows us to extract the distribution of the number of initially closed bonds. We also extract the molecular parameters of the adhesion bonds, in good agreement with earlier results from single bond experiments. Our analysis shows that the peaks in the measured histograms are not simple multiples of the single bond values, but follow from a superposition procedure which generates different peak positions.

  13. Modeling of Dynamic Fluid Forces in Fast Switching Valves

    DEFF Research Database (Denmark)

    Roemer, Daniel Beck; Johansen, Per; Pedersen, Henrik Clemmensen

    2015-01-01

    Switching valves experience opposing fluid forces due to movement of the moving member itself, as the surrounding fluid volume must move to accommodate the movement. This movement-induced fluid force may be divided into three main components; the added mass term, the viscous term and the socalled...... is given using an analytically solvable example, showing the explicit form of the force terms and highlighting the significance of the added mass and history term in certain fast switching valve applications. A general approximate model for arbitrary valve geometries is then proposed with offset...

  14. Single-cell force spectroscopy of the medically important Staphylococcus epidermidis-Candida albicans interaction

    Science.gov (United States)

    Beaussart, Audrey; Herman, Philippe; El-Kirat-Chatel, Sofiane; Lipke, Peter N.; Kucharíková, Soňa; van Dijck, Patrick; Dufrêne, Yves F.

    2013-10-01

    Despite the clinical importance of bacterial-fungal interactions, their molecular details are poorly understood. A hallmark of such medically important interspecies associations is the interaction between the two nosocomial pathogens Staphylococcus aureus and Candida albicans, which can lead to mixed biofilm-associated infections with enhanced antibiotic resistance. Here, we use single-cell force spectroscopy (SCFS) to quantify the forces engaged in bacterial-fungal co-adhesion, focusing on the poorly investigated S. epidermidis-C. albicans interaction. Force curves recorded between single bacterial and fungal germ tubes showed large adhesion forces (~5 nN) with extended rupture lengths (up to 500 nm). By contrast, bacteria poorly adhered to yeast cells, emphasizing the important role of the yeast-to-hyphae transition in mediating adhesion to bacterial cells. Analysis of mutant strains altered in cell wall composition allowed us to distinguish the main fungal components involved in adhesion, i.e. Als proteins and O-mannosylations. We suggest that the measured co-adhesion forces are involved in the formation of mixed biofilms, thus possibly as well in promoting polymicrobial infections. In the future, we anticipate that this SCFS platform will be used in nanomedicine to decipher the molecular mechanisms of a wide variety of pathogen-pathogen interactions and may help in designing novel anti-adhesion agents.

  15. Forces Mobilization Model (FORCEMOB): Unclassified Training Tutorial

    Science.gov (United States)

    2015-08-01

    industrial output occur 6. Models the use of emergency investment to redress shortfalls; computes investment demand iv Table 1. FORCEMOB Input...use of emergency investment to redress shortfalls and compute emergency investment demand  This section will give a high level overview of how...this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data

  16. Volcanic tremors and magma wagging: gas flux interactions and forcing mechanism

    Science.gov (United States)

    Bercovici, David; Jellinek, A. Mark; Michaut, Chloé; Roman, Diana C.; Morse, Robert

    2013-11-01

    Volcanic tremor is an important precursor to explosive eruptions and is ubiquitous across most silicic volcanic systems. Oscillations can persist for days and occur in a remarkably narrow frequency band (i.e. 0.5-7 Hz). The recently proposed magma-wagging model of Jellinek & Bercovici provides a basic explanation for the emergence and frequency evolution of tremor that is consistent with observations of many active silicic and andesitic volcanic systems. This model builds on work suggesting that the magma column rising in the volcanic conduit is surrounded by a permeable vesicular annulus of sheared bubbles. The magma-wagging model stipulates that the magma column rattles within the spring like foam of the annulus, and predicts oscillations at the range of observed tremor frequencies for a wide variety of volcanic environments. However, the viscous resistance of the magma column attenuates the oscillations and thus a forcing mechanism is required. Here we provide further development of the magma-wagging model and demonstrate that it implicitly has the requisite forcing to excite wagging behaviour. In particular, the extended model allows for gas flux through the annulus, which interacts with the wagging displacements and induces a Bernoulli effect that amplifies the oscillations. This effect leads to an instability involving growing oscillations at the lower end of the tremor frequency spectrum, and that drives the system against viscous damping of the wagging magma column. The fully non-linear model displays tremor oscillations associated with pulses in gas flux, analogous to observations of audible `chugging'. These oscillations also occur in clusters or envelopes that are consistent with observations of sporadic tremor envelopes. The wagging model further accurately predicts that seismic signals on opposite sides of a volcano are out of phase by approximately half a wagging or tremor period. Finally, peaks in gas flux occur at the end of the growing instability

  17. Adapted nested force-gradient integrators for the Schwinger model

    CERN Document Server

    Shcherbakov, Dmitry; Günther, Michael; Finkenrath, Jacob; Knechtli, Francesco; Peardon, Michael

    2016-01-01

    We study a novel class of numerical integrators, the adapted nested force-gradient schemes, used within the molecular dynamics step of the Hybrid Monte Carlo (HMC) algorithm. We test these methods in the Schwinger model on the lattice, a well known benchmark problem. We derive the analytical basis of nested force-gradient type methods and demonstrate the advantage of the proposed approach, namely reduced computational costs compared with other numerical integration schemes in HMC.

  18. Unified Model of Dynamic Forced Barrier Crossing in Single Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Friddle, R W

    2007-06-21

    Thermally activated barrier crossing in the presence of an increasing load can reveal kinetic rate constants and energy barrier parameters when repeated over a range of loading rates. Here we derive a model of the mean escape force for all relevant loading rates--the complete force spectrum. Two well-known approximations emerge as limiting cases; one of which confirms predictions that single-barrier spectra should converge to a phenomenological description in the slow loading limit.

  19. Highly asymmetric interaction forces induced by acoustic waves in coupled plate structures

    CERN Document Server

    Fan, Xiying; Zhang, Shenwei; Ke, Manzhu; Liu, Zhengyou

    2015-01-01

    Mutual forces can be induced between coupled structures when illuminated by external acoustic waves. In this Letter, we propose a concept of asymmetric interaction between two coupled plate-like structures, which is generated by oppositely incident plane waves. Besides the striking contrast in magnitude, the mutual force induced by one of the incidences can be tuned extremely strong due to the resonant excitation of the flexural plate modes. The highly asymmetric interaction with enhanced strength in single side should be potentially useful, such as in designing ultrasound instruments and sensors.

  20. Nonparametric Model of Smooth Muscle Force Production During Electrical Stimulation.

    Science.gov (United States)

    Cole, Marc; Eikenberry, Steffen; Kato, Takahide; Sandler, Roman A; Yamashiro, Stanley M; Marmarelis, Vasilis Z

    2017-03-01

    A nonparametric model of smooth muscle tension response to electrical stimulation was estimated using the Laguerre expansion technique of nonlinear system kernel estimation. The experimental data consisted of force responses of smooth muscle to energy-matched alternating single pulse and burst current stimuli. The burst stimuli led to at least a 10-fold increase in peak force in smooth muscle from Mytilus edulis, despite the constant energy constraint. A linear model did not fit the data. However, a second-order model fit the data accurately, so the higher-order models were not required to fit the data. Results showed that smooth muscle force response is not linearly related to the stimulation power.

  1. Modeling of Arc Force in Plasma Arc Welding

    Institute of Scientific and Technical Information of China (English)

    GAO Zhonglin; HU Shengsun; YIN Fengliang; WANG Rui

    2008-01-01

    A three. dimensional mathematical model for the transferred-type argon arc was developed to describe arc force on the anode surface. The software ANSYS was employed to solve the model. The model includes a part of torch and tungsten electrode to achieve m ore reasonable results. The arc temperature and flow fields were derived. And the influences of welding parameters on arc force were also studied. The simulated results show that arc pressure at the anode are dependent on the welding current, plasma gas flow rate and electrode neck-in, while not sensitive to arc length.

  2. Exact Casimir energies at nonzero temperature: Validity of proximity force approximation and interaction of semitransparent spheres

    CERN Document Server

    Milton, Kimball A; Wagner, Jef; Shajesh, K V

    2009-01-01

    In this paper, dedicated to the career of Tom Erber, we consider the Casimir interaction between weakly coupled bodies at nonzero temperature. For the case of semitransparent bodies, that is, ones described by delta-function potentials, we first examine the interaction between an infinite plane and an arbitrary curved surface. In weak coupling, such an interaction energy coincides with the exact form of the proximity force approximation obtained by summing the interaction between opposite surface elements at arbitrary temperature. This result generalizes a theorem proved recently by Decca et al. We also obtain exact closed-form results for the Casimir energy at arbitrary temperature for weakly coupled semitransparent spheres.

  3. A radial distribution function-based open boundary force model for multi-centered molecules

    KAUST Repository

    Neumann, Philipp

    2014-06-01

    We derive an expression for radial distribution function (RDF)-based open boundary forcing for molecules with multiple interaction sites. Due to the high-dimensionality of the molecule configuration space and missing rotational invariance, a computationally cheap, 1D approximation of the arising integral expressions as in the single-centered case is not possible anymore. We propose a simple, yet accurate model invoking standard molecule- and site-based RDFs to approximate the respective integral equation. The new open boundary force model is validated for ethane in different scenarios and shows very good agreement with data from periodic simulations. © World Scientific Publishing Company.

  4. DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes.

    Science.gov (United States)

    Reis, L A; Rocha, M S

    2017-05-01

    In this work, we use force spectroscopy to investigate the interaction between the DAPI fluorescent dye and the λ-DNA molecule under high (174 mM) and low (34 mM) ionic strengths. Firstly, we have measured the changes on the mechanical properties (persistence and contour lengths) of the DNA-DAPI complexes as a function of the dye concentration in the sample. Then, we use recently developed models in order to connect the behavior of both mechanical properties to the physical chemistry of the interaction. Such analysis has allowed us to identify and to decouple two main binding modes, determining the relevant physicochemical (binding) parameters for each of these modes: minor groove binding, which saturates at very low DAPI concentrations ( CT ∼ 0.50 μM) and presents equilibrium binding constants of the order of ∼10(7) M(-1) for the two ionic strengths studied; and intercalation, which starts to play a significant role only after the saturation of the first mode, presenting much smaller equilibrium binding constants (∼10(5) M(-1) ).

  5. Modeling the mechanics of cells in the cell-spreading process driven by traction forces

    Science.gov (United States)

    Fang, Yuqiang; Lai, King W. C.

    2016-04-01

    Mechanical properties of cells and their mechanical interaction with the extracellular environments are main factors influencing cellular function, thus indicating the progression of cells in different disease states. By considering the mechanical interactions between cell adhesion molecules and the extracellular environment, we developed a cell mechanical model that can characterize the mechanical changes in cells during cell spreading. A cell model was established that consisted of various main subcellular components, including cortical cytoskeleton, nuclear envelope, actin filaments, intermediate filaments, and microtubules. We demonstrated the structural changes in subcellular components and the changes in spreading areas during cell spreading driven by traction forces. The simulation of nanoindentation tests was conducted by integrating the indenting force to the cell model. The force-indentation curve of the cells at different spreading states was simulated, and the results showed that cell stiffness increased with increasing traction forces, which were consistent with the experimental results. The proposed cell mechanical model provides a strategy to investigate the mechanical interactions of cells with the extracellular environments through the adhesion molecules and to reveal the cell mechanical properties at the subcellular level as cells shift from the suspended state to the adherent state.

  6. A Possible Unification Model for All Basic Forces

    OpenAIRE

    Yue-Liang, Wu; Guang-Zhao, Zhou

    1997-01-01

    A unification model for strong, electromagnetic, weak and gravitational forces is proposed. The tangent space of ordinary coordinate 4-dimensional spacetime is a submanifold of an 14-dimensional internal spacetime spanned by four frame fields. The unification of the standard model with gravity is governed by gauge symmetry in the internal spacetime.

  7. A model of psychological resilience for the Netherlands Armed Forces

    NARCIS (Netherlands)

    Kamphuis, W.; Venrooij, W.; Berg, C. van den

    2012-01-01

    In the current study, a model of psychological resilience was developed for the Netherlands Armed Forces and a number of important relations were tested using a longitudinal design. The model of resilience was based on a systematic literature review of resilience in high-risk professions and intervi

  8. IMPLEMENTATION MODEL OF MOTOR TRACTION FORCE OF MAGLEV TRAIN

    Directory of Open Access Journals (Sweden)

    V. O. Polyakov

    2016-08-01

    Full Text Available Purpose. Traction force implementation (TFI by the motor of magnetic levitation train (MLT occurs in the process of electric-to-kinetic energy transformation at interaction of inductor and armature magnetic fields. Ac-cordingly, the aim of this study is to obtain a correct description of such energy transformation. Methodology. At the present stage, a mathematical and, in particular, computer simulation is the main and most universal tool for analysis and synthesis of processes and systems. At the same time, radical advantages of this tool make the precision of selection of a particular research methodology even more important. It is especially important for such a large and complex system as MLT. Therefore the special attention in the work is given to the rationale for choosing the research paradigm selective features. Findings. The analysis results of existing TFI process model versions indicate that each of them has both advantages and disadvantages. Therefore, one of the main results of this study was the creation of a mathematical model for such process that would preserve the advantages of previous versions, but would be free from their disadvantages. The work provides rationale for application (for the purposes of research of train motor TFI of the integrative holistic paradigm, which assimilates the advantages of the theory of electric circuit and magnetic field. Originality. The priority of creation of such paradigm and corresponding version of FI model constitute the originality of the research. Practical value. The main manifestation of practical value of this research in the opportunity, in case of use of its results, for significant increase in efficiency of MLT dynamic studies, on the condition that their generalized costs will not rise.

  9. Molecular theory for the effects of solute attractive forces on hydrophobic interactions

    CERN Document Server

    Chaudhari, M I; Asthagiri, D; Tan, L; Pratt, L R

    2015-01-01

    We consider the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions. The principal result of LMF theory is outlined, then tested by obtaining radial distribution functions (rdfs) for Ar atoms in water, with and without attractive interactions distinguished by the Weeks-Chandler-Andersen (WCA) separation. Change from purely repulsive atomic solute interactions to include realistic attractive interactions substantially \\emph{diminishes} the strength of hydrophobic bonds. Since attractions make a big contribution to hydrophobic interactions, Pratt-Chandler theory, which did not include attractions, should not be simply comparable to computer simulation results with general physical interactions, including attractions. The rdfs permit evaluation of osmotic second virial coefficients $B_2$. Those $B_2$ are consistent with the conclusion that incorporation of attractive interactions leads to more positive (repulsive) values. In all cases here, $B_2$ becomes mor...

  10. Study of deformation of droplet in external force field by using liquid-gas model of lattice-gas

    Energy Technology Data Exchange (ETDEWEB)

    Ebihara, Ken-ichi; Watanabe, Tadashi [Japan Atomic Energy Research Inst., Center for Promotion of Computational Science and Engineering, Tokai, Ibaraki (Japan)

    2000-10-01

    The deformation of the droplet by the external force which is assumed to be gravity is studied by using the liquid-gas model of lattice-gas. Two types of liquid-gas models, one is the minimal model and the other is the maximal model, which are distinguished from each other by the added long-range interactions are used for the simulation of the droplet deformation. The difference of the droplet deformation between the maximal model and the minimal model was observed. While the droplet of the minimal model elongates in the direction of the external force, the droplet of the maximal model elongates in the perpendicular direction to the external force. Therefore the droplet deformation in the external force field of the maximal model is more similar to the droplet deformation which is observed in experiments than that of the minimal model. (author)

  11. Van der Waals interaction torque and force between dielectrically anisotropic layered media

    CERN Document Server

    Lu, Bing-Sui

    2016-01-01

    We analyse the van der Waals interaction for a pair of dielectrically anisotropic plane-layered media interacting across a dielectrically isotropic medium. We investigate the van der Waals torque and force for the following cases: (i) a pair of single anisotropic layers, (ii) a single anisotropic layer interacting with a multilayered slab consisting of alternating anisotropic and isotropic layers, and (iii) a pair of multilayered slabs each consisting of alternating anisotropic and isotropic layers, looking at the cases where the optical axes lie parallel and/or perpendicular to the plane of the layers. For the first case, the optical axes of the oppositely facing anisotropic layers of the two interacting slabs generally have an angular mismatch, and within each multilayered slab the optical axes may either be the same, or undergo constant angular increments across the anisotropic layers. In particular, we examine how the behaviors of the van der Waals torque and force can be "tuned" by adjusting the layer th...

  12. Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

    Science.gov (United States)

    Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

    2013-10-08

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

  13. Modeling the Interaction between AFM Tips and Pinned Surface Nanobubbles.

    Science.gov (United States)

    Guo, Zhenjiang; Liu, Yawei; Xiao, Qianxiang; Schönherr, Holger; Zhang, Xianren

    2016-01-26

    Although the morphology of surface nanobubbles has been studied widely with different AFM modes, AFM images may not reflect the real shapes of the nanobubbles due to AFM tip-nanobubble interactions. In addition, the interplay between surface nanobubble deformation and induced capillary force has not been well understood in this context. In our work we used constraint lattice density functional theory to investigate the interaction between AFM tips and pinned surface nanobubbles systematically, especially concentrating on the effects of tip hydrophilicity and shape. For a hydrophilic tip contacting a nanobubble, its hydrophilic nature facilitates its departure from the bubble surface, displaying a weak and intermediate-range attraction. However, when the tip squeezes the nanobubble during the approach process, the nanobubble shows an elastic effect that prevents the tip from penetrating the bubble, leading to a strong nanobubble deformation and repulsive interactions. On the contrary, a hydrophobic tip can easily pierce the vapor-liquid interface of the nanobubble during the approach process, leading to the disappearance of the repulsive force. In the retraction process, however, the adhesion between the tip and the nanobubble leads to a much stronger lengthening effect on nanobubble deformation and a strong long-range attractive force. The trends of force evolution from our simulations agree qualitatively well with recent experimental AFM observations. This favorable agreement demonstrates that our model catches the main intergradient of tip-nanobubble interactions for pinned surface nanobubbles and may therefore provide important insight into how to design minimally invasive AFM experiments.

  14. Force Limited Random Vibration Test of TESS Camera Mass Model

    Science.gov (United States)

    Karlicek, Alexandra; Hwang, James Ho-Jin; Rey, Justin J.

    2015-01-01

    The Transiting Exoplanet Survey Satellite (TESS) is a spaceborne instrument consisting of four wide field-of-view-CCD cameras dedicated to the discovery of exoplanets around the brightest stars. As part of the environmental testing campaign, force limiting was used to simulate a realistic random vibration launch environment. While the force limit vibration test method is a standard approach used at multiple institutions including Jet Propulsion Laboratory (JPL), NASA Goddard Space Flight Center (GSFC), European Space Research and Technology Center (ESTEC), and Japan Aerospace Exploration Agency (JAXA), it is still difficult to find an actual implementation process in the literature. This paper describes the step-by-step process on how the force limit method was developed and applied on the TESS camera mass model. The process description includes the design of special fixtures to mount the test article for properly installing force transducers, development of the force spectral density using the semi-empirical method, estimation of the fuzzy factor (C2) based on the mass ratio between the supporting structure and the test article, subsequent validating of the C2 factor during the vibration test, and calculation of the C.G. accelerations using the Root Mean Square (RMS) reaction force in the spectral domain and the peak reaction force in the time domain.

  15. Logarithmic interaction under periodic boundary conditions: closed form formulas for energy and forces

    Science.gov (United States)

    Tyagi, Sandeep

    A method is given to obtain closed form formulas for the energy and forces for an aggregate of charges interacting via a logarithmic interaction under periodic boundary conditions. The work done here is a generalization of Glasser's results [J. Math. Phys., 15, 188 (1974)] and is obtained with a different and simpler method than that by Stremler [J. Math. Phys., 45, 3584 (2004)]. The simplicity of the formulas derived here makes them extremely convenient in a computer simulation.

  16. Logarithmic interaction under periodic boundary conditions: Closed form formulas for energy and forces

    OpenAIRE

    2005-01-01

    A method is given to obtain closed form formulas for the energy and forces for an aggregate of charges interacting via a logarithmic interaction under periodic boundary conditions. The work done here is a generalization of Glasser's results [M. L. Glasser, J. Math. Phys. 15, 188 (1974)] and is obtained with a different and simpler method than that by Stremler [M. A. Stremler, J. Math. Phys. 45, 3584 (2004)]. The simplicity of the formulas derived here makes them extremely convenient in a comp...

  17. Measurement of interaction forces between red blood cells in aggregates by optical tweezers

    Energy Technology Data Exchange (ETDEWEB)

    Maklygin, A Yu; Priezzhev, A V; Karmenian, A; Nikitin, Sergei Yu; Obolenskii, I S; Lugovtsov, Andrei E; Kisun Li

    2012-06-30

    We have fabricated double-beam optical tweezers and demonstrated the possibility of their use for measuring the interaction forces between red blood cells (erythrocytes). It has been established experimentally that prolonged trapping of red blood cells in a tightly focused laser beam does not cause any visible changes in their shape or size. We have measured the interaction between red blood cells in the aggregate, deformed by optical tweezers.

  18. INTERACTIONS: DESIGN, IMPLEMENTATION AND EVALUATION OF A COMPUTATIONAL TOOL FOR TEACHING INTERMOLECULAR FORCES IN HIGHER EDUCATION

    OpenAIRE

    Francisco Geraldo Barbosa; Jair Mafezoli; Mary Anne Sousa Lima; Francisco Serra Oliveira Alexandre; Diego Macedo de Almeida; Antonio José Melo Leite Junior; José Nunes da Silva Júnior

    2015-01-01

    Intermolecular forces are a useful concept that can explain the attraction between particulate matter as well as numerous phenomena in our lives such as viscosity, solubility, drug interactions, and dyeing of fibers. However, studies show that students have difficulty understanding this important concept, which has led us to develop a free educational software in English and Portuguese. The software can be used interactively by teachers and students, thus facilitating better understanding. Pr...

  19. Needle-Tissue Interaction Forces for Bevel-Tip Steerable Needles

    OpenAIRE

    Misra, Sarthak; Reed, Kyle B.; Douglas, Andrew S.; Ramesh, K. T.; Okamura, Allison M.

    2008-01-01

    The asymmetry of a bevel-tip needle results in the needle naturally bending when it is inserted into soft tissue. As a first step toward modeling the mechanics of deflection of the needle, we determine the forces at the bevel tip. In order to find the forces acting at the needle tip, we measure rupture toughness and nonlinear material elasticity parameters of several soft tissue simulant gels and chicken tissue. We incorporate these physical parameters into a finite element model that include...

  20. Phenomenological analysis of the interacting boson model

    Science.gov (United States)

    Hatch, R. L.; Levit, S.

    1982-01-01

    The classical Hamiltonian of the interacting boson model is defined and expressed in terms of the conventional quadrupole variables. This is used in the analyses of the dynamics in the various limits of the model. The purpose is to determine the range and the features of the collective phenomena which the interacting boson model is capable of describing. In the commonly used version of the interacting boson model with one type of the s and d bosons and quartic interactions, this capability has certain limitations and the model should be used with care. A more sophisticated version of the interacting boson model with neutron and proton bosons is not discussed. NUCLEAR STRUCTURE Interacting bosons, classical IBM Hamiltonian in quadrupole variables, phenomenological content of the IBM and its limitations.

  1. The relation between a microscopic threshold-force model and macroscopic models of adhesion

    Science.gov (United States)

    Hulikal, Srivatsan; Bhattacharya, Kaushik; Lapusta, Nadia

    2017-01-01

    This paper continues our recent work on the relationship between discrete contact interactions at the microscopic scale and continuum contact interactions at the macroscopic scale (Hulikal et al., J. Mech. Phys. Solids 76, 144-161, 2015). The focus of this work is on adhesion. We show that a collection of a large number of discrete elements governed by a threshold-force based model at the microscopic scale collectively gives rise to continuum fracture mechanics at the macroscopic scale. A key step is the introduction of an efficient numerical method that enables the computation of a large number of discrete contacts. Finally, while this work focuses on scaling laws, the methodology introduced in this paper can also be used to study rough-surface adhesion.

  2. A theoretical model for the Lorentz force particle analyzer

    Science.gov (United States)

    Moreau, René; Tao, Zhen; Wang, Xiaodong

    2016-07-01

    In a previous paper [X. Wang et al., J. Appl. Phys. 120, 014903 (2016)], several experimental devices have been presented, which demonstrate the efficiency of electromagnetic techniques for detecting and sizing electrically insulating particles entrained in the flow of a molten metal. In each case, a non-uniform magnetic field is applied across the flow of the electrically conducting liquid, thereby generating a braking Lorentz force on this moving medium and a reaction force on the magnet, which tends to be entrained in the flow direction. The purpose of this letter is to derive scaling laws for this Lorentz force from an elementary theoretical model. For simplicity, as in the experiments, the flowing liquid is modeled as a solid body moving with a uniform velocity U. The eddy currents in the moving domain are derived from the classic induction equation and Ohm's law, and expressions for the Lorentz force density j ×B and for its integral over the entire moving domain follow. The insulating particles that are eventually present and entrained with this body are then treated as small disturbances in a classic perturbation analysis, thereby leading to scaling laws for the pulses they generate in the Lorentz force. The purpose of this letter is both to illustrate the eddy currents without and with insulating particles in the electrically conducting liquid and to derive a key relation between the pulses in the Lorentz force and the main parameters (particle volume and dimensions of the region subjected to the magnetic field).

  3. Small forces that differ with prior motor experience can communicate movement goals during human-human physical interaction.

    Science.gov (United States)

    Sawers, Andrew; Bhattacharjee, Tapomayukh; McKay, J Lucas; Hackney, Madeleine E; Kemp, Charles C; Ting, Lena H

    2017-01-31

    Physical interactions between two people are ubiquitous in our daily lives, and an integral part of many forms of rehabilitation. However, few studies have investigated forces arising from physical interactions between humans during a cooperative motor task, particularly during overground movements. As such, the direction and magnitude of interaction forces between two human partners, how those forces are used to communicate movement goals, and whether they change with motor experience remains unknown. A better understanding of how cooperative physical interactions are achieved in healthy individuals of different skill levels is a first step toward understanding principles of physical interactions that could be applied to robotic devices for motor assistance and rehabilitation. Interaction forces between expert and novice partner dancers were recorded while performing a forward-backward partnered stepping task with assigned "leader" and "follower" roles. Their position was recorded using motion capture. The magnitude and direction of the interaction forces were analyzed and compared across groups (i.e. expert-expert, expert-novice, and novice-novice) and across movement phases (i.e. forward, backward, change of direction). All dyads were able to perform the partnered stepping task with some level of proficiency. Relatively small interaction forces (10-30N) were observed across all dyads, but were significantly larger among expert-expert dyads. Interaction forces were also found to be significantly different across movement phases. However, interaction force magnitude did not change as whole-body synchronization between partners improved across trials. Relatively small interaction forces may communicate movement goals (i.e. "what to do and when to do it") between human partners during cooperative physical interactions. Moreover, these small interactions forces vary with prior motor experience, and may act primarily as guiding cues that convey information about

  4. Interactions between Rotavirus and Suwannee River Organic Matter: Aggregation, Deposition, and Adhesion Force Measurement

    KAUST Repository

    Gutierrez, Leonardo

    2012-08-21

    Interactions between rotavirus and Suwannee River natural organic matter (NOM) were studied by time-resolved dynamic light scattering, quartz crystal microbalance, and atomic force microscopy. In NOM-containing NaCl solutions of up to 600 mM, rotavirus suspension remained stable for over 4 h. Atomic force microscopy (AFM) measurement for interaction force decay length at different ionic strengths showed that nonelectrostatic repulsive forces were mainly responsible for eliminating aggregation in NaCl solutions. Aggregation rates of rotavirus in solutions containing 20 mg C/L increased with divalent cation concentration until reaching a critical coagulation concentration of 30 mM CaCl2 or 70 mM MgCl2. Deposition kinetics of rotavirus on NOM-coated silica surface was studied using quartz crystal microbalance. Experimental attachment efficiencies for rotavirus adsorption to NOM-coated surface in MgCl2 solution were lower than in CaCl2 solution at a given divalent cation concentration. Stronger adhesion force was measured for virus-virus and virus-NOM interactions in CaCl2 solution compared to those in MgCl2 or NaCl solutions at the same ionic strength. This study suggested that divalent cation complexation with carboxylate groups in NOM and on virus surface was an important mechanism in the deposition and aggregation kinetics of rotavirus. © 2012 American Chemical Society.

  5. Modeling of Dynamic Fluid Forces in Fast Switching Valves

    DEFF Research Database (Denmark)

    Roemer, Daniel Beck; Johansen, Per; Pedersen, Henrik Clemmensen;

    2015-01-01

    Switching valves experience opposing fluid forces due to movement of the moving member itself, as the surrounding fluid volume must move to accommodate the movement. This movement-induced fluid force may be divided into three main components; the added mass term, the viscous term and the socalled...... history term. For general valve geometries there are no simple solution to either of these terms. During development and design of such switching valves, it is therefore, common practice to use simple models to describe the opposing fluid forces, neglecting all but the viscous term which is determined...... based on shearing areas and venting channels. For fast acting valves the opposing fluid force may retard the valve performance significantly, if appropriate measures are not taken during the valve design. Unsteady Computational Fluid Dynamics (CFD) simulations are available to simulate the total fluid...

  6. Flight Dynamics of Flexible Aircraft with Aeroelastic and Inertial Force Interactions

    Science.gov (United States)

    Nguyen, Nhan T.; Tuzcu, Ilhan

    2009-01-01

    This paper presents an integrated flight dynamic modeling method for flexible aircraft that captures coupled physics effects due to inertial forces, aeroelasticity, and propulsive forces that are normally present in flight. The present approach formulates the coupled flight dynamics using a structural dynamic modeling method that describes the elasticity of a flexible, twisted, swept wing using an equivalent beam-rod model. The structural dynamic model allows for three types of wing elastic motion: flapwise bending, chordwise bending, and torsion. Inertial force coupling with the wing elasticity is formulated to account for aircraft acceleration. The structural deflections create an effective aeroelastic angle of attack that affects the rigid-body motion of flexible aircraft. The aeroelastic effect contributes to aerodynamic damping forces that can influence aerodynamic stability. For wing-mounted engines, wing flexibility can cause the propulsive forces and moments to couple with the wing elastic motion. The integrated flight dynamics for a flexible aircraft are formulated by including generalized coordinate variables associated with the aeroelastic-propulsive forces and moments in the standard state-space form for six degree-of-freedom flight dynamics. A computational structural model for a generic transport aircraft has been created. The eigenvalue analysis is performed to compute aeroelastic frequencies and aerodynamic damping. The results will be used to construct an integrated flight dynamic model of a flexible generic transport aircraft.

  7. Development of a mechanistic model for forced convection subcooled boiling

    Science.gov (United States)

    Shaver, Dillon R.

    The focus of this work is on the formulation, implementation, and testing of a mechanistic model of subcooled boiling. Subcooled boiling is the process of vapor generation on a heated wall when the bulk liquid temperature is still below saturation. This is part of a larger effort by the US DoE's CASL project to apply advanced computational tools to the simulation of light water reactors. To support this effort, the formulation of the dispersed field model is described and a complete model of interfacial forces is formulated. The model has been implemented in the NPHASE-CMFD computer code with a K-epsilon model of turbulence. The interfacial force models are built on extensive work by other authors, and include novel formulations of the turbulent dispersion and lift forces. The complete model of interfacial forces is compared to experiments for adiabatic bubbly flows, including both steady-state and unsteady conditions. The same model is then applied to a transient gas/liquid flow in a complex geometry of fuel channels in a sodium fast reactor. Building on the foundation of the interfacial force model, a mechanistic model of forced-convection subcooled boiling is proposed. This model uses the heat flux partitioning concept and accounts for condensation of bubbles attached to the wall. This allows the model to capture the enhanced heat transfer associated with boiling before the point of net generation of vapor, a phenomenon consistent with existing experimental observations. The model is compared to four different experiments encompassing flows of light water, heavy water, and R12 at different pressures, in cylindrical channels, an internally heated annulus, and a rectangular channel. The experimental data includes axial and radial profiles of both liquid temperature and vapor volume fraction, and the agreement can be considered quite good. The complete model is then applied to simulations of subcooled boiling in nuclear reactor subchannels consistent with the

  8. No-Core Shell Model Calculations in Light Nuclei with Three-Nucleon Forces

    Energy Technology Data Exchange (ETDEWEB)

    Barrett, B R; Vary, J P; Nogga, A; Navratil, P; Ormand, W E

    2004-01-08

    The ab initio No-Core Shell Model (NCSM) has recently been expanded to include nucleon-nucleon (NN) and three-nucleon (3N) interactions at the three-body cluster level. Here it is used to predict binding energies and spectra of p-shell nuclei based on realistic NN and 3N interactions. It is shown that 3N force (3NF) properties can be studied in these nuclear systems. First results show that interactions based on chiral perturbation theory lead to a realistic description of {sup 6}Li.

  9. Classical and fluctuation-induced electromagnetic interactions in micronscale systems: designer bonding, antibonding, and Casimir forces

    CERN Document Server

    Rodriguez, Alejandro W; Woolf, David N; Johnson, Steven G; Loncar, Marko; Capasso, Federico

    2014-01-01

    Whether intentionally introduced to exert control over particles and macroscopic objects, such as for trapping or cooling, or whether arising from the quantum and thermal fluctuations of charges in otherwise neutral bodies, leading to unwanted stiction between nearby mechanical parts, electromagnetic interactions play a fundamental role in many naturally occurring processes and technologies. In this review, we survey recent progress in the understanding and experimental observation of optomechanical and quantum-fluctuation forces. Although both of these effects arise from exchange of electromagnetic momentum, their dramatically different origins, involving either real or virtual photons, lead to different physical manifestations and design principles. Specifically, we describe recent predictions and measurements of attractive and repulsive optomechanical forces, based on the bonding and antibonding interactions of evanescent waves, as well as predictions of modified and even repulsive Casimir forces between n...

  10. Lateral hydrodynamic interactions between an emulsion droplet and a flat surface evaluated by frictional force microscopy.

    Science.gov (United States)

    Vakarelski, Ivan U; Dagastine, Raymond R; Chan, Derek Y C; Stevens, Geoffrey W; Higashitani, Ko; Grieser, Franz

    2010-06-01

    We introduce a lateral atomic force microscopy (AFM) method to measure the hydrodynamic drag force acting on a microscopic emulsion droplet moving parallel to a flat surface. A tetradecane oil droplet formed in an aqueous solution of sodium dodecylsulfate was attached to a V-shaped atomic force microscopy cantilever, and lateral hydrodynamic interactions between the droplet and a flat glass surface were measured using a range of scanning velocities. The droplet was positioned either far from the oscillating surface or was pressed to the surface under a constant applied load. These measurements demonstrate the feasibility of using AFM to study lateral hydrodynamic interactions and lubricity between soft matter materials relevant to a large number of applications in areas as diverse as flavor delivery in foods to the applications of emulsions or emollients in personal care products.

  11. Influence of atomic force microscope tip-sample interaction on the study of scaling behavior

    NARCIS (Netherlands)

    Aue, J.; de Hosson, J.T.M.

    1997-01-01

    Images acquired with atomic force microscopy are based on tip-sample interaction. It is shown that using scanning probe techniques for determining scaling parameters of a surface leads to an underestimate of the actual scaling dimension, due to the dilation of tip and surface. How much we underestim

  12. Interaction forces between salivary proteins and Streptococcus mutans with and without antigen I/II

    NARCIS (Netherlands)

    Xu, C.P.; Belt-Gritter, van de B.; Dijkstra, R.J.B.; Norde, W.; Mei, van der H.C.; Busscher, H.J.

    2007-01-01

    The antigen I/II family of surface proteins is expressed by oral streptococci, including Streptococcus mutans, and mediates specific binding to, among others, salivary films. The aim of this study was to investigate the interaction forces between salivary proteins and S. mutans with (LT11) and witho

  13. Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective.

    Science.gov (United States)

    Hu, Xiaotang; Li, Hongbin

    2014-10-01

    Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  14. Interaction forces between salivary proteins and Streptococcus mutans with and without antigen I/II

    NARCIS (Netherlands)

    Xu, Chun-Ping; van de Belt-Gritter, Betsy; Dijkstra, Rene J. B.; Norde, Willem; van der Mei, Henny C.; Busscher, Henk J.

    2007-01-01

    The antigen I/II family of surface proteins is expressed by oral streptococci, including Streptococcus mutans, and mediates specific binding to, among others, salivary films. The aim of this study was to investigate the interaction forces between salivary proteins and S. mutans with (LT11) and

  15. Model based control of dynamic atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Chibum [Department of Mechanical System Design Engineering, Seoul National University of Science and Technology, Seoul 139-743 (Korea, Republic of); Salapaka, Srinivasa M., E-mail: salapaka@illinois.edu [Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)

    2015-04-15

    A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H{sub ∞} control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.

  16. Model based control of dynamic atomic force microscope.

    Science.gov (United States)

    Lee, Chibum; Salapaka, Srinivasa M

    2015-04-01

    A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H(∞) control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.

  17. Interaction of Volcanic Forcing and El Nino: Sensitivity to the Eruption Magnitude and El Nino Intensity

    KAUST Repository

    Predybaylo, Evgeniya

    2015-04-01

    Volcanic aerosols formed in the stratosphere after strong explosive eruptions influence Earth\\'s radiative balance, affecting atmospheric and oceanic temperatures and circulation. It was observed that the recent volcanic eruptions frequently occurred in El Nino years. Analysis of the paleo data confirms that the probability of a sequent El Nino occurrence after the eruption increases. To better understand the physical mechanism of this interaction we employed ocean-atmosphere coupled climate model CM2.1, developed in the Geophysical Fluid Dynamics Laboratory, and conducted a series of numerical experiments using initial conditions with different El Nino Southern Oscillation (ENSO) strengths forced by volcanic eruptions of different magnitudes, Pinatubo of June 1991 and Tambora of April 1815: (i) strong ENSO/Pinatubo, (ii) weak ENSO/Pinatubo, (iii) strong ENSO/Tambora. The amount of ejected material from the Tambora eruption was about three times greater than that of the Pinatubo eruption. The initial conditions with El Nino were sampled from the CM2.1 long control run. Our simulations show the enhancement of El Nino in the second year after an eruption. We found that the spatial-temporal structure of model responses is sensitive to both the magnitude of an eruption and the strength of El Nino. We analyzed the ocean dynamic in the tropical Pacific for all cases to uncover the physical mechanism, resulting in the enhanced and/or prolonged El Nino.

  18. A simple approach to adjust tidal forcing in fjord models

    Science.gov (United States)

    Hjelmervik, Karina; Kristensen, Nils Melsom; Staalstrøm, André; Røed, Lars Petter

    2017-07-01

    To model currents in a fjord accurate tidal forcing is of extreme importance. Due to complex topography with narrow and shallow straits, the tides in the innermost parts of a fjord are both shifted in phase and altered in amplitude compared to the tides in the open water outside the fjord. Commonly, coastal tide information extracted from global or regional models is used on the boundary of the fjord model. Since tides vary over short distances in shallower waters close to the coast, the global and regional tidal forcings are usually too coarse to achieve sufficiently accurate tides in fjords. We present a straightforward method to remedy this problem by simply adjusting the tides to fit the observed tides at the entrance of the fjord. To evaluate the method, we present results from the Oslofjord, Norway. A model for the fjord is first run using raw tidal forcing on its open boundary. By comparing modelled and observed time series of water level at a tidal gauge station close to the open boundary of the model, a factor for the amplitude and a shift in phase are computed. The amplitude factor and the phase shift are then applied to produce adjusted tidal forcing at the open boundary. Next, we rerun the fjord model using the adjusted tidal forcing. The results from the two runs are then compared to independent observations inside the fjord in terms of amplitude and phases of the various tidal components, the total tidal water level, and the depth integrated tidal currents. The results show improvements in the modelled tides in both the outer, and more importantly, the inner parts of the fjord.

  19. The Tip-Sample Interaction in Atomic Force Microscopy and its Implications for Biological Applications.

    Science.gov (United States)

    Baselt, David Randall

    This thesis describes the construction of an atomic force microscope and its application to the study of tip -sample interactions, primarily through the use of friction and hardness (elasticity) imaging. Part one describes the atomic force microscope, which consists of a scanned-cantilever stage (chapter 2); a versatile digital signal processor-based control system with self-optimizing feedback, lock-in amplifier emulation (for hardness imaging), and macro programmability (chapter 3); and image processing software (chapter 4). Part two describes a number of results that have helped to characterize the tip-sample interaction and the contact imaging modes used for its study. Meniscus forces act laterally as well as normally, and that they vary with position (chapter 5). Friction measurements couple with scanner position and feedback, and the meniscus effects friction images (chapter 6). Sliding of the tip over the sample surface introduces slope-dependence into hardness measurements (chapter 7). Dull tips can create prominent topography artifacts even on very flat surfaces (chapter 8). In an investigation of collagen fibrils, AFM has revealed the characteristic 65 nm banding pattern, a second, minor banding pattern, and microfibrils that run along the fibril axis. The distribution of proteoglycans along the fibrils creates a characteristic pattern in friction images. Although imaging in water reduces interaction forces, water can also make biological samples more sensitive to force. However, for robust biological samples imaged in air, tip shape presents a greater obstacle than tip -sample interaction forces to obtaining high-resolution images. Tip contamination increases tip-sample friction and can occasionally improve resolution (chapter 9). For a separate project I have designed a general -purpose nearfield scanning optical microscope (chapter 10).

  20. An optimized charge penetration model for use with the AMOEBA force field.

    Science.gov (United States)

    Rackers, Joshua A; Wang, Qiantao; Liu, Chengwen; Piquemal, Jean-Philip; Ren, Pengyu; Ponder, Jay W

    2016-12-21

    The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field. With a function derived from the charge distribution of a hydrogen-like atom and a limited number of parameters, our charge penetration model dramatically improves the description of electrostatics at short range. On a database of 101 biomolecular dimers, the charge penetration model brings the error in the electrostatic interaction energy relative to the ab initio SAPT electrostatic interaction energy from 13.4 kcal mol(-1) to 1.3 kcal mol(-1). The model is shown not only to be robust and transferable for the AMOEBA model, but also physically meaningful as it universally improves the description of the electrostatic potential around a given molecule.

  1. Evaluation of the interactions between polymeric chains and surfaces with different structures performed by an atomic force microscope

    Directory of Open Access Journals (Sweden)

    Oréfice Rodrigo Lambert

    1998-01-01

    Full Text Available Interactions between polymers and inorganic surfaces are present in a series of phenomena involving processes such as coagulation and deffloculation of ceramic powder and adsorption of organic macromolecules on the surface of implants, among others. In this work, Atomic Force Microscopy (AFM was modified to allow the evaluation of interactions between polymeric chains and inorganic surfaces (silica with different structures. Polymers (sulfonated polysulfone were grafted onto AFM cantilevers. AFM force-distance curves were obtained for this modified tip against a series of substrates produced by depositing silica films on silicon wafers. The structure of the silica layer was modified by employing heat treatments at different temperatures. The results showed that the interactions between polymer and surfaces are dependent on the structure of the surfaces. Penetration of the polymeric chains can occur through a soft gel layer (substrates treated at low temperature, 110 °C. For surfaces with dense silica layers, the results showed that not only the concentration of hydroxy groups but also their spatial distribution along the surfaces are important in defining the magnitude of interactions between polymers and surfaces. A model involving a molecular recognition process, in which interactions are maximized for inorganic surfaces with structures that can match the chemical architecture of the polymer, was then used to explain the obtained results.

  2. Inference of a nonlinear stochastic model of the cardiorespiratory interaction

    CERN Document Server

    Smelyanskiy, V N; Stefanovska, A; McClintock, P V E

    2005-01-01

    A new technique is introduced to reconstruct a nonlinear stochastic model of the cardiorespiratory interaction. Its inferential framework uses a set of polynomial basis functions representing the nonlinear force governing the system oscillations. The strength and direction of coupling, and the noise intensity are simultaneously inferred from a univariate blood pressure signal, monitored in a clinical environment. The technique does not require extensive global optimization and it is applicable to a wide range of complex dynamical systems subject to noise.

  3. Interaction of cationic hydrophobic surfactants at negatively charged surfaces investigated by atomic force microscopy.

    Science.gov (United States)

    McNamee, Cathy E; Butt, Hans-Jürgen; Higashitani, Ko; Vakarelski, Ivan U; Kappl, Michael

    2009-10-06

    Atomic force microscopy was used to study the adsorption of the surfactant octadecyl trimethyl ammonium chloride (C18TAC) at a low concentration (0.03 mM) to negatively charged surfaces in water. Atomic force microscopy tips were functionalized with dimethyloctadecyl(3-tripropyl)ammonium chloride (C18TAC-si) or N-trimethoxysilylpropyl-N,N,N-trimethylammomium chloride (hydrophilpos-si) to facilitate imaging of the adsorbed surfactant without artifacts. Tapping mode images and force measurements revealed C18TAC patches, identified as partial surfactant bilayers or hemimicelles. The forces controlling the adsorption process of the C18TAC to a negatively charged surface were investigated by measuring the forces between a C18TAC-si or a hydrophilpos-si tip and a silica surface in the presence of varying concentrations of either NaCl or NaNO3. Screening of forces with an increasing NaCl concentration was observed for the C18TAC-si and hydrophilpos-si tips, proving an electrostatic contribution. Screening was also observed for the hydrophilpos-si tip in NaNO3, whereas a long-range attraction was observed for the C18TAC-si tip for all NaNO3 concentrations. These results indicate that screening of the forces for the C18TAC-si tip depended on the type and/or size of the anion, possibly due to a different probability of the anions to enter the silane layers. The interaction of C18TAC patches with C18TAC-si tips in the presence of NaCl and the interaction of the patches with hydrophilpos-si tips in either NaCl or NaNO3 were repulsive and independent of the number of force curves measured, indicating a stable, positively charged C18TAC patch. However, the forces measured between the patches and a C18TAC-si tip in NaNO3 depended on the number of force curves measured, indicating a change in patch structure induced by the first interaction.

  4. NN Interaction in Chiral Constituent Quark Models

    CERN Document Server

    Valcarce, A; González, P

    2003-01-01

    We review the actual state in the description of the NN interaction by means of chiral constituent quark models. We present a series of relevant features that are nicely explained within the quark model framework.

  5. Semantic models for adaptive interactive systems

    CERN Document Server

    Hussein, Tim; Lukosch, Stephan; Ziegler, Jürgen; Calvary, Gaëlle

    2013-01-01

    Providing insights into methodologies for designing adaptive systems based on semantic data, and introducing semantic models that can be used for building interactive systems, this book showcases many of the applications made possible by the use of semantic models.Ontologies may enhance the functional coverage of an interactive system as well as its visualization and interaction capabilities in various ways. Semantic models can also contribute to bridging gaps; for example, between user models, context-aware interfaces, and model-driven UI generation. There is considerable potential for using

  6. Coordination between digit forces and positions: interactions between anticipatory and feedback control.

    Science.gov (United States)

    Fu, Qiushi; Santello, Marco

    2014-04-01

    Humans adjust digit forces to compensate for trial-to-trial variability in digit placement during object manipulation, but the underlying control mechanisms remain to be determined. We hypothesized that such digit position/force coordination was achieved by both visually guided feed-forward planning and haptic-based feedback control. The question arises about the time course of the interaction between these two mechanisms. This was tested with a task in which subjects generated torque (± 70 N·mm) on a virtual object to control a cursor moving to target positions to catch a falling ball, using a virtual reality environment and haptic devices. The width of the virtual object was varied between large (L) and small (S). These object widths result in significantly different horizontal digit relative positions and require different digit forces to exert the same task torque. After training, subjects were tested with random sequences of L and S widths with or without visual information about object width. We found that visual cues allowed subjects to plan manipulation forces before contact. In contrast, when visual cues were not available to predict digit positions, subjects implemented a "default" digit force plan that was corrected after digit contact to eventually accomplish the task. The time course of digit forces revealed that force development was delayed in the absence of visual cues. Specifically, the appropriate digit force adjustments were made 250-300 ms after initial object contact. This result supports our hypothesis and further reveals that haptic feedback alone is sufficient to implement digit force-position coordination.

  7. Interplay of Multiple Interaction Forces: Binding of Norfloxacin to Human Serum Albumin.

    Science.gov (United States)

    Paul, Bijan K; Ghosh, Narayani; Mukherjee, Saptarshi

    2015-10-15

    Herein, the binding interaction of a potential chemotherapeutic antibacterial drug norfloxacin (NOF) with a serum transport protein, human serum albumin (HSA), is investigated. The prototropic transformation of the drug (NOF) is found to be remarkably modified following interaction with the protein as manifested through significant modulations of the photophysics of the drug. The predominant zwitterionic form of NOF in aqueous buffer phase undergoes transformation to the cationic form within the protein-encapsulated state. This implies the possible role of electrostatic interaction force in NOF-HSA binding. This postulate is further substantiated from the effect of ionic strength on the interaction process. To this end, the detailed study of the thermodynamics of the drug-protein interaction process from isothermal titration calorimetric (ITC) experiments is found to unfold the signature of electrostatic as well as hydrophobic interaction forces underlying the binding process. Thus, interplay of more than one interaction forces is argued to be responsible for the overall drug-protein binding. The ITC results reveal an important finding in terms of enthalpy-entropy compensation (EEC) characterizing the NOF-HSA binding. The effect of drug-binding on the native protein conformation has also been evaluated from circular dichroism (CD) spectroscopy which unveils partial rupture of the protein secondary structure. In conjunction to this, the functionality of the native protein (in terms of esterase-like activity) is found to be lowered as a result of binding with NOF. The AutoDock-based docking simulation unravels the probable binding location of NOF within the hydrophilic subdomain IA of HSA. The present program also focuses on exploring the dynamical aspects of the drug-protein interaction scenario. The rotational-relaxation dynamics of the protein-bound drug reveals the not-so-common "dip-and-rise" pattern.

  8. Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy.

    Science.gov (United States)

    Jin, Albert J; Lafer, Eileen M; Peng, Jennifer Q; Smith, Paul D; Nossal, Ralph

    2013-03-01

    Atomic force microscopy (AFM), single molecule force spectroscopy (SMFS), and single particle force spectroscopy (SPFS) are used to characterize intermolecular interactions and domain structures of clathrin triskelia and clathrin-coated vesicles (CCVs). The latter are involved in receptor-mediated endocytosis (RME) and other trafficking pathways. Here, we subject individual triskelia, bovine-brain CCVs, and reconstituted clathrin-AP180 coats to AFM-SMFS and AFM-SPFS pulling experiments and apply novel analytics to extract force-extension relations from very large data sets. The spectroscopic fingerprints of these samples differ markedly, providing important new information about the mechanism of CCV uncoating. For individual triskelia, SMFS reveals a series of events associated with heavy chain alpha-helix hairpin unfolding, as well as cooperative unraveling of several hairpin domains. SPFS of clathrin assemblies exposes weaker clathrin-clathrin interactions that are indicative of inter-leg association essential for RME and intracellular trafficking. Clathrin-AP180 coats are energetically easier to unravel than the coats of CCVs, with a non-trivial dependence on force-loading rate.

  9. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

    Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...

  10. Rasch Model Based Analysis of the Force Concept Inventory

    Science.gov (United States)

    Planinic, Maja; Ivanjek, Lana; Susac, Ana

    2010-01-01

    The Force Concept Inventory (FCI) is an important diagnostic instrument which is widely used in the field of physics education research. It is therefore very important to evaluate and monitor its functioning using different tools for statistical analysis. One of such tools is the stochastic Rasch model, which enables construction of linear…

  11. Intersoliton forces in the Wess-Zumino model

    CERN Document Server

    Portugues, R; Portugues, Ruben; Townsend, Paul K.

    2002-01-01

    The spectrum of supersymmetric domain wall solitons of the Wess-Zumino model is known to be discontinuous across a curve (of marginal stability) in the moduli space of quartic superpotentials. Here we show how this phenomenom can be understood from the behavior of the long-range inter-soliton force.

  12. Interactive Water Resources Modeling and Model Use: An Overview

    Science.gov (United States)

    Loucks, Daniel P.; Kindler, Janusz; Fedra, Kurt

    1985-02-01

    This serves as an introduction for the following sequence of five papers on interactive water resources and environmental management, policy modeling, and model use. We review some important shortcomings of many management and policy models and argue for improved human-computer-model interaction and communication. This interaction can lead to more effective model use which in turn should facilitate the exploration, analysis, and synthesis of alternative designs, plans, and policies by those directly involved in the planning, management, or policy making process. Potential advantages of interactive modeling and model use, as well as some problems and research needs, are discussed.

  13. Parabolized Stability Equations analysis of nonlinear interactions with forced eigenmodes to control subsonic jet instabilities

    Energy Technology Data Exchange (ETDEWEB)

    Itasse, Maxime, E-mail: Maxime.Itasse@onera.fr; Brazier, Jean-Philippe, E-mail: Jean-Philippe.Brazier@onera.fr; Léon, Olivier, E-mail: Olivier.Leon@onera.fr; Casalis, Grégoire, E-mail: Gregoire.Casalis@onera.fr [Onera - The French Aerospace Lab, F-31055 Toulouse (France)

    2015-08-15

    Nonlinear evolution of disturbances in an axisymmetric, high subsonic, high Reynolds number hot jet with forced eigenmodes is studied using the Parabolized Stability Equations (PSE) approach to understand how modes interact with one another. Both frequency and azimuthal harmonic interactions are analyzed by setting up one or two modes at higher initial amplitudes and various phases. While single mode excitation leads to harmonic growth and jet noise amplification, controlling the evolution of a specific mode has been made possible by forcing two modes (m{sub 1}, n{sub 1}), (m{sub 2}, n{sub 2}), such that the difference in azimuth and in frequency matches the desired “target” mode (m{sub 1} − m{sub 2}, n{sub 1} − n{sub 2}). A careful setup of the initial amplitudes and phases of the forced modes, defined as the “killer” modes, has allowed the minimizing of the initially dominant instability in the near pressure field, as well as its estimated radiated noise with a 15 dB loss. Although an increase of the overall sound pressure has been found in the range of azimuth and frequency analyzed, the present paper reveals the possibility to make the initially dominant instability ineffective acoustically using nonlinear interactions with forced eigenmodes.

  14. Three-dimensional traction force microscopy: a new tool for quantifying cell-matrix interactions.

    Directory of Open Access Journals (Sweden)

    Christian Franck

    Full Text Available The interactions between biochemical processes and mechanical signaling play important roles during various cellular processes such as wound healing, embryogenesis, metastasis, and cell migration. While traditional traction force measurements have provided quantitative information about cell matrix interactions in two dimensions, recent studies have shown significant differences in the behavior and morphology of cells when placed in three-dimensional environments. Hence new quantitative experimental techniques are needed to accurately determine cell traction forces in three dimensions. Recently, two approaches both based on laser scanning confocal microscopy have emerged to address this need. This study highlights the details, implementation and advantages of such a three-dimensional imaging methodology with the capability to compute cellular traction forces dynamically during cell migration and locomotion. An application of this newly developed three-dimensional traction force microscopy (3D TFM technique to single cell migration studies of 3T3 fibroblasts is presented to show that this methodology offers a new quantitative vantage point to investigate the three-dimensional nature of cell-ECM interactions.

  15. Three-dimensional traction force microscopy: a new tool for quantifying cell-matrix interactions.

    Science.gov (United States)

    Franck, Christian; Maskarinec, Stacey A; Tirrell, David A; Ravichandran, Guruswami

    2011-03-29

    The interactions between biochemical processes and mechanical signaling play important roles during various cellular processes such as wound healing, embryogenesis, metastasis, and cell migration. While traditional traction force measurements have provided quantitative information about cell matrix interactions in two dimensions, recent studies have shown significant differences in the behavior and morphology of cells when placed in three-dimensional environments. Hence new quantitative experimental techniques are needed to accurately determine cell traction forces in three dimensions. Recently, two approaches both based on laser scanning confocal microscopy have emerged to address this need. This study highlights the details, implementation and advantages of such a three-dimensional imaging methodology with the capability to compute cellular traction forces dynamically during cell migration and locomotion. An application of this newly developed three-dimensional traction force microscopy (3D TFM) technique to single cell migration studies of 3T3 fibroblasts is presented to show that this methodology offers a new quantitative vantage point to investigate the three-dimensional nature of cell-ECM interactions.

  16. String Interactions in c=1 Matrix Model

    CERN Document Server

    De Boer, J; Verlinde, E; Yee, J T; Boer, Jan de; Sinkovics, Annamaria; Verlinde, Erik; Yee, Jung-Tay

    2004-01-01

    We study string interactions in the fermionic formulation of the c=1 matrix model. We give a precise nonperturbative description of the rolling tachyon state in the matrix model, and discuss S-matrix elements of the c=1 string. As a first step to study string interactions, we compute the interaction of two decaying D0-branes in terms of free fermions. This computation is compared with the string theory cylinder diagram using the rolling tachyon ZZ boundary states.

  17. Forced versus coupled dynamics in Earth system modelling and prediction

    Directory of Open Access Journals (Sweden)

    B. Knopf

    2005-01-01

    Full Text Available We compare coupled nonlinear climate models and their simplified forced counterparts with respect to predictability and phase space topology. Various types of uncertainty plague climate change simulation, which is, in turn, a crucial element of Earth System modelling. Since the currently preferred strategy for simulating the climate system, or the Earth System at large, is the coupling of sub-system modules (representing, e.g. atmosphere, oceans, global vegetation, this paper explicitly addresses the errors and indeterminacies generated by the coupling procedure. The focus is on a comparison of forced dynamics as opposed to fully, i.e. intrinsically, coupled dynamics. The former represents a particular type of simulation, where the time behaviour of one complex systems component is prescribed by data or some other external information source. Such a simplifying technique is often employed in Earth System models in order to save computing resources, in particular when massive model inter-comparisons need to be carried out. Our contribution to the debate is based on the investigation of two representative model examples, namely (i a low-dimensional coupled atmosphere-ocean simulator, and (ii a replica-like simulator embracing corresponding components.Whereas in general the forced version (ii is able to mimic its fully coupled counterpart (i, we show in this paper that for a considerable fraction of parameter- and state-space, the two approaches qualitatively differ. Here we take up a phenomenon concerning the predictability of coupled versus forced models that was reported earlier in this journal: the observation that the time series of the forced version display artificial predictive skill. We present an explanation in terms of nonlinear dynamical theory. In particular we observe an intermittent version of artificial predictive skill, which we call on-off synchronization, and trace it back to the appearance of unstable periodic orbits. We also

  18. Improved Generalized Force Model considering the Comfortable Driving Behavior

    Directory of Open Access Journals (Sweden)

    De-Jie Xu

    2015-01-01

    Full Text Available This paper presents an improved generalized force model (IGFM that considers the driver’s comfortable driving behavior. Through theoretical analysis, we propose the calculation methods of comfortable driving distance and velocity. Then the stability condition of the model is obtained by the linear stability analysis. The problems of the unrealistic acceleration of the leading car existing in the previous models were solved. Furthermore, the simulation results show that IGFM can predict correct delay time of car motion and kinematic wave speed at jam density, and it can exactly describe the driver’s behavior under an urgent case, where no collision occurs. The dynamic properties of IGFM also indicate that stability has improved compared to the generalized force model.

  19. Hydrodynamic Interactions between Two Forced Objects of Arbitrary Shape: II Relative Translation

    CERN Document Server

    Goldfriend, Tomer; Witten, Thomas A

    2015-01-01

    We study the relative translation of two arbitrarily shaped objects, caused by their hydrodynamic interaction as they are forced through a viscous fluid in the limit of zero Reynolds number. It is well known that in the case of two rigid spheres in an unbounded fluid, the hydrodynamic interaction does not produce relative translation. More generally such an effective pair-interaction vanishes in configurations with spatial inversion symmetry, for example, an enantiomorphic pair in mirror image positions has no relative translation. We show that the breaking of inversion symmetry by boundaries of the system accounts for the interactions between two spheres in confined geometries, as observed in experiments. The same general principle also provides new predictions for interactions in other object configurations near obstacles. We examine the time-dependent relative translation of two self-aligning objects, extending the numerical analysis of our preceding publication [Goldfriend, Diamant and Witten, arXiv:1502....

  20. Fragmentary model of exchange interactions

    CERN Document Server

    Kotov, V M

    2000-01-01

    This article makes attempt to refusal from using neutrino for explanation continuous distribution of beta particle energy by conversion to characteristic exchange interaction particles in nucleolus. It is taking formulation for nuclear position with many different fragments. It is computing half-value period of spontaneous fission of heavy nucleolus. (author)

  1. Modeling graphene-substrate interactions

    NARCIS (Netherlands)

    Amlaki, T.

    2016-01-01

    In this thesis I focussed on the interactions between graphene-like materials (grapheme and germanene) and various substrates. The attractive properties of graphene like a high carrier mobility, its single-atomic thickness and its theoretical magic have made graphene a very popular and promising can

  2. Modeling graphene-substrate interactions

    NARCIS (Netherlands)

    Amlaki, Taher

    2016-01-01

    In this thesis I focussed on the interactions between graphene-like materials (grapheme and germanene) and various substrates. The attractive properties of graphene like a high carrier mobility, its single-atomic thickness and its theoretical magic have made graphene a very popular and promising can

  3. Probing molecular interaction between transferrin and anti-transferrin by atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The interaction between transferrin (Tf) and its antibody was investigated by atomic force microscope. Tf-antibody was immobilized on the Au-coated glass slide, and the specific combination between antibody and antigen was also characterized by AFM. The results showed that holo-transferrin was jogged with anti-transferrin, and binded anti-tran- sferrin more tightly than apo-transferrin. The force- distance curves revealed that the affinity of anti-trans- ferrin and holo-transferrin was much stronger than that of apo-transferrin.

  4. Shock Particle Interaction - Fully Resolved Simulations and Modeling

    Science.gov (United States)

    Mehta, Yash; Neal, Chris; Jackson, Thomas L.; Balachandar, S. "Bala"; Thakur, Siddharth

    2016-11-01

    Currently there is a substantial lack of fully resolved data for shock interacting with multiple particles. In this talk we will fill this gap by presenting results of shock interaction with 1-D array and 3-D structured arrays of particles. Objectives of performing fully resolved simulations of shock propagation through packs of multiple particles are twofold, 1) To understand the complicated physical phenomena occurring during shock particle interaction, and 2) To translate the knowledge from microscale simulations in building next generation point-particle models for macroscale simulations that can better predict the motion (forces) and heat transfer for particles. We compare results from multiple particle simulations against the single particle simulations and make relevant observations. The drag history and flow field for multiple particle simulations are markedly different from those of single particle simluations, highlighting the effect of neighboring particles. We propose new models which capture this effect of neighboring particles. These models are called Pair-wise Interaction Extended Point Particle models (PIEP). Effect of multiple neighboring particles is broken down into pair-wise interactions, and these pair-wise interactions are superimposed to get the final model U.S. Department of Energy, National Nuclear Security Administration, Advanced Simulation and Computing Program, as a Cooperative Agreement under the Predictive Science Academic Alliance Program, under Contract No. DE-NA0002378.

  5. Effects of wave-induced forcing on a circulation model of the North Sea

    Science.gov (United States)

    Staneva, Joanna; Alari, Victor; Breivik, Øyvind; Bidlot, Jean-Raymond; Mogensen, Kristian

    2017-01-01

    The effect of wind waves on water level and currents during two storms in the North Sea is investigated using a high-resolution Nucleus for European Modelling of the Ocean (NEMO) model forced with fluxes and fields from a high-resolution wave model. The additional terms accounting for wave-current interaction that are considered in this study are the Stokes-Coriolis force, the sea-state-dependent energy and momentum fluxes. The individual and collective role of these processes is quantified and the results are compared with a control run without wave effects as well as against current and water-level measurements from coastal stations. We find a better agreement with observations when the circulation model is forced by sea-state-dependent fluxes, especially in extreme events. The two extreme events, the storm Christian (25-27 October 2013), and about a month later, the storm Xaver (5-7 December 2013), induce different wave and surge conditions over the North Sea. Including the wave effects in the circulation model for the storm Xaver raises the modelled surge by more than 40 cm compared with the control run in the German Bight area. For the storm Christian, a difference of 20-30 cm in the surge level between the wave-forced and the stand-alone ocean model is found over the whole southern part of the North Sea. Moreover, the modelled vertical velocity profile fits the observations very well when the wave forcing is accounted for. The contribution of wave-induced forcing has been quantified indicating that this represents an important mechanism for improving water-level and current predictions.

  6. A Simple Analytical Model for Batoid Wake topology and Propulsive Forces

    Science.gov (United States)

    Valdivia Y Alvarado, Pablo; Srivatsa, Karthik

    2013-11-01

    Batoids swim by forcing waves along their large pectoral fins. These waves determine the topology of the shed wakes and the resulting propulsive forces. An understanding of the relation between fin kinematics and wake topology is essential to control vehicles that use batoid-like fin propulsion. Simulations of the fluid-structure interactions during fin motions provide information of the changes in wake topology and the propulsive forces that result with variations in fin kinematics. However, simulations require computing power usually not available in mobile robots and cannot be used for real time control. An alternative is to develop simple qualitative models whose errors can be compensated by closed loop feedback controllers. Here we describe an analytical model that can be used to predict wake geometry and resulting propulsive forces in batoid-like fins. The model incorporates important fin kinematic parameters such as wave number, amplitude envelope, and flapping frequency. Dye flow visualization and particle image velocimetry along with force measurements confirm the model applicability to batoid-like fin propulsion. This work was funded in whole or in part by the Singapore National Research Foundation (NRF) through the Singapore-MIT Alliance for Research and Technology (SMART).

  7. Mathematical models and methods of localized interaction theory

    CERN Document Server

    Bunimovich, AI

    1995-01-01

    The interaction of the environment with a moving body is called "localized" if it has been found or assumed that the force or/and thermal influence of the environment on each body surface point is independent and can be determined by the local geometrical and kinematical characteristics of this point as well as by the parameters of the environment and body-environment interactions which are the same for the whole surface of contact.Such models are widespread in aerodynamics and gas dynamics, covering supersonic and hypersonic flows, and rarefied gas flows. They describe the influence of light

  8. Modelling time evolving interactions in networks through a non stationary extension of stochastic block models

    OpenAIRE

    2015-01-01

    National audience; In this paper, we focus on the stochastic block model (SBM),a probabilistic tool describing interactions between nodes of a network using latent clusters. The SBM assumes that the networkhas a stationary structure, in which connections of time varying intensity are not taken into account. In other words, interactions between two groups are forced to have the same features during the whole observation time. To overcome this limitation,we propose a partition of the whole time...

  9. Cytoplasmic membrane protonmotive force energizes periplasmic interactions between ExbD and TonB.

    Science.gov (United States)

    Ollis, Anne A; Manning, Marta; Held, Kiara G; Postle, Kathleen

    2009-08-01

    The TonB system of Escherichia coli (TonB/ExbB/ExbD) transduces the protonmotive force (pmf) of the cytoplasmic membrane to drive active transport by high-affinity outer membrane transporters. In this study, chromosomally encoded ExbD formed formaldehyde-linked complexes with TonB, ExbB and itself (homodimers) in vivo. Pmf was required for detectable cross-linking between TonB-ExbD periplasmic domains. Consistent with that observation, the presence of inactivating transmembrane domain mutations ExbD(D25N) or TonB(H20A) also prevented efficient formaldehyde cross-linking between ExbD and TonB. A specific site of periplasmic interaction occurred between ExbD(A92C) and TonB(A150C) and required functional transmembrane domains in both proteins. Conversely, neither TonB, ExbB nor pmf were required for ExbD dimer formation. These data suggest two possible models where either dynamic complex formation occurred through transmembrane domains or the transmembrane domains of ExbD and TonB configure their respective periplasmic domains. Analysis of T7-tagged ExbD with anti-ExbD antibodies revealed that a T7 tag was responsible both for our previous failure to detect T7-ExbD-ExbB and T7-ExbD-TonB formaldehyde-linked complexes and for the concomitant artefactual appearance of T7-ExbD trimers.

  10. Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

    Institute of Scientific and Technical Information of China (English)

    YAN XiuFen; JIANG Nan; MA Jing

    2009-01-01

    A series of theoretical approaches,including conventional FF03 and FF03-based polarization model,as well as the generalized energy-based fragmentation (GEBF) quantum chemistry method,have been applied to investigate the interactions between acetate ion (CH_3COO~-) and the α-subunit of human adult hemoglobin (designated as Hb-α) at four binding sites (Lys16,Lys90,Arg92,and Lys127),respectively.The FF03-based polarizable force fields show that the interaction energies between the CH_3COO~-group and Hb-α follow the trend of Arg92>Lys127>Lys90>Lys16.The complexation of CH_3COO~-with Hb-α is governed by the long-range electrostatic interactions and steric effect.

  11. Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A series of theoretical approaches,including conventional FF03 and FF03-based polarization model,as well as the generalized energy-based fragmentation(GEBF) quantum chemistry method,have been applied to investigate the interactions between acetate ion(CH3COO-) and the α-subunit of human adult hemoglobin(designated as Hb-α) at four binding sites(Lys16,Lys90,Arg92,and Lys127),respectively.The FF03-based polarizable force fields show that the interaction energies between the CH3COO-group and Hb-α follow the trend of Arg92>Lys127>Lys90>Lys16.The complexation of CH3COO-with Hb-α is governed by the long-range electrostatic interactions and steric effect.

  12. Density-dependent effective baryon-baryon interaction from chiral three-baryon forces

    Science.gov (United States)

    Petschauer, Stefan; Haidenbauer, Johann; Kaiser, Norbert; Meißner, Ulf-G.; Weise, Wolfram

    2017-01-01

    A density-dependent effective potential for the baryon-baryon interaction in the presence of the (hyper)nuclear medium is constructed, based on the leading (irreducible) three-baryon forces derived within SU(3) chiral effective field theory. We evaluate the contributions from three classes: contact terms, one-pion exchange and two-pion exchange. In the strangeness-zero sector we recover the known result for the in-medium nucleon-nucleon interaction. Explicit expressions for the ΛN in-medium potential in (asymmetric) nuclear matter are presented. Our results are suitable for implementation into calculations of (hyper)nuclear matter. In order to estimate the low-energy constants of the leading three-baryon forces we introduce the decuplet baryons as explicit degrees of freedom and construct the relevant terms in the minimal non-relativistic Lagrangian. With these, the constants are estimated through decuplet saturation. Utilizing this approximation we provide numerical results for the effect of the three-body force in symmetric nuclear matter and pure neutron matter on the ΛN interaction. A moderate repulsion that increases with density is found in comparison to the free ΛN interaction.

  13. Quantifying the adhesion and interaction forces between Pseudomonas aeruginosa and natural organic matter.

    Science.gov (United States)

    Abu-Lail, Laila I; Liu, Yatao; Atabek, Arzu; Camesano, Terri A

    2007-12-01

    Atomic force microscopy (AFM) was used to characterize interactions between natural organic matter (NOM), and glass or bacteria. Poly(methacrylic acid) (PMA), soil humic Acid (SHA), and Suwannee River humic Acid (SRHA), were adsorbed to silica AFM probes. Adhesion forces (Fadh) for the interaction of organic-probes and glass slides correlated with organic molecular weight (MW), but not with radius of the organic aggregate (R), charge density (Q), or zeta potential (zeta). Two Pseudomonas aeruginosa strains with different lipopolysaccharides (LPS) were chosen: PAO1 (A+B+), whose LPS have common antigen (A-band) + O-antigen (B-band); and mutant AK1401 (A+B-). Fadh between bacteria and organics correlated with organic MW, R, and Q, but not zeta. PAO1 had lower Fadh with silica than NOM, which was attributed to negative charges from the B-band polymers causing electrostatic repulsion. AK1401 adhered stronger to silica than to the organics, perhaps because the absence of the B-band exposed underlying positively charged proteins. DLVO calculations could not explain the differences in the two bacteria or predict qualitative or quantitative trends in interaction forces in these systems. Molecular-level information from AFM studies can bring us closer to understanding the complex nature of bacterial-NOM interactions.

  14. Adhesion force interactions between cyclopentane hydrate and physically and chemically modified surfaces.

    Science.gov (United States)

    Aman, Zachary M; Sloan, E Dendy; Sum, Amadeu K; Koh, Carolyn A

    2014-12-07

    Interfacial interactions between liquid-solid and solid-solid phases/surfaces are of fundamental importance to the formation of hydrate deposits in oil and gas pipelines. This work establishes the effect of five categories of physical and chemical modification to steel on clathrate hydrate adhesive force: oleamide, graphite, citric acid ester, nonanedithiol, and Rain-X anti-wetting agent. Hydrate adhesive forces were measured using a micromechanical force apparatus, under both dry and water-wet surface conditions. The results show that the graphite coating reduced hydrate-steel adhesion force by 79%, due to an increase in the water wetting angle from 42 ± 8° to 154 ± 7°. Two chemical surface coatings (nonanedithiol and the citric acid ester) induced rapid hydrate growth in the hydrate particles; nonanedithiol increased hydrate adhesive force by 49% from the baseline, while the citric acid ester coating reduced hydrate adhesion force by 98%. This result suggests that crystal growth may enable a strong adhesive pathway between hydrate and other crystalline structures, however this effect may be negated in cases where water-hydrocarbon interfacial tension is minimised. When a liquid water droplet was placed on the modified steel surfaces, the graphite and citric acid ester became less effective at reducing adhesive force. In pipelines containing a free water phase wetting the steel surface, chemical or physical surface modifications alone may be insufficient to eliminate hydrate deposition risk. In further tests, the citric acid ester reduced hydrate cohesive forces by 50%, suggesting mild activity as a hybrid anti-agglomerant suppressing both hydrate deposition and particle agglomeration. These results demonstrate a new capability to develop polyfunctional surfactants, which simultaneously limit the capability for hydrate particles to aggregate and deposit on the pipeline wall.

  15. The Characteristics of the Factors That Govern the Preferred Force in the Social Force Model of Pedestrian Movement

    CERN Document Server

    Shuaib, Mohammed Mahmod; Abu-Sulyman, Ibtesam M

    2010-01-01

    The social force model which belongs to the microscopic pedestrian studies has been considered as the supremacy by many researchers and due to the main feature of reproducing the self-organized phenomena resulted from pedestrian dynamic. The Preferred Force which is a measurement of pedestrian's motivation to adapt his actual velocity to his desired velocity is an essential term on which the model was set up. This Force has gone through stages of development: first of all, Helbing and Molnar (1995) have modeled the original force for the normal situation. Second, Helbing and his co-workers (2000) have incorporated the panic situation into this force by incorporating the panic parameter to account for the panic situations. Third, Lakoba and Kaup (2005) have provided the pedestrians some kind of intelligence by incorporating aspects of the decision-making capability. In this paper, the authors analyze the most important incorporations into the model regarding the preferred force. They make comparisons between t...

  16. Role of subgrid-scale modeling in large eddy simulation of wind turbine wake interactions

    DEFF Research Database (Denmark)

    Sarlak, Hamid; Meneveau, C.; Sørensen, Jens Nørkær

    2015-01-01

    A series of simulations are carried out to evaluate specific features of the Large Eddy Simulation (LES) technique in wind turbine wake interactions. We aim to model wake interactions of two aligned model rotors. The effects of the rotor resolution, actuator line force filter size, and Reynolds...

  17. Effects of wave-induced forcing on a circulation model of the North Sea

    Science.gov (United States)

    Staneva, Joanna; Alari, Victor; Breivik, Øyvind; Bidlot, Jean-Raymond; Mogensen, Kristian

    2017-04-01

    The effect of wind waves on water level and currents during two storms in the North Sea is investigated using a high-resolution NEMO model forced with fluxes and fields from a high-resolution wave model. The additional terms accounting for wave-current interaction that are considered in this study are the Stokes-Coriolis force and the sea-state dependent energy and momentum fluxes. The individual and collective role of these processes is quantified and the results are compared with a control run without wave effects as well as against current and water level measurements from coastal stations. We find a better agreement with observations when the circulation model is forced by sea-state dependent fluxes, especially in extreme events. The two extreme events, the storm Christian (25-27 October 2013), and about a month later, the storm Xaver (5-7 December 2013), induce different wave and surge conditions over the North Sea. Including the wave effects in the circulation model for the storm Xaver raises the modelled surge by more than 40 cm compared with the control run in the German Bight area. For the storm Christian, a difference of 20-30 cm in the surge level between the wave-forced and the stand-alone ocean model is found over the whole southern part of the North Sea. Moreover, the modelled vertical velocity profile fits the observations very well when the wave forcing is accounted for. The contribution of wave-induced forcing has been quantified indicating that this represents an important mechanism for improving water level and current predictions.

  18. Applying forces to elastic network models of large biomolecules using a haptic feedback device.

    Science.gov (United States)

    Stocks, M B; Laycock, S D; Hayward, S

    2011-03-01

    Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version.

  19. Modeling of soil-water-structure interaction

    DEFF Research Database (Denmark)

    Tang, Tian

    to dynamic ocean waves. The goal of this research project is to develop numerical soil models for computing realistic seabed response in the interacting offshore environment, where ocean waves, seabed and offshore structure highly interact with each other. The seabed soil models developed are based...... as the developed nonlinear soil displacements and stresses under monotonic and cyclic loading. With the FVM nonlinear coupled soil models as a basis, multiphysics modeling of wave-seabed-structure interaction is carried out. The computations are done in an open source code environment, OpenFOAM, where FVM models...... of Computational Fluid Dynamics (CFD) and structural mechanics are available. The interaction in the system is modeled in a 1-way manner: First detailed free surface CFD calculations are executed to obtain a realistic wave field around a given structure. Then the dynamic structural response, due to the motions...

  20. Use of Atomic Force Microscopy to Study the Multi-Modular Interaction of Bacterial Adhesins to Mucins

    Directory of Open Access Journals (Sweden)

    A. Patrick Gunning

    2016-11-01

    Full Text Available The mucus layer covering the gastrointestinal (GI epithelium is critical in selecting and maintaining homeostatic interactions with our gut bacteria. However, the molecular details of these interactions are not well understood. Here, we provide mechanistic insights into the adhesion properties of the canonical mucus-binding protein (MUB, a large multi-repeat cell–surface adhesin found in Lactobacillus inhabiting the GI tract. We used atomic force microscopy to unravel the mechanism driving MUB-mediated adhesion to mucins. Using single-molecule force spectroscopy we showed that MUB displayed remarkable adhesive properties favouring a nanospring-like adhesion model between MUB and mucin mediated by unfolding of the multiple repeats constituting the adhesin. We obtained direct evidence for MUB self-interaction; MUB–MUB followed a similar binding pattern, confirming that MUB modular structure mediated such mechanism. This was in marked contrast with the mucin adhesion behaviour presented by Galectin-3 (Gal-3, a mammalian lectin characterised by a single carbohydrate binding domain (CRD. The binding mechanisms reported here perfectly match the particular structural organization of MUB, which maximizes interactions with the mucin glycan receptors through its long and linear multi-repeat structure, potentiating the retention of bacteria within the outer mucus layer.

  1. Use of Atomic Force Microscopy to Study the Multi-Modular Interaction of Bacterial Adhesins to Mucins.

    Science.gov (United States)

    Gunning, A Patrick; Kavanaugh, Devon; Thursby, Elizabeth; Etzold, Sabrina; MacKenzie, Donald A; Juge, Nathalie

    2016-11-08

    The mucus layer covering the gastrointestinal (GI) epithelium is critical in selecting and maintaining homeostatic interactions with our gut bacteria. However, the molecular details of these interactions are not well understood. Here, we provide mechanistic insights into the adhesion properties of the canonical mucus-binding protein (MUB), a large multi-repeat cell-surface adhesin found in Lactobacillus inhabiting the GI tract. We used atomic force microscopy to unravel the mechanism driving MUB-mediated adhesion to mucins. Using single-molecule force spectroscopy we showed that MUB displayed remarkable adhesive properties favouring a nanospring-like adhesion model between MUB and mucin mediated by unfolding of the multiple repeats constituting the adhesin. We obtained direct evidence for MUB self-interaction; MUB-MUB followed a similar binding pattern, confirming that MUB modular structure mediated such mechanism. This was in marked contrast with the mucin adhesion behaviour presented by Galectin-3 (Gal-3), a mammalian lectin characterised by a single carbohydrate binding domain (CRD). The binding mechanisms reported here perfectly match the particular structural organization of MUB, which maximizes interactions with the mucin glycan receptors through its long and linear multi-repeat structure, potentiating the retention of bacteria within the outer mucus layer.

  2. Spatial interactions in agent-based modeling

    CERN Document Server

    Ausloos, Marcel; Merlone, Ugo

    2014-01-01

    Agent Based Modeling (ABM) has become a widespread approach to model complex interactions. In this chapter after briefly summarizing some features of ABM the different approaches in modeling spatial interactions are discussed. It is stressed that agents can interact either indirectly through a shared environment and/or directly with each other. In such an approach, higher-order variables such as commodity prices, population dynamics or even institutions, are not exogenously specified but instead are seen as the results of interactions. It is highlighted in the chapter that the understanding of patterns emerging from such spatial interaction between agents is a key problem as much as their description through analytical or simulation means. The chapter reviews different approaches for modeling agents' behavior, taking into account either explicit spatial (lattice based) structures or networks. Some emphasis is placed on recent ABM as applied to the description of the dynamics of the geographical distribution o...

  3. An Interactive Whiteboard Model Survey: Reliable Development

    Directory of Open Access Journals (Sweden)

    Bih-Yaw Shih

    2012-04-01

    Full Text Available Applications and practices of interactive whiteboards (IWBs in school learning is important focus and development trend for developmented countries in recent years. There are rare researches and discussions about IWB teaching materials for course teaching and teaching effectiveness. As for the aspect of academic studies, there is more practical teaching sharing for subjects such as language learning, mathematical learning and physical science learning; however, it is rarely seen empirical research on the application of IWB for educational acceptances of interactive whiteboards. Based on its imporatances, we summarize previous literatures to establish a theoretical model for interactive whiteboards (IWBs. Variables in this model are then discussed to find out the interaction between each other. The contribution of the study develops an innovative model for educational acceptances of interactive whiteboards using hybrid TAM, ECM, and Flow models.

  4. Error sources in atomic force microscopy for dimensional measurements: Taxonomy and modeling

    DEFF Research Database (Denmark)

    Marinello, F.; Voltan, A.; Savio, E.

    2010-01-01

    This paper aimed at identifying the error sources that occur in dimensional measurements performed using atomic force microscopy. In particular, a set of characterization techniques for errors quantification is presented. The discussion on error sources is organized in four main categories......: scanning system, tip-surface interaction, environment, and data processing. The discussed errors include scaling effects, squareness errors, hysteresis, creep, tip convolution, and thermal drift. A mathematical model of the measurement system is eventually described, as a reference basis for errors...

  5. Active contour model based on force field analysis

    Institute of Scientific and Technical Information of China (English)

    HOU Zhi-qiang; HAN Chong-zhao

    2006-01-01

    The traditional snake initial contour should be close to the true boundary of an object of interest in an image;otherwise,an incorrect result will be obtained.Next,active contours have difficulties progressing into boundary concavities.Moreover,the traditional snake as well as almost all of its improved methods can be easily obtained from the local minimum because snake models are nonconvex.An active contour model based on force field analysis (FFA),namely,FFA snake model,is presented in this paper.Based on analyzing force distribution rules of the distance potential force field,a standard is introduced here to distinguish the false one from contour points.The result is not considered as the final solution when the snake energy is minimal.Furthermore,estimation and calculation should be made according to the established standard;only then can the result be considered final.Thus,the snake is prevented from running into the local minimum.The simulation results show that the FFA snake model has a large capture range and can move a snake into the boundary concavities,and that it is able to obtain the object of interest's contour precisely.Compared with the gradient vector flow snake,this new model has a low computational cost.

  6. Modeling Rotating Turbulent Flows with the Body Force Potential Model.

    Science.gov (United States)

    Bhattacharya, Amitabh; Perot, Blair

    2000-11-01

    Like a Reynolds Stress Transport equation model, the turbulent potential model has an explicit Coriolis acceleration term that appears in the model that accounts for rotation effects. In this work the additional secondary effects that system rotation has on the dissipation rate, return-to-isotropy, and fast pressure strain terms are also included in the model. The resulting model is tested in the context of rotating isotropic turbulence, rotating homogeneous shear flow, rotating channel flow, and swirling pipe flow. Many of the model changes are applicable to Reynolds stress transport equation models. All model modifications are frame indifferent.

  7. Attractive particle interaction forces and packing density of fine glass powders.

    Science.gov (United States)

    Parteli, Eric J R; Schmidt, Jochen; Blümel, Christina; Wirth, Karl-Ernst; Peukert, Wolfgang; Pöschel, Thorsten

    2014-09-02

    We study the packing of fine glass powders of mean particle diameter in the range (4-52) μm both experimentally and by numerical DEM simulations. We obtain quantitative agreement between the experimental and numerical results, if both types of attractive forces of particle interaction, adhesion and non-bonded van der Waals forces are taken into account. Our results suggest that considering only viscoelastic and adhesive forces in DEM simulations may lead to incorrect numerical predictions of the behavior of fine powders. Based on the results from simulations and experiments, we propose a mathematical expression to estimate the packing fraction of fine polydisperse powders as a function of the average particle size.

  8. Interaction of red blood cells with a polarized electrode: evidence of long-range intermolecular forces.

    Science.gov (United States)

    Gingell, D; Fornes, J A

    1976-10-01

    We have investigated the electrostatic interaction of glutaraldehyde-fixed human red cells with a polarizable electrode carrying a defined surface charge density which can be varied continuously through a wide range. Cells in a dilute salt solution are unable to adhere to the electrode at high negative charge, but at lower negative charge densities they are reversibly adherent and can be forced off by increasing the negative polarization. Near zero electrode charge they become irreversibly stuck to the electrode and cannot be evicted even at maximum electrode polarization. Calculation of the electrostatic repulsive force using measured charge densities indicates the existence of an attractive force which may be acting over several hundred angstroms.

  9. Understanding Peptide Dendrimer Interactions with Model Cell Membrane Mimics

    DEFF Research Database (Denmark)

    Lind, Tania Kjellerup

    membranes or highly conserved motifs, effectively making resistance due to mutations less likely to develop and spread. For this we studied the conditions to form supported lipid bilayers with basic systems and further established a protocol for producing biomimetic bacterial model membranes via the vesicle...... fusion method, which presents improved means for studying drug-membrane interactions in the future. The interaction mechanism of a family of dendrimers was examined and in particular one dendrimer (BALY) was extensively studied by the combined use of quartz crystal microbalance, atomic force microscopy...... and neutron reection. The application of several complementary surface-sensitive techniques allowed for systematically addressing the interface-related processes and gain insights into different aspects of the interaction. BALY was found to interact via a uidity-dependent mechanism. It inserted into the outer...

  10. Terahertz vibrations of crystalline acyclic and cyclic diglycine: benchmarks for London force correction models.

    Science.gov (United States)

    Juliano, Thomas R; Korter, Timothy M

    2013-10-10

    Terahertz spectroscopy provides direct information concerning weak intermolecular forces in crystalline molecular solids and therefore acts as an excellent method for calibrating and evaluating computational models for noncovalent interactions. In this study, the low-frequency vibrations of two dipeptides were compared, acyclic diglycine and cyclic diglycine, as benchmark systems for gauging the performance of semiempirical London force correction approaches. The diglycine samples were investigated using pulsed terahertz spectroscopy from 10 to 100 cm(-1) and then analyzed using solid-state density functional theory (DFT) augmented with existing London force corrections, as well as a new parametrization (DFT-DX) based on known experimental values. The two diglycine molecules provide a useful test for the applied models given their similarities, but more importantly the differences in the intermolecular forces displayed by each. It was found that all of the considered London force correction models were able to generate diglycine crystal structures of similar accuracy, but considerable variation occurred in their abilities to predict terahertz frequency vibrations. The DFT-DX parametrization was particularly successful in this investigation and shows promise for the improved analysis of low-frequency spectra.

  11. Interactive Multimedia Software on Fundamental Particles and Forces. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Jack Sculley

    1999-04-27

    Research in the SBIR Phase 2 grant number 95 ER 81944 centered on creating interactive multimedia software for teaching basic concepts in particle physics on fundamental particles and forces. The work was undertaken from February 1997 through July 1998. Overall the project has produced some very encouraging results in terms of product development, interest from the general public and interest from potential Phase 3 funders. Although the original Phase 3 publisher, McGraw Hill Home Interactive, was dissolved by its parent company, and other changes in the CD-ROM industry forced them to change their focus from CD-ROM to the Internet, there has been substantial interest from software publishers and online content providers in the content developed in the course of the Phase 2 research. Results are summarized.

  12. INTERACTIONS: DESIGN, IMPLEMENTATION AND EVALUATION OF A COMPUTATIONAL TOOL FOR TEACHING INTERMOLECULAR FORCES IN HIGHER EDUCATION

    Directory of Open Access Journals (Sweden)

    Francisco Geraldo Barbosa

    2015-12-01

    Full Text Available Intermolecular forces are a useful concept that can explain the attraction between particulate matter as well as numerous phenomena in our lives such as viscosity, solubility, drug interactions, and dyeing of fibers. However, studies show that students have difficulty understanding this important concept, which has led us to develop a free educational software in English and Portuguese. The software can be used interactively by teachers and students, thus facilitating better understanding. Professors and students, both graduate and undergraduate, were questioned about the software quality and its intuitiveness of use, facility of navigation, and pedagogical application using a Likert scale. The results led to the conclusion that the developed computer application can be characterized as an auxiliary tool to assist teachers in their lectures and students in their learning process of intermolecular forces.

  13. Interactive Multimedia Software on Fundamental Particles and Forces. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Jack Sculley

    1999-04-27

    Research in the SBIR Phase 2 grant number 95 ER 81944 centered on creating interactive multimedia software for teaching basic concepts in particle physics on fundamental particles and forces. The work was undertaken from February 1997 through July 1998. Overall the project has produced some very encouraging results in terms of product development, interest from the general public and interest from potential Phase 3 funders. Although the original Phase 3 publisher, McGraw Hill Home Interactive, was dissolved by its parent company, and other changes in the CD-ROM industry forced them to change their focus from CD-ROM to the Internet, there has been substantial interest from software publishers and online content providers in the content developed in the course of the Phase 2 research. Results are summarized.

  14. Research on Evacuation Based on Social Force Model

    Science.gov (United States)

    Liu, W.; Deng, Z.; Li, W.; Lin, J.

    2017-09-01

    Crowded centers always cause personnel casualties in evacuation operations. Stampede events often occur by hit, squeeze and crush due to panic. It is of vital important to alleviate such situation. With the deepening of personnel evacuation research, more and more researchers are committed to study individual behaviors and self-organization phenomenon in evacuation process. The study mainly includes: 1, enrich the social force model from different facets such as visual, psychological, external force to descript more realistic evacuation; 2, research on causes and effects of self - organization phenomenon. In this paper, we focus on disorder motion that occurs in the crowded indoor publics, especially the narrow channel and safety exits and other special arteries. We put forward the improved social force model to depict pedestrians' behaviors, an orderly speed-stratification evacuation method to solve disorder problem, and shape-changed export to alleviate congestion. The result of this work shows an improvement of evacuation efficiency by 19.5 %. Guiding pedestrians' direction to slow down the influence of social forces has a guidance function in improving the efficiency of indoor emergency evacuation.

  15. Corrections to the Casimir Force Due to Interactions of Plasmons and Electromagnetic Field

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Considering the interaction between the electromagnetic field and matter field, a concise method is used to calculate the ground-state energy of the interacting system. With the assumption of squeezed-like state, a new vacuum state is obtained for the interacting system. The energy of the new vacuum state is obviously lower than that of unperturbed vacuum state. Based on the new vacuum state, the correction to the Casimir force is obtained.The result shows that the contribution of the interaction is a repulsive one and the Casimir effect is attributed to both electromagnetic field and matter field. On the basis of the obtained results, the recent experimental data can be explained reasonably.

  16. Interaction of quercetin with ovalbumin: Spectroscopic and molecular modeling studies

    Energy Technology Data Exchange (ETDEWEB)

    Lu Yan, E-mail: yanlu2001@sohu.co [College of Chemistry and Environmental Science, Henan Normal University, Xinxiang, Henan 453007 (China); Wang Yunlai; Gao Shenghua; Wang Gongke; Yan Changling; Chen Dejun [College of Chemistry and Environmental Science, Henan Normal University, Xinxiang, Henan 453007 (China)

    2009-09-15

    The binding of quercetin (QCT) to ovalbumin (OVA) in aqueous solution was investigated by molecular spectroscopy and modeling at pH 7.4. The fluorescence, synchronous fluorescence and UV-absorption spectroscopies were employed to study the mode and the mechanism for this interaction. QCT binding is characterized by one high affinity binding site with the association constants of the order of 10{sup 5}. The distance between donor (OVA) and acceptor (QCT) was estimated according to Forster's theory of non-radiation energy transfer. Molecular docking showed that the QCT can bind to the active site of OVA. The binding dynamics was expounded by thermodynamic parameters, molecular modeling and accessible surface area calculation, which entails that hydrophobic interactions, hydrogen bonding and electrostatic forces stabilizes the interaction.

  17. Cold-atom physics using ultrathin optical fibers: light-induced dipole forces and surface interactions.

    Science.gov (United States)

    Sagué, G; Vetsch, E; Alt, W; Meschede, D; Rauschenbeutel, A

    2007-10-19

    The strong evanescent field around ultrathin unclad optical fibers bears a high potential for detecting, trapping, and manipulating cold atoms. Introducing such a fiber into a cold-atom cloud, we investigate the interaction of a small number of cold cesium atoms with the guided fiber mode and with the fiber surface. Using high resolution spectroscopy, we observe and analyze light-induced dipole forces, van der Waals interaction, and a significant enhancement of the spontaneous emission rate of the atoms. The latter can be assigned to the modification of the vacuum modes by the fiber.

  18. Measuring the interaction force between a high temperature superconductor and a permanent magnet

    OpenAIRE

    Valenzuela, S. O.; Jorge, G. A.; Rodriguez, E.

    1999-01-01

    Repulsive and attractive forces are both possible between a superconducting sample and a permanent magnet, and they can give place to magnetic levitation or free-suspension phenomena, respectively. We show experiments to quantify this magnetic interaction which represents a promising field regarding to short-term technological applications of high temperature superconductors. The measuring technique employs an electronic balance and a rare-earth magnet that induces a magnetic moment in a melt...

  19. Mooring Model Experiment and Mooring Line Force Calculation

    Institute of Scientific and Technical Information of China (English)

    向溢; 谭家华; 杨建民; 张承懿

    2001-01-01

    Mooring model experiment and mooring line tension determination are of significance to the design of mooring systems and berthing structures. This paper mainly involves: (a) description and analysis of a mooring model experiment;(b) derivation of static equilibrium equations for a moored ship subjected to wind, current and waves; (c) solution of mo.oring equations with the Monte Carlo method; (d) qualitative analysis of effects of pier piles on mooring line forces. Special emphasis is placed on the derivation ofstatic equilibrium equations, solution method and the mooring model experiment.

  20. A Method for Model Checking Feature Interactions

    DEFF Research Database (Denmark)

    Pedersen, Thomas; Le Guilly, Thibaut; Ravn, Anders Peter;

    2015-01-01

    This paper presents a method to check for feature interactions in a system assembled from independently developed concurrent processes as found in many reactive systems. The method combines and refines existing definitions and adds a set of activities. The activities describe how to populate the ...... the definitions with models to ensure that all interactions are captured. The method is illustrated on a home automation example with model checking as analysis tool. In particular, the modelling formalism is timed automata and the analysis uses UPPAAL to find interactions....

  1. Research on the Earth system multi-body force system dynamical model

    Institute of Scientific and Technical Information of China (English)

    CHEN; Xiaofei; BI; Siwen; WU; Fei; DONG; Qianlin

    2006-01-01

    This paper presents an overview of the binding force and freedom force of Earth system, and describes force moment to point and line and force system in the Earth system. It introduces the force theory of the Earth system multi-body force system from special or equivalent force system of Earth system mechanics, general force and no-power force of Earth system. Finally it describes the force and moment of nodes of Earth system and provides basic model for the research of the Earth system multi-body dynamics.

  2. Force nanoscopy of hydrophobic interactions in the fungal pathogen Candida glabrata.

    Science.gov (United States)

    El-Kirat-Chatel, Sofiane; Beaussart, Audrey; Derclaye, Sylvie; Alsteens, David; Kucharíková, Soňa; Van Dijck, Patrick; Dufrêne, Yves F

    2015-02-24

    Candida glabrata is an opportunistic human fungal pathogen which binds to surfaces mainly through the Epa family of cell adhesion proteins. While some Epa proteins mediate specific lectin-like interactions with human epithelial cells, others promote adhesion and biofilm formation on plastic surfaces via nonspecific interactions that are not yet elucidated. We report the measurement of hydrophobic forces engaged in Epa6-mediated cell adhesion by means of atomic force microscopy (AFM). Using single-cell force spectroscopy, we found that C. glabrata wild-type (WT) cells attach to hydrophobic surfaces via strongly adhesive macromolecular bonds, while mutant cells impaired in Epa6 expression are weakly adhesive. Nanoscale mapping of yeast cells using AFM tips functionalized with hydrophobic groups shows that Epa6 is massively exposed on WT cells and conveys strong hydrophobic properties to the cell surface. Our results demonstrate that Epa6 mediates strong hydrophobic interactions, thereby providing a molecular basis for the ability of this adhesin to drive biofilm formation on abiotic surfaces.

  3. An investigation of ab initio shell-model interactions derived by no-core shell model

    Science.gov (United States)

    Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing

    2016-09-01

    The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.

  4. Integral bubble and jet models with pressure forces

    Science.gov (United States)

    Vulfson, A. N.; Nikolaev, P. V.

    2017-07-01

    Modifications of integral bubble and jet models including the pressure force are proposed. Exact solutions are found for the modified model of a stationary convective jet from a point source of buoyancy and momentum. The exact solutions are compared against analytical solutions of the integral models for a stationary jet that are based on the approximation of the vertical boundary layer. It is found that the modified integral models of convective jets retain the power-law dependences on the altitude for the vertical velocity and buoyancy obtained in classical models. For a buoyant jet in a neutrally stratified atmosphere, the inclusion of the pressure force increases the amplitude of buoyancy and decreases the amplitude of vertical velocity. The total amplitude change is about 10%. It is shown that in this model there is a dynamic invariant expressing the law of a uniform distribution of the potential and kinetic energy along the jet axis. For a spontaneous jet rising in an unstably stratified atmosphere, the inclusion of the pressure force retains the amplitude of buoyancy and increases the amplitude of vertical velocity by about 15%. It is shown that in the model of a spontaneous jet there is a dynamic invariant expressing the law of a uniform distribution of the available potential and kinetic energy along the jet axis. The results are of interest for the problems of anthropogenic pollution diffusion in the air and water environments and the formulation of models for statistical and stochastic ensembles of thermals in a mass-flux parameterization of turbulent moments.

  5. Dynamical Models of Dyadic Interactions with Delay

    CERN Document Server

    Bielczyk, Natalia; Płatkowski, Tadeusz

    2012-01-01

    When interpersonal interactions between individuals are described by the (discrete or continuous) dynamical systems, the interactions are usually assumed to be instantaneous: the rates of change of the actual states of the actors at given instant of time are assumed to depend on their states at the same time. In reality the natural time delay should be included in the corresponding models. We investigate a general class of linear models of dyadic interactions with a constant discrete time delay. We prove that in such models the changes of stability of the stationary points from instability to stability or vice versa occur for various intervals of the parameters which determine the intensity of interactions. The conditions guaranteeing arbitrary number (zero, one ore more) of switches are formulated and the relevant theorems are proved. A systematic analysis of all generic cases is carried out. It is obvious that the dynamics of interactions depend both on the strength of reactions of partners on their own sta...

  6. Matrix models with Penner interaction inspired by interacting ribonucleic acid

    Indian Academy of Sciences (India)

    Pradeep Bhadola; N Deo

    2015-02-01

    The Penner interaction known in studies of moduli space of punctured Riemann surfaces is introduced and studied in the context of random matrix model of homo RNA. An analytic derivation of the generating function is given and the corresponding partition function is derived numerically. An additional dependence of the structure combinatorics factor on (related to the size of the matrix and the interaction strength) is obtained. This factor has a strong effect on the structure combinatorics in the low regime. Databases are scanned for real ribonucleic acid (RNA) structures and pairing information for these RNA structures is computationally extracted. Then the genus is calculated for every structure and plotted as a function of length. The genus distribution function is compared with the prediction from the nonlinear (NL) model. The specific heat and distribution of structure with temperature calculated from the NL model shows that the NL inter-action is biased towards planar structures. The second derivative of specific heat changes phase from a double peaked function for small to a single peak for large . Detailed analysis reveals the presence of the double peak only for genus 0 structures, the higher genii behave normally with . Comparable behaviour is found in studies involving interactions of RNA with osmolytes and monovalent cations in unfolding experiments.

  7. Towards a unified realistic shell-model Hamiltonian with the monopole-based universal force

    CERN Document Server

    Kaneko, K; Sun, Y; Tazaki, S

    2013-01-01

    We propose a unified realistic shell-model Hamiltonian employing the pairing plus multipole Hamiltonian combined with the monopole interaction constructed starting from the monopole-based universal force by Otsuka it et al. (Phys. Rev. Lett. 104, 012501 (2010)). It is demonstrated that the proposed PMMU model can consistently describe a large amount of spectroscopic data as well as binding energies in the pf and pf5/2g9/2 shell spaces, and could serve as a practical shell model for even heavier mass regions.

  8. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

    Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...... by various electronic structure methods, where part of the enzyme is represented by a force field description and the effects of the solvent are represented by a continuum model. The relative energies vary by several hundreds of kJ/mol between the transition structures, and tests showed that a large part...... of this variation is due to changes in the enzyme structure at distances more than 5 Å from the active site. There are significant differences between the results obtained by pure quantum methods and those from mixed quantum and molecular mechanics methods....

  9. Guided crowd dynamics via modified social force model

    Science.gov (United States)

    Yang, Xiaoxia; Dong, Hairong; Wang, Qianling; Chen, Yao; Hu, Xiaoming

    2014-10-01

    Pedestrian dynamics is of great theoretical significance for strategy design of emergency evacuation. Modification of pedestrian dynamics based on the social force model is presented to better reflect pedestrians' behavioral characteristics in emergency. Specifically, the modified model can be used for guided crowd dynamics in large-scale public places such as subway stations and stadiums. This guided crowd model is validated by explicitly comparing its density-speed and density-flow diagrams with fundamental diagrams. Some social phenomena such as gathering, balance and conflicts are clearly observed in simulation, which further illustrate the effectiveness of the proposed modeling method. Also, time delay for pedestrians with time-dependent desired velocities is observed and explained using the established model in this paper. Furthermore, this guided crowd model is applied to the simulation system of Beijing South Railway Station for predictive evacuation experiments.

  10. Using Interaction Scenarios to Model Information Systems

    DEFF Research Database (Denmark)

    Bækgaard, Lars; Bøgh Andersen, Peter

    The purpose of this paper is to define and discuss a set of interaction primitives that can be used to model the dynamics of socio-technical activity systems, including information systems, in a way that emphasizes structural aspects of the interaction that occurs in such systems. The primitives...

  11. Effect of attractive interactions between polymers on the effective force acting between colloids immersed in a polymer system: Analytic liquid-state theory.

    Science.gov (United States)

    Chervanyov, A I

    2016-12-28

    By making use of the polymer reference interaction site model, we analytically study the effect of attractive interactions between polymers on the effective forces acting between colloids immersed in a polymer system. The performed theoretical analysis has no restrictions with respect to the polymer density and relative sizes of the colloids and polymers. The polymer mediated (PM) potential acting between colloids is shown to significantly depend on the strength and range of the polymer-polymer interactions. In the nano-particle limit, where the colloid radius is much smaller than the polymer gyration radius, the presence of attractive polymer-polymer interactions causes only quantitative changes to the PM potential. In the opposite limit of relatively large colloids, the polymer-polymer interactions revert the sign of the total effective force acting between colloids so that this force becomes attractive at sufficiently large polymer densities. With the objective to study an intricate interplay between the attractive PM forces and steric repulsion in different polymer density regimes, we calculate the second virial coefficient B of the total effective potential acting between colloids. The dependence of B on the polymer density is discussed in detail, revealing several novel features of the PM interactions caused by the presence of attractive polymer-polymer interactions.

  12. Air Force Enlisted Personnel Retention-Accession Model.

    Science.gov (United States)

    1980-06-01

    axes are made, with the implcation that they are career choices. In this model, corner or interior solutions may occur with interior or mixed career...with the enlistment data for mental category IV and high school 32 ...... *1 non-graduates, suggests that for all practical purposes the Air Force...the full information available and should, other things equal, provide the best point estimates. Except for the 1959-1967 period, the point estimate

  13. Modeling Tractive Force Requirements of Wheel Tractors for Disc Harrowing in Loamy Sand Soil

    Directory of Open Access Journals (Sweden)

    S O Nkakini

    2012-10-01

    Full Text Available In this research study, disc harrowing operations in a loamy sand soil, on an experimental plot of twenty different soil moisture levels at tillage speeds of 1.94m/s, 2.22m/s and 2.5m/s were conducted, using trace tractor techniques. The independent variables: drawbar pull force, rolling (motion resistance, wheel slip, moisture content, cone index, wheel numeric, contact pressure, speed, width of harrow, depth of harrow, and dependent variable (Tractive force were measured. Mathematical models using dimensional analysis, describing the tractor tyre-soil interaction were developed and validated. Regression analysis, was used to depict the relationships between independent variables and dependent variable. Analysis of variance using Randomized Complete Block Design in two way analysis was also used to study the effects and interactions of variables on tractive forces.Validation results of the developed tractive force models conducted, revealed that harrowing operations recorded the highest coefficient of determination, R2 = 0.995 at 2.5m/s tillage speed, while R2 =0.990 and 0. 9 were obtained at tillage speeds of 1.94m/s and 2,22m/s respectively. Analysis of variance between measured and predicted tractive forces showed correlation coefficients, R2 = 0.9308, 0.8999, 0.9958 and standard errors of 0.5844, 0.8628 and 0.78476 for harrowing at tillage speeds of 1.94m/s, 2.22m/s, and 2.5m/s respectively. The residuals analysis ranged from between – 138.95 and 48.7117, -98.6106 and 451.474, -33.3709 and 32.5384,and percentage (% errors from -0.83458466 and 0.27430385, -0.396874637 and 2.546385 and -0.191731686 and 0.189232 respectively. These indicate that there are no significant difference (P > 0.05 between the measured and predicted tractive forces, which are clear evidences of the test of goodness of fits of the models Tillage speed of 2.5m/s illustrated the highest correlation coefficient of 0.9958 in this tillage operation. The tractive force

  14. Information Retrieval Interaction: an Analysis of Models

    Directory of Open Access Journals (Sweden)

    Farahnaz Sadoughi

    2012-03-01

    Full Text Available Information searching process is an interactive process; thus users has control on searching process, and they can manage the results of the search process. In this process, user's question became more mature, according to retrieved results. In addition, on the side of the information retrieval system, there are some processes that could not be realized, unless by user. Practically, this issue, is egregious in “Interaction” -i.e. process of user connection to other system elements- and in “Relevance judgment”. This paper had a glance to existence of “Interaction” in information retrieval, in first. Then the tradition model of information retrieval and its strenght and weak points were reviewed. Finally, the current models of interactive information retrieval includes: Belkin episodic model, Ingwersen cognitive model, Sarasevic stratified model, and Spinks interactive feedback model were elucidated.

  15. Syndetic model of fundamental interactions

    Directory of Open Access Journals (Sweden)

    Ernest Ma

    2015-02-01

    Full Text Available The standard model of quarks and leptons is extended to connect three outstanding issues in particle physics and astrophysics: (1 the absence of strong CP nonconservation, (2 the existence of dark matter, and (3 the mechanism of nonzero neutrino masses, and that of the first family of quarks and leptons, all in the context of having only one Higgs boson in a renormalizable theory. Some phenomenological implications are discussed.

  16. Alternative methods for specification of observed forcing in single-column models and cloud system models

    Science.gov (United States)

    Randall, David A.; Cripe, Douglas G.

    1999-10-01

    We discuss alternative methods for prescribing advective tendencies in single-column models (SCMs) and cloud system models. These include "revealed forcing," in which the total advective tendency is prescribed from observations; "horizontal advective forcing," in which the horizontal advective tendencies are prescribed, together with the observed vertical motion which is combined with the predicted sounding to determine the tendencies due to vertical advection; and "relaxation forcing," in which the horizontal advective tendencies are computed by relaxing the sounding toward the observed upstream sounding, with a relaxation timescale determined by the time required for the wind to carry parcels across the grid column. When relaxation forcing is used, the horizontal advective tendencies can be diagnosed from the model output and compared with the corresponding observed tendencies. We present SCM results to illustrate these three forcing methods, based on data from several field experiments in both the tropics and the midlatitudes. Each method is shown to have its strengths and weaknesses. Overall, the results presented here do not show unambiguous differences between revealed forcing and horizontal advective forcing. The two methods appear to be generally comparable. Revealed forcing may therefore be preferred for its simplicity. Relaxation forcing guarantees realistic soundings of the state variables but can produce large errors in parameterized processes which are driven by rates (e.g., fluxes) rather than states. In particular, relaxation forcing gives large errors in the precipitation rate in this model. We demonstrate that relaxation forcing leads to unrealistically high (low) precipitation in versions of the model which tend to produce unrealistically dry (humid) soundings. The observed horizontal advective tendencies in the tropics are so weak, especially for temperature, that small absolute errors in the diabatic tendencies diagnosed with relaxation forcing

  17. Advances in modeling of biomolecular interactions

    Institute of Scientific and Technical Information of China (English)

    Cong-zhongCAI; Ze-rongLI; Wan-luWANG; Yu-zongCHEN

    2004-01-01

    Modeling of molecular interactions is increasingly used in life science research and biotechnology development.Examples are computer aided drug design, prediction of protein interactions with other molecules, and simulation of networks of biomolecules in a particular process in human body. This article reviews recent progress in the related fields and provides a brief overview on the methods used in molecular modeling of biological systems.

  18. Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.

    Science.gov (United States)

    Stark, Austin C; Andrews, Casey T; Elcock, Adrian H

    2013-09-10

    Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.

  19. Mathematical models for plant-herbivore interactions

    Science.gov (United States)

    Feng, Zhilan; DeAngelis, Donald L.

    2017-01-01

    Mathematical Models of Plant-Herbivore Interactions addresses mathematical models in the study of practical questions in ecology, particularly factors that affect herbivory, including plant defense, herbivore natural enemies, and adaptive herbivory, as well as the effects of these on plant community dynamics. The result of extensive research on the use of mathematical modeling to investigate the effects of plant defenses on plant-herbivore dynamics, this book describes a toxin-determined functional response model (TDFRM) that helps explains field observations of these interactions. This book is intended for graduate students and researchers interested in mathematical biology and ecology.

  20. A Model of Elementary Particle Interactions

    CERN Document Server

    Khan, I

    2000-01-01

    There is a second kind of light which does not interact with our electrons. However it interacts with some of our protons (p) and some of our neutrons (n) which are both of two kinds: protons (p, p`), neutrons (n`, n) differing in the two kinds of charges (Q1, Q2) associated with the two kinds of light. p [p`] and n` [n] have (Q1, Q2) values equal to (1, 1) [(1, 0)] and (0, 0) [(0, 1)] respectively. There is also a second kind of electron (Q2 =1, Q1= 0), equal in mass to our electron (Q1 = -1, Q2= 0), which does not interact with our (the first) kind of light. Three major scenarios S1, S2 and X4 arise. In S1, matter in the solar system on large scales is predominantly neutralized in both kinds of charges and the weak forces of attraction among the sun and planets are due to a fundamental force of nature. However in this scenario we must postulate that human consciousness is locked on to chemical reactions in the retina involving the first kind of light and the first kind of electrons only. It is oblivious to ...

  1. Modeling Effects on Forces in Shear Wall-Frame Structures

    Directory of Open Access Journals (Sweden)

    Adang Surahman

    2015-05-01

    Full Text Available Shear walls are added to a structural system to reduce lateral deformations in moment resisting frames and are designed to carry a major portion of lateral load induced by an earthquake. A small percentage error in the shear wall calculation will have a significant effect on the frame forces. The results show that even a slight difference in structural assumption, or modeling, results in significant differences. Some of these differences are beyond the values that are covered by safety factors for errors in modeling. The differences are more obvious in the upper stories. It is not recommended to overestimate shear wall stiffness, nor underestimate frame stiffness.

  2. Forced thermal cycling of catalytic reactions: experiments and modelling

    DEFF Research Database (Denmark)

    Jensen, Søren; Olsen, Jakob Lind; Thorsteinsson, Sune;

    2007-01-01

    Recent studies of catalytic reactions subjected to fast forced temperature oscillations have revealed a rate enhancement increasing with temperature oscillation frequency. We present detailed studies of the rate enhancement up to frequencies of 2.5 Hz. A maximum in the rate enhancement is observed...... at about 1 Hz. A model for the rate enhancement that includes the surface kinetics and the dynamic partial pressure variations in the reactor is introduced. The model predicts a levelling off of the rate enhancement with frequency at about 1 Hz. The experimentally observed decrease above 1 Hz is explained...... by dynamic thermal limitations of the reactor. (c) 2007 Elsevier B.V. All rights reserved....

  3. Modeling of Laser Material Interactions

    Science.gov (United States)

    Garrison, Barbara

    2009-03-01

    Irradiation of a substrate by laser light initiates the complex chemical and physical process of ablation where large amounts of material are removed. Ablation has been successfully used in techniques such as nanolithography and LASIK surgery, however a fundamental understanding of the process is necessary in order to further optimize and develop applications. To accurately describe the ablation phenomenon, a model must take into account the multitude of events which occur when a laser irradiates a target including electronic excitation, bond cleavage, desorption of small molecules, ongoing chemical reactions, propagation of stress waves, and bulk ejection of material. A coarse grained molecular dynamics (MD) protocol with an embedded Monte Carlo (MC) scheme has been developed which effectively addresses each of these events during the simulation. Using the simulation technique, thermal and chemical excitation channels are separately studied with a model polymethyl methacrylate system. The effects of the irradiation parameters and reaction pathways on the process dynamics are investigated. The mechanism of ablation for thermal processes is governed by a critical number of bond breaks following the deposition of energy. For the case where an absorbed photon directly causes a bond scission, ablation occurs following the rapid chemical decomposition of material. The study provides insight into the influence of thermal and chemical processes in polymethyl methacrylate and facilitates greater understanding of the complex nature of polymer ablation.

  4. Biomechanically inspired modelling of pedestrian-induced forces on laterally oscillating structures

    Science.gov (United States)

    Bocian, M.; Macdonald, J. H. G.; Burn, J. F.

    2012-07-01

    Despite considerable interest among engineers and scientists, bi-directional interaction between walking pedestrians and lively bridges has still not been well understood. In an attempt to bridge this gap a biomechanically inspired model of the human response to lateral bridge motion is presented and explored. The simple inverted pendulum model captures the key features of pedestrian lateral balance and the resulting forces on the structure. The forces include self-excited components that can be effectively modelled as frequency-dependent added damping and mass to the structure. The results of numerical simulations are in reasonable agreement with recent experimental measurements of humans walking on a laterally oscillating treadmill, and in very good agreement with measurements on full-scale bridges. In contrast to many other models of lateral pedestrian loading, synchronisation with the bridge motion is not involved. A parametric study of the model is conducted, revealing that as pedestrians slow down as a crowd becomes more dense, their resulting lower pacing rates generate larger self-excited forces. For typical pedestrian parameters, the potential to generate negative damping arises for any lateral bridge vibration frequency above 0.43 Hz, depending on the walking frequency. Stability boundaries of the combined pedestrian-structure system are presented in terms of the structural damping ratio and pedestrian-to-bridge mass ratio, revealing complex relations between damping demand and bridge and pedestrian frequencies, due to the added mass effect. Finally it is demonstrated that the model can produce simultaneous self-excited forces on multiple structural modes, and a realistic full simulation of a large number of pedestrians, walking randomly and interacting with a bridge, produces structural behaviour in very good agreement with site observations.

  5. Accurate Force Field Development for Modeling Conjugated Polymers.

    Science.gov (United States)

    DuBay, Kateri H; Hall, Michelle Lynn; Hughes, Thomas F; Wu, Chuanjie; Reichman, David R; Friesner, Richard A

    2012-11-13

    The modeling of the conformational properties of conjugated polymers entails a unique challenge for classical force fields. Conjugation imposes strong constraints upon bond rotation. Planar configurations are favored, but the concomitantly shortened bond lengths result in moieties being brought into closer proximity than usual. The ensuing steric repulsions are particularly severe in the presence of side chains, straining angles, and stretching bonds to a degree infrequently found in nonconjugated systems. We herein demonstrate the resulting inaccuracies by comparing the LMP2-calculated inter-ring torsion potentials for a series of substituted stilbenes and bithiophenes to those calculated using standard classical force fields. We then implement adjustments to the OPLS-2005 force field in order to improve its ability to model such systems. Finally, we show the impact of these changes on the dihedral angle distributions, persistence lengths, and conjugation length distributions observed during molecular dynamics simulations of poly[2-methoxy-5-(2'-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV) and poly 3-hexylthiophene (P3HT), two of the most widely used conjugated polymers.

  6. Study of the interactions between endolysin and bacterial peptidoglycan on S. aureus by dynamic force spectroscopy

    Science.gov (United States)

    Liu, Jianli; Zhang, Xuejie; Yang, Hang; Yuan, Jinghe; Wei, Hongping; Yu, Junping; Fang, Xiaohong

    2015-09-01

    The cell wall binding domain (CBD) of bacteriophage lysins can recognize target bacteria with extraordinary specificity through binding to bacterial peptidoglycan, thus it is a promising new probe to identify the corresponding bacterial pathogen. In this work, we used atomic force microscopy (AFM) based single-molecule force spectroscopy to investigate the interaction between the CBD of lysin PlyV12 (PlyV12C) and pathogenic bacterium Staphylococcus aureus (S. aureus). The binding forces of PlyV12C with S. aureus have been measured, and the dissociation process of their binding complex has been characterized. Furthermore, we compared the interactions of PlyV12C-S. aureus and antibody-S. aureus. It is revealed that PlyV12C has a comparable affinity to bacterial peptidoglycans as that of the S. aureus antibody. The results provide new information on the binding properties of lysin CBD with bacterium, and the application of lysin CBD in bacterium detection.

  7. Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins.

    Science.gov (United States)

    Mera-Adasme, Raúl; Sadeghian, Keyarash; Sundholm, Dage; Ochsenfeld, Christian

    2014-11-20

    Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site.

  8. Study of the interactions between endolysin and bacterial peptidoglycan on S. aureus by dynamic force spectroscopy.

    Science.gov (United States)

    Liu, Jianli; Zhang, Xuejie; Yang, Hang; Yuan, Jinghe; Wei, Hongping; Yu, Junping; Fang, Xiaohong

    2015-10-07

    The cell wall binding domain (CBD) of bacteriophage lysins can recognize target bacteria with extraordinary specificity through binding to bacterial peptidoglycan, thus it is a promising new probe to identify the corresponding bacterial pathogen. In this work, we used atomic force microscopy (AFM) based single-molecule force spectroscopy to investigate the interaction between the CBD of lysin PlyV12 (PlyV12C) and pathogenic bacterium Staphylococcus aureus (S. aureus). The binding forces of PlyV12C with S. aureus have been measured, and the dissociation process of their binding complex has been characterized. Furthermore, we compared the interactions of PlyV12C-S. aureus and antibody-S. aureus. It is revealed that PlyV12C has a comparable affinity to bacterial peptidoglycans as that of the S. aureus antibody. The results provide new information on the binding properties of lysin CBD with bacterium, and the application of lysin CBD in bacterium detection.

  9. Mapping force of interaction between PLGA nanoparticle with cell membrane using optical tweezers

    Science.gov (United States)

    Chhajed, Suyash; Gu, Ling; Homayoni, Homa; Nguyen, Kytai; Mohanty, Samarendra

    2011-03-01

    Drug delivery using magnetic (Fe 3 O4) Poly Lactic-co-Glycolic Acid (PLGA) nanoparticles is finding increasing usage in therapeutic applications due to its biodegradability, biocompatibility and targeted localization. Since optical tweezers allow non-contact, highly sensitive force measurement, we utilized optical tweezers for studying interaction forces between the Fe 3 O4 -PLGA nanoparticles with prostate cancer PC3 cells. Presence of Fe 3 O4 within the PLGA shell allowed efficient trapping of these nanoparticles in near-IR optical tweezers. The conglomerated PLGA nanoparticles could be dispersed by use of the optical tweezers. Calibration of trapping stiffness as a function of laser beam power was carried out using equipartition theorem method, where the mean square displacement was measured with high precision using time-lapse fluorescence imaging of the nanoparticles. After the trapped PLGA nanoparticle was brought in close vicinity of the PC3 cell membrane, displacement of the nanoparticle from trap center was measured as a function of time. In short time scale (30 sec) , whiletheforceofinteractionwaswithin 0.2 pN , theforceincreasedbeyond 1 pNatlongertimescales (~ 10 min). We will present the results of the time-varying force of interactions between PLGA nanoparticles with PC3 cells using optical tweezers.

  10. Electroweak and Strong Interactions Phenomenology, Concepts, Models

    CERN Document Server

    Scheck, Florian

    2012-01-01

    Electroweak and Strong Interaction: Phenomenology, Concepts, Models, begins with relativistic quantum mechanics and some quantum field theory which lay the foundation for the rest of the text. The phenomenology and the physics of the fundamental interactions are emphasized through a detailed discussion of the empirical fundamentals of unified theories of strong, electromagnetic, and weak interactions. The principles of local gauge theories are described both in a heuristic and a geometric framework. The minimal standard model of the fundamental interactions is developed in detail and characteristic applications are worked out. Possible signals of physics beyond that model, notably in the physics of neutrinos are also discussed. Among the applications scattering on nucleons and on nuclei provide salient examples. Numerous exercises with solutions make the text suitable for advanced courses or individual study. This completely updated revised new edition contains an enlarged chapter on quantum chromodynamics an...

  11. Numerical modelling of steel tubes under oblique crushing forces

    Science.gov (United States)

    Ismail, A. E.; Rahman, M. Q. Abdul; Nezere, N.; Jamian, S.; Kamarudin, K. A.; Awang, M. K.; Nor, M. K. Mohd; Ibrahim, M. N.; Rasidi Ibrahim, M.; Zulafif Rahim, M.; Fahrul Hassan, Mohd; Nor, Nik Hisyamudin Muhd; Arifin, A. M. T.; Zaini Yunos, Muhamad

    2017-08-01

    This paper presents the numerical assessment of crushing responses of elliptical tubes under crushing forces. Based on the literature survey, tremendous amount of works on the axial crushing behaviour can be found. However, the studies on the oblique crushing responses are rarely found. Therefore, this work investigates numerically the elliptical tubes under compressions. The numerical model of the tubes are developed using ANSYS finite element program. Two important parameters are used such as elliptical ratios and oblique angles. The tubes are compressed quasi-statically and the force-displacement curves are extracted. Then, the area under the curves are calculated and it is represented the performances of energy absorptions. It is found numerically that the introductions of oblique angles during the crushing processes decrease the crushing performances. However, the elliptical-shaped tubes capable to enhance the energy absorption capabilities. On the other hand, the elliptical-shaped tubes produced the enhancement on the energy absorption capabilities.

  12. A Multibody Knee Model Corroborates Subject-Specific Experimental Measurements of Low Ligament Forces and Kinematic Coupling During Passive Flexion.

    Science.gov (United States)

    Kia, Mohammad; Schafer, Kevin; Lipman, Joseph; Cross, Michael; Mayman, David; Pearle, Andrew; Wickiewicz, Thomas; Imhauser, Carl

    2016-05-01

    A multibody model of the knee was developed and the predicted ligament forces and kinematics during passive flexion corroborated subject-specific measurements obtained from a human cadaveric knee that was tested using a robotic manipulator. The model incorporated a novel strategy to estimate the slack length of ligament fibers based on experimentally measured ligament forces at full extension and included multifiber representations for the cruciates. The model captured experimentally measured ligament forces (≤ 5.7 N root mean square (RMS) difference), coupled internal rotation (≤ 1.6 deg RMS difference), and coupled anterior translation (≤ 0.4 mm RMS difference) through 130 deg of passive flexion. This integrated framework of model and experiment improves our understanding of how passive structures, such as ligaments and articular geometries, interact to generate knee kinematics and ligament forces.

  13. Multi-sensorial interaction with a nano-scale phenomenon : the force curve

    CERN Document Server

    Marliere, Sylvain; Florens, Jean-Loup; Marchi, Florence

    2010-01-01

    Using Atomic Force Microscopes (AFM) to manipulate nano-objects is an actual challenge for surface scientists. Basic haptic interfacesbetween the AFM and experimentalists have already been implemented. Themulti-sensory renderings (seeing, hearing and feeling) studied from acognitive point of view increase the efficiency of the actual interfaces. Toallow the experimentalist to feel and touch the nano-world, we add mixedrealities between an AFM and a force feedback device, enriching thus thedirect connection by a modeling engine. We present in this paper the firstresults from a real-time remote-control handling of an AFM by our ForceFeedback Gestural Device through the example of the approach-retract curve.

  14. Intra-Articular Knee Contact Force Estimation During Walking Using Force-Reaction Elements and Subject-Specific Joint Model.

    Science.gov (United States)

    Jung, Yihwan; Phan, Cong-Bo; Koo, Seungbum

    2016-02-01

    Joint contact forces measured with instrumented knee implants have not only revealed general patterns of joint loading but also showed individual variations that could be due to differences in anatomy and joint kinematics. Musculoskeletal human models for dynamic simulation have been utilized to understand body kinetics including joint moments, muscle tension, and knee contact forces. The objectives of this study were to develop a knee contact model which can predict knee contact forces using an inverse dynamics-based optimization solver and to investigate the effect of joint constraints on knee contact force prediction. A knee contact model was developed to include 32 reaction force elements on the surface of a tibial insert of a total knee replacement (TKR), which was embedded in a full-body musculoskeletal model. Various external measurements including motion data and external force data during walking trials of a subject with an instrumented knee implant were provided from the Sixth Grand Challenge Competition to Predict in vivo Knee Loads. Knee contact forces in the medial and lateral portions of the instrumented knee implant were also provided for the same walking trials. A knee contact model with a hinge joint and normal alignment could predict knee contact forces with root mean square errors (RMSEs) of 165 N and 288 N for the medial and lateral portions of the knee, respectively, and coefficients of determination (R2) of 0.70 and -0.63. When the degrees-of-freedom (DOF) of the knee and locations of leg markers were adjusted to account for the valgus lower-limb alignment of the subject, RMSE values improved to 144 N and 179 N, and R2 values improved to 0.77 and 0.37, respectively. The proposed knee contact model with subject-specific joint model could predict in vivo knee contact forces with reasonable accuracy. This model may contribute to the development and improvement of knee arthroplasty.

  15. Modeling Tractive Force Requirements of Wheel tractors For Disc Ploughing in Sandy Loam Soil

    Directory of Open Access Journals (Sweden)

    S O Nkakini

    2012-10-01

    Full Text Available Tractive force models at different tillage speeds were developed using dimensional analysis, describing the tractor tyre - soil interaction. In this research study, disc ploughing on an experimental plot at twenty different soil moisture levels in loamy sand soil was carried out using trace tractor techniques. The independent variables: drawbar pull force, rolling (motion resistance, wheel slip, moisture content, cone index, wheel numeric, contact pressure, speed, width of plough, depth of plough, and dependent variable (Tractive force were measured and compared to computed values. High coefficients of determination R2 = 0.9492, 0.9555 and 0.9447 for ploughing at tillage speeds of 1.94m/s, 2.22m/s and 2.5m/s were obtained respectively. Standard errors of 0.3672552, 0.8628 and 0.8047 and the percentage (% errors of -2.272608059 and 2.45655144,-2.304946155 and 2.523126085,-1.424947801 and 2.020155232 at minimum and maximum values, were obtained. These results are clear evidence of the test of goodness of fit of the models between predictive and measured parameters for ploughing at different tillage speeds. The models were verified and validated by comparing the predicted with the measured tractive forces, and shown to closely followed the experimental results.

  16. Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy.

    Science.gov (United States)

    Yang, Yong; Wang, Hong; Erie, Dorothy A

    2003-02-01

    Atomic force microscopy (AFM) has been applied in many biological investigations in the past 15 years. This review focuses on the application of AFM for quantitatively characterizing the structural and thermodynamic properties of protein-protein and protein-nucleic acid complexes. AFM can be used to determine the stoichiometries and association constants of multiprotein assemblies and to quantify changes in conformations of proteins and protein-nucleic acid complexes. In addition, AFM in solution permits the observation of the dynamic properties of biomolecular complexes and the measurement of intermolecular forces between biomolecules. Recent advances in cryogenic AFM, AFM on two-dimensional crystals, carbon nanotube probes, solution imaging, high-speed AFM, and manipulation capabilities enhance these applications by improving AFM resolution and the dynamic and operative capabilities of the AFM. These developments make AFM a powerful tool for investigating the biomolecular assemblies and interactions that govern gene regulation.

  17. Three-quark interaction: The driving force in the inhomogeneous evolution equations

    Energy Technology Data Exchange (ETDEWEB)

    Bartnik, E.A.; Namyslowski, J.M.

    1984-09-01

    Using perturbative QCD on the light cone (A/sub +/ = 0 gauge), and the Brodsky-Lepage collinear projection, we make a partial-wave projection (in the l/sub z/ component) of the Weinberg equation, and find a set of evolution equations for distribution amplitudes. For l/sub z/not =0 our equations are inhomogeneous, and their solutions show an increasing QCD perturbative effect for the currently available momentum transfers. The driving force of the inhomogenous evolution equations is a three-quark irreducible interaction, which gives terms approx.(1-x)/sup 3/ in the proton's deep-inelastic structure function, breaks the SU(6) symmetry, and contributes to the deviation of the d/u ratio for proton from the value 1/2. That force couples a qq-bar pair to one transverse gluon and one Coulomb gluon.

  18. Measuring the interaction force between a high temperature superconductor and a permanent magnet

    Science.gov (United States)

    Valenzuela, S. O.; Jorge, G. A.; Rodríguez, E.

    1999-11-01

    Repulsive and attractive forces are both possible between a superconducting sample and a permanent magnet, and they can give rise to magnetic levitation or free-suspension phenomena, respectively. We show experiments to quantify this magnetic interaction, which represents a promising field with regard to short-term technological applications of high temperature superconductors. The measuring technique employs an electronic balance and a rare-earth magnet that induces a magnetic moment in a melt-textured YBa2Cu3O7 superconductor immersed in liquid nitrogen. The simple design of the experiments allows a fast and easy implementation in the advanced physics laboratory with a minimum cost. Actual levitation and suspension demonstrations can be done simultaneously as a help to interpret magnetic force measurements.

  19. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.;

    2013-01-01

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were...

  20. Modeling of hydrogen interactions with beryllium

    Energy Technology Data Exchange (ETDEWEB)

    Longhurst, G.R. [Lockheed Martin Idaho Technologies Co., Idaho Falls, ID (United States)

    1998-01-01

    In this paper, improved mathematical models are developed for hydrogen interactions with beryllium. This includes the saturation effect observed for high-flux implantation of ions from plasmas and retention of tritium produced from neutronic transmutations in beryllium. Use of the models developed is justified by showing how they can replicated experimental data using the TMAP4 tritium transport code. (author)

  1. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.

    2013-01-01

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were t...

  2. Supermodel - Interactive Ensemble of Low-dimensional Models

    Science.gov (United States)

    Basnarkov, Lasko; Duane, Gregory; Kocarev, Ljupco

    2013-04-01

    The accuracy of numerical weather prediction is steadily increasing due to the advances in different scientific disciplines. One of them aims at understanding the physics that underlies the atmospheric dynamics. Although the basic laws are well known there is large room for improvement in modeling various small scale processes. Currently they are generally parametrized and thus we are facing dozens of atmospheric models that are used in different meteorological centers around the world. The models are based on the same fluid dynamics laws, but generally differ in spatial resolution, parametrisation of the unresolved processes and also in the corresponding parameter values. Another key factor that contributes to the prediction improvement is the increase of the available computational power. As one consequence the grid resolution is getting smaller. As another, the contemporary numerical weather prediction schemes consider combinations of the outputs of the ensembles of models -- different perturbations of the same model or even different models. Considering interactive ensembles- with dynamical exchange of information between models that run simultaneously-is a novel approach toward improving the weather forecast or climate projection. Although flux exchange between different ocean and atmospheric models has some history, coupling different atmospheric models is rather new. The coupling schemes can be different and the first approaches are those that combine corresponding dynamical variables or tendency components. In this work we present an example with an artificial toy model- the Lorenz 96 model-that shares some properties with the atmosphere. As reality (the atmosphere) we consider one Lorenz 96 class III system, while as its imperfect models are taken three class II systems that have different forcing terms. The interactive ensemble has tendencies that are weighted combinations of the individual models' tendencies. The weights are obtained with statistical

  3. Statistical mechanics models for motion and force planning

    Science.gov (United States)

    Rodriguez, G.

    1990-01-01

    The models of statistical mechanics provide an alternative to the methods of classical mechanics more traditionally used in robotics. They have a potential to: improve analysis of object collisions; handle kinematic and dynamic contact interactions within the same frmework; and reduce the need for perfect deterministic world model information. The statistical mechanics models characterize the state of the system as a probability density function (p.d.f.) whose time evolution is governed by a partial differential equation subject to boundary and initial conditions. The boundary conditions when rigid objects collide reflect the conservation of momentum. The models are being developed to embedd in remote semi-autonomous systems with a need to reason and interact with a multiobject environment.

  4. Interacting Dark Energy Models -- Scalar Linear Perturbations

    CERN Document Server

    Perico, E L D

    2016-01-01

    We extend the dark sector interacting models assuming the dark energy as the sum of independent contributions $\\rho_{\\Lambda} =\\sum_i\\rho_{\\Lambda i}$, associated with (and interacting with) each of the $i$ material species. We derive the linear scalar perturbations for two interacting dark energy scenarios, modeling its cosmic evolution and identifying their different imprints in the CMB and matter power spectrum. Our treatment was carried out for two phenomenological motivated expressions of the dark energy density, $\\rho_\\Lambda(H^2)$ and $\\rho_\\Lambda(R)$. The $\\rho_\\Lambda(H^2)$ description turned out to be a full interacting model, i.e., the dark energy interacts with everyone material species in the universe, whereas the $\\rho_\\Lambda(R)$ description only leads to interactions between dark energy and the non-relativistic matter components; which produces different imprints of the two models on the matter power spectrum. A comparison with the Planck 2015 data was made in order to constrain the free para...

  5. Top-down and bottom-up forces interact at thermal range extremes on American lobster.

    Science.gov (United States)

    Boudreau, Stephanie A; Anderson, Sean C; Worm, Boris

    2015-05-01

    Exploited marine populations are thought to be regulated by the effects of fishing, species interactions and climate. Yet, it is unclear how these forces interact and vary across a species' range. We conducted a meta-analysis of American lobster (Homarus americanus) abundance data throughout the entirety of the species' range, testing competing hypotheses about bottom-up (climate, temperature) vs. top-down (predation, fishing) regulation along a strong thermal gradient. Our results suggest an interaction between predation and thermal range - predation effects dominated at the cold and warm extremes, but not at the centre of the species' range. Similarly, there was consistent support for a positive climate effect on lobster recruitment at warm range extremes. In contrast, fishing effort followed, rather than led changes in lobster abundance over time. Our analysis suggests that the relative effects of top-down and bottom-up forcing in regulating marine populations may intensify at thermal range boundaries and weaken at the core of a species' range.

  6. Empirical tight-binding force model for molecular-dynamics simulation of Si

    Science.gov (United States)

    Wang, C. Z.; Chan, C. T.; Ho, K. M.

    1989-04-01

    A scheme of molecular-dynamics simulation using the empirical tight-binding force model is proposed. The scheme allows the interatomic interactions involved in the molecular dynamics to be determined by first-principles total-energy and electronic-structure calculations without resorting to fitting experimental data. For a first application of the scheme we show that a very simple nearest-neighbor two-center empirical tight-binding force model is able to stabilize the diamond structure of Si within a reasonable temperature range. We also show that the scheme makes possible the quantitative calculation of the temperature dependence of various anharmonic effects such as lattice thermal expansion, temperature-dependent phonon linewidths, and phonon frequency shifts.

  7. Critical Casimir forces between defects in the 2D Ising model

    Science.gov (United States)

    Nowakowski, P.; Maciołek, A.; Dietrich, S.

    2016-12-01

    An exact statistical mechanical derivation is given of the critical Casimir interactions between two defects in a planar lattice-gas Ising model. Each defect is a finite group of nearest-neighbor spins with modified coupling constants. Such a system can be regarded as a model of a binary liquid mixture with the molecules confined to a membrane and the defects mimicking protein inclusions embedded into the membrane. As suggested by recent experiments, certain cellular membranes appear to be tuned to the proximity of a critical demixing point belonging to the two-dimensional Ising universality class. Therefore one can expect the emergence of critical Casimir forces between membrane inclusions. These forces are governed by universal scaling functions, which we derive for simple defects. We prove that the scaling law appearing at criticality is the same for all types of defects considered here.

  8. Polarizable water model for the coarse-grained MARTINI force field.

    Directory of Open Access Journals (Sweden)

    Semen O Yesylevskyy

    2010-06-01

    Full Text Available Coarse-grained (CG simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models.

  9. Measurement strategy and analytic model to determine firing pin force

    Science.gov (United States)

    Lesenciuc, Ioan; Suciu, Cornel

    2016-12-01

    As illustrated in literature, ballistics is a branch of theoretical mechanics, which studies the construction and working principles of firearms and ammunition, their effects, as well as the motions of projectiles and bullets1. Criminalistics identification, as part of judiciary identification represents an activity aimed at finding common traits of different objects, objectives, phenomena and beings, but more importantly, traits that differentiate each of them from similar ones2-4. In judicial ballistics, in the case of rifled firearms it is relatively simple for experts to identify the used weapon from traces left on the projectile, as the rifling of the barrel leaves imprints on the bullet, which remain approximately identical even after the respective weapon is fired 100 times with the same barrel. However, in the case of smoothbore firearms, their identification becomes much more complicated. As the firing cap suffers alterations from being hit by the firing pin, determination of the force generated during impact creates the premises for determining the type of firearm used to shoot the respective cartridge. The present paper proposes a simple impact model that can be used to evaluate the force generated by the firing pin during its impact with the firing cap. The present research clearly showed that each rifle, by the combination of the three investigated parameters (impact force maximum value, its variation diagram, and impact time) leave a unique trace. Application of such a method in ballistics can create the perspectives for formulating clear conclusions that eliminate possible judicial errors in this field.

  10. Ion size effect on colloidal forces within the primitive model

    Directory of Open Access Journals (Sweden)

    J.Wu

    2005-01-01

    Full Text Available The effect of ion size on the mean force between a pair of isolated charged particles in an electrolyte solution is investigated using Monte Carlo simulations within the framework of the primitive model where both colloidal particles and small ions are represented by charged hard spheres and the solvent is treated as a dielectric continuum. It is found that the short-ranged attraction between like-charged macroions diminishes as the diameter of the intermediating divalent counterions and coions increases and the maximum attractive force is approximately a linear function of the counterion diameter. This size effect contradicts the prediction of the Asakura-Oosawa theory suggesting that an increase in the excluded volume of small ions would lead to a stronger depletion between colloidal particles. Interestingly, the simulation results indicate that both the hard-sphere collision and the electrostatic contributions to the mean force are insensitive to the size disparity of colloidal particles with the same average diameter.

  11. Multisite Interactions in Lattice-Gas Models

    Science.gov (United States)

    Einstein, T. L.; Sathiyanarayanan, R.

    For detailed applications of lattice-gas models to surface systems, multisite interactions often play at least as significant a role as interactions between pairs of adatoms that are separated by a few lattice spacings. We recall that trio (3-adatom, non-pairwise) interactions do not inevitably create phase boundary asymmetries about half coverage. We discuss a sophisticated application to an experimental system and describe refinements in extracting lattice-gas energies from calculations of total energies of several different ordered overlayers. We describe how lateral relaxations complicate matters when there is direct interaction between the adatoms, an issue that is important when examining the angular dependence of step line tensions. We discuss the connector model as an alternative viewpoint and close with a brief account of recent work on organic molecule overlayers.

  12. Application of atomic force microscopy to the study of natural and model soil particles.

    Science.gov (United States)

    Cheng, S; Bryant, R; Doerr, S H; Rhodri Williams, P; Wright, C J

    2008-09-01

    The structure and surface chemistry of soil particles has extensive impact on many bulk scale properties and processes of soil systems and consequently the environments that they support. There are a number of physiochemical mechanisms that operate at the nanoscale which affect the soil's capability to maintain native vegetation and crops; this includes soil hydrophobicity and the soil's capacity to hold water and nutrients. The present study used atomic force microscopy in a novel approach to provide unique insight into the nanoscale properties of natural soil particles that control the physiochemical interaction of material within the soil column. There have been few atomic force microscopy studies of soil, perhaps a reflection of the heterogeneous nature of the system. The present study adopted an imaging and force measurement research strategy that accounted for the heterogeneity and used model systems to aid interpretation. The surface roughness of natural soil particles increased with depth in the soil column a consequence of the attachment of organic material within the crevices of the soil particles. The roughness root mean square calculated from ten 25 microm(2) images for five different soil particles from a Netherlands soil was 53.0 nm, 68.0 nm, 92.2 nm and 106.4 nm for the respective soil depths of 0-10 cm, 10-20 cm, 20-30 cm and 30-40 cm. A novel analysis method of atomic force microscopy phase images based on phase angle distribution across a surface was used to interpret the nanoscale distribution of organic material attached to natural and model soil particles. Phase angle distributions obtained from phase images of model surfaces were found to be bimodal, indicating multiple layers of material, which changed with the concentration of adsorbed humic acid. Phase angle distributions obtained from phase images of natural soil particles indicated a trend of decreasing surface coverage with increasing depth in the soil column. This was consistent with

  13. Modeling attacker-defender interactions in information networks.

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Michael Joseph

    2010-09-01

    The simplest conceptual model of cybersecurity implicitly views attackers and defenders as acting in isolation from one another: an attacker seeks to penetrate or disrupt a system that has been protected to a given level, while a defender attempts to thwart particular attacks. Such a model also views all non-malicious parties as having the same goal of preventing all attacks. But in fact, attackers and defenders are interacting parts of the same system, and different defenders have their own individual interests: defenders may be willing to accept some risk of successful attack if the cost of defense is too high. We have used game theory to develop models of how non-cooperative but non-malicious players in a network interact when there is a substantial cost associated with effective defensive measures. Although game theory has been applied in this area before, we have introduced some novel aspects of player behavior in our work, including: (1) A model of how players attempt to avoid the costs of defense and force others to assume these costs; (2) A model of how players interact when the cost of defending one node can be shared by other nodes; and (3) A model of the incentives for a defender to choose less expensive, but less effective, defensive actions.

  14. Modelling earthquake interaction and seismicity statistics

    Science.gov (United States)

    Steacy, S.; Hetherington, A.

    2009-04-01

    The effects of earthquake interaction and fault complexity on seismicity statistics are investigated in a 3D model composed of a number of cellular automata (each representing an individual fault) distributed in a volume. Each automaton is assigned a fractal distribution of strength. Failure occurs when the 3D Coulomb stress on any cell exceeds its strength and stress transfer during simulated earthquake rupture is via nearest-neighbor rules formulated to give realistic stress concentrations. An event continues until all neighboring cells whose stresses exceed their strengths have ruptured and the size of the event is determined from its area and stress drop. Long-range stress interactions are computed following the termination of simulated ruptures using a boundary element code. In practice, these stress perturbations are only computed for events above a certain size (e.g. a threshold length of 10 km) and stresses are updated on nearby structures. Events which occur as a result of these stress interactions are considered to be "triggered" earthquakes and they, in turn, can trigger further seismic activity. The threshold length for computing interaction stresses is a free parameter and hence interaction can be "turned off" by setting this to an unrealistically high value. We consider 3 synthetic fault networks of increasing degrees of complexity - modelled on the North Anatolian fault system, the structures in the San Francisco Bay Area, and the Southern California fault network. We find that the effect of interaction is dramatically different in networks of differing complexity. In the North Anatolian analogue, for example, interaction leads to a decreased number of events, increased b-values, and an increase in recurrence intervals. In the Bay Area model, by contrast, we observe that interaction increases the number of events, decreases the b-values, and has little effect on recurrence intervals. For all networks, we find that interaction can activate mis

  15. Material dependence of Casimir interaction between a sphere and a plate: First analytic correction beyond proximity force approximation

    CERN Document Server

    Teo, L P

    2013-01-01

    We derive analytically the asymptotic behavior of the Casimir interaction between a sphere and a plate when the distance between them, $d$, is much smaller than the radius of the sphere, $R$. The leading order and next-to-leading order terms are derived from the exact formula for the Casimir interaction energy. They are found to depend nontrivially on the dielectric functions of the objects. As expected, the leading order term coincides with that derived using the proximity force approximation. The result on the next-to-leading order term complements that found by Bimonte, Emig and Kardar [Appl. Phys. Lett. \\textbf{100}, 074110 (2012)] using derivative expansion. Numerical results are presented when the dielectric functions are given by the plasma model or the Drude model, with the plasma frequency (for plasma and Drude models) and relaxation frequency (for Drude model) given respectively by 9eV and 0.035eV, the conventional values used for gold metal. It is found that if plasma model is used instead of Drude...

  16. Visualization of interaction between ribosome-inactivating proteins and supercoiled DNA with an atomic force microscope

    Institute of Scientific and Technical Information of China (English)

    吴晓华; 刘望夷; 欧阳振乾; 李民乾

    1997-01-01

    The interaction between ribosome-inactivating proteins (RIPs) and supercoiled DNA was observed with an atomic force microscope (AFM). It was found that RIPs can bind to both supercoiled DNA and the unwound double stranded loop region in supercoiled DNA. The RIPs hound to the supercoils can induce the conformational change of supercoiled DNA. Furthermore, the supercoiled DNA was relaxed and cleaved into nick or linear form by RIPs. It indicated that RIP seemed to be a supercoil-dependent DNA binding protein and exhibited the activity of su-percoil-dependent DNA endonuclease.

  17. Non Linear Force Free Field Modeling for a Pseudostreamer

    Science.gov (United States)

    Karna, Nishu; Savcheva, Antonia; Gibson, Sarah; Tassev, Svetlin V.

    2017-08-01

    In this study we present a magnetic configuration of a pseudostreamer observed on April 18, 2015 on southern west limb embedding a filament cavity. We constructed Non Linear Force Free Field (NLFFF) model using the flux rope insertion method. The NLFFF model produces the three-dimensional coronal magnetic field constrained by observed coronal structures and photospheric magnetogram. SDO/HMI magnetogram was used as an input for the model. The high spatial and temporal resolution of the SDO/AIA allows us to select best-fit models that match the observations. The MLSO/CoMP observations provide full-Sun observations of the magnetic field in the corona. The primary observables of CoMP are the four Stokes parameters (I, Q, U, V). In addition, we perform a topology analysis of the models in order to determine the location of quasi-separatrix layers (QSLs). QSLs are used as a proxy to determine where the strong electric current sheets can develop in the corona and also provide important information about the connectivity in complicated magnetic field configuration. We present the major properties of the 3D QSL and FLEDGE maps and the evolution of 3D coronal structures during the magnetofrictional process. We produce FORWARD-modeled observables from our NLFFF models and compare to a toy MHD FORWARD model and the observations.

  18. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.;

    2013-01-01

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were...... then successfully applied to activity recognition, activity simulation and multi-target tracking. Our method compares favourably with respect to previously reported results using Hidden Markov Models and Relational Particle Filtering....

  19. Stochastic effects in a seasonally forced epidemic model

    Science.gov (United States)

    Rozhnova, G.; Nunes, A.

    2010-10-01

    The interplay of seasonality, the system’s nonlinearities and intrinsic stochasticity, is studied for a seasonally forced susceptible-exposed-infective-recovered stochastic model. The model is explored in the parameter region that corresponds to childhood infectious diseases such as measles. The power spectrum of the stochastic fluctuations around the attractors of the deterministic system that describes the model in the thermodynamic limit is computed analytically and validated by stochastic simulations for large system sizes. Size effects are studied through additional simulations. Other effects such as switching between coexisting attractors induced by stochasticity often mentioned in the literature as playing an important role in the dynamics of childhood infectious diseases are also investigated. The main conclusion is that stochastic amplification, rather than these effects, is the key ingredient to understand the observed incidence patterns.

  20. Stochastic effects in a seasonally forced epidemic model

    CERN Document Server

    Rozhnova, Ganna

    2010-01-01

    The interplay of seasonality, the system's nonlinearities and intrinsic stochasticity is studied for a seasonally forced susceptible-exposed-infective-recovered stochastic model. The model is explored in the parameter region that corresponds to childhood infectious diseases such as measles. The power spectrum of the stochastic fluctuations around the attractors of the deterministic system that describes the model in the thermodynamic limit is computed analytically and validated by stochastic simulations for large system sizes. Size effects are studied through additional simulations. Other effects such as switching between coexisting attractors induced by stochasticity often mentioned in the literature as playing an important role in the dynamics of childhood infectious diseases are also investigated. The main conclusion is that stochastic amplification, rather than these effects, is the key ingredient to understand the observed incidence patterns.

  1. Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo

    CERN Document Server

    Thomas, Robert E; Overy, Catherine; Knowles, Peter J; Alavi, Ali; Booth, George H

    2015-01-01

    Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, "replica" ensemble of walkers, whose population evolves in imaginary time independently from the first, and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality, and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, the present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where suf...

  2. SOFTWARE RELIABILITY MODEL FOR COMPONENT INTERACTION MODE

    Institute of Scientific and Technical Information of China (English)

    Wang Qiang; Lu Yang; Xu Zijun; Han Jianghong

    2011-01-01

    With the rapid progress of component technology,the software development methodology of gathering a large number of components for designing complex software systems has matured.But,how to assess the application reliability accurately with the information of system architecture and the components reliabilities together has become a knotty problem.In this paper,the defects in formal description of software architecture and the limitations in existed model assumptions are both analyzed.Moreover,a new software reliability model called Component Interaction Mode (CIM) is proposed.With this model,the problem for existed component-based software reliability analysis models that cannot deal with the cases of component interaction with non-failure independent and non-random control transition is resolved.At last,the practice examples are presented to illustrate the effectiveness of this model

  3. Charge-Spot Model for Electrostatic Forces in Simulation of Fine Particulates

    Science.gov (United States)

    Walton, Otis R.; Johnson, Scott M.

    2010-01-01

    The charge-spot technique for modeling the static electric forces acting between charged fine particles entails treating electric charges on individual particles as small sets of discrete point charges, located near their surfaces. This is in contrast to existing models, which assume a single charge per particle. The charge-spot technique more accurately describes the forces, torques, and moments that act on triboelectrically charged particles, especially image-charge forces acting near conducting surfaces. The discrete element method (DEM) simulation uses a truncation range to limit the number of near-neighbor charge spots via a shifted and truncated potential Coulomb interaction. The model can be readily adapted to account for induced dipoles in uncharged particles (and thus dielectrophoretic forces) by allowing two charge spots of opposite signs to be created in response to an external electric field. To account for virtual overlap during contacts, the model can be set to automatically scale down the effective charge in proportion to the amount of virtual overlap of the charge spots. This can be accomplished by mimicking the behavior of two real overlapping spherical charge clouds, or with other approximate forms. The charge-spot method much more closely resembles real non-uniform surface charge distributions that result from tribocharging than simpler approaches, which just assign a single total charge to a particle. With the charge-spot model, a single particle may have a zero net charge, but still have both positive and negative charge spots, which could produce substantial forces on the particle when it is close to other charges, when it is in an external electric field, or when near a conducting surface. Since the charge-spot model can contain any number of charges per particle, can be used with only one or two charge spots per particle for simulating charging from solar wind bombardment, or with several charge spots for simulating triboelectric charging

  4. The standard model of electroweak interactions

    CERN Document Server

    Pich, Antonio

    1994-01-01

    What follows is an updated version of the lectures given at the CERN Academic Training (November 1993) and at the Jaca Winter Meeting (February 1994). The aim is to provide a pedagogical introduction to the Standard Model of electroweak interactions. After briefly reviewing the empirical considerations which lead to the construction of the Standard Model Lagrangian, the particle content, structure and symmetries of the theory are discussed. Special emphasis is given to the many phenomenological tests (universality, flavour-changing neutral currents, precision measurements, quark mixing, etc.) which have established this theoretical framework as the Standard Theory of electroweak interactions.

  5. Long-wave forcing for regional atmospheric modelling

    Energy Technology Data Exchange (ETDEWEB)

    Storch, H. von; Langenberg, H.; Feser, F. [GKSS-Forschungszentrum Geesthacht GmbH (Germany). Inst. fuer Hydrophysik

    1999-07-01

    A new method, named 'spectral nudging', of linking a regional model to the driving large-scale model simulated or analyzed by a global model is proposed and tested. Spectral nudging is based on the idea that regional-scale climate statistics are conditioned by the interplay between continental-scale atmospheric conditions and such regional features as marginal seas and mountain ranges. Following this 'downscaling' idea, the regional model is forced to satisfy not only boundary conditions, possibly in a boundary sponge region, but also large-scale flow conditions inside the integration area. We demonstrate that spectral nudging succeeds in keeping the simulated state close to the driving state at large scales, while generating smaller-scale features. We also show that the standard boundary forcing technique in current use allows the regional model to develop internal states conflicting with the large-scale state. It is concluded that spectral nudging may be seen as a suboptimal and indirect data assimilation technique. (orig.) [German] Eine neue Methode, genannt 'spektrales nudging', ein Regionalmodell an das durch ein Globalmodell simulierte grossskalige Antriebsfeld zu koppeln, wird vorgestellt und getestet. Das spektrale nudging basiert auf der Annahme, dass regionale Klimastatistik durch die Wechselwirkung zwischen dem kontinental-skaligen atmosphaerischen Zustand und regionalen Gegebenheiten, wie kleinere Seen und Gebirgszuege, bestimmt wird. Demnach muss das Regionalmodell nicht nur die Randbedingungen erfuellen, sondern auch die grossskaligen Zustaende innerhalb des Integrationsgebietes wiedergeben koennen. Wir zeigen, dass durch das spektrale nudging der grossskalige modellierte Zustand nahe an dem des Antriebsfeldes liegt, ohne die Modellierung regionaler Phaenomene zu beeintraechtigen. Ausserdem zeigen wir, dass das Regionalmodell durch die zur Zeit benutzte Antriebstechnik ueber den Modellrand interne Felder produzieren kann

  6. Hydrophobic pore array surfaces: wetting and interaction forces in water/ethanol mixtures.

    Science.gov (United States)

    Hansson, Petra M; Hormozan, Yashar; Brandner, Birgit D; Linnros, Jan; Claesson, Per M; Swerin, Agne; Schoelkopf, Joachim; Gane, Patrick A C; Thormann, Esben

    2013-04-15

    Interactions between and wetting behavior of structured hydrophobic surfaces using different concentrations of water/ethanol mixtures have been investigated. Silica surfaces consisting of pore arrays with different pore spacings and pore depths were made hydrophobic by silanization. Their static and dynamic contact angles were found to be independent of the pore depth while fewer pores on the surface, i.e. a closer resemblance to a flat surface, gave a lower contact angle. As expected, a higher amount of ethanol facilitated wetting on all the surfaces tested. Confocal Raman microscopy measurements proved both water and ethanol to penetrate into the pores. AFM colloidal probe force measurements clearly showed that formation of air cavitation was hindered between the hydrophobic surfaces in presence of ethanol, and an increase in ethanol concentration was followed by a smaller jump-in distance and a weaker adhesion force. On separation, an immediate jump-out of contact occurred. The measured forces were interpreted as being due to capillary condensation of ethanol between the surfaces giving rise to very unstable cavities immediately rupturing on surface separation.

  7. Effects of interactive technology, teacher scaffolding and feedback on university students' conceptual development in motion and force concepts

    Science.gov (United States)

    Stecklein, Jason Jeffrey

    The utilization of interactive technologies will affect learning in science classrooms of the future. And although these technologies have improved in form and function, their effective employment in university science classrooms has lagged behind the rapid development of new constructivist pedagogies and means of instruction. This dissertation examines the enlistment of instructional technologies, in particular tablet PCs and DyKnow Interactive Software, in a technologically enhanced, university-level, introductory physics course. Results of this qualitative case study of three university students indicate that (1) the use of interactive technology positively affects both student learning within force and motion and self-reported beliefs about physics, (2) ad hoc use of instructional technologies may not sufficient for effective learning in introductory physics, (3) student learners dictate the leveraging of technology in any classroom, and (4) that purposeful teacher structuring of classroom activities with technologies are essential for student construction of knowledge. This includes designing activities to elicit attention and make knowledge visible for low-level content, while augmenting student interactions and modelling procedural steps for higher-level content.

  8. A Model to Predict Rolling Force of Finishing Stands with RBF Neural Networks

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    In view of intrinsic imperfection of traditional models of rolling force, in order to improve the prediction accuracy of rolling force, a new method combining radial basis function (RBF) neural networks with traditional models to predict rolling force was proposed. The off-line simulation indicates that the predicted results are much more accurate than that with traditional models.

  9. Model Testing of Forces in the Reflector Joint and Mooring Forces on Wave Dragon

    DEFF Research Database (Denmark)

    Gilling, Lasse; Kofoed, Jens Peter; Tedd, James

    This report aims to present the results of a test series analysing the forces in the redesigned reflector joint and the forces in the main mooring link. The resluts presented are intended to be used by WD project partners, for the design and construction of the joint on the prototype Wave Dragon...... at Nissum Bredning and for future North Sea scale Wave Dragon. Lengths, forces and other dimentions presented are scaled to the North sea Wave Dragon unless otherwise specified....

  10. Model Testing of Forces in the Reflector Joint and Mooring Forces on Wave Dragon

    DEFF Research Database (Denmark)

    Gilling, Lasse; Kofoed, Jens Peter; Tedd, James

    This report aims to present the results of a test series analysing the forces in the redesigned reflector joint and the forces in the main mooring link. The resluts presented are intended to be used by WD project partners, for the design and construction of the joint on the prototype Wave Dragon...... at Nissum Bredning and for future North Sea scale Wave Dragon. Lengths, forces and other dimentions presented are scaled to the North sea Wave Dragon unless otherwise specified....

  11. Global Quantitative Modeling of Chromatin Factor Interactions

    Science.gov (United States)

    Zhou, Jian; Troyanskaya, Olga G.

    2014-01-01

    Chromatin is the driver of gene regulation, yet understanding the molecular interactions underlying chromatin factor combinatorial patterns (or the “chromatin codes”) remains a fundamental challenge in chromatin biology. Here we developed a global modeling framework that leverages chromatin profiling data to produce a systems-level view of the macromolecular complex of chromatin. Our model ultilizes maximum entropy modeling with regularization-based structure learning to statistically dissect dependencies between chromatin factors and produce an accurate probability distribution of chromatin code. Our unsupervised quantitative model, trained on genome-wide chromatin profiles of 73 histone marks and chromatin proteins from modENCODE, enabled making various data-driven inferences about chromatin profiles and interactions. We provided a highly accurate predictor of chromatin factor pairwise interactions validated by known experimental evidence, and for the first time enabled higher-order interaction prediction. Our predictions can thus help guide future experimental studies. The model can also serve as an inference engine for predicting unknown chromatin profiles — we demonstrated that with this approach we can leverage data from well-characterized cell types to help understand less-studied cell type or conditions. PMID:24675896

  12. Density-dependent effective baryon-baryon interaction from chiral three-baryon forces

    CERN Document Server

    Petschauer, Stefan; Kaiser, Norbert; Meißner, Ulf-G; Weise, Wolfram

    2016-01-01

    A density-dependent effective potential for the baryon-baryon interaction in the presence of the (hyper)nuclear medium is constructed, based on the leading (irreducible) three-baryon forces derived within SU(3) chiral effective field theory. We evaluate the contributions from three classes: contact terms, one-pion exchange and two-pion exchange. In the strangeness-zero sector we recover the known result for the in-medium nucleon-nucleon interaction. Explicit expressions for the Lambda-nucleon in-medium potential in (asymmetric) nuclear matter are presented. Our results are suitable for implementation into calculations of (hyper)nuclear matter. In order to estimate the low-energy constants of the leading three-baryon forces we introduce the decuplet baryons as explicit degrees of freedom and construct the relevant terms in the minimal non-relativistic Lagrangian. With these, the constants are estimated through decuplet saturation. Utilizing this approximation we provide numerical results for the effect of the ...

  13. Vegetation Monitoring with Gaussian Processes and Latent Force Models

    Science.gov (United States)

    Camps-Valls, Gustau; Svendsen, Daniel; Martino, Luca; Campos, Manuel; Luengo, David

    2017-04-01

    Monitoring vegetation by biophysical parameter retrieval from Earth observation data is a challenging problem, where machine learning is currently a key player. Neural networks, kernel methods, and Gaussian Process (GP) regression have excelled in parameter retrieval tasks at both local and global scales. GP regression is based on solid Bayesian statistics, yield efficient and accurate parameter estimates, and provides interesting advantages over competing machine learning approaches such as confidence intervals. However, GP models are hampered by lack of interpretability, that prevented the widespread adoption by a larger community. In this presentation we will summarize some of our latest developments to address this issue. We will review the main characteristics of GPs and their advantages in vegetation monitoring standard applications. Then, three advanced GP models will be introduced. First, we will derive sensitivity maps for the GP predictive function that allows us to obtain feature ranking from the model and to assess the influence of examples in the solution. Second, we will introduce a Joint GP (JGP) model that combines in situ measurements and simulated radiative transfer data in a single GP model. The JGP regression provides more sensible confidence intervals for the predictions, respects the physics of the underlying processes, and allows for transferability across time and space. Finally, a latent force model (LFM) for GP modeling that encodes ordinary differential equations to blend data-driven modeling and physical models of the system is presented. The LFM performs multi-output regression, adapts to the signal characteristics, is able to cope with missing data in the time series, and provides explicit latent functions that allow system analysis and evaluation. Empirical evidence of the performance of these models will be presented through illustrative examples.

  14. Mechanistic Multidimensional Modeling of Forced Convection Boiling Heat Transfer

    Directory of Open Access Journals (Sweden)

    Michael Z. Podowski

    2009-01-01

    Full Text Available Due to the importance of boiling heat transfer in general, and boiling crisis in particular, for the analysis of operation and safety of both nuclear reactors and conventional thermal power systems, extensive efforts have been made in the past to develop a variety of methods and tools to evaluate the boiling heat transfer coefficient and to assess the onset of temperature excursion and critical heat flux (CHF at various operating conditions of boiling channels. The objective of this paper is to present mathematical modeling concepts behind the development of mechanistic multidimensional models of low-quality forced convection boiling, including the mechanisms leading to temperature excursion and the onset of CHF.

  15. Modeling the desired direction in a force-based model for pedestrian dynamics

    CERN Document Server

    Chraibi, Mohcine; Schadschneider, Andreas; Seyfried, Armin

    2012-01-01

    We introduce an enhanced model based on the generalized centrifugal force model. Furthermore, the desired direction of pedestrians is investigated. A new approach leaning on the well-known concept of static and dynamic floor-fields in cellular automata is presented. Numerical results of the model are presented and compared with empirical data.

  16. Extraction of user's navigation commands from upper body force interaction in walker assisted gait

    Directory of Open Access Journals (Sweden)

    Pons José L

    2010-08-01

    Full Text Available Abstract Background The advances in technology make possible the incorporation of sensors and actuators in rollators, building safer robots and extending the use of walkers to a more diverse population. This paper presents a new method for the extraction of navigation related components from upper-body force interaction data in walker assisted gait. A filtering architecture is designed to cancel: (i the high-frequency noise caused by vibrations on the walker's structure due to irregularities on the terrain or walker's wheels and (ii the cadence related force components caused by user's trunk oscillations during gait. As a result, a third component related to user's navigation commands is distinguished. Results For the cancelation of high-frequency noise, a Benedict-Bordner g-h filter was designed presenting very low values for Kinematic Tracking Error ((2.035 ± 0.358·10-2 kgf and delay ((1.897 ± 0.3697·101ms. A Fourier Linear Combiner filtering architecture was implemented for the adaptive attenuation of about 80% of the cadence related components' energy from force data. This was done without compromising the information contained in the frequencies close to such notch filters. Conclusions The presented methodology offers an effective cancelation of the undesired components from force data, allowing the system to extract in real-time voluntary user's navigation commands. Based on this real-time identification of voluntary user's commands, a classical approach to the control architecture of the robotic walker is being developed, in order to obtain stable and safe user assisted locomotion.

  17. Morphodynamic modeling of an embayed beach under wave group forcing

    Science.gov (United States)

    Reniers, A. J. H. M.; Roelvink, J. A.; Thornton, E. B.

    2004-01-01

    The morphodynamic response of the nearshore zone of an embayed beach induced by wave groups is examined with a numerical model. The model utilizes the nonlinear shallow water equations to phase resolve the mean and infragravity motions in combination with an advection-diffusion equation for the sediment transport. The sediment transport associated with the short-wave asymmetry is accounted for by means of a time-integrated contribution of the wave nonlinearity using stream function theory. The two-dimensional (2-D) computations consider wave group energy made up of directionally spread, short waves with a zero mean approach angle with respect to the shore normal, incident on an initially alongshore uniform barred beach. Prior to the 2-D computations, the model is calibrated with prototype flume measurements of waves, currents, and bed level changes during erosive and accretive conditions. The most prominent feature of the 2-D model computations is the development of an alongshore quasi-periodic bathymetry of shoals cut by rip channels. Without directional spreading, the smallest alongshore separation of the rip channels is obtained, and the beach response is self-organizing in nature. Introducing a small amount of directional spreading (less than 2°) results in a strong increase in the alongshore length scales as the beach response changes from self-organizing to being quasi-forced. A further increase in directional spreading leads again to smaller length scales. The hypothesized correlation between the observed rip spacing and wave group forced edge waves over the initially alongshore uniform bathymetry is not found. However, there is a correlation between the alongshore length scales of the wave group-induced quasi-steady flow circulations and the eventual alongshore spacing of the rip channels. This suggests that the scouring associated with the quasi-steady flow induced by the initial wave groups triggers the development of rip channels via a positive feedback

  18. Modelling hadronic interactions in HEP MC generators

    CERN Document Server

    Skands, Peter

    2015-01-01

    HEP event generators aim to describe high-energy collisions in full exclusive detail. They combine perturbative matrix elements and parton showers with dynamical models of less well-understood phenomena such as hadronization, diffraction, and the so-called underlying event. We briefly summarise some of the main concepts relevant to the modelling of soft/inclusive hadron interactions in MC generators, in particular PYTHIA, with emphasis on questions recently highlighted by LHC data.

  19. Defining a 21st Century Air Force (Services) Business Model

    Science.gov (United States)

    2014-05-10

    recognize purchasing habits and preferences of millennials from a marketing perspective in order to develop a relevant services model. Based on... Millennial shopping habits indicate that youthful and future patrons want more on-line and interactive programs. In a recent world-wide survey...conducted by the company, eMarketer, 40 percent of male millennial respondents indicated they would buy everything online if they could. 11 The

  20. Experimental identification and analytical modelling of human walking forces: Literature review

    Science.gov (United States)

    Racic, V.; Pavic, A.; Brownjohn, J. M. W.

    2009-09-01

    Dynamic forces induced by humans walking change simultaneously in time and space, being random in nature and varying considerably not only between different people but also for a single individual who cannot repeat two identical steps. Since these important aspects of walking forces have not been adequately researched in the past, the corresponding lack of knowledge has reflected badly on the quality of their mathematical models used in vibration assessments of pedestrian structures such as footbridges, staircases and floors. To develop better force models which can be used with more confidence in the structural design, an adequate experimental and analytical approach must be taken to account for their complexity. This paper is the most comprehensive review published to date, of 270 references dealing with different experimental and analytical characterizations of human walking loading. The source of dynamic human-induced forces is in fact in the body motion. To date, human motion has attracted a lot of interest in many scientific branches, particularly in medical and sports science, bioengineering, robotics, and space flight programs. Other fields include biologists of various kinds, physiologists, anthropologists, computer scientists (graphics and animation), human factors and ergonomists, etc. It resulted in technologically advanced tools that can help understanding the human movement in more detail. Therefore, in addition to traditional direct force measurements utilizing a force plate and an instrumented treadmill, this review also introduces methods for indirect measurement of time-varying records of walking forces via combination of visual motion tracking (imaging) data and known body mass distribution. The review is therefore an interdisciplinary article that bridges the gaps between biomechanics of human gait and civil engineering dynamics. Finally, the key reason for undertaking this review is the fact that human-structure dynamic interaction and

  1. A fashion model with social interaction

    Science.gov (United States)

    Nakayama, Shoichiro; Nakamura, Yasuyuki

    2004-06-01

    In general, it is difficult to investigate social phenomena mathematically or quantitatively due to non-linear interactions. Statistical physics can provide powerful methods for studying social phenomena with interactions, and could be very useful for them. In this study, we take a focus on fashion as a social phenomenon with interaction. The social interaction considered here are “bandwagon effect” and “snob effect.” In the bandwagon effect, the correlation between one's behavior and others is positive. People feel fashion weary or boring when it is overly popular. This is the snob effect. It is assumed that the fashion phenomenon is formed by the aggregation of individual's binary choice, that is, the fashion is adopted or not. We formulate the fashion phenomenon as the logit model, which is based on the random utility theory in social science, especially economics. The model derived here basically has the similarity with the pioneering model by Weidlich (Phys. Rep. 204 (1991) 1), which was derived from the master equation, the Langevin equation, or the Fokker-Planck equation. This study seems to give the behavioral or behaviormetrical foundation to his model. As a result of dynamical analysis, it is found that in the case that both the bandwagon effect and the snob effect work, periodic or chaotic behavior of fashion occurs under certain conditions.

  2. Parameter Symmetry of the Interacting Boson Model

    CERN Document Server

    Shirokov, A M; Smirnov, Yu F; Shirokov, Andrey M.; Smirnov, Yu. F.

    1998-01-01

    We discuss the symmetry of the parameter space of the interacting boson model (IBM). It is shown that for any set of the IBM Hamiltonian parameters (with the only exception of the U(5) dynamical symmetry limit) one can always find another set that generates the equivalent spectrum. We discuss the origin of the symmetry and its relevance for physical applications.

  3. A yarn interaction model for circular braiding

    NARCIS (Netherlands)

    Ravenhorst, van J.H.; Akkerman, R.

    2016-01-01

    Machine control data for the automation of the circular braiding process has been generated using previously published mathematical models that neglect yarn interaction. This resulted in a significant deviation from the required braid angle at mandrel cross-sectional changes, likely caused by an inc

  4. Intuitionistic preference modeling and interactive decision making

    CERN Document Server

    Xu, Zeshui

    2014-01-01

    This book offers an in-depth and comprehensive introduction to the priority methods of intuitionistic preference relations, the consistency and consensus improving procedures for intuitionistic preference relations, the approaches to group decision making based on intuitionistic preference relations, the approaches and models for interactive decision making with intuitionistic fuzzy information, and the extended results in interval-valued intuitionistic fuzzy environments.

  5. 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

  6. Proximity effect on hydrodynamic interaction between a sphere and a plane measured by force feedback microscopy at different frequencies

    Science.gov (United States)

    Carpentier, Simon; Rodrigues, Mario S.; Charlaix, Elisabeth; Chevrier, Joël

    2015-07-01

    In this article, we measure the viscous damping G″, and the associated stiffness G', of a liquid flow in sphere-plane geometry over a large frequency range. In this regime, the lubrication approximation is expected to dominate. We first measure the static force applied to the tip. This is made possible thanks to a force feedback method. Adding a sub-nanometer oscillation of the tip, we obtain the dynamic part of the interaction with solely the knowledge of the lever properties in the experimental context using a linear transformation of the amplitude and phase change. Using a Force Feedback Microscope (FFM), we are then able to measure simultaneously the static force, the stiffness, and the dissipative part of the interaction in a broad frequency range using a single AFM probe. Similar measurements have been performed by the Surface Force Apparatus (SFA) with a probe radius hundred times bigger. In this context, the FFM can be called nano-SFA.

  7. Proximity effect on hydrodynamic interaction between a sphere and a plane measured by Force Feedback Microscopy at different frequencies

    CERN Document Server

    Carpentier, Simon; Charlaix, Elisabeth; Chevrier, Joel

    2015-01-01

    In this article, we measure the viscous damping $G'',$ and the associated stiffness $G',$ of a liquid flow in sphere-plane geometry in a large frequency range. In this regime, the lubrication approximation is expected to dominate. We first measure the static force applied to the tip. This is made possible thanks to a force feedback method. Adding a sub-nanometer oscillation of the tip, we obtain the dynamic part of the interaction with solely the knowledge of the lever properties in the experimental context using a linear transformation of the amplitude and phase change. Using a Force Feedback Microscope (FFM)we are then able to measure simultaneously the static force, the stiffness and the dissipative part of the interaction in a broad frequency range using a single AFM probe. Similar measurements have been performed by the Surface Force Apparatus with a probe radius hundred times bigger. In this context the FFM can be called nano-SFA.

  8. Statistical pairwise interaction model of stock market

    Science.gov (United States)

    Bury, Thomas

    2013-03-01

    Financial markets are a classical example of complex systems as they are compound by many interacting stocks. As such, we can obtain a surprisingly good description of their structure by making the rough simplification of binary daily returns. Spin glass models have been applied and gave some valuable results but at the price of restrictive assumptions on the market dynamics or they are agent-based models with rules designed in order to recover some empirical behaviors. Here we show that the pairwise model is actually a statistically consistent model with the observed first and second moments of the stocks orientation without making such restrictive assumptions. This is done with an approach only based on empirical data of price returns. Our data analysis of six major indices suggests that the actual interaction structure may be thought as an Ising model on a complex network with interaction strengths scaling as the inverse of the system size. This has potentially important implications since many properties of such a model are already known and some techniques of the spin glass theory can be straightforwardly applied. Typical behaviors, as multiple equilibria or metastable states, different characteristic time scales, spatial patterns, order-disorder, could find an explanation in this picture.

  9. The interaction of respiration and visual feedback on the control of force and neural activation of the agonist muscle.

    Science.gov (United States)

    Baweja, Harsimran S; Patel, Bhavini K; Neto, Osmar P; Christou, Evangelos A

    2011-12-01

    The purpose of this study was to compare force variability and the neural activation of the agonist muscle during constant isometric contractions at different force levels when the amplitude of respiration and visual feedback were varied. Twenty young adults (20-32 years, 10 men and 10 women) were instructed to accurately match a target force at 15% and 50% of their maximal voluntary contraction (MVC) with abduction of the index finger while controlling their respiration at different amplitudes (85%, 100% and 125% normal) in the presence and absence of visual feedback. Each trial lasted 22s and visual feedback was removed from 8-12 and 16-20s. Each subject performed three trials with each respiratory condition at each force level. Force variability was quantified as the standard deviation of the detrended force data. The neural activation of the first dorsal interosseus (FDI) was measured with bipolar surface electrodes placed distal to the innervation zone. Relative to normal respiration, force variability increased significantly only during high-amplitude respiration (∼63%). The increase in force variability from normal- to high-amplitude respiration was strongly associated with amplified force oscillations from 0 to 3 Hz (R(2) ranged from .68 to .84, phigh-amplitude respiration and visual feedback of force interact and amplify force variability in young adults during moderate levels of effort.

  10. Structural impact of cations on lipid bilayer models: nanomechanical properties by AFM-force spectroscopy.

    Science.gov (United States)

    Redondo-Morata, Lorena; Giannotti, Marina I; Sanz, Fausto

    2014-02-01

    Atomic Force Microscopy (AFM) has become an invaluable tool for studying the micro- and nanoworlds. As a stand-alone, high-resolution imaging technique and force transducer, it defies most other surface instrumentation in ease of use, sensitivity and versatility. The main strength of AFM relies on the possibility to operate in an aqueous environment on a wide variety of biological samples, from single molecules - DNA or proteins - to macromolecular assemblies like biological membranes. Understanding the effect of mechanical stress on membranes is of primary importance in biophysics, since cells are known to perform their function under a complex combination of forces. In the later years, AFM-based Force-Spectroscopy (AFM-FS) has provided a new vista on membrane mechanics in a confined area within the nanometer realm, where most of the specific molecular interactions take place. Lipid membranes are electrostatically charged entities that physiologically coexist with electrolyte solutions. Thus, specific interactions with ions are a matter of considerable interest. The distribution of ions in the solution and their interaction with the membranes are factors that substantially modify the structure and dynamics of the cell membranes. Furthermore, signaling processes are modified by the membrane capability of retaining ions. Supported Lipid Bilayers (SLBs) are a versatile tool to investigate phospholipid membranes mimicking biological surfaces. In the present contribution, we review selected experiments on the mechanical stability of SLBs as models of lipid membranes by means of AFM-FS, with special focus on the effect of cations and ionic strength in the overall nanomechanical stability.

  11. Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations.

    Science.gov (United States)

    Mao, Yuezhi; Demerdash, Omar; Head-Gordon, Martin; Head-Gordon, Teresa

    2016-11-08

    AMOEBA is a molecular mechanics force field that addresses some of the shortcomings of a fixed partial charge model, by including permanent atomic point multipoles through quadrupoles, as well as many-body polarization through the use of point inducible dipoles. In this work, we investigate how well AMOEBA formulates its non-bonded interactions, and how it implicitly incorporates quantum mechanical effects such as charge penetration (CP) and charge transfer (CT), for water-water and water-ion interactions. We find that AMOEBA's total interaction energies, as a function of distance and over angular scans for the water dimer and for a range of water-monovalent cations, agree well with an advanced density functional theory (DFT) model, whereas the water-halides and water-divalent cations show significant disagreement with the DFT result, especially in the compressed region when the two fragments overlap. We use a second-generation energy decomposition analysis (EDA) scheme based on absolutely localized molecular orbitals (ALMOs) to show that in the best cases AMOEBA relies on cancellation of errors by softening of the van der Waals (vdW) wall to balance permanent electrostatics that are too unfavorable, thereby compensating for the missing CP effect. CT, as another important stabilizing effect not explicitly taken into account in AMOEBA, is also found to be incorporated by the softened vdW interaction. For the water-halides and water-divalent cations, this compensatory approach is not as well executed by AMOEBA over all distances and angles, wherein permanent electrostatics remains too unfavorable and polarization is overdamped in the former while overestimated in the latter. We conclude that the DFT-based EDA approach can help refine a next-generation AMOEBA model that either realizes a better cancellation of errors for problematic cases like those illustrated here, or serves to guide the parametrization of explicit functional forms for short-range contributions from

  12. Evaluating interaction forces between BSA and rabbit anti-BSA in sulphathiazole sodium, tylosin and levofloxacin solution by AFM

    Science.gov (United States)

    Wang, Congzhou; Wang, Jianhua; Deng, Linhong

    2011-11-01

    Protein-protein interactions play crucial roles in numerous biological processes. However, it is still challenging to evaluate the protein-protein interactions, such as antigen and antibody, in the presence of drug molecules in physiological liquid. In this study, the interaction between bovine serum albumin (BSA) and rabbit anti-BSA was investigated using atomic force microscopy (AFM) in the presence of various antimicrobial drugs (sulphathiazole sodium, tylosin and levofloxacin) under physiological condition. The results show that increasing the concentration of tylosin decreased the single-molecule-specific force between BSA and rabbit anti-BSA. As for sulphathiazole sodium, it dramatically decreased the specific force at a certain critical concentration, but increased the nonspecific force as its concentration increasing. In addition, the presence of levofloxacin did not greatly influence either the specific or nonspecific force. Collectively, these results suggest that these three drugs may adopt different mechanisms to affect the interaction force between BSA and rabbit anti-BSA. These findings may enhance our understanding of antigen/antibody binding processes in the presence of drug molecules, and hence indicate that AFM could be helpful in the design and screening of drugs-modulating protein-protein interaction processes.

  13. Force modulating dynamic disorder: A physical model of catch-slip bond transitions in receptor-ligand forced dissociation experiments

    Science.gov (United States)

    Liu, Fei; Ou-Yang, Zhong-Can

    2006-11-01

    Recent experiments found that some adhesive receptor-ligand complexes have counterintuitive catch-slip transition behaviors: the mean lifetimes of these complexes first increase (catch) with initial application of a small external force, and then decrease (slip) when the force is beyond some threshold. In this work we suggest that the forced dissociation of these complexes might be a typical rate process with dynamic disorder. The one-dimensional force modulating Agmon-Hopfield model is used to describe the transitions in the single-bond P-selectin glycoprotein ligand 1-P-selectin forced dissociation experiments, which were respectively performed in the constant force [Marshall , Nature (Landon) 423, 190 (2003)] and the ramping force [Evans , Proc. Natl. Acad. Sci. U.S.A 98, 11281 (2004)] modes. We find that, an external force can not only accelerate the bond dissociation, but also modulate the complex from the lower-energy barrier to the higher one; the catch-slip bond transition can arise from a particular energy barrier shape. The agreement between our calculation and the experimental data is satisfactory.

  14. Spin-dependent two-body interactions from gravitational self-force computations

    CERN Document Server

    Bini, Donato; Geralico, Andrea

    2015-01-01

    We analytically compute, through the eight-and-a-half post-Newtonian order and the fourth-order in spin, the gravitational self-force correction to Detweiler's gauge invariant redshift function for a small mass in circular orbit around a Kerr black hole. Using the first law of mechanics for black hole binaries with spin [L.~Blanchet, A.~Buonanno and A.~Le Tiec, Phys.\\ Rev.\\ D {\\bf 87}, 024030 (2013)] we transcribe our results into a knowledge of various spin-dependent couplings, as encoded within the spinning effective-one-body model of T.~Damour and A.~Nagar [Phys.\\ Rev.\\ D {\\bf 90}, 044018 (2014)]. We also compare our analytical results to the (corrected) numerical self-force results of A.~G.~Shah, J.~L.~Friedman and T.~S.~Keidl [Phys.\\ Rev.\\ D {\\bf 86}, 084059 (2012)], from which we show how to directly extract physically relevant spin-dependent couplings.

  15. Pre-industrial to Present Day Chemistry Model Simulations: The Role of Different Forcings

    Science.gov (United States)

    Young, P. J.; Lamarque, J.; Kinnison, D. E.; Vitt, F.

    2011-12-01

    We will present the results from several CAM-Chem simulations that span 1850-2010. Simulations where one forcing is fixed at 1850 (or 1930) levels are compared against a "base" simulation, where all the forcings evolve through time. The "fixed" simulations respectively hold (1) methane, (2) all surface/aloft emissions, (3) only aerosol emissions, (4) sea surface temperatures/CO2 (i.e. climate) at their 1850 level, and (5) CFCs at their 1930 level. We will examine the sensitivity of the ozone budget and methane lifetime results under these various scenarios. In particular, we will discuss the potential role of complex interactions in defining the tropospheric ozone burden change. We will make use of those results as a basis for the understanding of the spread in fields from the ongoing Atmospheric Chemistry and Climate Model Intercomparison Project (ACCMIP).

  16. Coarse-grained models for interacting, flapping swimmers

    Science.gov (United States)

    Oza, Anand; Ristroph, Leif; Shelley, Michael; Courant Institute Applied Math Lab Collaboration

    2016-11-01

    We present the results of a theoretical investigation into the dynamics of interacting flapping swimmers. Our study is motivated by ongoing experiments in the NYU Applied Math Lab, in which freely-translating, heaving airfoils interact hydrodynamically to choose their relative positions and velocities. We develop a discrete dynamical system in which flapping swimmers shed point vortices during each flapping cycle, which in turn exert forces on the swimmers. We present a framework for finding exact solutions to the evolution equations and for assessing their stability, giving physical insight into the preference for certain observed "schooling states". The model may be extended to arrays of flapping swimmers, and configurations in which the swimmers' flapping frequencies are incommensurate. Generally, our results indicate how hydrodynamics may mediate schooling and flocking behavior in biological contexts. A. Oza acknowledges the support of the NSF Mathematical Sciences Postdoctoral Fellowship.

  17. Prosthetic finger phalanges with lifelike skin compliance for low-force social touching interactions

    Directory of Open Access Journals (Sweden)

    Ge Shuzhi

    2011-03-01

    Full Text Available Abstract Background Prosthetic arms and hands that can be controlled by the user's electromyography (EMG signals are emerging. Eventually, these advanced prosthetic devices will be expected to touch and be touched by other people. As realistic as they may look, the currently available prosthetic hands have physical properties that are still far from the characteristics of human skins because they are much stiffer. In this paper, different configurations of synthetic finger phalanges have been investigated for their skin compliance behaviour and have been compared with the phalanges of the human fingers and a phalanx from a commercially available prosthetic hand. Methods Handshake tests were performed to identify which areas on the human hand experience high contact forces. After these areas were determined, experiments were done on selected areas using an indenting probe to obtain the force-displacement curves. Finite element simulations were used to compare the force-displacement results of the synthetic finger phalanx designs with that of the experimental results from the human and prosthetic finger phalanges. The simulation models were used to investigate the effects of (a varying the internal topology of the finger phalanx and (b varying different materials for the internal and external layers. Results and Conclusions During handshake, the high magnitudes of contact forces were observed at the areas where the full grasping enclosure of the other person's hand can be achieved. From these areas, the middle phalanges of the (a little, (b ring, and (c middle fingers were selected. The indentation experiments on these areas showed that a 2 N force corresponds to skin tissue displacements of more than 2 mm. The results from the simulation model show that introducing an open pocket with 2 mm height on the internal structure of synthetic finger phalanges increased the skin compliance of the silicone material to 235% and the polyurethane material to

  18. Energy Landscape of Alginate-Epimerase Interactions Assessed by Optical Tweezers and Atomic Force Microscopy.

    Directory of Open Access Journals (Sweden)

    Armend Gazmeno Håti

    Full Text Available Mannuronan C-5 epimerases are a family of enzymes that catalyze epimerization of alginates at the polymer level. This group of enzymes thus enables the tailor-making of various alginate residue sequences to attain various functional properties, e.g. viscosity, gelation and ion binding. Here, the interactions between epimerases AlgE4 and AlgE6 and alginate substrates as well as epimerization products were determined. The interactions of the various epimerase-polysaccharide pairs were determined over an extended range of force loading rates by the combined use of optical tweezers and atomic force microscopy. When studying systems that in nature are not subjected to external forces the access to observations obtained at low loading rates, as provided by optical tweezers, is a great advantage since the low loading rate region for these systems reflect the properties of the rate limiting energy barrier. The AlgE epimerases have a modular structure comprising both A and R modules, and the role of each of these modules in the epimerization process were examined through studies of the A- module of AlgE6, AlgE6A. Dynamic strength spectra obtained through combination of atomic force microscopy and the optical tweezers revealed the existence of two energy barriers in the alginate-epimerase complexes, of which one was not revealed in previous AFM based studies of these complexes. Furthermore, based on these spectra estimates of the locations of energy transition states (xβ, lifetimes in the absence of external perturbation (τ0 and free energies (ΔG# were determined for the different epimerase-alginate complexes. This is the first determination of ΔG# for these complexes. The values determined were up to 8 kBT for the outer barrier, and smaller values for the inner barriers. The size of the free energies determined are consistent with the interpretation that the enzyme and substrate are thus not tightly locked at all times but are able to relocate

  19. Energy Landscape of Alginate-Epimerase Interactions Assessed by Optical Tweezers and Atomic Force Microscopy.

    Science.gov (United States)

    Håti, Armend Gazmeno; Aachmann, Finn Lillelund; Stokke, Bjørn Torger; Skjåk-Bræk, Gudmund; Sletmoen, Marit

    2015-01-01

    Mannuronan C-5 epimerases are a family of enzymes that catalyze epimerization of alginates at the polymer level. This group of enzymes thus enables the tailor-making of various alginate residue sequences to attain various functional properties, e.g. viscosity, gelation and ion binding. Here, the interactions between epimerases AlgE4 and AlgE6 and alginate substrates as well as epimerization products were determined. The interactions of the various epimerase-polysaccharide pairs were determined over an extended range of force loading rates by the combined use of optical tweezers and atomic force microscopy. When studying systems that in nature are not subjected to external forces the access to observations obtained at low loading rates, as provided by optical tweezers, is a great advantage since the low loading rate region for these systems reflect the properties of the rate limiting energy barrier. The AlgE epimerases have a modular structure comprising both A and R modules, and the role of each of these modules in the epimerization process were examined through studies of the A- module of AlgE6, AlgE6A. Dynamic strength spectra obtained through combination of atomic force microscopy and the optical tweezers revealed the existence of two energy barriers in the alginate-epimerase complexes, of which one was not revealed in previous AFM based studies of these complexes. Furthermore, based on these spectra estimates of the locations of energy transition states (xβ), lifetimes in the absence of external perturbation (τ0) and free energies (ΔG#) were determined for the different epimerase-alginate complexes. This is the first determination of ΔG# for these complexes. The values determined were up to 8 kBT for the outer barrier, and smaller values for the inner barriers. The size of the free energies determined are consistent with the interpretation that the enzyme and substrate are thus not tightly locked at all times but are able to relocate. Together with the

  20. Energy Landscape of Alginate-Epimerase Interactions Assessed by Optical Tweezers and Atomic Force Microscopy

    Science.gov (United States)

    Håti, Armend Gazmeno; Aachmann, Finn Lillelund; Stokke, Bjørn Torger; Skjåk-Bræk, Gudmund; Sletmoen, Marit

    2015-01-01

    Mannuronan C-5 epimerases are a family of enzymes that catalyze epimerization of alginates at the polymer level. This group of enzymes thus enables the tailor-making of various alginate residue sequences to attain various functional properties, e.g. viscosity, gelation and ion binding. Here, the interactions between epimerases AlgE4 and AlgE6 and alginate substrates as well as epimerization products were determined. The interactions of the various epimerase–polysaccharide pairs were determined over an extended range of force loading rates by the combined use of optical tweezers and atomic force microscopy. When studying systems that in nature are not subjected to external forces the access to observations obtained at low loading rates, as provided by optical tweezers, is a great advantage since the low loading rate region for these systems reflect the properties of the rate limiting energy barrier. The AlgE epimerases have a modular structure comprising both A and R modules, and the role of each of these modules in the epimerization process were examined through studies of the A- module of AlgE6, AlgE6A. Dynamic strength spectra obtained through combination of atomic force microscopy and the optical tweezers revealed the existence of two energy barriers in the alginate-epimerase complexes, of which one was not revealed in previous AFM based studies of these complexes. Furthermore, based on these spectra estimates of the locations of energy transition states (xβ), lifetimes in the absence of external perturbation (τ0) and free energies (ΔG#) were determined for the different epimerase–alginate complexes. This is the first determination of ΔG# for these complexes. The values determined were up to 8 kBT for the outer barrier, and smaller values for the inner barriers. The size of the free energies determined are consistent with the interpretation that the enzyme and substrate are thus not tightly locked at all times but are able to relocate. Together with the

  1. Transient aerodynamic forces on a fighter model during simulated approach and landing with thrust reversers

    Science.gov (United States)

    Humphreys, A. P.; Paulson, J. W., Jr.; Kemmerly, G. T.

    1988-01-01

    Previous wind tunnel tests of fighter configurations have shown that thrust reverser jets can induce large, unsteady aerodynamic forces and moments during operation in ground proximity. This is a concern for STOL configurations using partial reversing to spoil the thrust while keeping the engine output near military (MIL) power during landing approach. A novel test technique to simulate approach and landing was developed under a cooperative Northrop/NASA/USAF program. The NASA LaRC Vortex Research Facility was used for the experiments in which a 7-percent F-18 model was moved horizontally at speeds of up to 100 feet per second over a ramp simulating an aircraft to ground rate of closure similar to a no-flare STOL approach and landing. This paper presents an analysis of data showing the effect of reverser jet orientation and jet dynamic pressure ratio on the transient forces for different angles of attack, and flap and horizontal tail deflection. It was found, for reverser jets acting parallel to the plane of symmetry, that the jets interacted strongly with the ground, starting approximately half a span above the ground board. Unsteady rolling moment transients, large enough to cause the probable upset of an aircraft, and strong normal force and pitching moment transients were measured. For jets directed 40 degrees outboard, the transients were similar to the jet-off case, implying only minor interaction.

  2. Van der Waals forces and electron-electron interactions in two strained graphene layers

    Science.gov (United States)

    Sharma, Anand; Harnish, Peter; Sylvester, Alexander; Kotov, Valeri N.

    2014-03-01

    We evaluate the van der Waals (vdW) interaction energy at T=0 between two undoped graphene layers which are separated by a finite distance. Our study is carried out within the Random Phase Approximation and the interaction energy is obtained for variation in the strength of effective Coulomb interaction and anisotropy due to applied uniaxial strain. We consider the following three models for the anisotropic case: a) where one of the two layers is uniaxially strained, b) the two layers are strained in the same direction, and c) one of the layers is strained in the perpendicular direction. We find that for all the three models and any given value of the coupling, the vdW interaction energy increases with increasing anisotropy. The effect is most striking for the case when both the layers are strained in the parallel direction where we observe up to an order of magnitude increase in the strained graphene relative to the unstrained case. We also investigate the effect of intra-layer electron-electron interactions in the region of large separation between the strained graphene layers. We conclude that the many-body contributions to the correlation energy are non-negligible and the vdW interaction energy decreases as a function of increasing distance between the layers. Alexander Sylvester acknowledges financial assistance from the Research Experiences for Undergraduates (REU) Program of the National Science Foundation (NSF) focussing on complex materials.

  3. A global modeling study on carbonaceous aerosol microphysical characteristics and radiative forcing

    Directory of Open Access Journals (Sweden)

    S. E. Bauer

    2010-02-01

    Full Text Available Recently, attention has been drawn towards black carbon aerosols as a short-term climate warming mitigation candidate. However the global and regional impacts of the direct, cloud-indirect and semi-direct forcing effects are highly uncertain, due to the complex nature of aerosol evolution and the way that mixed, aged aerosols interact with clouds and radiation. A detailed aerosol microphysical scheme, MATRIX, embedded within the GISS climate model is used in this study to present a quantitative assessment of the impact of microphysical processes involving black carbon, such as emission size distributions and optical properties on aerosol cloud activation and radiative forcing.

    Our best estimate for net direct and indirect aerosol radiative forcing between 1750 and 2000 is −0.56 W/m2. However, the direct and indirect aerosol effects are quite sensitive to the black and organic carbon size distribution and consequential mixing state. The net radiative forcing can vary between −0.32 to −0.75 W/m2 depending on these carbonaceous particle properties at emission. Assuming that sulfates, nitrates and secondary organics form a coating around a black carbon core, rather than forming a uniformly mixed particle, changes the overall net aerosol radiative forcing from negative to positive. Taking into account internally mixed black carbon particles let us simulate correct aerosol absorption. Black carbon absorption is amplified by sulfate and nitrate coatings, but even more strongly by organic coatings. Black carbon mitigation scenarios generally showed reduced radiative forcing when sources with a large proportion of black carbon, such as diesel, are reduced; however reducing sources with a larger organic carbon component as well, such as bio-fuels, does not necessarily lead to climate benefits.

  4. Light weakly coupled axial forces: models, constraints, and projections

    Science.gov (United States)

    Kahn, Yonatan; Krnjaic, Gordan; Mishra-Sharma, Siddharth; Tait, Tim M. P.

    2017-05-01

    We investigate the landscape of constraints on MeV-GeV scale, hidden U(1) forces with nonzero axial-vector couplings to Standard Model fermions. While the purely vector-coupled dark photon, which may arise from kinetic mixing, is a well-motivated scenario, several MeV-scale anomalies motivate a theory with axial couplings which can be UV-completed consistent with Standard Model gauge invariance. Moreover, existing constraints on dark photons depend on products of various combinations of axial and vector couplings, making it difficult to isolate the effects of axial couplings for particular flavors of SM fermions. We present a representative renormalizable, UV-complete model of a dark photon with adjustable axial and vector couplings, discuss its general features, and show how some UV constraints may be relaxed in a model with nonrenormalizable Yukawa couplings at the expense of fine-tuning. We survey the existing parameter space and the projected reach of planned experiments, briefly commenting on the relevance of the allowed parameter space to low-energy anomalies in π0 and 8Be∗ decay.

  5. Light Weakly Coupled Axial Forces: Models, Constraints, and Projections

    CERN Document Server

    Kahn, Yonatan; Mishra-Sharma, Siddharth; Tait, Tim M P

    2016-01-01

    We investigate the landscape of constraints on MeV-GeV scale, hidden U(1) forces with nonzero axial-vector couplings to Standard Model fermions. While the purely vector-coupled dark photon, which may arise from kinetic mixing, is a well-motivated scenario, several MeV-scale anomalies motivate a theory with axial couplings which can be UV-completed consistent with Standard Model gauge invariance. Moreover, existing constraints on dark photons depend on products of various combinations of axial and vector couplings, making it difficult to isolate the effects of axial couplings for particular flavors of SM fermions. We present a representative renormalizable, UV-complete model of a dark photon with adjustable axial and vector couplings, discuss its general features, and show how some UV constraints may be relaxed in a model with nonrenormalizable Yukawa couplings at the expense of fine-tuning. We survey the existing parameter space and the projected reach of planned experiments, briefly commenting on the relevan...

  6. Light Weakly Coupled Axial Forces: Models, Constraints, and Projections

    Energy Technology Data Exchange (ETDEWEB)

    Kahn, Yonatan [Princeton U.; Krnjaic, Gordan [Fermilab; Mishra-Sharma, Siddharth [Princeton U.; Tait, Tim P. [UC, Irvine

    2016-09-28

    We investigate the landscape of constraints on MeV-GeV scale, hidden U(1) forces with nonzero axial-vector couplings to Standard Model fermions. While the purely vector-coupled dark photon, which may arise from kinetic mixing, is a well-motivated scenario, several MeV-scale anomalies motivate a theory with axial couplings which can be UV-completed consistent with Standard Model gauge invariance. Moreover, existing constraints on dark photons depend on products of various combinations of axial and vector couplings, making it difficult to isolate the effects of axial couplings for particular flavors of SM fermions. We present a representative renormalizable, UV-complete model of a dark photon with adjustable axial and vector couplings, discuss its general features, and show how some UV constraints may be relaxed in a model with nonrenormalizable Yukawa couplings at the expense of fine-tuning. We survey the existing parameter space and the projected reach of planned experiments, briefly commenting on the relevance of the allowed parameter space to low-energy anomalies in pi^0 and 8-Be* decay.

  7. Gravitational Interactions in a General Multibrane Model

    CERN Document Server

    Bloomfield, Jolyon K

    2010-01-01

    The gravitational interactions of the four-dimensional effective theory describing a general N-brane model in five dimensions without radion stabilization are analyzed. The parameter space is constrained by requiring that there be no ghost modes in the theory, and that the Eddington parameterized post-Newtonian parameter gamma be consistent with observations. We show that we must reside on the brane on which the warp factor is maximized. The resultant theory contains N-1 radion modes in a nonlinear sigma model, with the target space being a subset of hyperbolic space. Imposing observational constraints on the relative strengths of gravitational interactions of dark and visible matter shows that at least 99.8% of the dark matter must live on our brane in this model.

  8. Algebraic Turbulence-Chemistry Interaction Model

    Science.gov (United States)

    Norris, Andrew T.

    2012-01-01

    The results of a series of Perfectly Stirred Reactor (PSR) and Partially Stirred Reactor (PaSR) simulations are compared to each other over a wide range of operating conditions. It is found that the PaSR results can be simulated by a PSR solution with just an adjusted chemical reaction rate. A simple expression has been developed that gives the required change in reaction rate for a PSR solution to simulate the PaSR results. This expression is the basis of a simple turbulence-chemistry interaction model. The interaction model that has been developed is intended for use with simple one-step global reaction mechanisms and for steady-state flow simulations. Due to the simplicity of the model there is very little additional computational cost in adding it to existing CFD codes.

  9. A closer look at the complex hydrophilic/hydrophobic interactions forces at the human hair surface

    Science.gov (United States)

    Baghdadli, N.; Luengo, G. S.; Recherche, L.

    2008-03-01

    The complex chemical structure of the hair surface is far from being completely understood. Current understanding is based on Rivett's model1 that was proposed to explain the macroscopic hydrophobic nature of the surface of natural hair. In this model covalently-linked fatty acids are chemically grafted to the amorphous protein (keratin) through a thio-ester linkage2,3. Nevertheless, experience like wetting and electrical properties of human hair surface4 shows that the complexity of the hair surface is not fully understand based on this model in literature. Recent studies in our laboratory show for the first time microscopic evidence of the heterogeneous physico-chemical character of the hair surface. By using Chemical Force Microscopy, the presence of hydrophobic and ionic species are detected and localized, before and after a cosmetic treatment (bleaching). Based on force curve analysis the mapping of the local distribution of hydrophilic and hydrophobic groups of hair surface is obtained. A discussion on a more plausible hair model and its implications will be presented based on these new results.

  10. A closer look at the complex hydrophilic/hydrophobic interactions forces at the human hair surface

    Energy Technology Data Exchange (ETDEWEB)

    Baghdadli, N; Luengo, G S; Recherche, L [Avenue Eugene Schueller, Aulnay-Sous Bois, 93100 (France)], E-mail: nbaghdadli@rd.loreal.com, E-mail: gluengo@rd.loreal.com

    2008-03-15

    The complex chemical structure of the hair surface is far from being completely understood. Current understanding is based on Rivett's model{sup 1} that was proposed to explain the macroscopic hydrophobic nature of the surface of natural hair. In this model covalently-linked fatty acids are chemically grafted to the amorphous protein (keratin) through a thio-ester linkage{sup 2,3}. Nevertheless, experience like wetting and electrical properties of human hair surface{sup 4} shows that the complexity of the hair surface is not fully understand based on this model in literature. Recent studies in our laboratory show for the first time microscopic evidence of the heterogeneous physico-chemical character of the hair surface. By using Chemical Force Microscopy, the presence of hydrophobic and ionic species are detected and localized, before and after a cosmetic treatment (bleaching). Based on force curve analysis the mapping of the local distribution of hydrophilic and hydrophobic groups of hair surface is obtained. A discussion on a more plausible hair model and its implications will be presented based on these new results.

  11. An Atomic Force Microscopy Study of the Interactions Involving Polymers and Silane Networks

    Directory of Open Access Journals (Sweden)

    Rodrigo L. Oréfice

    1998-12-01

    Full Text Available ABSTRACT: Silane coupling agents have been frequently used as interfacial agents in polymer composites to improve interfacial strength and resistance to fluid migration. Although the capability of these agents in improving properties and performance of composites has been reported, there are still many uncertainties regarding the processing-structure-property relationships and the mechanisms of coupling developed by silane agents. In this work, an Atomic Force Microscope (AFM was used to measure interactions between polymers and silica substrates, where silane networks with a series of different structures were processed. The influence of the structure of silane networks on the interactions with polymers was studied and used to determine the mechanisms involved in the coupling phenomenon. The AFM results showed that phenomena such as chain penetration, entanglements, intersegment bonding, chain conformation in the vicinities of rigid surfaces were identified as being relevant for the overall processes of adhesion and adsorption of polymeric chains within a silane network. AFM adhesion curves showed that penetration of polymeric chains through a more open silane network can lead to higher levels of interactions between polymer and silane agents.

  12. Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, G.; Garcia, A.E. [Los Alamos National Lab., NM (United States). Theoretical Biology and Biophysics Group; Soumpasis, D.M. [Max-Planck-Inst for Biophysical Chemistry, Goettingen (Germany). Biocomputation Group

    1994-10-01

    To understand the functioning of living organisms on a molecular level, it is crucial to dissect the intricate interplay of the immense number of biological molecules. Most of the biochemical processes in cells occur in a liquid environment formed mainly by water and ions. This solvent environment plays an important role in biological systems. The potential-of-mean-force (PMF) formalism attempts to describe quantitatively the interactions of the solvent with biological macromolecules on the basis of an approximate statistical-mechanical representation. At its current status of development, it deals with ionic effects on the biomolecular structure and with the structural hydration of biomolecules. The underlying idea of the PMF formalism is to identify the dominant sources of interactions and incorporate these interactions into the theoretical formalism using PMF`s (or particle correlation functions) extracted from bulk-liquid systems. In the following, the authors shall briefly outline the statistical-mechanical foundation of the PMF formalism and introduce the PMF expansion formalism, which is intimately linked to superposition approximations for higher-order particle correlation functions. The authors shall then sketch applications, which describe the effects of the ionic environment on nucleic-acid structure. Finally, the authors shall present the more recent extension of the PMF idea to describe quantitatively the structural hydration of biomolecules. Results for the interface of ice and water and for the hydration of deoxyribonucleic acid (DNA) will be discussed.

  13. Secret neutrino interactions: a pseudoscalar model

    Science.gov (United States)

    Archidiacono, Maria; Hannestad, Steen; Sloth Hansen, Rasmus; Tram, Thomas

    2016-05-01

    Neutrino oscillation experiments point towards the existence of additional mostly sterile neutrino mass eigenstates in the eV mass range. At the same time, such sterile neutrinos are disfavoured by cosmology (Big Bang Nucleosynthesis, Cosmic Microwave Background and Large Scale Structure), unless they can be prevented from being thermalised in the early Universe. To this aim, we introduce a model of sterile neutrino secret interactions mediated by a new light pseudoscalar: The new interactions can accomodate sterile neutrinos in the early Universe, providing a good fit to all the up to date cosmological data.

  14. Physical Forces between Humans and How Humans Attract and Repel Each Other Based on Their Social Interactions in an Online World.

    Directory of Open Access Journals (Sweden)

    Stefan Thurner

    Full Text Available Physical interactions between particles are the result of the exchange of gauge bosons. Human interactions are mediated by the exchange of messages, goods, money, promises, hostilities, etc. While in the physical world interactions and their associated forces have immediate dynamical consequences (Newton's laws the situation is not clear for human interactions. Here we quantify the relative acceleration between humans who interact through the exchange of messages, goods and hostilities in a massive multiplayer online game. For this game we have complete information about all interactions (exchange events between about 430,000 players, and about their trajectories (movements in the metric space of the game universe at any point in time. We use this information to derive "interaction potentials" for communication, trade and attacks and show that they are harmonic in nature. Individuals who exchange messages and trade goods generally attract each other and start to separate immediately after exchange events end. The form of the interaction potential for attacks mirrors the usual "hit-and-run" tactics of aggressive players. By measuring interaction intensities as a function of distance, velocity and acceleration, we show that "forces" between players are directly related to the number of exchange events. We find an approximate power-law decay of the likelihood for interactions as a function of distance, which is in accordance with previous real world empirical work. We show that the obtained potentials can be understood with a simple model assuming an exchange-driven force in combination with a distance-dependent exchange rate.

  15. Force fields for simulating the interaction of surfaces with biological molecules

    Science.gov (United States)

    Martin, Lewis; Bilek, Marcela M.; Weiss, Anthony S.; Kuyucak, Serdar

    2016-01-01

    The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide–surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data. PMID:26855748

  16. As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

    Science.gov (United States)

    Rottler, Jörg; Plotkin, Steven S.

    2016-01-01

    Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered. PMID:27898663

  17. Evacuation in the Social Force Model is not stationary

    CERN Document Server

    Gawroński, P; Kämpf, M; Kantelhardt, J W

    2011-01-01

    An evacuation process is simulated within the Social Force Model. Thousand pedestrians are leaving a room by one exit. We investigate the stationarity of the distribution of time lags between instants when two successive pedestrians cross the exit. The exponential tail of the distribution is shown to gradually vanish. Taking fluctuations apart, the time lags decrease in time till there are only about 50 pedestrians in the room, then they start to increase. This suggests that at the last stage the flow is laminar. In the first stage, clogging events slow the evacuation down. As they are more likely for larger crowds, the flow is not stationary. The data are investigated with detrended fluctuation analysis.

  18. Interaction between pheromone and its receptor of the fission yeast Schizosaccharomyces pombe examined by a force spectroscopy study.

    Science.gov (United States)

    Sasuga, Shintaro; Abe, Ryohei; Nikaido, Osamu; Kiyosaki, Shoichi; Sekiguchi, Hiroshi; Ikai, Atsushi; Osada, Toshiya

    2012-01-01

    Interaction between P-factor, a peptide pheromone composed of 23 amino acid residues, and its pheromone receptor, Mam2, on the cell surface of the fission yeast Schizosaccharomyces pombe was examined by an atomic force microscope (AFM). An AFM tip was modified with P-factor derivatives to perform force curve measurements. The specific interaction force between P-factor and Mam2 was calculated to be around 120 pN at a probe speed of 1.74 μm/s. When the AFM tip was modified with truncated P-factor derivative lacking C-terminal Leu, the specific interaction between the tip and the cell surface was not observed. These results were also confirmed with an assay system using a green fluorescent protein (GFP) reporter gene to monitor the activation level of signal transduction following the interaction of Mam2 with P-factor.

  19. Interaction between Pheromone and Its Receptor of the Fission Yeast Schizosaccharomyces pombe Examined by a Force Spectroscopy Study

    Directory of Open Access Journals (Sweden)

    Shintaro Sasuga

    2012-01-01

    Full Text Available Interaction between P-factor, a peptide pheromone composed of 23 amino acid residues, and its pheromone receptor, Mam2, on the cell surface of the fission yeast Schizosaccharomyces pombe was examined by an atomic force microscope (AFM. An AFM tip was modified with P-factor derivatives to perform force curve measurements. The specific interaction force between P-factor and Mam2 was calculated to be around 120 pN at a probe speed of 1.74 μm/s. When the AFM tip was modified with truncated P-factor derivative lacking C-terminal Leu, the specific interaction between the tip and the cell surface was not observed. These results were also confirmed with an assay system using a green fluorescent protein (GFP reporter gene to monitor the activation level of signal transduction following the interaction of Mam2 with P-factor.

  20. Comparision of atomic force microscopy interaction forces between bacteria and silicon nitride substrata for three commonly used immobilization methods

    NARCIS (Netherlands)

    Vadillo-Rodríguez, Virginia; Busscher, Henk J; Norde, Willem; de Vries, Joop; Dijkstra, René JB; Stokroos, Ietse; van der Mei, Henderina

    2004-01-01

    Atomic force microscopy (AFM) has emerged as a powerful technique for mapping the surface morphology of biological specimens, including bacterial cells. Besides creating topographic images, AFM enables us to probe both physicochemical and mechanical properties of bacterial cell surfaces on a nanomet

  1. Comparison of Atomic Force Microscopy interaction forces between bacteria and silicon nitride substrata for three commonly used immobilization methods

    NARCIS (Netherlands)

    Vadillo-Rodriguez, V.; Busscher, H.J.; Norde, W.; Vries, de J.; Dijkstra, R.J.B.; Stokroos, I.; Mei, van der H.C.

    2004-01-01

    Atomic force microscopy (AFM) has emerged as a powerful technique for mapping the surface morphology of biological specimens, including bacterial cells. Besides creating topographic images, AFM enables us to probe both physicochemical and mechanical properties of bacterial cell surfaces on a nanomet

  2. Comparision of atomic force microscopy interaction forces between bacteria and silicon nitride substrata for three commonly used immobilization methods

    NARCIS (Netherlands)

    Vadillo-Rodríguez, Virginia; Busscher, Henk J; Norde, Willem; de Vries, Joop; Dijkstra, René JB; Stokroos, Ietse; van der Mei, Henderina

    2004-01-01

    Atomic force microscopy (AFM) has emerged as a powerful technique for mapping the surface morphology of biological specimens, including bacterial cells. Besides creating topographic images, AFM enables us to probe both physicochemical and mechanical properties of bacterial cell surfaces on a nanomet

  3. Comparison of Atomic Force Microscopy interaction forces between bacteria and silicon nitride substrata for three commonly used immobilization methods

    NARCIS (Netherlands)

    Vadillo-Rodriguez, V.; Busscher, H.J.; Norde, W.; Vries, de J.; Dijkstra, R.J.B.; Stokroos, I.; Mei, van der H.C.

    2004-01-01

    Atomic force microscopy (AFM) has emerged as a powerful technique for mapping the surface morphology of biological specimens, including bacterial cells. Besides creating topographic images, AFM enables us to probe both physicochemical and mechanical properties of bacterial cell surfaces on a nanomet

  4. Intermolecular forces, spontaneous emission, and superradiance in a dielectric medium : Polariton-mediated interactions

    NARCIS (Netherlands)

    Knoester, Jasper; Mukamel, Shaul

    1989-01-01

    A reduced equation of motion that describes the excited-state dynamics of interacting two-level impurity molecules in a dielectric host crystal is derived starting from a microscopic model for the total system. Our theory generalizes the derivation of the conventional superradiance master equation f

  5. Modeling Hydraulic Responses to Meteorological Forcing: fromCanopy to Aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Lehua; Jin, Jiming; Miller, Norman; Wu, Yu-Shu; Bodvarsson,Gudmundur

    2007-02-08

    An understanding of the hydrologic interactions amongatmosphere, land surface, and subsurface is one of the keys tounderstanding the water cycling system that supports our life system onearth. Properly modeling such interactionsis a difficult task because oftheinherent coupled processes and complex feedback structures amongsubsystems. In this paper, we present a model that simulates thelandsurface and subsurface hydrologic response to meteorological forcing.This model combines a state of the art landsurface model, the NCARCommunity Land Model version 3 (CLM3), with a variablysaturatedgroundwater model, the TOUGH2, through an internal interfacethat includes flux and state variables shared by the two submodels.Specifically, TOUGH2, in its simulation, uses infiltration, evaporation,and rootuptake rates, calculated by CLM3, as source/sink terms? CLM3, inits simulation, uses saturation and capillary pressure profiles,calculated by TOUGH2, as state variables. This new model, CLMT2,preserves the best aspects of both submodels: the state of the artmodeling capability of surface energy and hydrologic processes from CLM3and the more realistic physical process based modeling capability ofsubsurface hydrologic processes from TOUGH2. The preliminary simulationresults show that the coupled model greatly improves the predictions ofthe water table, evapotranspiration, surface temperature, and moisture inthe top 20 cm of soil at a real watershed, as evaluated from 18 years ofobserved data. The new model is also ready to be coupled with anatmospheric simulation model, representing one of the first models thatare capable to simulate hydraulic processes from top of the atmosphere todeep ground.

  6. Aespoe modelling task force - experiences of the site specific flow and transport modelling (in detailed and site scale)

    Energy Technology Data Exchange (ETDEWEB)

    Gustafson, Gunnar [Chalmers Univ. of Technology, Goeteborg (Sweden); Stroem, A.; Wikberg, P. [Swedish Nuclear Fuel and Waste Management Co. , Stockholm (Sweden)

    1998-09-01

    The Aespoe Task Force on modelling of groundwater flow and transport of solutes was initiated in 1992. The Task Force shall be a forum for the organisations supporting the Aespoe Hard Rock Laboratory Project to interact in the area of conceptual and numerical modelling of groundwater flow and solute transport in fractured rock. Much emphasis is put on building of confidence in the approaches and methods in use for modelling of groundwater flow and nuclide migration in order to demonstrate their use for performance and safety assessment. The modelling work within the Task Force is linked to the experiments performed at the Aespoe Laboratory. As the first Modelling Task, a large scale pumping and tracer experiment called LPT2 was chosen. This was the final part of the characterisation work for the Aespoe site before the construction of the laboratory in 1990. The construction of the Aespoe HRL access tunnel caused an even larger hydraulic disturbance on a much larger scale than that caused by the LPT2 pumping test. This was regarded as an interesting test case for the conceptual and numerical models of the Aespoe site developed during Task No 1, and was chosen as the third Modelling Task. The aim of Task 3 can be seen from two different perspectives. The Aespoe HRL project saw it as a test of their ability to define a conceptual and structural model of the site that can be utilised by independent modelling groups and be transformed to a predictive groundwater flow model. The modelling groups saw it as a means of understanding groundwater flow in a large fractured rock volume and of testing their computational tools. A general conclusion is that Task 3 has served these purposes well. Non-sorbing tracers tests, made as a part of the TRUE-experiments were chosen as the next predictive modelling task. A preliminary comparison between model predictions made by the Aespoe Task Force and the experimental results, shows that most modelling teams predicted breakthrough from

  7. Measurement of the Interaction Force between Dust Particles within a Glass Box in a GEC RF Reference Cell

    Science.gov (United States)

    Chen, Mudi; Kong, Jie; Qiao, Ke; Carmona-Reyes, Jorge; Harris, Brandon; Matthews, Lorin; Hyde, Truell

    2013-10-01

    A wide variety of structural states (for example, Coulomb balls, one-dimensional vertically aligned dust particle chains, helical dust structures, etc.) have been observed for dust particles confined within a glass box placed on the lower electrode of a GEC rf reference cell. Both the interparticle interaction force and the confinement force play important roles in the formation of these structures. Unfortunately, since the exact nature of the confinement force produced by the walls of the glass box is yet unclear, it is difficult to differentiate between the effects produced by the interparticle interaction force and the effects created by the confinement force. In this experiment, a free-falling dust particle in the box acts as an in-situ probe, providing information on the structure of the confinement force. It will be shown that the data provided by this mapping procedure allows the interaction force between particles within various dust particle structures to be measured through perturbation of individual particles employing a diode pumped solid state laser (Coherent VERDI).

  8. Narcissistic Force Meets Systemic Resistance: The Energy Clash Model.

    Science.gov (United States)

    Sedikides, Constantine; Campbell, W Keith

    2017-05-01

    This article focuses on the interplay between narcissistic leaders and organizations. It attempts to capture the gist of this interplay with a model outlining the narcissistic organizational trajectory. The Energy Clash Model borrows and adapts a phase/state physics metaphor to conceptualize narcissism as a force that enters or emerges in a stable system (i.e., organization) as a leader, destabilizes it, and stabilizes it at a different state or is expelled. The model consists of three time-contingent phases: perturbation, conflict, and resolution. Narcissists create instability through waves of excitement, proposed reforms, and an inspiring vision for organization's future ( perturbation). With the passage of time, though, systemic awareness and alertness intensify, as organizational costs-in terms of human resources and monetary losses-accrue. Narcissistic energy clashes directly with the organization ( conflict), a clash likely to restabilize the system eventually. The conflict may provoke the exit of the narcissistic leader or his or her accommodation, that is, steps or controls negotiated between the system and the leader ( resolution). Although narcissism is subject to organizational liability, narcissistic energy, when managed and directed properly, may contribute to organizational innovation and evolution. Thus, several interventions for working with narcissistic leaders are discussed.

  9. Implementing Nonlinear Buoyancy and Excitation Forces in the WEC-Sim Wave Energy Converter Modeling Tool: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Lawson, M.; Yu, Y. H.; Nelessen, A.; Ruehl, K.; Michelen, C.

    2014-05-01

    Wave energy converters (WECs) are commonly designed and analyzed using numerical models that combine multi-body dynamics with hydrodynamic models based on the Cummins Equation and linearized hydrodynamic coefficients. These modeling methods are attractive design tools because they are computationally inexpensive and do not require the use of high performance computing resources necessitated by high-fidelity methods, such as Navier Stokes computational fluid dynamics. Modeling hydrodynamics using linear coefficients assumes that the device undergoes small motions and that the wetted surface area of the devices is approximately constant. WEC devices, however, are typically designed to undergo large motions in order to maximize power extraction, calling into question the validity of assuming that linear hydrodynamic models accurately capture the relevant fluid-structure interactions. In this paper, we study how calculating buoyancy and Froude-Krylov forces from the instantaneous position of a WEC device (referred to as instantaneous buoyancy and Froude-Krylov forces from herein) changes WEC simulation results compared to simulations that use linear hydrodynamic coefficients. First, we describe the WEC-Sim tool used to perform simulations and how the ability to model instantaneous forces was incorporated into WEC-Sim. We then use a simplified one-body WEC device to validate the model and to demonstrate how accounting for these instantaneously calculated forces affects the accuracy of simulation results, such as device motions, hydrodynamic forces, and power generation.

  10. Atomic forces between noble gas atoms, alkali ions, and halogen ions for surface interactions

    Science.gov (United States)

    Wilson, J. W.; Outlaw, R. A.; Heinbockel, J. H.

    1988-01-01

    The components of the physical forces between noble gas atoms, alkali ions, and halogen ions are analyzed and a data base developed from analysis of the two-body potential data, the alkali-halide molecular data, and the noble gas crystal and salt crystal data. A satisfactory global fit to this molecular and crystal data is then reproduced by the model to within several percent. Surface potentials are evaluated for noble gas atoms on noble gas surfaces and salt crystal surfaces with surface tension neglected. Within this context, the noble gas surface potentials on noble gas and salt crystals are considered to be accurate to within several percent.

  11. Interaction forces between red cells agglutinated by antibody. IV. Time and force dependence of break-up.

    Science.gov (United States)

    Tees, D F; Coenen, O; Goldsmith, H L

    1993-09-01

    We report on an extension of a previously described method to measure the hydrodynamic force to separate doublets of fixed, sphered and swollen red cells cross-linked by antibody (S. P. Tha, J. Shuster, and H. L. Goldsmith. 1986. Biophys. J. 50:1117-1126). With a traveling microtube apparatus, doublets are tracked and videotaped in a slowly accelerating Poiseuille flow in 150-microns-diameter tubes, and the hydrodynamic normal force at break-up, Fn, is computed from the measured doublet velocity and radial position. Previous results showed a large range of Fn, the mean of which increased with [antiserum], and an absence of clustering at discrete values of Fn. Since it was assumed that the cells separate the instant a critical force to break all crossbridges was reached, lack of clustering could have been due to the use of a polyclonal antiserum. We therefore studied the effect of monoclonal IgM or IgA antibody on the distribution of Fn. The results showed that the data are as scattered as ever, with Fn varying from 2 to 200 pN, and exhibit no evidence of clustering. However, the scatter in Fn could be due to the stochastic nature of intercellular bonds (E. Evans, D. Berk, and A. Leung. 1991a. Biophys. J. 59:838-848). We therefore studied the force dependence of the time to break-up under constant shear stress (Fn from 30 to 200 pN), both in Poiseuille and Couette flow, the latter by using a counter-rotating cone and plate rheoscope. When 280 doublets were rapidly accelerated in the traveling microtube and then allowed to coast in steady flow for up to 180 s, 91% survived into the constant force region; 16% of these broke up after time intervals, tP, of 2-30s. Of 340 doublets immediately exposed to constant shear in the rheoscope, 37% broke after time intervals, tc, from 5. In the rheoscope, the time intervals and number of rotations to break-up, tc, were quite well reproduced assuming (Nb) = 4. The similarity of (Fn) for monoclonal IgM and IgA for doublet break

  12. Interacting Dark Energy Models and Observations

    Science.gov (United States)

    Shojaei, Hamed; Urioste, Jazmin

    2017-01-01

    Dark energy is one of the mysteries of the twenty first century. Although there are candidates resembling some features of dark energy, there is no single model describing all the properties of dark energy. Dark energy is believed to be the most dominant component of the cosmic inventory, but a lot of models do not consider any interaction between dark energy and other constituents of the cosmic inventory. Introducing an interaction will change the equation governing the behavior of dark energy and matter and creates new ways to explain cosmic coincidence problem. In this work we studied how the Hubble parameter and density parameters evolve with time in the presence of certain types of interaction. The interaction serves as a way to convert dark energy into matter to avoid a dark energy-dominated universe by creating new equilibrium points for the differential equations. Then we will use numerical analysis to predict the values of distance moduli at different redshifts and compare them to the values for the distance moduli obtained by WMAP (Wilkinson Microwave Anisotropy Probe). Undergraduate Student

  13. A Predictive Model of Cell Traction Forces Based on Cell Geometry

    OpenAIRE

    Lemmon, Christopher A.; Romer, Lewis H

    2010-01-01

    Recent work has indicated that the shape and size of a cell can influence how a cell spreads, develops focal adhesions, and exerts forces on the substrate. However, it is unclear how cell shape regulates these events. Here we present a computational model that uses cell shape to predict the magnitude and direction of forces generated by cells. The predicted results are compared to experimentally measured traction forces, and show that the model can predict traction force direction, relative m...

  14. Comments on interactions in the SUSY models

    CERN Document Server

    Upadhyay, Sudhakar; Mandal, Bhabani Prasad

    2016-01-01

    We consider the special supersymmetry (SUSY) transformations with $m$ generators $\\overleftarrow{s}_\\alpha,$ for some class of the models and study the physical consequences when making the Grassmann-odd transformations to form an Abelian supergroup with finite parameters and set of group-like elements with finite parameters being by a functionals of field variables. The SUSY-invariant path integral measure within conventional quantization scheme leads to appearance of the Jacobian under change of variables generated by such SUSY transformations, which is explicitly calculated. The Jacobian leads, first, to appearance of only trivial interactions in the transformed action, second, to the presence of modified Ward identity, which reduceds to the standard Ward identities for constant parameters. We examine the case of ${N}=1$, $N=2$ supersymmetric harmonic oscillator to illustrate the general concept on a free simple model with $(1,1)$ physical degrees of freedom. It is shown that the interaction terms, $U_{tr}...

  15. Modeling of soil-water-structure interaction

    DEFF Research Database (Denmark)

    Tang, Tian

    The trend towards the installation of more offshore constructions for the production and transmission of marine oil, gas and wind power is expected to continue over the coming years. An important process in the offshore construction design is the assessment of seabed soil stability exposed...... to dynamic ocean waves. The goal of this research project is to develop numerical soil models for computing realistic seabed response in the interacting offshore environment, where ocean waves, seabed and offshore structure highly interact with each other. The seabed soil models developed are based...... on the ’modified’ Biot’s consolidation equations, in which the soil-pore fluid coupling is extended to account for the various nonlinear soil stress-strain relations included. The Finite volume method (FVM) together with a segregated solution strategy has been used to numerically solve the governing equations...

  16. Force-time course parameters and force fatigue model during an intermittent fatigue protocol in motorcycle race riders.

    Science.gov (United States)

    Marina, M; Rios, M; Torrado, P; Busquets, A; Angulo-Barroso, R

    2015-06-01

    Fatigue in forearm muscles may be critical for motorcycle riders in relation to performance and forearm disorders. Force-time course parameters were examined to better characterize the reduction in the maximal force generating capacity (MVC) during an intermittent fatigue protocol (IFP) specifically designed for motorcycle riders. Also, a mathematical force fatigue model is proposed. Forty motorcyclists (aged 27.6 ± 6.8 years) performed an IFP that simulated the braking gesture and posture of a rider. Fatigue was confirmed by a 40% decrement of the normalized MVC in comparison with basal value. Contraction time increased in comparison with basal condition (P ≤ 0.034). Relaxation kinetics presented two phases: (a) a pre-fatigue phase where half relaxation time (HRTraw ) and normalized (HRTnor ) decreased (P ≤ 0.013) while relaxation rate (RRraw ) remained unchanged; and (b) a fatiguing phase where HRTraw , HRTnor increased and RRraw decreased (P ≤ 0.047). Normalized RRraw (RRnor ) declined progressively (P ≤ 0.016). The proposed nonlinear force fatigue model confirmed a satisfactory adjustment (R(2)  = 0.977 ± 0.018). This mathematical expression derived three patterns of force fatigue: three-phase, exponential and linear, representing 70%, 13%, and 17% of the participants, respectively. Overall, these results provided further support to force fatigue theoretical and applied proposals.

  17. A phenomenological continuum model for force-driven nano-channel liquid flows

    Science.gov (United States)

    Ghorbanian, Jafar; Celebi, Alper T.; Beskok, Ali

    2016-11-01

    A phenomenological continuum model is developed using systematic molecular dynamics (MD) simulations of force-driven liquid argon flows confined in gold nano-channels at a fixed thermodynamic state. Well known density layering near the walls leads to the definition of an effective channel height and a density deficit parameter. While the former defines the slip-plane, the latter parameter relates channel averaged density with the desired thermodynamic state value. Definitions of these new parameters require a single MD simulation performed for a specific liquid-solid pair at the desired thermodynamic state and used for calibration of model parameters. Combined with our observations of constant slip-length and kinematic viscosity, the model accurately predicts the velocity distribution and volumetric and mass flow rates for force-driven liquid flows in different height nano-channels. Model is verified for liquid argon flow at distinct thermodynamic states and using various argon-gold interaction strengths. Further verification is performed for water flow in silica and gold nano-channels, exhibiting slip lengths of 1.2 nm and 15.5 nm, respectively. Excellent agreements between the model and the MD simulations are reported for channel heights as small as 3 nm for various liquid-solid pairs.

  18. 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.

  19. Interacting holographic generalized cosmic Chaplygin gas model

    Science.gov (United States)

    Naji, Jalil

    2014-03-01

    In this paper we consider a correspondence between the holographic dark energy density and interacting generalized cosmic Chaplygin gas energy density in flat FRW universe. Then, we reconstruct the potential of the scalar field which describe the generalized cosmic Chaplygin cosmology. In the special case we obtain time-dependent energy density and study cosmological parameters. We find stability condition of this model which is depend on cosmic parameter.

  20. PRIMO: An Interactive Homology Modeling Pipeline

    Science.gov (United States)

    Glenister, Michael

    2016-01-01

    The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO’s automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/. PMID:27855192

  1. PRIMO: An Interactive Homology Modeling Pipeline.

    Science.gov (United States)

    Hatherley, Rowan; Brown, David K; Glenister, Michael; Tastan Bishop, Özlem

    2016-01-01

    The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO's automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/.

  2. Composite Higgs Boson in the Unified Subquark Model of All Fundamental Particles and Forces

    CERN Document Server

    Terazawa, Hidezumi

    2014-01-01

    In the unified subquark model of all fundamental particles and forces, the mass of the Higgs boson in the standard model of electroweak interactions ($m_H$) is predicted to be about $2\\sqrt{6}m_W/3$ (where $m_W$ is the mass of the charged weak boson), which agrees well with the experimental values of $125-126$ GeV recently found by the ATLAS and CMS Colaborations at the LHC. It seems to indicate that the Higgs boson is a composite of the iso-doublet subquark-antisubquark pairs well described by the unified subquark model with either one of subquark masses vanishing or being very small compared to the other.

  3. Method of and apparatus for modeling interactions

    Science.gov (United States)

    Budge, Kent G.

    2004-01-13

    A method and apparatus for modeling interactions can accurately model tribological and other properties and accommodate topological disruptions. Two portions of a problem space are represented, a first with a Lagrangian mesh and a second with an ALE mesh. The ALE and Lagrangian meshes are constructed so that each node on the surface of the Lagrangian mesh is in a known correspondence with adjacent nodes in the ALE mesh. The interaction can be predicted for a time interval. Material flow within the ALE mesh can accurately model complex interactions such as bifurcation. After prediction, nodes in the ALE mesh in correspondence with nodes on the surface of the Lagrangian mesh can be mapped so that they are once again adjacent to their corresponding Lagrangian mesh nodes. The ALE mesh can then be smoothed to reduce mesh distortion that might reduce the accuracy or efficiency of subsequent prediction steps. The process, from prediction through mapping and smoothing, can be repeated until a terminal condition is reached.

  4. Modeling Users' Experiences with Interactive Systems

    CERN Document Server

    Karapanos, Evangelos

    2013-01-01

    Over the past decade the field of Human-Computer Interaction has evolved from the study of the usability of interactive products towards a more holistic understanding of how they may mediate desired human experiences.  This book identifies the notion of diversity in usersʼ experiences with interactive products and proposes methods and tools for modeling this along two levels: (a) interpersonal diversity in usersʽ responses to early conceptual designs, and (b) the dynamics of usersʼ experiences over time. The Repertory Grid Technique is proposed as an alternative to standardized psychometric scales for modeling interpersonal diversity in usersʼ responses to early concepts in the design process, and new Multi-Dimensional Scaling procedures are introduced for modeling such complex quantitative data. iScale, a tool for the retrospective assessment of usersʼ experiences over time is proposed as an alternative to longitudinal field studies, and a semi-automated technique for the analysis of the elicited exper...

  5. Nagaoka's atomic model and hyperfine interactions.

    Science.gov (United States)

    Inamura, Takashi T

    2016-01-01

    The prevailing view of Nagaoka's "Saturnian" atom is so misleading that today many people have an erroneous picture of Nagaoka's vision. They believe it to be a system involving a 'giant core' with electrons circulating just outside. Actually, though, in view of the Coulomb potential related to the atomic nucleus, Nagaoka's model is exactly the same as Rutherford's. This is true of the Bohr atom, too. To give proper credit, Nagaoka should be remembered together with Rutherford and Bohr in the history of the atomic model. It is also pointed out that Nagaoka was a pioneer of understanding hyperfine interactions in order to study nuclear structure.

  6. Isard's contributions to spatial interaction modeling

    Science.gov (United States)

    O'Kelly, M. E.

    . This short review, surveys Isard's role in promoting what has become known as spatial interaction modeling. Some contextual information on the milieu from which his work emerged is given, together with a selected number of works that are judged to have been influenced (directly and indirectly) by his work. It is suggested that this burgeoning field owes a lot to the foundations laid in the gravity model chapter of ``Methods''. The review is supplemented by a rather extensive bibliography of additional works that are indicative of the breadth of the impact of this field.

  7. Modeling Tractive Force Requirements of Wheel Tractors for Disc Ridging in Loamy Sand Soil

    Directory of Open Access Journals (Sweden)

    S O Nkakini

    2012-10-01

    Full Text Available The efficiency with which a soil can transmit energy from a traction device on a tractor to the drawbar has been called the tractive efficiency of soil. Experiments were conducted for disc ridging operations in a loamy sand soil, at tillage speeds of 1.94m/s, 2.22m/s and 2.5m/s, using trace tractor techniques. Tractive force models at different tillage speeds were developed using dimensional analysis, describing the tractors tyre - soil interaction. The measured independent variables such as drawbar pull force, rolling (motion resistance, wheel slip, moisture content, cone index, wheel numeric, contact pressure, speed, width of ridge and height of ridge were used in the developed models. Values of the measured dependent variable (Tractive force were compared with computed values. High coefficients of determination R2 = 0.996, 0.996 and 0.986, percentage (% errors of -0.122620038 and 0.11606597,-0.126307491 and 0.215127604 ,-0.603425382 and 0.372951166 at minimum and maximum values, for disc ridging at tillage speeds of 1.94m/s, 2.22m/s and 2.5m/s were obtained respectively. Analysis of variance between measured and predicted tractive force values indicated standard errors of 11.15346, 10.15346 and 8.24219, while correlation coefficients of R2 = 0.996, 0.768 and 0.9674 were obtained for disc ridging at tillage speeds of 1.94m/s, 2.22m/s, and 2.5m/s respectively . These results are clear evidence of the test of goodness of fit of the models between the measured and predicted tractive forces for disc ridging at the various tillage speeds. Disc ridging speed of 2.5m/s illustrated the lowest coefficient of determination R2 = 0.986. The developed models were validated by comparing the predicted with the measured tractive forces, and shown to closely followed the experimental results.

  8. A modified social force model for crowd dynamics

    Science.gov (United States)

    Hassan, Ummi Nurmasyitah; Zainuddin, Zarita; Abu-Sulyman, Ibtesam M.

    2017-08-01

    The Social Force Model (SFM) is one of the most successful models in microscopic pedestrian studies that is used to study the movement of pedestrians. Many modifications have been done to improvise the SFM by earlier researchers such as the incorporation of a constant respect factor into the self-stopping mechanism. Before the new mechanism is introduced, the researchers found out that a pedestrian will immediately come to a halt if other pedestrians are near to him, which seems to be an unrealistic behavior. Therefore, researchers introduce a self-slowing mechanism to gradually stop a pedestrian when he is approaching other pedestrians. Subsequently, the dynamic respect factor is introduced into the self-slowing mechanism based on the density of the pedestrians to make the model even more realistic. In real life situations, the respect factor of the pedestrians should be dynamic values instead of a constant value. However, when we reproduce the simulation of the dynamic respect factor, we found that the movement of the pedestrians are unrealistic because the pedestrians are lacking perception of the pedestrians in front of him. In this paper, we adopted both dynamic respect factor and dynamic angular parameter, called modified dynamic respect factor, which is dependent on the density of the pedestrians. Simulations are performed in a normal unidirectional walkway to compare the simulated pedestrians' movements produced by both models. The results obtained showed that the modified dynamic respect factor produces more realistic movement of the pedestrians which conform to the real situation. Moreover, we also found that the simulations endow the pedestrian with a self-slowing mechanism and a perception of other pedestrians in front of him.

  9. Mutable polyelectrolyte tube arrays: mesoscale modeling and lateral force microscopy.

    Science.gov (United States)

    Cranford, Steven W; Han, Lin; Ortiz, Christine; Buehler, Markus J

    2017-08-23

    In this study, the pH-dependent friction of layer-by-layer assemblies of poly(allylamine hydrochloride) and poly(acrylic acid) (PAH/PAA) are quantified for microtube array structures via experimental and simulated lateral force microscopy (LFM). A novel coarse-grain tube model is developed, utilizing a molecular dynamics (MD) framework with a Hertzian soft contact potential (such that F ∼ δ(3/2)) to allow the efficient dynamic simulation of 3D arrays consisting of hundreds of tubes at micrometer length scales. By quantitatively comparing experimental LFM and computational results, the coupling between geometry (tube spacing and swelling) and material properties (intrinsic stiffness) results in a transition from bending dominated deformation to bending combined with inter-tube contact, independent of material adhesion assumptions. Variation of tube spacing (and thus control of contact) can be used to exploit the normal and lateral resistance of the tube arrays as a function of pH (2.0/5.5), beyond the effect of areal tube density, with increased resistances (potential mutability) up to a factor of ∼60. This study provides a novel modeling platform to assess and design dynamic polyelectrolyte-based substrates/coatings with tailorable stimulus-responsive surface friction. Our results show that micro-geometry can be used alongside stimulus-responsive material changes to amplify and systematically tune mutability.

  10. Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo.

    Science.gov (United States)

    Thomas, Robert E; Opalka, Daniel; Overy, Catherine; Knowles, Peter J; Alavi, Ali; Booth, George H

    2015-08-07

    Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, "replica" ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, the present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation.

  11. Different patterns of collagen-proteoglycan interaction: a scanning electron microscopyand atomic force microscopy study

    Directory of Open Access Journals (Sweden)

    A Ruggeri

    2009-12-01

    Full Text Available The extracellular matrix of unfixed, unstained rat corneal stroma, visualized with high-resolution scanning electron microscopy and atomic force microscopy after minimal preliminary treatment, appears composed of straight, parallel, uniform collagen fibrils regularly spaced by a three-dimensional, irregular network of thin, delicate proteoglycan filaments. Rat tail tendon, observed under identical conditions, appears instead made of heterogeneous, closely packed fibrils interwoven with orthogonal proteoglycan filaments. Pre-treatment with cupromeronic blue just thickens the filaments without affecting their spatial layout. Digestion with chondroitinase ABC rids the tendon matrix of all its interconnecting filaments while the corneal stroma architecture remains virtually unaffected, its fibrils always being separated by an evident interfibrillar spacing which is never observed in tendon. Our observations indicate that matrix proteoglycans are responsible for both the highly regular interfibrillar spacing which is distinctive of corneal stroma, and the strong interfibrillar binding observed in tendon. These opposite interaction patterns appear to be distinctive of different proteo- glycan species. The molecular details of proteoglycan interactions are still incompletely understood and are the subject of ongoing research.

  12. Hydrodynamic Interactions between Two Forced Objects of Arbitrary Shape: I Effect on Alignment

    CERN Document Server

    Goldfriend, Tomer; Witten, Thomas A

    2015-01-01

    We study the properties and symmetries governing the hydrodynamic interaction between two identical, arbitrarily shaped objects, driven through a viscous fluid. We treat analytically the leading (dipolar) terms of the pair-mobility matrix, affecting the instantaneous relative linear and angular velocities of the two objects at large separation. We find that the ability to align asymmetric objects by an external time-dependent drive [Moths and Witten, Phys. Rev. Lett. 110, 028301 (2013)] is degraded by the hydrodynamic interaction. The effects of hydrodynamic interactions are explicitly demonstrated through numerically calculated time-dependent trajectories of model alignable objects composed of four stokeslets. In addition to the orientational effect, we find that the two objects generally repel each other, thus restoring full alignment at long times.

  13. Developing Snow Model Forcing Data From WRF Model Output to Aid in Water Resource Forecasting

    Science.gov (United States)

    Havens, S.; Marks, D. G.; Watson, K. A.; Masarik, M.; Flores, A. N.; Kormos, P.; Hedrick, A. R.

    2015-12-01

    Traditional operational modeling tools used by water managers in the west are challenged by more frequently occurring uncharacteristic stream flow patterns caused by climate change. Water managers are now turning to new models based on the physical processes within a watershed to combat the increasing number of events that do not follow the historical patterns. The USDA-ARS has provided near real time snow water equivalent (SWE) maps using iSnobal since WY2012 for the Boise River Basin in southwest Idaho and since WY2013 for the Tuolumne Basin in California that feeds the Hetch Hetchy reservoir. The goal of these projects is to not only provide current snowpack estimates but to use the Weather Research and Forecasting (WRF) model to drive iSnobal in order to produce a forecasted stream flow when coupled to a hydrology model. The first step is to develop methods on how to create snow model forcing data from WRF outputs. Using a reanalysis 1km WRF dataset from WY2009 over the Boise River Basin, WRF model results like surface air temperature, relative humidity, wind, precipitation, cloud cover, and incoming long wave radiation must be downscaled for use in iSnobal. iSnobal results forced with WRF output are validated at point locations throughout the basin, as well as compared with iSnobal results forced with traditional weather station data. The presentation will explore the differences in forcing data derived from WRF outputs and weather stations and how this affects the snowpack distribution.

  14. Polyelectrolyte Building Blocks for Nanotechnology: Atomic Force Microscopy Investigations of Polyelectrolyte-Lipid Interactions, Polyelectrolyte Brushes and Viral Cages

    OpenAIRE

    2013-01-01

    The work presented here has a multidisciplinary character, having as a common factor the characterization of self-assembled nanostructures through force spectroscopy. Exploring AFM as a tool for characterizing self-assembly and interaction forces in soft matter nanostructures, three different Bio and nonbiological systems where investigated, all of them share the common characteristic of being soft matter molecular structures at the nanoscale. The studied systems in question are: a) Polyelect...

  15. An Approach for Simulation of the Muscle Force Modeling It by Summation of Motor Unit Contraction Forces

    Directory of Open Access Journals (Sweden)

    Rositsa Raikova

    2013-01-01

    Full Text Available Muscle force is due to the cumulative effect of repetitively contracting motor units (MUs. To simulate the contribution of each MU to whole muscle force, an approach implemented in a novel computer program is proposed. The individual contraction of an MU (the twitch is modeled by a 6-parameter analytical function previously proposed; the force of one MU is a sum of its contractions due to an applied stimulation pattern, and the muscle force is the sum of the active MUs. The number of MUs, the number of slow, fast-fatigue-resistant, and fast-fatigable MUs, and their six parameters as well as a file with stimulation patterns for each MU are inputs for the developed software. Different muscles and different firing patterns can be simulated changing the input data. The functionality of the program is illustrated with a model consisting of 30 MUs of rat medial gastrocnemius muscle. The twitches of these MUs were experimentally measured and modeled. The forces of the MUs and of the whole muscle were simulated using different stimulation patterns that included different regular, irregular, synchronous, and asynchronous firing patterns of MUs. The size principle of MUs for recruitment and derecruitment was also demonstrated using different stimulation paradigms.

  16. A validation study of a stochastic model of human interaction

    Science.gov (United States)

    Burchfield, Mitchel Talmadge

    The purpose of this dissertation is to validate a stochastic model of human interactions which is part of a developmentalism paradigm. Incorporating elements of ancient and contemporary philosophy and science, developmentalism defines human development as a progression of increasing competence and utilizes compatible theories of developmental psychology, cognitive psychology, educational psychology, social psychology, curriculum development, neurology, psychophysics, and physics. To validate a stochastic model of human interactions, the study addressed four research questions: (a) Does attitude vary over time? (b) What are the distributional assumptions underlying attitudes? (c) Does the stochastic model, {-}N{intlimitssbsp{-infty}{infty}}varphi(chi,tau)\\ Psi(tau)dtau, have utility for the study of attitudinal distributions and dynamics? (d) Are the Maxwell-Boltzmann, Fermi-Dirac, and Bose-Einstein theories applicable to human groups? Approximately 25,000 attitude observations were made using the Semantic Differential Scale. Positions of individuals varied over time and the logistic model predicted observed distributions with correlations between 0.98 and 1.0, with estimated standard errors significantly less than the magnitudes of the parameters. The results bring into question the applicability of Fisherian research designs (Fisher, 1922, 1928, 1938) for behavioral research based on the apparent failure of two fundamental assumptions-the noninteractive nature of the objects being studied and normal distribution of attributes. The findings indicate that individual belief structures are representable in terms of a psychological space which has the same or similar properties as physical space. The psychological space not only has dimension, but individuals interact by force equations similar to those described in theoretical physics models. Nonlinear regression techniques were used to estimate Fermi-Dirac parameters from the data. The model explained a high degree

  17. Visible Geology - Interactive online geologic block modelling

    Science.gov (United States)

    Cockett, R.

    2012-12-01

    Geology is a highly visual science, and many disciplines require spatial awareness and manipulation. For example, interpreting cross-sections, geologic maps, or plotting data on a stereonet all require various levels of spatial abilities. These skills are often not focused on in undergraduate geoscience curricula and many students struggle with spatial relations, manipulations, and penetrative abilities (e.g. Titus & Horsman, 2009). A newly developed program, Visible Geology, allows for students to be introduced to many geologic concepts and spatial skills in a virtual environment. Visible Geology is a web-based, three-dimensional environment where students can create and interrogate their own geologic block models. The program begins with a blank model, users then add geologic beds (with custom thickness and color) and can add geologic deformation events like tilting, folding, and faulting. Additionally, simple intrusive dikes can be modelled, as well as unconformities. Students can also explore the interaction of geology with topography by drawing elevation contours to produce their own topographic models. Students can not only spatially manipulate their model, but can create cross-sections and boreholes to practice their visual penetrative abilities. Visible Geology is easy to access and use, with no downloads required, so it can be incorporated into current, paper-based, lab activities. Sample learning activities are being developed that target introductory and structural geology curricula with learning objectives such as relative geologic history, fault characterization, apparent dip and thickness, interference folding, and stereonet interpretation. Visible Geology provides a richly interactive, and immersive environment for students to explore geologic concepts and practice their spatial skills.; Screenshot of Visible Geology showing folding and faulting interactions on a ridge topography.

  18. Force modeling for incisions into various tissues with MRF haptic master

    Science.gov (United States)

    Kim, Pyunghwa; Kim, Soomin; Park, Young-Dai; Choi, Seung-Bok

    2016-03-01

    This study proposes a new model to predict the reaction force that occurs in incisions during robot-assisted minimally invasive surgery. The reaction force is fed back to the manipulator by a magneto-rheological fluid (MRF) haptic master, which is featured by a bi-directional clutch actuator. The reaction force feedback provides similar sensations to laparotomy that cannot be provided by a conventional master for surgery. This advantage shortens the training period for robot-assisted minimally invasive surgery and can improve the accuracy of operations. The reaction force modeling of incisions can be utilized in a surgical simulator that provides a virtual reaction force. In this work, in order to model the reaction force during incisions, the energy aspect of the incision process is adopted and analyzed. Each mode of the incision process is classified by the tendency of the energy change, and modeled for realistic real-time application. The reaction force model uses actual reaction force information with three types of actual tissues: hard tissue, medium tissue, and soft tissue. This modeled force is realized by the MRF haptic master through an algorithm based on the position and velocity of a scalpel using two different control methods: an open-loop algorithm and a closed-loop algorithm. The reaction forces obtained from the proposed model are compared with a desired force in time domain.

  19. Nanofibre optic force transducers with sub-piconewton resolution via near-field plasmon-dielectric interactions

    Science.gov (United States)

    Huang, Qian; Lee, Joon; Arce, Fernando Teran; Yoon, Ilsun; Angsantikul, Pavimol; Liu, Justin; Shi, Yuesong; Villanueva, Josh; Thamphiwatana, Soracha; Ma, Xuanyi; Zhang, Liangfang; Chen, Shaochen; Lal, Ratnesh; Sirbuly, Donald J.

    2017-06-01

    Ultrasensitive nanomechanical instruments, including the atomic force microscope (AFM) and optical and magnetic tweezers, have helped shed new light on the complex mechanical environments of biological processes. However, it is difficult to scale down the size of these instruments due to their feedback mechanisms, which, if overcome, would enable high-density nanomechanical probing inside materials. A variety of molecular force probes including mechanophores, quantum dots, fluorescent pairs and molecular rotors have been designed to measure intracellular stresses; however, fluorescence-based techniques can have short operating times due to photo-instability and it is still challenging to quantify the forces with high spatial and mechanical resolution. Here, we develop a compact nanofibre optic force transducer (NOFT) that utilizes strong near-field plasmon-dielectric interactions to measure local forces with a sensitivity of <200 fN. The NOFT system is tested by monitoring bacterial motion and heart-cell beating as well as detecting infrasound power in solution.

  20. Modeling of adhesion in tablet compression - I. atomic force microscopy and molecular simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Wang, J. J.; Li, T.; Bateman, S. D.; Erck, R.; Morris, K. R.; Energy Technology; Purdue Univ.; Novartis Pharmaceutical Corp.

    2003-04-01

    Adhesion problems during tablet manufacturing have been observed to be dependent on many formulation and process factors including the run time on the tablet press. Consequently, problems due to sticking may only become apparent towards the end of the development process when a prolonged run on the tablet press is attempted for the first time. It would be beneficial to predict in a relative sense if a formulation or new chemical entity has the potential for adhesion problems early in the development process. It was hypothesized that favorable intermolecular interaction between the drug molecules and the punch face is the first step or criterion in the adhesion process. Therefore, the rank order of adhesion during tablet compression should follow the rank order of these energies of interaction. The adhesion phenomenon was investigated using molecular simulations and contact mode atomic force microscopy (AFM). Three model compounds were chosen from a family of profen compounds. Silicon nitride AFM tips were modified by coating a 20-nm iron layer on the surfaces by sputter coating. Profen flat surfaces were made by melting and recrystallization. The modified AFM probe and each profen surface were immersed in the corresponding profen saturated water during force measurements using AFM. The work of adhesion between iron and ibuprofen, ketoprofen, and flurbiprofen in vacuum were determined to be -184.1, -2469.3, -17.3 mJ {center_dot} m-2, respectively. The rank order of the work of adhesion between iron and profen compounds decreased in the order: ketoprofen > ibuprofen > flurbiprofen. The rank order of interaction between the drug molecules and the iron superlattice as predicted by molecular simulation using Cerius2 is in agreement with the AFM measurements. It has been demonstrated that Atomic Force Microscopy is a powerful tool in studying the adhesion phenomena between organic drug compounds and metal surface. The study has provided insight into the adhesion problems