Science.gov

Sample records for reconstructed dynamic forces

  1. Sequential reconstruction of driving-forces from nonlinear nonstationary dynamics

    NASA Astrophysics Data System (ADS)

    Güntürkün, Ulaş

    2010-07-01

    This paper describes a functional analysis-based method for the estimation of driving-forces from nonlinear dynamic systems. The driving-forces account for the perturbation inputs induced by the external environment or the secular variations in the internal variables of the system. The proposed algorithm is applicable to the problems for which there is too little or no prior knowledge to build a rigorous mathematical model of the unknown dynamics. We derive the estimator conditioned on the differentiability of the unknown system’s mapping, and smoothness of the driving-force. The proposed algorithm is an adaptive sequential realization of the blind prediction error method, where the basic idea is to predict the observables, and retrieve the driving-force from the prediction error. Our realization of this idea is embodied by predicting the observables one-step into the future using a bank of echo state networks (ESN) in an online fashion, and then extracting the raw estimates from the prediction error and smoothing these estimates in two adaptive filtering stages. The adaptive nature of the algorithm enables to retrieve both slowly and rapidly varying driving-forces accurately, which are illustrated by simulations. Logistic and Moran-Ricker maps are studied in controlled experiments, exemplifying chaotic state and stochastic measurement models. The algorithm is also applied to the estimation of a driving-force from another nonlinear dynamic system that is stochastic in both state and measurement equations. The results are judged by the posterior Cramer-Rao lower bounds. The method is finally put into test on a real-world application; extracting sun’s magnetic flux from the sunspot time series.

  2. Reconstruction of dynamic forces during impact tests of a crushable structure

    SciTech Connect

    Bateman, V.I.; Carne, T.G.; Mayes, R.L.; Davie, N.T.

    1993-12-31

    A force reconstruction technique is being used to assess the dynamic performance of a crushable structure (a bomb nose) in both the axial (90{degree}) and slapdown (30{degree}) impact conditions. The dynamic force characteristics for the current nose design, determined from these tests, will be used to write a dynamic force specification for a new nose design that will replace the current nose. Two structures for experimentally determining the dynamic force -- deflection characteristics of the old and new noses have been designed and constructed. One structure has the same dynamic characteristics as the bomb and is being used for axial and slapdown orientations with rocket-propelled testing. The second structure has the same mass as the bomb and is being used for iterative axial testing of candidate designs with a pneumatic ram. The structural characteristics of these two structures have been determined and are presented. A force reconstruction algorithm using the Sum of Weighted Accelerations Technique (SWAT) has been developed for each of the two structures. The force reconstruction algorithms have been verified for both structures using laboratory data. The force reconstruction process and the resulting algorithms are described. Data verifying the force reconstruction algorithms is presented.

  3. Crushable structure performance determined from reconstructed dynamic forces during impact tests

    SciTech Connect

    Bateman, V.I.

    1995-01-01

    A force reconstruction technique has been used to assess the dynamic performance of a crushable structure (a bomb nose) in both the axial (90{degrees}) and slapdown (30{degrees}) impact conditions. The dynamic force characteristics for the nose design, determined from these test results, have been used to write a dynamic force specification for a new nose design that will replace the old nose. The dynamic forces are reconstructed from measured acceleration responses with the Sum of Weighted Accelerations Technique (SWAT) developed at Sandia National Laboratories. Axial characterizations for the old nose are presented from tests at two SNL facilities: a rocket rail launcher facility and an 18-Inch horizontal actuator facility. The characterizations for the old nose are compared to the characterizations for two new nose designs. Slapdown characterizations for the old nose are presented. Incorporation of the test results into a dynamic force specification is discussed.

  4. An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics.

    PubMed

    Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki

    2014-05-14

    We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.

  5. An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics

    SciTech Connect

    Nakamura, Makoto Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki

    2014-05-14

    We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.

  6. Dynamic Reconstruction and Multivariable Control for Force-Actuated, Thin Facesheet Adaptive Optics

    NASA Technical Reports Server (NTRS)

    Grocott, Simon C. O.; Miller, David W.

    1997-01-01

    The Multiple Mirror Telescope (MMT) under development at the University of Arizona takes a new approach in adaptive optics placing a large (0.65 m) force-actuated, thin facesheet deformable mirror at the secondary of an astronomical telescope, thus reducing the effects of emissivity which are important in IR astronomy. However, The large size of the mirror and low stiffness actuators used drive the natural frequencies of the mirror down into the bandwidth of the atmospheric distortion. Conventional adaptive optics takes a quasi-static approach to controlling the, deformable mirror. However, flexibility within the control bandwidth calls for a new approach to adaptive optics. Dynamic influence functions are used to characterize the influence of each actuator on the surface of the deformable mirror. A linearized model of atmospheric distortion is combined with dynamic influence functions to produce a dynamic reconstructor. This dynamic reconstructor is recognized as an optimal control problem. Solving the optimal control problem for a system with hundreds of actuators and sensors is formidable. Exploiting the circularly symmetric geometry of the mirror, and a suitable model of atmospheric distortion, the control problem is divided into a number of smaller decoupled control problems using circulant matrix theory. A hierarchic control scheme which seeks to emulate the quasi-static control approach that is generally used in adaptive optics is compared to the proposed dynamic reconstruction technique. Although dynamic reconstruction requires somewhat more computational power to implement, it achieves better performance with less power usage, and is less sensitive than the hierarchic technique.

  7. Reconstructing Volcanic Forcing of Climate: Past, Present and Future

    NASA Astrophysics Data System (ADS)

    Toohey, M.; Timmreck, C.; Sigl, M.

    2015-12-01

    Radiative forcing resulting from major volcanic eruptions has been a dominant driver of climate variability during Earth's history. Including volcanic forcing in climate model simulations is therefore essential to recreate past climate variability, and provides the opportunity to test the ability of models to respond accurately to external forcing. Ice cores provide estimates of the volcanic sulfate loadings from past eruptions, from which radiative forcing can be reconstructed, with associated uncertainties. Using prior reconstructions, climate models have reproduced the gross features of global mean temperature variability reconstructed from climate proxies, although some significant differences between model results and reconstructions remain. There is much less confidence in the accuracy of the dynamical responses to volcanic forcing produced by climate models, and thus the regional aspects of post-volcanic climate anomalies are much more uncertain—a result which mirrors uncertainties in the dynamical responses to future climate change. Improvements in model's response to volcanic forcing may be possible through improving the accuracy of the forcing data. Recent advances on multiple fronts have motivated the development of a next-generation volcanic forcing timeseries for use in climate models, based on (1) improved dating and precision of ice core records, (2) better understanding of the atmospheric transport and microphysical evolution of volcanic aerosol, including its size distribution, and (3) improved representations of the spatiotemporal structure of volcanic radiative forcing. A new volcanic forcing data set, covering the past 2500 years, will be introduced and compared with prior reconstructions. Preliminary results of climate model simulations using the new forcing will also be shown, and current and future applications of the forcing set discussed.

  8. Synchronized dynamic dose reconstruction

    SciTech Connect

    Litzenberg, Dale W.; Hadley, Scott W.; Tyagi, Neelam; Balter, James M.; Ten Haken, Randall K.; Chetty, Indrin J.

    2007-01-15

    Variations in target volume position between and during treatment fractions can lead to measurable differences in the dose distribution delivered to each patient. Current methods to estimate the ongoing cumulative delivered dose distribution make idealized assumptions about individual patient motion based on average motions observed in a population of patients. In the delivery of intensity modulated radiation therapy (IMRT) with a multi-leaf collimator (MLC), errors are introduced in both the implementation and delivery processes. In addition, target motion and MLC motion can lead to dosimetric errors from interplay effects. All of these effects may be of clinical importance. Here we present a method to compute delivered dose distributions for each treatment beam and fraction, which explicitly incorporates synchronized real-time patient motion data and real-time fluence and machine configuration data. This synchronized dynamic dose reconstruction method properly accounts for the two primary classes of errors that arise from delivering IMRT with an MLC: (a) Interplay errors between target volume motion and MLC motion, and (b) Implementation errors, such as dropped segments, dose over/under shoot, faulty leaf motors, tongue-and-groove effect, rounded leaf ends, and communications delays. These reconstructed dose fractions can then be combined to produce high-quality determinations of the dose distribution actually received to date, from which individualized adaptive treatment strategies can be determined.

  9. Force reconstruction from tapping mode force microscopy experiments.

    PubMed

    Payam, Amir F; Martin-Jimenez, Daniel; Garcia, Ricardo

    2015-05-01

    Fast, accurate, and robust nanomechanical measurements are intensely studied in materials science, applied physics, and molecular biology. Amplitude modulation force microscopy (tapping mode) is the most established nanoscale characterization technique of surfaces for air and liquid environments. However, its quantitative capabilities lag behind its high spatial resolution and robustness. We develop a general method to transform the observables into quantitative force measurements. The force reconstruction algorithm has been deduced on the assumption that the observables (amplitude and phase shift) are slowly varying functions of the tip-surface separation. The accuracy and applicability of the method is validated by numerical simulations and experiments. The method is valid for liquid and air environments, small and large free amplitudes, compliant and rigid materials, and conservative and non-conservative forces.

  10. Force reconstruction using the inverse of the mode-shape matrix

    SciTech Connect

    Carne, T.G.; Bateman, V.I.; Dohrman, C.R.

    1991-01-01

    Force reconstruction is a process in which response signals from a dynamic event are used to infer what the applied force must have been to produce these responses. Force reconstruction is of interest when the input force cannot be directly measured, while the response signals are easily obtained using transducers such as accelerometers or strain gages. In many evaluation tests of a structure, the dynamic response is not sufficient information; one may really need a description of the input force. A new technique for force reconstruction is developed. To estimate the externally applied force, this technique sums the weight-scaled acceleration signals, and is referred to as the Sum of Weighted Accelerations Technique (SWAT). To obtain the scalar weights the inverse of the mode shape matrix is used. Application of this technique is illustrated with both numerical calculations using a mass-spring model and experimental data from a structure impacting a rigid barrier. 16 refs., 13 figs.

  11. The Dynamic Force Table

    ERIC Educational Resources Information Center

    Geddes, John B.; Black, Kelly

    2008-01-01

    We examine an experimental apparatus that is used to motivate the connections between the basic properties of vectors, potential functions, systems of nonlinear equations, and Newton's method for nonlinear systems of equations. The apparatus is an adaptation of a force table where we remove the center-pin and allow the center-ring to move freely.…

  12. Dynamic properties of force fields.

    PubMed

    Vitalini, F; Mey, A S J S; Noé, F; Keller, B G

    2015-02-28

    Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A10) differ when simulated with different force fields (AMBER ff99SB-ILDN, AMBER ff03, OPLS-AA/L, CHARMM27, and GROMOS43a1). The dynamic properties are extracted using Markov state models. For single-residue models (Ac-A-NHMe, Ac-V-NHMe), the slow conformational exchange processes are similar in all force fields, but the associated relaxation timescales differ by up to an order of magnitude. For the peptide systems, not only the relaxation timescales, but also the conformational exchange processes differ considerably across force fields. This finding calls the significance of dynamic interpretations of molecular-dynamics simulations into question.

  13. Exploring the topology of dynamical reconstructions

    NASA Astrophysics Data System (ADS)

    Garland, Joshua; Bradley, Elizabeth; Meiss, James D.

    2016-11-01

    Computing the state-space topology of a dynamical system from scalar data requires accurate reconstruction of those dynamics and construction of an appropriate simplicial complex from the results. The reconstruction process involves a number of free parameters and the computation of homology for a large number of simplices can be expensive. This paper is a study of how to compute the homology efficiently and effectively without a full (diffeomorphic) reconstruction. Using trajectories from the classic Lorenz system, we reconstruct the dynamics using the method of delays, then build a simplicial complex whose vertices are a small subset of the data: the "witness complex". Surprisingly, we find that the witness complex correctly resolves the homology of the underlying invariant set from noisy samples of that set even if the reconstruction dimension is well below the thresholds for assuring topological conjugacy between the true and reconstructed dynamics that are specified in the embedding theorems. We conjecture that this is because the requirements for reconstructing homology are less stringent: a homeomorphism is sufficient-as opposed to a diffeomorphism, as is necessary for the full dynamics. We provide preliminary evidence that a homeomorphism, in the form of a delay-coordinate reconstruction map, may exist at a lower dimension than that required to achieve an embedding.

  14. Reconstruction of electrostatic force microscopy images

    NASA Astrophysics Data System (ADS)

    Strassburg, E.; Boag, A.; Rosenwaks, Y.

    2005-08-01

    An efficient algorithm to restore the actual surface potential image from Kelvin probe force microscopy measurements of semiconductors is presented. The three-dimensional potential of the tip-sample system is calculated using an integral equation-based boundary element method combined with modeling the semiconductor by an equivalent dipole-layer and image-charge model. The derived point spread function of the measuring tip is then used to restore the actual surface potential from the measured image, using noise filtration and deconvolution algorithms. The model is then used to restore high-resolution Kelvin probe microscopy images of semiconductor surfaces.

  15. Mechanical Forces Governing Tissue Dynamics

    NASA Astrophysics Data System (ADS)

    Edwards, Glenn

    2002-10-01

    We have refined a UV-laser microbeam to investigate the forces at play during morphogenesis, i.e. early biological development, in the fruit fly Drosophila (1). While the microbeam typically is used to ablate tissue with cellular spatial resolution, it has the capability for submicron and thus subcellular spatial resolution. The microbeam can be steered in two-dimensions and UV-laser dissection occurred in vivo while the tissue was imaged in real time using a (visible) laser-scanning confocal microscope. We investigated a morphogenic process, known as dorsal closure, in a genetically engineered strain of Drosophila where green fluorescent protein has been fused to a fragment of a native structural protein (2). This allowed us to visualize the fluorescing contours of two opposing, outer sheets of tissue closing over an inner tissue sheet. Time-lapse imaging captured the contours in native closure as well as in response to UV-laser dissection. Specific patterns of dissection essentially eliminated a selected force: by tracking the changes in contour geometry we estimated the relative magnitude of that force (mechanical jump). Using this approach we identified and characterized a set of forces governing tissue dynamics. We have developed a mechanical model for the dynamics of dorsal closure based on this data set. This model provides a theoretical framework for investigating defective closure in mutant flies. Dorsal closure is a model system for various aspects of cell movement in wound healing and vertebrate development. This research has been supported by the DoD MFEL Program as administered by the AFOSR and by the NIH. 1. M.S. Hutson, Y. Tokutake, M-S. Chang, J.W. Bloor, S. Venakides, D.P. Kiehart, and G.S. Edwards. "Laser dissection of morphogenetic dynamics in Drosophila dorsal closure." In preparation. 2. D.P. Kiehart, et al, J. Cell Biol. 149, 471 (2000).

  16. Dynamic force microscopy in liquids

    NASA Astrophysics Data System (ADS)

    Dreier, M.; Anselmetti, D.; Richmond, T.; Dammer, U.; Guentherodt, H.-J.

    1994-11-01

    We applied dynamic force microscopy in a liquid environment to silanized and derivatized glass surfaces, InGaAs, as well as to biological materials such as hexagonally packed intermediate layers of deinococcus radiodurans. The vertical and lateral resolution were estimated to be less than 1 A and 7 - 10 nm, respectively. Upon immersing the cantilever into water, the resonance frequency was found to be reduced by a factor of two and the Q factor was lowered to 20 - 30. The experimental working distance between sensor and sample was determined with approach curves indicating that the range of interaction in water is much shorter compared to air.

  17. Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

    PubMed Central

    Woodside, Michael T.; Block, Steven M.

    2015-01-01

    Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate. PMID:24895850

  18. Reconstructing folding energy landscapes by single-molecule force spectroscopy.

    PubMed

    Woodside, Michael T; Block, Steven M

    2014-01-01

    Folding may be described conceptually in terms of trajectories over a landscape of free energies corresponding to different molecular configurations. In practice, energy landscapes can be difficult to measure. Single-molecule force spectroscopy (SMFS), whereby structural changes are monitored in molecules subjected to controlled forces, has emerged as a powerful tool for probing energy landscapes. We summarize methods for reconstructing landscapes from force spectroscopy measurements under both equilibrium and nonequilibrium conditions. Other complementary, but technically less demanding, methods provide a model-dependent characterization of key features of the landscape. Once reconstructed, energy landscapes can be used to study critical folding parameters, such as the characteristic transition times required for structural changes and the effective diffusion coefficient setting the timescale for motions over the landscape. We also discuss issues that complicate measurement and interpretation, including the possibility of multiple states or pathways and the effects of projecting multiple dimensions onto a single coordinate.

  19. Reconstructing Directed Networks From Noisy Dynamics

    NASA Astrophysics Data System (ADS)

    Tam, Hiu Ching; Ching, Emily Sc

    Complex systems can be fruitfully studied as networks of many elementary units, known as nodes, interacting with one another with the interactions being the links between the nodes. The overall behavior of the systems depends crucially on the network structure depicting how the nodes are linked with each other. It is usually possible to measure the dynamics of the individual nodes but difficult, if not impossible, to directly measure the interactions or links between the nodes. For most systems of interest, the links are directional in that one node affects the dynamics of the other but not vice versa. Moreover, the strength of interaction can vary for different links. Reconstructing directed and weighted networks from dynamics is one of the biggest challenges in network research. We have studied directed and weighted networks modelled by noisy dynamical systems with nonlinear dynamics and developed a method that reconstructs the links and their directions using only the dynamics of the nodes as input. Our method is motivated by a mathematical result derived for dynamical systems that approach a fixed point in the noise-free limit. We show that our method gives good reconstruction results for several directed and weighted networks with different nonlinear dynamics. Supported by Hong Kong Research Grants Council under Grant No. CUHK 14300914.

  20. Reconstruction of dynamic gated cardiac SPECT

    SciTech Connect

    Jin Mingwu; Yang Yongyi; King, Michael A.

    2006-11-15

    In this paper we propose an image reconstruction procedure which aims to unify gated single photon emission computed tomography (SPECT) and dynamic SPECT into a single method. We divide the cardiac cycle into a number of gate intervals as in gated SPECT, but treat the tracer distribution for each gate as a time-varying signal. By using both dynamic and motion-compensated temporal regularization, our reconstruction procedure will produce an image sequence that shows both cardiac motion and time-varying tracer distribution simultaneously. To demonstrate the proposed reconstruction method, we simulated gated cardiac perfusion imaging using the gated mathematical cardiac-torso (gMCAT) phantom with Tc99m-Teboroxime as the imaging agent. Our results show that the proposed method can produce more accurate reconstruction of gated dynamic images than independent reconstruction of individual gate frames with spatial smoothness alone. In particular, our results show that the former could improve the contrast to noise ratio of a simulated perfusion defect by as much as 100% when compared to the latter.

  1. Fusion of intraoperative force sensoring, surface reconstruction and biomechanical modeling

    NASA Astrophysics Data System (ADS)

    Röhl, S.; Bodenstedt, S.; Küderle, C.; Suwelack, S.; Kenngott, H.; Müller-Stich, B. P.; Dillmann, R.; Speidel, S.

    2012-02-01

    Minimally invasive surgery is medically complex and can heavily benefit from computer assistance. One way to help the surgeon is to integrate preoperative planning data into the surgical workflow. This information can be represented as a customized preoperative model of the surgical site. To use it intraoperatively, it has to be updated during the intervention due to the constantly changing environment. Hence, intraoperative sensor data has to be acquired and registered with the preoperative model. Haptic information which could complement the visual sensor data is still not established. In addition, biomechanical modeling of the surgical site can help in reflecting the changes which cannot be captured by intraoperative sensors. We present a setting where a force sensor is integrated into a laparoscopic instrument. In a test scenario using a silicone liver phantom, we register the measured forces with a reconstructed surface model from stereo endoscopic images and a finite element model. The endoscope, the instrument and the liver phantom are tracked with a Polaris optical tracking system. By fusing this information, we can transfer the deformation onto the finite element model. The purpose of this setting is to demonstrate the principles needed and the methods developed for intraoperative sensor data fusion. One emphasis lies on the calibration of the force sensor with the instrument and first experiments with soft tissue. We also present our solution and first results concerning the integration of the force sensor as well as accuracy to the fusion of force measurements, surface reconstruction and biomechanical modeling.

  2. Dynamic Force Measurement with Strain Gauges

    ERIC Educational Resources Information Center

    Lee, Bruce E.

    1974-01-01

    Discusses the use of four strain gauges, a Wheatstone bridge, and an oscilloscope to measure forces dynamically. Included is an example of determining the centripetal force of a pendulum in a general physics laboratory. (CC)

  3. A dynamic 3D foot reconstruction system.

    PubMed

    Thabet, Ali K; Trucco, Emanuele; Salvi, Joaquim; Wang, Weijie; Abboud, Rami J

    2011-01-01

    Foot problems are varied and range from simple disorders through to complex diseases and joint deformities. Wherever possible, the use of insoles, or orthoses, is preferred over surgery. Current insole design techniques are based on static measurements of the foot, despite the fact that orthoses are prevalently used in dynamic conditions while walking or running. This paper presents the design and implementation of a structured-light prototype system providing dense three dimensional (3D) measurements of the foot in motion, and its use to show that foot measurements in dynamic conditions differ significantly from their static counterparts. The input to the system is a video sequence of a foot during a single step; the output is a 3D reconstruction of the plantar surface of the foot for each frame of the input. Engineering and clinical tests were carried out for the validation of the system. The accuracy of the system was found to be 0.34 mm with planar test objects. In tests with real feet, the system proved repeatable, with reconstruction differences between trials one week apart averaging 2.44 mm (static case) and 2.81 mm (dynamic case). Furthermore, a study was performed to compare the effective length of the foot between static and dynamic reconstructions using the 4D system. Results showed an average increase of 9 mm for the dynamic case. This increase is substantial for orthotics design, cannot be captured by a static system, and its subject-specific measurement is crucial for the design of effective foot orthoses.

  4. Dynamical numerical model for nematic order reconstruction.

    PubMed

    Lombardo, G; Ayeb, H; Barberi, R

    2008-05-01

    In highly frustrated calamitic nematic liquid crystals, a strong elastic distortion can be confined on a few nanometers. The classical elastic theory fails to describe such systems and a more complete description based on the tensor order parameter Q is required. A finite element method is used to implement the Q dynamics by a variational principle and it is shown that a uniaxial nematic configuration can evolve passing through transient biaxial states. This solution, which connects two competing uniaxial nematic textures, is known as "nematic order reconstruction."

  5. Dynamical numerical model for nematic order reconstruction

    NASA Astrophysics Data System (ADS)

    Lombardo, G.; Ayeb, H.; Barberi, R.

    2008-05-01

    In highly frustrated calamitic nematic liquid crystals, a strong elastic distortion can be confined on a few nanometers. The classical elastic theory fails to describe such systems and a more complete description based on the tensor order parameter Q is required. A finite element method is used to implement the Q dynamics by a variational principle and it is shown that a uniaxial nematic configuration can evolve passing through transient biaxial states. This solution, which connects two competing uniaxial nematic textures, is known as “nematic order reconstruction.”

  6. Supersonic Flight Dynamics Test: Trajectory, Atmosphere, and Aerodynamics Reconstruction

    NASA Technical Reports Server (NTRS)

    Kutty, Prasad; Karlgaard, Christopher D.; Blood, Eric M.; O'Farrell, Clara; Ginn, Jason M.; Shoenenberger, Mark; Dutta, Soumyo

    2015-01-01

    The Supersonic Flight Dynamics Test is a full-scale flight test of a Supersonic Inflatable Aerodynamic Decelerator, which is part of the Low Density Supersonic Decelerator technology development project. The purpose of the project is to develop and mature aerodynamic decelerator technologies for landing large mass payloads on the surface of Mars. The technologies include a Supersonic Inflatable Aerodynamic Decelerator and Supersonic Parachutes. The first Supersonic Flight Dynamics Test occurred on June 28th, 2014 at the Pacific Missile Range Facility. This test was used to validate the test architecture for future missions. The flight was a success and, in addition, was able to acquire data on the aerodynamic performance of the supersonic inflatable decelerator. This paper describes the instrumentation, analysis techniques, and acquired flight test data utilized to reconstruct the vehicle trajectory, atmosphere, and aerodynamics. The results of the reconstruction show significantly higher lofting of the trajectory, which can partially be explained by off-nominal booster motor performance. The reconstructed vehicle force and moment coefficients fall well within pre-flight predictions. A parameter identification analysis indicates that the vehicle displayed greater aerodynamic static stability than seen in pre-flight computational predictions and ballistic range tests.

  7. Undulator with dynamic compensation of magnetic forces

    DOEpatents

    Gluskin, Efim; Trakhtenberg, Emil; Xu, Joseph Z.

    2016-05-31

    A method and apparatus for implementing dynamic compensation of magnetic forces for undulators are provided. An undulator includes a respective set of magnet arrays, each attached to a strongback, and placed on horizontal slides and positioned parallel relative to each other with a predetermined gap. Magnetic forces are compensated by a set of compensation springs placed along the strongback. The compensation springs are conical springs having exponential-force characteristics that substantially match undulator magnetic forces independently of the predetermined gap. The conical springs are positioned along the length of the magnets.

  8. Estimation of the shear force in transverse dynamic force microscopy using a sliding mode observer

    NASA Astrophysics Data System (ADS)

    Nguyen, Thang; Hatano, Toshiaki; Khan, Said G.; Zhang, Kaiqiang; Edwards, Christopher; Harniman, Robert; Burgess, Stuart C.; Antognozzi, Massimo; Miles, Mervyn; Herrmann, Guido

    2015-09-01

    In this paper, the problem of estimating the shear force affecting the tip of the cantilever in a Transverse Dynamic Force Microscope (TDFM) using a real-time implementable sliding mode observer is addressed. The behaviour of a vertically oriented oscillated cantilever, in close proximity to a specimen surface, facilitates the imaging of the specimen at nano-metre scale. Distance changes between the cantilever tip and the specimen can be inferred from the oscillation amplitudes, but also from the shear force acting at the tip. Thus, the problem of accurately estimating the shear force is of significance when specimen images and mechanical properties need to be obtained at submolecular precision. A low order dynamic model of the cantilever is derived using the method of lines, for the purpose of estimating the shear force. Based on this model, an estimator using sliding mode techniques is presented to reconstruct the unknown shear force, from only tip position measurements and knowledge of the excitation signal applied to the top of the cantilever. Comparisons to methods assuming a quasi-static harmonic balance are made.

  9. Force dynamics in fixed-ratio schedules.

    PubMed

    Pinkston, Jonathan W; McBee, Lindsey N

    2014-03-01

    Fixed-ratio schedules are widely used in behavioral research. Although fixed-ratio schedules often conjure up relationships to work and effort, little is known about effort-related measures in these schedules. Early research had shown that force and effort of operant behavior vary systematically during the execution of ratio schedules, and the goal of the present study was to revisit early research on force dynamics in fixed-ratio schedules. Four rats earned sucrose by pressing an isometric force transducer. Presses produced sucrose after ten or twenty responses. In general, the force of responses increased then decreased systematically across the ratio. The possibility that decreases in force during ratio execution was due to a trade-off with the differential reinforcement of short inter-response times (IRT) was investigated in an additional condition where sucrose was made available according to a tandem fixed-ratio 19 inter-response (IRT)> t schedule. The tandem IRT requirement did not eliminate decreasing trends in force across the ratio; unexpectedly, the tandem requirement did eliminate increases in force early in the ratio, which may reflect sequence-level organization operating in the control of force dynamics. PMID:24315798

  10. Tensor-based dictionary learning for dynamic tomographic reconstruction

    NASA Astrophysics Data System (ADS)

    Tan, Shengqi; Zhang, Yanbo; Wang, Ge; Mou, Xuanqin; Cao, Guohua; Wu, Zhifang; Yu, Hengyong

    2015-04-01

    In dynamic computed tomography (CT) reconstruction, the data acquisition speed limits the spatio-temporal resolution. Recently, compressed sensing theory has been instrumental in improving CT reconstruction from far few-view projections. In this paper, we present an adaptive method to train a tensor-based spatio-temporal dictionary for sparse representation of an image sequence during the reconstruction process. The correlations among atoms and across phases are considered to capture the characteristics of an object. The reconstruction problem is solved by the alternating direction method of multipliers. To recover fine or sharp structures such as edges, the nonlocal total variation is incorporated into the algorithmic framework. Preclinical examples including a sheep lung perfusion study and a dynamic mouse cardiac imaging demonstrate that the proposed approach outperforms the vectorized dictionary-based CT reconstruction in the case of few-view reconstruction.

  11. Tensor-based Dictionary Learning for Dynamic Tomographic Reconstruction

    PubMed Central

    Tan, Shengqi; Zhang, Yanbo; Wang, Ge; Mou, Xuanqin; Cao, Guohua; Wu, Zhifang; Yu, Hengyong

    2015-01-01

    In dynamic computed tomography (CT) reconstruction, the data acquisition speed limits the spatio-temporal resolution. Recently, compressed sensing theory has been instrumental in improving CT reconstruction from far few-view projections. In this paper, we present an adaptive method to train a tensor-based spatio-temporal dictionary for sparse representation of an image sequence during the reconstruction process. The correlations among atoms and across phases are considered to capture the characteristics of an object. The reconstruction problem is solved by the alternating direction method of multipliers. To recover fine or sharp structures such as edges, the nonlocal total variation is incorporated into the algorithmic framework. Preclinical examples including a sheep lung perfusion study and a dynamic mouse cardiac imaging demonstrate that the proposed approach outperforms the vectorized dictionary-based CT reconstruction in the case of few-view reconstruction. PMID:25779991

  12. Forced synchronization of autonomous dynamical Boolean networks

    SciTech Connect

    Rivera-Durón, R. R. Campos-Cantón, E.; Campos-Cantón, I.; Gauthier, Daniel J.

    2015-08-15

    We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics.

  13. Forced synchronization of autonomous dynamical Boolean networks.

    PubMed

    Rivera-Durón, R R; Campos-Cantón, E; Campos-Cantón, I; Gauthier, Daniel J

    2015-08-01

    We present the design of an autonomous time-delay Boolean network realized with readily available electronic components. Through simulations and experiments that account for the detailed nonlinear response of each circuit element, we demonstrate that a network with five Boolean nodes displays complex behavior. Furthermore, we show that the dynamics of two identical networks display near-instantaneous synchronization to a periodic state when forced by a common periodic Boolean signal. A theoretical analysis of the network reveals the conditions under which complex behavior is expected in an individual network and the occurrence of synchronization in the forced networks. This research will enable future experiments on autonomous time-delay networks using readily available electronic components with dynamics on a slow enough time-scale so that inexpensive data collection systems can faithfully record the dynamics.

  14. 4-D reconstruction for dynamic fluorescence diffuse optical tomography.

    PubMed

    Liu, Xin; Zhang, Bin; Luo, Jianwen; Bai, Jing

    2012-11-01

    Dynamic fluorescence diffuse optical tomography (FDOT) is important for the research of drug delivery, medical diagnosis and treatment. Conventionally, dynamic tomographic images are reconstructed frame by frame, independently. This approach fails to account for the temporal correlations in measurement data. Ideally, the entire image sequence should be considered as a whole and a four-dimensional (4-D) reconstruction should be performed. However, the fully 4-D reconstruction is computationally intensive. In this paper, we propose a new 4-D reconstruction approach for dynamic FDOT, which is achieved by applying a temporal Karhunen-Loève (KL) transformation to the imaging equation. By taking advantage of the decorrelation and compression properties of the KL transformation, the complex 4-D optical reconstruction problem is greatly simplified. To evaluate the performance of the method, simulation, phantom, and in vivo experiments (N=7) are performed on a hybrid FDOT/x-ray computed tomography imaging system. The experimental results indicate that the reconstruction images obtained by the KL method provide good reconstruction quality. Additionally, by discarding high-order KL components, the computation time involved with fully 4-D reconstruction can be greatly reduced in contrast to the conventional frame-by-frame reconstruction.

  15. Identification of dynamic forces using group-sparsity in frequency domain

    NASA Astrophysics Data System (ADS)

    Rezayat, A.; Nassiri, V.; De Pauw, B.; Ertveldt, J.; Vanlanduit, S.; Guillaume, P.

    2016-03-01

    The knowledge of acting dynamic forces is required for the design of structures. Given the structural model, inverse techniques offer the possibility to reconstruct the system's input forces from vibration data. The inverse problem is highly sensitive to measurement noise, and the classical pseudo-inverse method generally fails to find the correct loads. In this paper we propose a new penalty function that combines the advantages of the ℓp-norm properties, together with a modified iterative optimization technique. The new algorithm (G-FISTA) is used to localize and reconstruct dynamic point-forces on a beam structure, with no prior knowledge on the force locations. The algorithm is validated by means of several simulations and experiments. The strain data is measured using Fiber Bragg Gratings (FBG) attached to the beam. The obtained results show that the location and time history of point forces are better estimated using the proposed technique.

  16. Reconstruction of dynamic structural inputs in the presence of noise

    SciTech Connect

    Bateman, V.I.; Solomon, O.M. Jr.

    1986-08-01

    This report describes a technique to reconstruct dynamic structural inputs by deconvolution of measured data. The structure to which this technique has been applied is a mild steel bar (3 in diameter and 60 in. long) with a conical nose which provides some geometric simulation of penetrating structures which are used in field test. The deconvolution technique successfully reconstructs dynamic inputs to the bar with and without additive white noise present in the measured response.

  17. Debye Entropic Force and Modified Newtonian Dynamics

    NASA Astrophysics Data System (ADS)

    Li, Xin; Chang, Zhe

    2011-04-01

    Verlinde has suggested that the gravity has an entropic origin, and a gravitational system could be regarded as a thermodynamical system. It is well-known that the equipartition law of energy is invalid at very low temperature. Therefore, entropic force should be modified while the temperature of the holographic screen is very low. It is shown that the modified entropic force is proportional to the square of the acceleration, while the temperature of the holographic screen is much lower than the Debye temperature TD. The modified entropic force returns to the Newton's law of gravitation while the temperature of the holographic screen is much higher than the Debye temperature. The modified entropic force is connected with modified Newtonian dynamics (MOND). The constant a0 involved in MOND is linear in the Debye frequency ωD, which can be regarded as the largest frequency of the bits in screen. We find that there do have a strong connection between MOND and cosmology in the framework of Verlinde's entropic force, if the holographic screen is taken to be bound of the Universe. The Debye frequency is linear in the Hubble constant H0.

  18. A comparison of force reconstruction methods for a lumped mass beam

    SciTech Connect

    Bateman, V.I.; Mayes, R.L.; Carne, T.G.

    1992-11-01

    Two extensions of the force reconstruction method, the Sum of Weighted Accelerations Technique (SWAT), are presented in this paper; and the results are compared to those obtained using SWAT. SWAT requires the use of the structure`s elastic mode shapes for reconstruction of the applied force. Although based on the same theory, the two, new techniques do not rely on mode shapes to reconstruct the applied force and may be applied to structures whose mode shapes are not available. One technique uses the measured force and acceleration responses with the rigid body mode shapes to calculate the scalar weighting vector, so the technique is called SWAT-CAL (SWAT using a CALibrated force input). The second technique uses only the free-decay time response of the structure with the rigid body mode shapes to calculate the scalar weighting vector and is called SWAT-TEEM (SWAT using Time Eliminated Elastic Modes).

  19. A comparison of force reconstruction methods for a lumped mass beam

    SciTech Connect

    Bateman, V.I.; Mayes, R.L.; Carne, T.G.

    1992-01-01

    Two extensions of the force reconstruction method, the Sum of Weighted Accelerations Technique (SWAT), are presented in this paper; and the results are compared to those obtained using SWAT. SWAT requires the use of the structure's elastic mode shapes for reconstruction of the applied force. Although based on the same theory, the two, new techniques do not rely on mode shapes to reconstruct the applied force and may be applied to structures whose mode shapes are not available. One technique uses the measured force and acceleration responses with the rigid body mode shapes to calculate the scalar weighting vector, so the technique is called SWAT-CAL (SWAT using a CALibrated force input). The second technique uses only the free-decay time response of the structure with the rigid body mode shapes to calculate the scalar weighting vector and is called SWAT-TEEM (SWAT using Time Eliminated Elastic Modes).

  20. Dynamics of weakly coupled parametrically forced oscillators

    NASA Astrophysics Data System (ADS)

    Salgado Sánchez, P.; Porter, J.; Tinao, I.; Laverón-Simavilla, A.

    2016-08-01

    The dynamics of two weakly coupled parametric oscillators are studied in the neighborhood of the primary subharmonic instability. The nature of both primary and secondary instabilities depends in a critical way on the permutation symmetries, if any, that remain after coupling is considered, and this depends on the relative phases of the parametric forcing terms. Detailed bifurcation sets, revealing a complex series of transitions organized in part by Bogdanov-Takens points, are calculated for representative sets of parameters. In the particular case of out-of-phase forcing the predictions of the coupled oscillator model are compared with direct numerical simulations and with recent experiments on modulated cross waves. Both the initial Hopf bifurcation and the subsequent saddle-node heteroclinic bifurcation are confirmed.

  1. Dynamics of weakly coupled parametrically forced oscillators.

    PubMed

    Salgado Sánchez, P; Porter, J; Tinao, I; Laverón-Simavilla, A

    2016-08-01

    The dynamics of two weakly coupled parametric oscillators are studied in the neighborhood of the primary subharmonic instability. The nature of both primary and secondary instabilities depends in a critical way on the permutation symmetries, if any, that remain after coupling is considered, and this depends on the relative phases of the parametric forcing terms. Detailed bifurcation sets, revealing a complex series of transitions organized in part by Bogdanov-Takens points, are calculated for representative sets of parameters. In the particular case of out-of-phase forcing the predictions of the coupled oscillator model are compared with direct numerical simulations and with recent experiments on modulated cross waves. Both the initial Hopf bifurcation and the subsequent saddle-node heteroclinic bifurcation are confirmed.

  2. Dynamics of Turing Patterns under Spatiotemporal Forcing

    NASA Astrophysics Data System (ADS)

    Rüdiger, S.; Míguez, D. G.; Muñuzuri, A. P.; Sagués, F.; Casademunt, J.

    2003-03-01

    We study, both theoretically and experimentally, the dynamical response of Turing patterns to a spatiotemporal forcing in the form of a traveling-wave modulation of a control parameter. We show that from strictly spatial resonance, it is possible to induce new, generic dynamical behaviors, including temporally modulated traveling waves and localized traveling solitonlike solutions. The latter make contact with the soliton solutions of Coullet [

    Phys. Rev. Lett.PRLTAO0031-9007 56, 724 (1986)
    ] and generalize them. The stability diagram for the different propagating modes in the Lengyel-Epstein model is determined numerically. Direct observations of the predicted solutions in experiments carried out with light modulations in the photosensitive chlorine dioxide-iodine-malonic acid reaction are also reported.

  3. Impact-force sparse reconstruction from highly incomplete and inaccurate measurements

    NASA Astrophysics Data System (ADS)

    Qiao, Baijie; Zhang, Xingwu; Gao, Jiawei; Chen, Xuefeng

    2016-08-01

    The classical l2-norm-based regularization methods applied for force reconstruction inverse problem require that the number of measurements should not be less than the number of unknown sources. Taking into account the sparse nature of impact-force in time domain, we develop a general sparse methodology based on minimizing l1-norm for solving the highly underdetermined model of impact-force reconstruction. A monotonic two-step iterative shrinkage/thresholding (MTWIST) algorithm is proposed to find the sparse solution to such an underdetermined model from highly incomplete and inaccurate measurements, which can be problematic with Tikhonov regularization. MTWIST is highly efficient for large-scale ill-posed problems since it mainly involves matrix-vector multiplies without matrix factorization. In sparsity frame, the proposed sparse regularization method can not only determine the actual impact location from many candidate sources but also simultaneously reconstruct the time history of impact-force. Simulation and experiment including single-source and two-source impact-force reconstruction are conducted on a simply supported rectangular plate and a shell structure to illustrate the effectiveness and applicability of MTWIST, respectively. Both the locations and force time histories of the single-source and two-source cases are accurately reconstructed from a single accelerometer, where the high noise level is considered in simulation and the primary noise in experiment is supposed to be colored noise. Meanwhile, the consecutive impact-forces reconstruction in a large-scale (greater than 104) sparse frame illustrates that MTWIST has advantages of computational efficiency and identification accuracy over Tikhonov regularization.

  4. Forced and internal variability in temperature simulations and reconstructions of the Common Era

    NASA Astrophysics Data System (ADS)

    Fernández-Donado, Laura; Fidel González-Rouco, J.; Garcia-Bustamante, Elena; Smerdon, Jason S.; Luterbacher, Juerg; Raible, Christoph C.

    2016-04-01

    The relatively short ranges of external forcing variability within the CE represent a challenge in as much as the consistency between simulations and reconstructions can be affected by the large uncertainties in their respective responses to the external forcings. One of the core questions within this work relates therefore the extent to which a straight response to the external forcing can be identified during the period under study and whether this signal is common to simulated and reconstructed temperature. This study is based on an exhaustive compilation, analysis and intercomparison of the available hemispherical and global temperature reconstructions as well as a complete ensemble of simulations including both PMIP3/CMIP5 and non-PMIP3 model experiments. In addition, the various external forcing configurations applied to the models are characterized and a Total External Forcing, including all the individual forcing contributors, is developed for each experiment. Based on the linear relationship found at multidecadal and longer timescales during the last millennium between the temperature and the total external forcing, a quantitative metric of the ratio of response, the so-called Last Millennium Transient Climate Response (LMTCR), is obtained and compared for simulations and reconstructions. Within the LMTCR context, a significant quantitative consistency between the simulations and reconstructions is addressed. This work also offers a discussion about the impact that a range of generally accepted methodological approaches might have on the reconstructed ensemble uncertainties and their influences on model-data comparison exercises. A segregation among the various existing spatial targets within the NH, based on the different level of temperatura variability observed in the series, suggests a lower level of model-data consistency during the MCA than previously reported.

  5. Dynamic Ising model: reconstruction of evolutionary trees

    NASA Astrophysics Data System (ADS)

    de Oliveira, P. M. C.

    2013-09-01

    An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. ‘Species’ here is a general denomination for biological species, spoken languages or any other entity which evolves through heredity. From the N currently alive species within a clade, distances are measured through pairwise comparisons made by geneticists, linguists, etc. The larger is such a distance that, for a pair of species, the older is their last common ancestor. The aim is to reconstruct the previously unknown bifurcations, i.e. the whole clade, from knowledge of the N(N - 1)/2 quoted distances, which are taken for granted. A mechanical method is presented and its applicability is discussed.

  6. Force Production and Reactive Strength Capabilities After Anterior Cruciate Ligament Reconstruction

    PubMed Central

    Flanagan, Eamonn P; Galvin, Lorcan; Harrison, Andrew J

    2008-01-01

    Context: Ambiguity exists in the literature regarding whether individuals can restore function to 100% after anterior cruciate ligament (ACL) reconstruction. The response of force production and reactive strength in stretch-shortening cycle activities after surgery has not been established. Objective: To compare reactive strength and force production capabilities between the involved and uninvolved legs of participants who had undergone ACL reconstruction and rehabilitation with the reactive strength and force production capabilities of a control group. Design: Repeated measures, cross-sectional. Setting: Research laboratory. Patients or Other Participants: Ten participants with ACL reconstructions who had returned to their chosen sports and 10 age-matched and activity-matched control subjects. Intervention(s): We screened the ACL group with the International Knee Documentation Committee Subjective Knee Evaluation Form and functional performance tests to measure a basic level of function. We assessed force production capabilities and reactive strength using squat, countermovement, drop, and rebound jump protocols on a force sledge apparatus. Main Outcome Measure(s): The dependent variables were flight time, peak vertical ground reaction force, leg spring stiffness, and reactive strength index. Results: No participant in the ACL group exhibited functional deficits in comparison with normative values or the control group. Using the force sledge apparatus, we found no notable differences in force production capabilities and reactive strength in the ACL group when comparing the involved with uninvolved legs or the degree of difference between legs with the control group. Conclusions: After ACL reconstruction, rehabilitated participants did not exhibit deficits in force production or reactive strength capabilities. Our results suggest that force production and reactive strength capabilities can be restored to levels comparable with the uninjured control limb and may not

  7. Reconstruction dynamics of recorded holograms in photochromic glass.

    PubMed

    Mihailescu, Mona; Pavel, Eugen; Nicolae, Vasile B

    2011-06-20

    We have investigated the dynamics of the record-erase process of holograms in photochromic glass using continuum Nd:YVO₄ laser radiation (λ=532 nm). A bidimensional microgrid pattern was formed and visualized in photochromic glass, and its diffraction efficiency decay versus time (during reconstruction step) gave us information (D, Δn) about the diffusion process inside the material. The recording and reconstruction processes were carried out in an off-axis setup, and the images of the reconstructed object were recorded by a CCD camera. Measurements realized on reconstructed object images using holograms recorded at a different incident power laser have shown a two-stage process involved in silver atom kinetics. PMID:21691352

  8. Climate Forcing Reconstructions for Use in PMIP Simulations of the Last Millennium (v1.0)

    NASA Technical Reports Server (NTRS)

    Schmidt, Gavin A.; Jungclaus, J.H.; Steinhilber, F.; Vieira, L. E. A.; Ammann, C. M.; Bard, E.; Braconnot, P.; Crowley, T. J.; Delayque, G.; Joos, F.; Krivova, N. A.; Muscheler, R.; Otto-Bliesner, B. L.; Pongratz, J.; Shindell, D. T.; Solanki, S. K.

    2011-01-01

    Simulations of climate over the Last Millennium (850-1850 CE) have been incorporated into the third phase of the Paleoclimate Modelling Intercomparison Project (PMIP3). The drivers of climate over this period are chiefly orbital, solar, volcanic, changes in land use/land cover and some variation in greenhouse gas levels. While some of these effects can be easily defined, the reconstructions of solar, volcanic and land use-related forcing are more uncertain. We describe here the approach taken in defining the scenarios used in PMIP3, document the forcing reconstructions and discuss likely implications.

  9. External force back-projective composition and globally deformable optimization for 3-D coronary artery reconstruction

    NASA Astrophysics Data System (ADS)

    Yang, Jian; Cong, Weijian; Chen, Yang; Fan, Jingfan; Liu, Yue; Wang, Yongtian

    2014-02-01

    The clinical value of the 3D reconstruction of a coronary artery is important for the diagnosis and intervention of cardiovascular diseases. This work proposes a method based on a deformable model for reconstructing coronary arteries from two monoplane angiographic images acquired from different angles. First, an external force back-projective composition model is developed to determine the external force, for which the force distributions in different views are back-projected to the 3D space and composited in the same coordinate system based on the perspective projection principle of x-ray imaging. The elasticity and bending forces are composited as an internal force to maintain the smoothness of the deformable curve. Second, the deformable curve evolves rapidly toward the true vascular centerlines in 3D space and angiographic images under the combination of internal and external forces. Third, densely matched correspondence among vessel centerlines is constructed using a curve alignment method. The bundle adjustment method is then utilized for the global optimization of the projection parameters and the 3D structures. The proposed method is validated on phantom data and routine angiographic images with consideration for space and re-projection image errors. Experimental results demonstrate the effectiveness and robustness of the proposed method for the reconstruction of coronary arteries from two monoplane angiographic images. The proposed method can achieve a mean space error of 0.564 mm and a mean re-projection error of 0.349 mm.

  10. Validation of a Laboratory Method for Evaluating Dynamic Properties of Reconstructed Equine Racetrack Surfaces

    PubMed Central

    Setterbo, Jacob J.; Chau, Anh; Fyhrie, Patricia B.; Hubbard, Mont; Upadhyaya, Shrini K.; Symons, Jennifer E.; Stover, Susan M.

    2012-01-01

    Background Racetrack surface is a risk factor for racehorse injuries and fatalities. Current research indicates that race surface mechanical properties may be influenced by material composition, moisture content, temperature, and maintenance. Race surface mechanical testing in a controlled laboratory setting would allow for objective evaluation of dynamic properties of surface and factors that affect surface behavior. Objective To develop a method for reconstruction of race surfaces in the laboratory and validate the method by comparison with racetrack measurements of dynamic surface properties. Methods Track-testing device (TTD) impact tests were conducted to simulate equine hoof impact on dirt and synthetic race surfaces; tests were performed both in situ (racetrack) and using laboratory reconstructions of harvested surface materials. Clegg Hammer in situ measurements were used to guide surface reconstruction in the laboratory. Dynamic surface properties were compared between in situ and laboratory settings. Relationships between racetrack TTD and Clegg Hammer measurements were analyzed using stepwise multiple linear regression. Results Most dynamic surface property setting differences (racetrack-laboratory) were small relative to surface material type differences (dirt-synthetic). Clegg Hammer measurements were more strongly correlated with TTD measurements on the synthetic surface than the dirt surface. On the dirt surface, Clegg Hammer decelerations were negatively correlated with TTD forces. Conclusions Laboratory reconstruction of racetrack surfaces guided by Clegg Hammer measurements yielded TTD impact measurements similar to in situ values. The negative correlation between TTD and Clegg Hammer measurements confirms the importance of instrument mass when drawing conclusions from testing results. Lighter impact devices may be less appropriate for assessing dynamic surface properties compared to testing equipment designed to simulate hoof impact (TTD

  11. Free energy reconstruction from steered dynamics without post-processing

    SciTech Connect

    Athenes, Manuel; Marinica, Mihai-Cosmin

    2010-09-20

    Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable one to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes theorem, we propose a more direct method in which a posterior likelihood function is used both to construct the steered dynamics and to infer the contribution to equilibrium of all the sampled states. The method is implemented with two steering schedules. First, using non-autonomous steering, we calculate the migration barrier of the vacancy in Fe-{alpha}. Second, using an autonomous scheduling related to metadynamics and equivalent to temperature-accelerated molecular dynamics, we accurately reconstruct the two-dimensional free energy landscape of the 38-atom Lennard-Jones cluster as a function of an orientational bond-order parameter and energy, down to the solid-solid structural transition temperature of the cluster and without maximum-likelihood post-processing.

  12. Reconstructing embedding spaces of coupled dynamical systems from multivariate data.

    PubMed

    Boccaletti, S; Valladares, D L; Pecora, Louis M; Geffert, Hite P; Carroll, T

    2002-03-01

    A method for reconstructing dimensions of subspaces for weakly coupled dynamical systems is offered. The tool is able to extrapolate the subspace dimensions from the zero coupling limit, where the division of dimensions as per the algorithm is exact. Implementation of the proposed technique to multivariate data demonstrates its effectiveness in disentangling subspace dimensionalities also in the case of emergent synchronized motions, for both numerical and experimental systems.

  13. Dynamic force patterns of an undulatory microswimmer

    NASA Astrophysics Data System (ADS)

    Schulman, Rafael D.; Backholm, Matilda; Ryu, William S.; Dalnoki-Veress, Kari

    2014-05-01

    We probe the viscous forces involved in the undulatory swimming of the model organism C. elegans. Using micropipette deflection, we attain direct measurements of lateral and propulsive forces produced in response to the motion of the worm. We observe excellent agreement of the results with resistive force theory, through which we determine the drag coefficients of this organism. The drag coefficients are in accordance with theoretical predictions. Using a simple scaling argument, we obtain a relationship between the size of the worm and the forces that we measure, which well describes our data.

  14. Simulated and reconstructed climate in Europe during the last five centuries: joint evaluation of climate models performance and the dynamical consistency of gridded reconstructions

    NASA Astrophysics Data System (ADS)

    José Gómez-Navarro, Juan; Bothe, Oliver; Wagner, Sebastian; Zorita, Eduardo; Werner, Johannes P.; Luterbacher, Jürg; Raible, Christoph C.; Montávez, Juan Pedro

    2015-04-01

    This study jointly analyses European winter and summer temperature and precipitation gridded climate reconstructions and a regional climate simulation reaching a resolution of 45 km over the period 1501-1990. In a first step, the simulation is compared to observational records to establish the model performance and to identify the most prominent caveats. It is found that the regional simulation is able to add value to the driving global simulation, which allows it to reproduce accurately the most prominent characteristics of the European climate, although remarkable biases can also be identified. In a second step, the simulation is compared to a set on independent reconstructions. The high-resolution of the simulation and the reconstructions allows to analyse the European area for nine sub-areas. An overall good agreement is found between the reconstructed and simulated climate variability across different areas, supporting a consistency of both products and the proper calibration of the reconstructions. However, biases appear between both datasets, that thanks to the evaluation of the model performance carried out before, can be attributed to deficiencies in the simulation. Although the simulation responds to external forcing, it largely differers with reconstructions in their estimates of the past climate evolution for European sub-regions. In particular, there are deviations between simulated and reconstructed anomalies during the Maunder and Dalton minima, i.e. the simulated response is much stronger than the reconstructed. This disagreement is to some extent expected given the prominent role of internal variability in the regional evolution of temperature and precipitation. However the inability of the model to reproduce any warm period similar to that recorded around 1740 in the reconstructions indicates fundamental limitations in the simulation that preclude reproducing exceptionally anomalous conditions. Despite these limitations, the simulated climate is a

  15. Static and dynamical Meissner force fields

    NASA Technical Reports Server (NTRS)

    Weinberger, B. R.; Lynds, L.; Hull, J. R.; Mulcahy, T. M.

    1991-01-01

    The coupling between copper-based high temperature superconductors (HTS) and magnets is represented by a force field. Zero-field cooled experiments were performed with several forms of superconductors: 1) cold-pressed sintered cylindrical disks; 2) small particles fixed in epoxy polymers; and 3) small particles suspended in hydrocarbon waxes. Using magnets with axial field symmetries, direct spatial force measurements in the range of 0.1 to 10(exp 4) dynes were performed with an analytical balance and force constants were obtained from mechanical vibrational resonances. Force constants increase dramatically with decreasing spatial displacement. The force field displays a strong temperature dependence between 20 and 90 K and decreases exponentially with increasing distance of separation. Distinct slope changes suggest the presence of B-field and temperature-activated processes that define the forces. Hysteresis measurements indicated that the magnitude of force scales roughly with the volume fraction of HTS in composite structures. Thus, the net force resulting from the field interaction appears to arise from regions as small or smaller than the grain size and does not depend on contiguous electron transport over large areas. Results of these experiments are discussed.

  16. Dictionary learning and time sparsity for dynamic MR data reconstruction.

    PubMed

    Caballero, Jose; Price, Anthony N; Rueckert, Daniel; Hajnal, Joseph V

    2014-04-01

    The reconstruction of dynamic magnetic resonance data from an undersampled k-space has been shown to have a huge potential in accelerating the acquisition process of this imaging modality. With the introduction of compressed sensing (CS) theory, solutions for undersampled data have arisen which reconstruct images consistent with the acquired samples and compliant with a sparsity model in some transform domain. Fixed basis transforms have been extensively used as sparsifying transforms in the past, but recent developments in dictionary learning (DL) have been shown to outperform them by training an overcomplete basis that is optimal for a particular dataset. We present here an iterative algorithm that enables the application of DL for the reconstruction of cardiac cine data with Cartesian undersampling. This is achieved with local processing of spatio-temporal 3D patches and by independent treatment of the real and imaginary parts of the dataset. The enforcement of temporal gradients is also proposed as an additional constraint that can greatly accelerate the convergence rate and improve the reconstruction for high acceleration rates. The method is compared to and shown to systematically outperform k- t FOCUSS, a successful CS method that uses a fixed basis transform. PMID:24710166

  17. Reconstruction of Holocene carbon dynamics in a large boreal peatland complex, southern Finland

    NASA Astrophysics Data System (ADS)

    Mathijssen, Paul J. H.; Väliranta, Minna; Korrensalo, Aino; Alekseychik, Pavel; Vesala, Timo; Rinne, Janne; Tuittila, Eeva-Stiina

    2016-06-01

    Holocene peatland development and associated carbon (C) dynamics were reconstructed for a southern boreal Finnish peatland complex with fen and bog areas. In order to assess the role of local factors and long-term allogenic climate forcing in peatland development patterns, we studied a total of 18 peat cores and reconstructed vertical peat growth and lateral peat area expansion rates, the C accumulation rate (CAR), past vegetation composition and past methane (CH4) fluxes. We combined fossil plant data with measured contemporary CH4 flux - vegetation relationship data to reconstruct CH4 fluxes over time. When these reconstructions were added to the CAR estimations, a more complete picture of Holocene-scale C dynamics was achieved. Basal peat ages showed that expansion of the peat area was rapid between 11,000 and 8000 cal. BP, but decreased during the dry mid-Holocene and is probably currently limited by basal topography. A similar pattern was observed for peat growth and CAR in the fen core, whereas in the bog core CAR increased after ombrotrophication, i.e. after 4400 cal. BP. The effect of fire on vegetation and CAR was more conspicuous at the bog site than at the fen site. The CH4 flux reconstructions showed that during the Holocene CH4 emissions at the fen site decreased from 19 ± 15 to 16 ± 8 g CH4 m-2 yr-1 and at the bog site from 20 ± 15 to 14 ± 8 g CH4 m-2 yr-1. Our results suggest that a combination of changing climate, fire events and local conditions have modified the autogenic peatland development and C dynamics.

  18. Simultaneous reconstruction and segmentation for dynamic SPECT imaging

    NASA Astrophysics Data System (ADS)

    Burger, Martin; Rossmanith, Carolin; Zhang, Xiaoqun

    2016-10-01

    This work deals with the reconstruction of dynamic images that incorporate characteristic dynamics in certain subregions, as arising for the kinetics of many tracers in emission tomography (SPECT, PET). We make use of a basis function approach for the unknown tracer concentration by assuming that the region of interest can be divided into subregions with spatially constant concentration curves. Applying a regularised variational framework reminiscent of the Chan-Vese model for image segmentation we simultaneously reconstruct both the labelling functions of the subregions as well as the subconcentrations within each region. Our particular focus is on applications in SPECT with the Poisson noise model, resulting in a Kullback-Leibler data fidelity in the variational approach. We present a detailed analysis of the proposed variational model and prove existence of minimisers as well as error estimates. The latter apply to a more general class of problems and generalise existing results in literature since we deal with a nonlinear forward operator and a nonquadratic data fidelity. A computational algorithm based on alternating minimisation and splitting techniques is developed for the solution of the problem and tested on appropriately designed synthetic data sets. For those we compare the results to those of standard EM reconstructions and investigate the effects of Poisson noise in the data.

  19. Single-molecule reconstruction of oligonucleotide secondary structure by atomic force microscopy.

    PubMed

    Pyne, Alice; Thompson, Ruth; Leung, Carl; Roy, Debdulal; Hoogenboom, Bart W

    2014-08-27

    Based on soft-touch atomic force microscopy, a method is described to reconstruct the secondary structure of single extended biomolecules, without the need for crystallization. The method is tested by accurately reproducing the dimensions of the B-DNA crystal structure. Importantly, intramolecular variations in groove depth of the DNA double helix are resolved, which would be inaccessible for methods that rely on ensemble-averaging.

  20. Force reconstruction using the sum of weighted accelerations technique -- Max-Flat procedure

    SciTech Connect

    Carne, T.G.; Mayes, R.L.; Bateman, V.I.

    1993-12-31

    Force reconstruction is a procedure in which the externally applied force is inferred from measured structural response rather than directly measured. In a recently developed technique, the response acceleration time-histories are multiplied by scalar weights and summed to produce the reconstructed force. This reconstruction is called the Sum of Weighted Accelerations Technique (SWAT). One step in the application of this technique is the calculation of the appropriate scalar weights. In this paper a new method of estimating the weights, using measured frequency response function data, is developed and contrasted with the traditional SWAT method of inverting the mode-shape matrix. The technique uses frequency response function data, but is not based on deconvolution. An application that will be discussed as part of this paper is the impact into a rigid barrier of a weapon system with an energy-absorbing nose. The nose had been designed to absorb the energy of impact and to mitigate the shock to the interior components.

  1. Corticomuscular synchronization with small and large dynamic force output

    PubMed Central

    Andrykiewicz, Agnieszka; Patino, Luis; Naranjo, Jose Raul; Witte, Matthias; Hepp-Reymond, Marie-Claude; Kristeva, Rumyana

    2007-01-01

    Background Over the last few years much research has been devoted to investigating the synchronization between cortical motor and muscular activity as measured by EEG/MEG-EMG coherence. The main focus so far has been on corticomuscular coherence (CMC) during static force condition, for which coherence in beta-range has been described. In contrast, we showed in a recent study [1] that dynamic force condition is accompanied by gamma-range CMC. The modulation of the CMC by various dynamic force amplitudes, however, remained uninvestigated. The present study addresses this question. We examined eight healthy human subjects. EEG and surface EMG were recorded simultaneously. The visuomotor task consisted in isometric compensation for 3 forces (static, small and large dynamic) generated by a manipulandum. The CMC, the cortical EEG spectral power (SP), the EMG SP and the errors in motor performance (as the difference between target and exerted force) were analyzed. Results For the static force condition we found the well-documented, significant beta-range CMC (15–30 Hz) over the contralateral sensorimotor cortex. Gamma-band CMC (30–45 Hz) occurred in both small and large dynamic force conditions without any significant difference between both conditions. Although in some subjects beta-range CMC was observed during both dynamic force conditions no significant difference between conditions could be detected. With respect to the motor performance, the lowest errors were obtained in the static force condition and the highest ones in the dynamic condition with large amplitude. However, when we normalized the magnitude of the errors to the amplitude of the applied force (relative errors) no significant difference between both dynamic conditions was observed. Conclusion These findings confirm that during dynamic force output the corticomuscular network oscillates at gamma frequencies. Moreover, we show that amplitude modulation of dynamic force has no effect on the gamma CMC

  2. Cranial myology and bite force performance of Erlikosaurus andrewsi: a novel approach for digital muscle reconstructions

    PubMed Central

    Lautenschlager, Stephan

    2013-01-01

    The estimation of bite force and bite performance in fossil and extinct animals is a challenging subject in palaeontology and is highly dependent on the reconstruction of the cranial myology. Furthermore, the morphology and arrangement of the adductor muscles considerably affect feeding processes and mastication and thus also have important dietary and ecological ramifications. However, in the past, the reconstruction of the (cranial) muscles was restricted to the identification of muscle attachment sites or simplified computer models. This study presents a detailed reconstruction of the adductor musculature of the Cretaceous therizinosaur Erlikosaurus andrewsi based on a stepwise and iterative approach. The detailed, three-dimensional models of the individual muscles allow for more accurate measurements of the muscle properties (length, cross-section, attachment angle and volume), from which muscle and bite force estimates are calculated. Bite force estimations are found to be the lowest at the tip of the snout (43–65 N) and respectively higher at the first (59–88 N) and last tooth (90–134 N) position. Nevertheless, bite forces are comparatively low for E. andrewsi, both in actual numbers as well as in comparison with other theropod dinosaurs. The results further indicate that the low bite performance was mainly used for leaf-stripping and plant cropping, rather than active mastication or chewing processes. Muscle and thus bite force in E. andrewsi (and most likely all therizinosaurs) is considerably constrained by the cranial anatomy and declines in derived taxa of this clade. This trend is reflected in the changes of dietary preferences from carnivory to herbivory in therizinosaurs. PMID:23061752

  3. Traceable dynamic calibration of force transducers by primary means

    NASA Astrophysics Data System (ADS)

    Vlajic, Nicholas; Chijioke, Ako

    2016-08-01

    We describe an apparatus for traceable, dynamic calibration of force transducers using harmonic excitation, and report calibration measurements of force transducers using this apparatus. In this system, the force applied to the transducer is produced by the acceleration of an attached mass, and is determined according to Newton’s second law, F  =  ma. The acceleration is measured by primary means, using laser interferometry. The capabilities of this system are demonstrated by performing dynamic calibrations of two shear-web-type force transducers up to a frequency of 2 kHz, with an expanded uncertainty below 1.2%. We give an account of all significant sources of uncertainty, including a detailed consideration of the effects of dynamic tilting (rocking), which is a leading source of uncertainty in such harmonic force calibration systems.

  4. Effective reconstruction of dynamics of medium response spectrum

    NASA Astrophysics Data System (ADS)

    Trofimov, Vyacheslav A.; Varentsova, Svetlana A.

    2008-10-01

    A new algorithm is suggested to visualize the dynamics of medium response spectrum in terahertz diapason by the singly measured set of partially intersected integral characteristics of the signal. The algorithm is based on SVD method and window sliding method. The analysis, we carried out, demonstrates many advantages of the new algorithm in com-parison with the Gabor-Fourier approach, which allows obtaining the dynamics of only one spectral line for one set of measurements. Among which it is necessary to mention the possibility to get the dynamics of many spectral components simultaneously for one set of measurements as well and therefore to get the complete information about the spectrum dynamics. This allows to identify specific materials with known spectral lines and to distinguish materials with similar spectra, which is of great importance for the detection and identification of different chemicals, pharmaceutical substances and explosives. To demonstrate the efficiency of a proposed algorithm, we compare spectrum dynamics of chocolate and soap, which possess the similar spectra. Our investigation shows that their dynamics widely vary in spec-tral lines. The proposed algorithm can be also applied to voice identification and to reconstruction of a laser beam profile with a great number of local maxima. Developed algorithm allows to measure the characteristic time of medium responce. It is very important for various problems of spectroscopy.

  5. Stable dynamics in forced systems with sufficiently high/low forcing frequency.

    PubMed

    Bartuccelli, M; Gentile, G; Wright, J A

    2016-08-01

    We consider parametrically forced Hamiltonian systems with one-and-a-half degrees of freedom and study the stability of the dynamics when the frequency of the forcing is relatively high or low. We show that, provided the frequency is sufficiently high, Kolmogorov-Arnold-Moser (KAM) theorem may be applied even when the forcing amplitude is far away from the perturbation regime. A similar result is obtained for sufficiently low frequency, but in that case we need the amplitude of the forcing to be not too large; however, we are still able to consider amplitudes which are outside of the perturbation regime. In addition, we find numerically that the dynamics may be stable even when the forcing amplitude is very large, well beyond the range of validity of the analytical results, provided the frequency of the forcing is taken correspondingly low. PMID:27586604

  6. Stable dynamics in forced systems with sufficiently high/low forcing frequency

    NASA Astrophysics Data System (ADS)

    Bartuccelli, M.; Gentile, G.; Wright, J. A.

    2016-08-01

    We consider parametrically forced Hamiltonian systems with one-and-a-half degrees of freedom and study the stability of the dynamics when the frequency of the forcing is relatively high or low. We show that, provided the frequency is sufficiently high, Kolmogorov-Arnold-Moser (KAM) theorem may be applied even when the forcing amplitude is far away from the perturbation regime. A similar result is obtained for sufficiently low frequency, but in that case we need the amplitude of the forcing to be not too large; however, we are still able to consider amplitudes which are outside of the perturbation regime. In addition, we find numerically that the dynamics may be stable even when the forcing amplitude is very large, well beyond the range of validity of the analytical results, provided the frequency of the forcing is taken correspondingly low.

  7. Dynamic Forces in Spur Gears - Measurement, Prediction, and Code Validation

    NASA Technical Reports Server (NTRS)

    Oswald, Fred B.; Townsend, Dennis P.; Rebbechi, Brian; Lin, Hsiang Hsi

    1996-01-01

    Measured and computed values for dynamic loads in spur gears were compared to validate a new version of the NASA gear dynamics code DANST-PC. Strain gage data from six gear sets with different tooth profiles were processed to determine the dynamic forces acting between the gear teeth. Results demonstrate that the analysis code successfully simulates the dynamic behavior of the gears. Differences between analysis and experiment were less than 10 percent under most conditions.

  8. Experiments of reconstructing discrete atmospheric dynamic models from data (I)

    NASA Astrophysics Data System (ADS)

    Lin, Zhenshan; Zhu, Yanyu; Deng, Ziwang

    1995-03-01

    In this paper, we give some experimental results of our study in reconstructing discrete atmospheric dynamic models from data. After a great deal of numerical experiments, we found that the logistic map, x n + 1 = 1- μx {2/n}, could be used in monthly mean temperature prediction when it was approaching the chaotic region, and its predictive results were in reverse states to the practical data. This means that the nonlinear developing behavior of the monthly mean temperature system is bifurcating back into the critical chaotic states from the chaotic ones.

  9. Dynamic Force Patterns of an Undulatory Microswimmer

    NASA Astrophysics Data System (ADS)

    Schulman, Rafael; Backholm, Matilda; Ryu, William; Dalnoki-Veress, Kari

    2014-03-01

    C. elegans is a millimeter-sized nematode which has served as a model organism in biology for several decades, primarily due to its simple anatomy. Using an undulatory form of locomotion, this worm is capable of propelling itself through various media. Due to the small length scales involved, swimming in this regime is qualitatively different from macroscopic locomotion because the swimmers can be considered to have no inertia. In order to understand the microswimming that this worm exhibits, it is crucial to determine the viscous forces experienced during its motion. Using a micropipette deflection technique in conjunction with high speed imaging, we have directly measured the time-varying forces generated by C. elegans during swimming. Furthermore, by analyzing the body's kinematics over time and applying a model of locomotion, we can compute the theoretical force curves. We observe excellent agreement between the measured and calculated forces. The success of this simple model has important implications in the understanding of microswimming in general.

  10. Liquid contact resonance atomic force microscopy via experimental reconstruction of the hydrodynamic function

    NASA Astrophysics Data System (ADS)

    Tung, Ryan C.; Killgore, Jason P.; Hurley, Donna C.

    2014-06-01

    We present a method to correct for surface-coupled inertial and viscous fluid loading forces in contact resonance (CR) atomic force microscopy (AFM) experiments performed in liquid. Based on analytical hydrodynamic theory, the method relies on experimental measurements of the AFM cantilever's free resonance peaks near the sample surface. The free resonance frequencies and quality factors in both air and liquid allow reconstruction of a continuous hydrodynamic function that can be used to adjust the CR data in liquid. Validation experiments utilizing thermally excited free and in-contact spectra were performed to assess the accuracy of our approach. Results show that the method recovers the air frequency values within approximately 6%. Knowledge of fluid loading forces allows current CR analysis techniques formulated for use in air and vacuum environments to be applied to liquid environments. Our technique greatly extends the range of measurement environments available to CR-AFM.

  11. Dimensional characterization of anesthesia dynamic in reconstructed embedding space.

    PubMed

    Gifani, P; Rabiee, H R; Hashemi, M; Ghanbari, M

    2007-01-01

    The depth of anesthesia quantification has been one of the most research interests in the field of EEG signal processing and nonlinear dynamical analysis has emerged as a novel method for the study of complex systems in the past few decades. In this investigation we use the concept of nonlinear time series analysis techniques to reconstruct the attractor of anesthesia from EEG signal which have been obtained from different hypnotic states during surgery to give a characterization of the dimensional complexity of EEG by Correlation Dimension estimation. The dimension of the anesthesia strange attractor can be thought of as a measure of the degrees of freedom or the ;complexity' of the dynamics at different hypnotic levels. The results imply that for awaked state the correlation dimension is high, On the other hand, for light, moderate and deep hypnotic states these values decrease respectively; which means for anesthetized situation we expect lower correlation dimension.

  12. Reconstructing dynamic molecular states from single-cell time series.

    PubMed

    Huang, Lirong; Pauleve, Loic; Zechner, Christoph; Unger, Michael; Hansen, Anders S; Koeppl, Heinz

    2016-09-01

    The notion of state for a system is prevalent in the quantitative sciences and refers to the minimal system summary sufficient to describe the time evolution of the system in a self-consistent manner. This is a prerequisite for a principled understanding of the inner workings of a system. Owing to the complexity of intracellular processes, experimental techniques that can retrieve a sufficient summary are beyond our reach. For the case of stochastic biomolecular reaction networks, we show how to convert the partial state information accessible by experimental techniques into a full system state using mathematical analysis together with a computational model. This is intimately related to the notion of conditional Markov processes and we introduce the posterior master equation and derive novel approximations to the corresponding infinite-dimensional posterior moment dynamics. We exemplify this state reconstruction approach using both in silico data and single-cell data from two gene expression systems in Saccharomyces cerevisiae, where we reconstruct the dynamic promoter and mRNA states from noisy protein abundance measurements. PMID:27605167

  13. Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics

    NASA Astrophysics Data System (ADS)

    Ehrlicher, Allen

    2012-02-01

    Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.

  14. Reconstructing the micrometeorological dynamics of the southern Amazonian transitional forest

    NASA Astrophysics Data System (ADS)

    de Paulo, Sergio Roberto; de Paulo, Iramaia Jorge Cabral; De Decker, Yannick

    2015-12-01

    In this work, we reconstruct and analyze the micrometeorological dynamics of the transitional forest located south of the Amazon basin. For this, we use time series of micrometeorological variables collected over five years in the transitional forest of Mato Grosso (Brazil). We employ local feature analysis, a recently proposed extension of principal component analysis, to extract the most relevant physical variables from this set. We show in this way that temperature records contain most of the dynamical information in all seasons. Based on this result, the dimensionality of the space spanned by the system's dynamics and the properties of the so defined attractors are obtained. In the dry season, the system presents a robust oscillatory character described by a well-defined limit cycle. In the wet season, the dynamics becomes more irregular but can still be seen as a periodic behavior affected by external noise. These results can help to develop accurate models for the meteorology of the Amazonian transitional forest and can thus lead to a better understanding of this important ecosystem.

  15. Dynamic Data-Driven Event Reconstruction for Atmospheric Releases

    SciTech Connect

    Kosovic, B; Belles, R; Chow, F K; Monache, L D; Dyer, K; Glascoe, L; Hanley, W; Johannesson, G; Larsen, S; Loosmore, G; Lundquist, J K; Mirin, A; Neuman, S; Nitao, J; Serban, R; Sugiyama, G; Aines, R

    2007-02-22

    Accidental or terrorist releases of hazardous materials into the atmosphere can impact large populations and cause significant loss of life or property damage. Plume predictions have been shown to be extremely valuable in guiding an effective and timely response. The two greatest sources of uncertainty in the prediction of the consequences of hazardous atmospheric releases result from poorly characterized source terms and lack of knowledge about the state of the atmosphere as reflected in the available meteorological data. In this report, we discuss the development of a new event reconstruction methodology that provides probabilistic source term estimates from field measurement data for both accidental and clandestine releases. Accurate plume dispersion prediction requires the following questions to be answered: What was released? When was it released? How much material was released? Where was it released? We have developed a dynamic data-driven event reconstruction capability which couples data and predictive models through Bayesian inference to obtain a solution to this inverse problem. The solution consists of a probability distribution of unknown source term parameters. For consequence assessment, we then use this probability distribution to construct a ''''composite'' forward plume prediction which accounts for the uncertainties in the source term. Since in most cases of practical significance it is impossible to find a closed form solution, Bayesian inference is accomplished by utilizing stochastic sampling methods. This approach takes into consideration both measurement and forward model errors and thus incorporates all the sources of uncertainty in the solution to the inverse problem. Stochastic sampling methods have the additional advantage of being suitable for problems characterized by a non-Gaussian distribution of source term parameters and for cases in which the underlying dynamical system is non-linear. We initially developed a Markov Chain Monte

  16. Dynamics of gecko locomotion: a force-measuring array to measure 3D reaction forces.

    PubMed

    Dai, Zhendong; Wang, Zhouyi; Ji, Aihong

    2011-03-01

    Measuring the interaction between each foot of an animal and the substrate is one of the most effective ways to understand the dynamics of legged locomotion. Here, a new facility - the force-measuring array (FMA) - was developed and applied to measure 3D reaction forces of geckos on different slope surfaces. The FMA consists of 16 3D sensors with resolution to the mN level. At the same time the locomotion behaviour of geckos freely moving on the FMA was recorded by high speed camera. The reaction forces acting on the gecko's individual feet measured by the FMA and correlated with locomotion behaviour provided enough information to reveal the mechanical and dynamic secrets of gecko locomotion. Moreover, dynamic forces were also measured by a force platform and correlated with locomotion behaviour. The difference between the forces measured by the two methods is discussed. From the results we conclude that FMA is the best way to obtain true reaction forces acting on the gecko's individual feet.

  17. Software for Correcting the Dynamic Error of Force Transducers

    PubMed Central

    Miyashita, Naoki; Watanabe, Kazuhide; Irisa, Kyouhei; Iwashita, Hiroshi; Araki, Ryosuke; Takita, Akihiro; Yamaguchi, Takao; Fujii, Yusaku

    2014-01-01

    Software which corrects the dynamic error of force transducers in impact force measurements using their own output signal has been developed. The software corrects the output waveform of the transducers using the output waveform itself, estimates its uncertainty and displays the results. In the experiment, the dynamic error of three transducers of the same model are evaluated using the Levitation Mass Method (LMM), in which the impact forces applied to the transducers are accurately determined as the inertial force of the moving part of the aerostatic linear bearing. The parameters for correcting the dynamic error are determined from the results of one set of impact measurements of one transducer. Then, the validity of the obtained parameters is evaluated using the results of the other sets of measurements of all the three transducers. The uncertainties in the uncorrected force and those in the corrected force are also estimated. If manufacturers determine the correction parameters for each model using the proposed method, and provide the software with the parameters corresponding to each model, then users can obtain the waveform corrected against dynamic error and its uncertainty. The present status and the future prospects of the developed software are discussed in this paper. PMID:25004158

  18. Software for correcting the dynamic error of force transducers.

    PubMed

    Miyashita, Naoki; Watanabe, Kazuhide; Irisa, Kyouhei; Iwashita, Hiroshi; Araki, Ryosuke; Takita, Akihiro; Yamaguchi, Takao; Fujii, Yusaku

    2014-01-01

    Software which corrects the dynamic error of force transducers in impact force measurements using their own output signal has been developed. The software corrects the output waveform of the transducers using the output waveform itself, estimates its uncertainty and displays the results. In the experiment, the dynamic error of three transducers of the same model are evaluated using the Levitation Mass Method (LMM), in which the impact forces applied to the transducers are accurately determined as the inertial force of the moving part of the aerostatic linear bearing. The parameters for correcting the dynamic error are determined from the results of one set of impact measurements of one transducer. Then, the validity of the obtained parameters is evaluated using the results of the other sets of measurements of all the three transducers. The uncertainties in the uncorrected force and those in the corrected force are also estimated. If manufacturers determine the correction parameters for each model using the proposed method, and provide the software with the parameters corresponding to each model, then users can obtain the waveform corrected against dynamic error and its uncertainty. The present status and the future prospects of the developed software are discussed in this paper. PMID:25004158

  19. Spatio-Temporal Reconstruction of Vortex Dynamics in Axisymmetric Wakes

    NASA Astrophysics Data System (ADS)

    Brücker, C.

    2001-04-01

    With time recording Digital-Particle-Image Velocimetry and spatio-temporal reconstruction technique, we obtained detailed quantitative results of the evolution of the velocity and vorticity field in the wake of axisymmetric bluff bodies-a sphere and an axially oriented cylinder with an elliptic nose and a blunt base. Experiments were carried out for Reynolds numbers of Re=500, 700 and 1000 in the transition range from ``regular'' to ``irregular'' shedding. DPIV-recordings in radial cross-sections at several distances downstream of the bodies allowed us to reconstruct the dynamics of the streamwise vorticity over a large number of shedding cycles. Our results prove that the wake in this regime consists of a double-sided chain of oppositely oriented hairpin vortices. In addition, the results show a well-defined low-frequency modulation of the vortex shedding, with a distinct peak in the frequency spectrum at a Strouhal number of about Sr~0.05 (in case of the sphere). The wake pattern in this ``irregular'' shedding regime typically exhibits periodic packets of 3-4 ``regular'' shedding cycles which are interrupted by phases with less action. The results indicate the coexistence of a long-wave instability of axisymmetric wakes against helical waves in addition to the primary instability causing the vortex shedding process.

  20. Application of DIRI dynamic infrared imaging in reconstructive surgery

    NASA Astrophysics Data System (ADS)

    Pawlowski, Marek; Wang, Chengpu; Jin, Feng; Salvitti, Matthew; Tenorio, Xavier

    2006-04-01

    We have developed the BioScanIR System based on QWIP (Quantum Well Infrared Photodetector). Data collected by this sensor are processed using the DIRI (Dynamic Infrared Imaging) algorithms. The combination of DIRI data processing methods with the unique characteristics of the QWIP sensor permit the creation of a new imaging modality capable of detecting minute changes in temperature at the surface of the tissue and organs associated with blood perfusion due to certain diseases such as cancer, vascular disease and diabetes. The BioScanIR System has been successfully applied in reconstructive surgery to localize donor flap feeding vessels (perforators) during the pre-surgical planning stage. The device is also used in post-surgical monitoring of skin flap perfusion. Since the BioScanIR is mobile; it can be moved to the bedside for such monitoring. In comparison to other modalities, the BioScanIR can localize perforators in a single, 20 seconds scan with definitive results available in minutes. The algorithms used include (FFT) Fast Fourier Transformation, motion artifact correction, spectral analysis and thermal image scaling. The BioScanIR is completely non-invasive and non-toxic, requires no exogenous contrast agents and is free of ionizing radiation. In addition to reconstructive surgery applications, the BioScanIR has shown promise as a useful functional imaging modality in neurosurgery, drug discovery in pre-clinical animal models, wound healing and peripheral vascular disease management.

  1. Reconstruction of missing daily streamflow data using dynamic regression models

    NASA Astrophysics Data System (ADS)

    Tencaliec, Patricia; Favre, Anne-Catherine; Prieur, Clémentine; Mathevet, Thibault

    2015-12-01

    River discharge is one of the most important quantities in hydrology. It provides fundamental records for water resources management and climate change monitoring. Even very short data-gaps in this information can cause extremely different analysis outputs. Therefore, reconstructing missing data of incomplete data sets is an important step regarding the performance of the environmental models, engineering, and research applications, thus it presents a great challenge. The objective of this paper is to introduce an effective technique for reconstructing missing daily discharge data when one has access to only daily streamflow data. The proposed procedure uses a combination of regression and autoregressive integrated moving average models (ARIMA) called dynamic regression model. This model uses the linear relationship between neighbor and correlated stations and then adjusts the residual term by fitting an ARIMA structure. Application of the model to eight daily streamflow data for the Durance river watershed showed that the model yields reliable estimates for the missing data in the time series. Simulation studies were also conducted to evaluate the performance of the procedure.

  2. Curl force dynamics: symmetries, chaos and constants of motion

    NASA Astrophysics Data System (ADS)

    Berry, M. V.; Shukla, Pragya

    2016-06-01

    This is a theoretical study of Newtonian trajectories governed by curl forces, i.e. position-dependent but not derivable from a potential, investigating in particular the possible existence of conserved quantities. Although nonconservative and nonhamiltonian, curl forces are not dissipative because volume in the position-velocity state space is preserved. A physical example is the effective forces exerted on small particles by light. When the force has rotational symmetry, for example when generated by an isolated optical vortex, particles spiral outwards and escape, even with an attractive gradient force, however strong. Without rotational symmetry, and for dynamics in the plane, the state space is four-dimensional, and to search for possible constants of motion we introduce the Volume of section: a numerical procedure, in which orbits are plotted as dots in a three-dimensional subspace. For some curl forces, e.g. optical fields with two opposite-strength vortices, the dots lie on a surface, indicating a hidden constant of motion. For other curl forces, e.g. those from four vortices, the dots explore clouds, in an unfamiliar kind of chaos, suggesting that no constant of motion exists. The curl force dynamics generated by optical vortices could be studied experimentally.

  3. Curl force dynamics: symmetries, chaos and constants of motion

    NASA Astrophysics Data System (ADS)

    Berry, M. V.; Shukla, Pragya

    2016-06-01

    This is a theoretical study of Newtonian trajectories governed by curl forces, i.e. position-dependent but not derivable from a potential, investigating in particular the possible existence of conserved quantities. Although nonconservative and nonhamiltonian, curl forces are not dissipative because volume in the position–velocity state space is preserved. A physical example is the effective forces exerted on small particles by light. When the force has rotational symmetry, for example when generated by an isolated optical vortex, particles spiral outwards and escape, even with an attractive gradient force, however strong. Without rotational symmetry, and for dynamics in the plane, the state space is four-dimensional, and to search for possible constants of motion we introduce the Volume of section: a numerical procedure, in which orbits are plotted as dots in a three-dimensional subspace. For some curl forces, e.g. optical fields with two opposite-strength vortices, the dots lie on a surface, indicating a hidden constant of motion. For other curl forces, e.g. those from four vortices, the dots explore clouds, in an unfamiliar kind of chaos, suggesting that no constant of motion exists. The curl force dynamics generated by optical vortices could be studied experimentally.

  4. Seasonally forced disease dynamics explored as switching between attractors

    NASA Astrophysics Data System (ADS)

    Keeling, Matt J.; Rohani, Pejman; Grenfell, Bryan T.

    2001-01-01

    Biological phenomena offer a rich diversity of problems that can be understood using mathematical techniques. Three key features common to many biological systems are temporal forcing, stochasticity and nonlinearity. Here, using simple disease models compared to data, we examine how these three factors interact to produce a range of complicated dynamics. The study of disease dynamics has been amongst the most theoretically developed areas of mathematical biology; simple models have been highly successful in explaining the dynamics of a wide variety of diseases. Models of childhood diseases incorporate seasonal variation in contact rates due to the increased mixing during school terms compared to school holidays. This ‘binary’ nature of the seasonal forcing results in dynamics that can be explained as switching between two nonlinear spiral sinks. Finally, we consider the stability of the attractors to understand the interaction between the deterministic dynamics and demographic and environmental stochasticity. Throughout attention is focused on the behaviour of measles, whooping cough and rubella.

  5. Motion predicted online dynamic MRI reconstruction from partially sampled k-space data.

    PubMed

    Majumdar, Angshul

    2013-11-01

    In this work we address the problem of reconstructing dynamic MRI sequences in an online fashion, i.e. reconstructing the current frame given that the previous frames have been already reconstructed. The reconstruction consists of a prediction and a correction step. The prediction step is based on an Auto-Regressive AR(1) model. Assuming that the prediction is good, the difference between the predicted frame and the actual frame (to be reconstructed) will be sparse. In the correction step, the difference between the predicted frame and the actual frame is estimated from partially sampled K-space data via a sparsity promoting least squares minimization problem. We have compared the proposed method with state-of-the-art methods in online dynamic MRI reconstruction. The experiments have been carried out on 2D and 3D Dynamic Contrast Enhanced (DCE) MRI datasets. Results show that our method yields the least reconstruction error.

  6. Spin motive force driven by skyrmion dynamics in magnetic nanodisks

    NASA Astrophysics Data System (ADS)

    Shimada, Yuhki; Ohe, Jun-ichiro

    2015-05-01

    The spin motive force driven by the dynamics of the skyrmion structure formed in a nanomagnetic disk is numerically investigated. Due to the existence of the magnetic structure along the disk edge, the collective mode of the magnetization is modified from that of the bulk skyrmion lattice obtained by using the periodic boundary condition. For a single-skyrmion disk, the dynamics of the skyrmion core and the edge magnetization induce the spin motive force, and a measurable AC voltage is obtained by two probes on the disk. For a multi-skyrmions disk, the phase-locked collective mode of skyrmions is found in the lowest resonant frequency where the amplitude of the AC voltage is enhanced by the cascade effect of the spin motive force. We also investigate the effect of the Rashba spin-orbit coupling on the spin motive force.

  7. Force reconstruction for impact tests of an energy-absorbing nose

    SciTech Connect

    Bateman, V.I.; Garne, T.G.; McCall, D.M.

    1990-01-01

    Delivery of a bomb into hard targets at speeds of up to 120 fps required the design of an energy-absorbing nose. The purpose of the nose is to decelerate the projectile and, by absorbing the kinetic energy with deformation, protect the projectile's internal components from high-level (shock) decelerations. A structural simulation of the projectile was designed to test the dynamic deformation characteristics of the energy-absorbing nose. The simulated projectile was instrumented with eight accelerometers mounted with a shock isolation technique. The dynamic force as a function of nose deformation was the desired result from the impact tests because it provides the designer with a performance criterion for the nose design. The dynamic force was obtained by combining the accelerations using the Sum of Weighted Accelerations Technique (SWAT). Results from two field tests are presented. 12 refs., 8 figs.

  8. Dynamic Forces Between Two Deformable Oil Droplets in Water

    NASA Astrophysics Data System (ADS)

    Dagastine, Raymond R.; Manica, Rogério; Carnie, Steven L.; Chan, D. Y. C.; Stevens, Geoffrey W.; Grieser, Franz

    2006-07-01

    The understanding of static interactions in colloidal suspensions is well established, whereas dynamic interactions more relevant to biological and other suspended soft-matter systems are less well understood. We present the direct force measurement and quantitative theoretical description for dynamic forces for liquid droplets in another immiscible fluid. Analysis of this system demonstrates the strong link between interfacial deformation, static surface forces, and hydrodynamic drainage, which govern dynamic droplet-droplet interactions over the length scale of nanometers and over the time scales of Brownian collisions. The results and analysis have direct bearing on the control and manipulation of suspended droplets in soft-matter systems ranging from the emulsions in shampoo to cellular interactions.

  9. Identifying the Stern-Gerlach force of classical electron dynamics.

    PubMed

    Wen, Meng; Bauke, Heiko; Keitel, Christoph H

    2016-01-01

    Different classical theories are commonly applied in various branches of physics to describe the relativistic dynamics of electrons by coupled equations for the orbital motion and spin precession. Exemplarily, we benchmark the Frenkel model and the classical Foldy-Wouthuysen model with spin-dependent forces (Stern-Gerlach forces) to the quantum dynamics as predicted by the Dirac equation. Both classical theories can lead to different or even contradicting predictions how the Stern-Gerlach forces modify the electron's orbital motion, when the electron moves in strong electromagnetic field configurations of emerging high-intensity laser facilities. In this way, one may evaluate the validity and identify the limits of these classical theories via a comparison with possible experiments to provide a proper description of spin-induced dynamics. Our results indicate that the Foldy-Wouthuysen model is qualitatively in better agreement with the Dirac theory than the widely used Frenkel model. PMID:27546820

  10. Identifying the Stern-Gerlach force of classical electron dynamics

    PubMed Central

    Wen, Meng; Bauke, Heiko; Keitel, Christoph H.

    2016-01-01

    Different classical theories are commonly applied in various branches of physics to describe the relativistic dynamics of electrons by coupled equations for the orbital motion and spin precession. Exemplarily, we benchmark the Frenkel model and the classical Foldy-Wouthuysen model with spin-dependent forces (Stern-Gerlach forces) to the quantum dynamics as predicted by the Dirac equation. Both classical theories can lead to different or even contradicting predictions how the Stern-Gerlach forces modify the electron’s orbital motion, when the electron moves in strong electromagnetic field configurations of emerging high-intensity laser facilities. In this way, one may evaluate the validity and identify the limits of these classical theories via a comparison with possible experiments to provide a proper description of spin-induced dynamics. Our results indicate that the Foldy-Wouthuysen model is qualitatively in better agreement with the Dirac theory than the widely used Frenkel model. PMID:27546820

  11. Identifying the Stern-Gerlach force of classical electron dynamics

    NASA Astrophysics Data System (ADS)

    Wen, Meng; Bauke, Heiko; Keitel, Christoph H.

    2016-08-01

    Different classical theories are commonly applied in various branches of physics to describe the relativistic dynamics of electrons by coupled equations for the orbital motion and spin precession. Exemplarily, we benchmark the Frenkel model and the classical Foldy-Wouthuysen model with spin-dependent forces (Stern-Gerlach forces) to the quantum dynamics as predicted by the Dirac equation. Both classical theories can lead to different or even contradicting predictions how the Stern-Gerlach forces modify the electron’s orbital motion, when the electron moves in strong electromagnetic field configurations of emerging high-intensity laser facilities. In this way, one may evaluate the validity and identify the limits of these classical theories via a comparison with possible experiments to provide a proper description of spin-induced dynamics. Our results indicate that the Foldy-Wouthuysen model is qualitatively in better agreement with the Dirac theory than the widely used Frenkel model.

  12. Identifying the Stern-Gerlach force of classical electron dynamics.

    PubMed

    Wen, Meng; Bauke, Heiko; Keitel, Christoph H

    2016-08-22

    Different classical theories are commonly applied in various branches of physics to describe the relativistic dynamics of electrons by coupled equations for the orbital motion and spin precession. Exemplarily, we benchmark the Frenkel model and the classical Foldy-Wouthuysen model with spin-dependent forces (Stern-Gerlach forces) to the quantum dynamics as predicted by the Dirac equation. Both classical theories can lead to different or even contradicting predictions how the Stern-Gerlach forces modify the electron's orbital motion, when the electron moves in strong electromagnetic field configurations of emerging high-intensity laser facilities. In this way, one may evaluate the validity and identify the limits of these classical theories via a comparison with possible experiments to provide a proper description of spin-induced dynamics. Our results indicate that the Foldy-Wouthuysen model is qualitatively in better agreement with the Dirac theory than the widely used Frenkel model.

  13. Towards a myocardial contraction force reconstruction technique for heart disease assessment and therapy planning

    NASA Astrophysics Data System (ADS)

    Haddad, Seyyed M. H.; Drangova, Maria; White, James A.; Samani, Abbas

    2014-03-01

    Cardiac ischemic injuries can be classified into two main categories: reversible and irreversible. Treatment of reversible damages is possible through revascularization therapies. Clinically, it is quite vital to determine the reversibility of ischemic injuries and local efficiency using accurate diagnostics techniques. For this purpose, a number of imaging techniques have been developed. To our knowledge, while some of these techniques are capable of assessing tissue viability which is believed to be correlated with ischemic injuries reversibility, none of them are capable of providing information about local myocardial tissue efficiency. Note that this efficiency indicates the local tissue contribution to the overall (global) heart mechanical function which is characterized by parameters such as ejection fraction. While contraction force generation of the myocardium is a reliable and straightforward mechanical measure for the local myocardium functionality, it is also hypothesized that the level of damage reversibility expected from therapy is proportional to the intensity and distribution of these forces. As such this research involves developing a new imaging technique for cardiac contraction force quantification. This work is also geared towards another application, namely Cardiac Resynchronization Therapy (CRT), specifically for electrode leads configuration optimization. The latter has not been tackled through a systematic technique thus far. In the proposed method, contraction force reconstruction is accomplished by an inverse problem algorithm solved through an optimization framework which uses forward mechanical modelling of the myocardium iteratively to obtain the contraction forces field. As a result, the method requires a forward mechanical model of the myocardium which is computationally efficient and robust against divergence. Therefore, we developed such a model which considers all aspects of the myocardial mechanics including hyperelasticity

  14. Force identification of dynamic systems using virtual work principle

    NASA Astrophysics Data System (ADS)

    Xu, Xun; Ou, Jinping

    2015-02-01

    One of the key inverse problems for estimating dynamic forces acting on a structure is to determine the force expansion and the corresponding solving method. This paper presents a moving least square (MLS) method for fitting dynamic forces, which improves the existing traditional methods. The simulation results show that the force expansion order has a tiny effect on the types of forces, which indicates the MLS method's excellent ability for local approximation and noise immunity as well as good fitting function. Then, the differential equation of motion for the system is transformed into an integral equation by using the virtual work principle, which can eliminate the structural acceleration response without introducing the calculation error. Besides, the transformation derives an expression of velocity by integrating by parts, which diminishes the error propagation of the velocity. Hence, the integral equation of motion for the system has a strong constraint to noise with zero mean value. Finally, this paper puts forward an optimization method to solve the equation. The numerical stability can be enhanced as the matrix inversion calculation is avoided. Illustrative examples involving different types of forces demonstrate that the transformation of the differential equation proposed through virtual work principle can eliminate interference efficiently and is robust for dynamic calculation.

  15. Dynamic Force Sensing Using an Optically Trapped Probing System

    PubMed Central

    Huang, Yanan; Cheng, Peng; Menq, Chia-Hsiang

    2013-01-01

    This paper presents the design of an adaptive observer that is implemented to enable real-time dynamic force sensing and parameter estimation in an optically trapped probing system. According to the principle of separation of estimation and control, the design of this observer is independent of that of the feedback controller when operating within the linear range of the optical trap. Dynamic force sensing, probe steering/clamping, and Brownian motion control can, therefore, be developed separately and activated simultaneously. The adaptive observer utilizes the measured motion of the trapped probe and input control effort to recursively estimate the probe–sample interaction force in real time, along with the estimation of the probing system’s trapping bandwidth. This capability is very important to achieving accurate dynamic force sensing in a time-varying process, wherein the trapping dynamics is nonstationary due to local variations of the surrounding medium. The adaptive estimator utilizes the Kalman filter algorithm to compute the time-varying gain in real time and minimize the estimation error for force probing. A series of experiments are conducted to validate the design of and assess the performance of the adaptive observer. PMID:24382944

  16. Dislocation dynamical approach to force fluctuations in nanoindentation experiments

    NASA Astrophysics Data System (ADS)

    Ananthakrishna, G.; Katti, Rohit; K, Srikanth

    2014-09-01

    We develop an approach that combines the power of nonlinear dynamics with the evolution equations for the mobile and immobile dislocation densities and force to explain force fluctuations in nanoindentation experiments. The model includes nucleation, multiplication, and propagation thresholds for mobile dislocations, and other well known dislocation transformation mechanisms. The model predicts all the generic features of nanoindentation such as the Hertzian elastic branch followed by several force drops of decreasing magnitudes, and residual plasticity after unloading. The stress corresponding to the elastic force maximum is close to the yield stress of an ideal solid. The predicted values for all the quantities are close to those reported by experiments. Our model allows us to address the indentation-size effect including the ambiguity in defining the hardness in the force drop dominated regime. At large indentation depths, the hardness remains nearly constant with a marginal decreasing trend.

  17. Dynamics of Cell Area and Force during Spreading

    PubMed Central

    Brill-Karniely, Yifat; Nisenholz, Noam; Rajendran, Kavitha; Dang, Quynh; Krishnan, Ramaswamy; Zemel, Assaf

    2014-01-01

    Experiments on human pulmonary artery endothelial cells are presented to show that cell area and the force exerted on a substrate increase simultaneously, but with different rates during spreading; rapid-force increase systematically occurred several minutes past initial spreading. We examine this theoretically and present three complementary mechanisms that may accompany the development of lamellar stress during spreading and underlie the observed behavior. These include: 1), the dynamics of cytoskeleton assembly at the cell basis; 2), the strengthening of acto-myosin forces in response to the generated lamellar stresses; and 3), the passive strain-stiffening of the cytoskeleton. PMID:25517168

  18. Approximate photochemical dynamics of azobenzene with reactive force fields

    SciTech Connect

    Li, Yan; Hartke, Bernd

    2013-12-14

    We have fitted reactive force fields of the ReaxFF type to the ground and first excited electronic states of azobenzene, using global parameter optimization by genetic algorithms. Upon coupling with a simple energy-gap transition probability model, this setup allows for completely force-field-based simulations of photochemical cis→trans- and trans→cis-isomerizations of azobenzene, with qualitatively acceptable quantum yields. This paves the way towards large-scale dynamics simulations of molecular machines, including bond breaking and formation (via the reactive force field) as well as photochemical engines (presented in this work)

  19. Dynamics of the force exchanged between membrane inclusions.

    PubMed

    Fournier, Jean-Baptiste

    2014-03-28

    We study the dynamical response of a fluid membrane to the sudden conformation change of active inclusions linearly coupled to the membrane curvature. The mutual force between two inclusions triggered simultaneously is shown to exhibit a transient maximum much larger than the equilibrium force. Even in the presence of tension, this dynamical interaction is long range over distances much larger than the correlation length. We derive the scaling laws describing these phenomena analytically, and we stress the importance of the damping due to intermonolayer friction. PMID:24724681

  20. Multiple impact regimes in liquid environment dynamic atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Melcher, John; Xu, Xin; Raman, Arvind

    2008-09-01

    A canonical assumption in dynamic atomic force microscopy is that the probe tip interacts with the sample once per oscillation cycle. We show this key ansatz breaks down for soft cantilevers in liquid environments. Such probes exhibit "drum roll" like dynamics with sequential bifurcations between oscillations with single, double, and triple impacts that can be clearly identified in the phase of the response. This important result is traced to a momentary excitation of the second flexural mode induced by tip-sample forces and low quality factors. Experiments performed on supported biological membranes in buffer solutions are used to demonstrate the findings.

  1. Gamma-range corticomuscular coherence during dynamic force output.

    PubMed

    Omlor, Wolfgang; Patino, Luis; Hepp-Reymond, Marie-Claude; Kristeva, Rumyana

    2007-02-01

    The beta-range synchronization between cortical motor and muscular activity as revealed by EEG/MEG-EMG coherence has been extensively investigated for steady-state motor output. However, there is a lack of information on the modulation of the corticomuscular coherence in conjunction with dynamic force output. We addressed this question comparing the EEG-EMG coherence and the cortical motor spectral power in eight healthy subjects in a visuomotor task, in which the subjects exerted a steady-state or periodically modulated dynamic isometric force output with their right-index finger to keep a visual cursor within a target zone. In the static condition, significant coherence was confined to the beta-range. In the dynamic condition, the most distinct coherence occurred in the gamma-range and the significant beta-range coherence was strikingly reduced. The cortical motor power in the beta-range during dynamic force output was decreased, whereas the power in the gamma-range remained without significant change. We conclude that during dynamic force the corticospinal oscillation mode of the sensorimotor system shifts towards higher (principally gamma) frequencies for the rapid integration of the visual and somatosensory information required to produce the appropriate motor command.

  2. Reconstructing representations of dynamic visual objects in early visual cortex

    PubMed Central

    Chong, Edmund; Familiar, Ariana M.; Shim, Won Mok

    2016-01-01

    As raw sensory data are partial, our visual system extensively fills in missing details, creating enriched percepts based on incomplete bottom-up information. Despite evidence for internally generated representations at early stages of cortical processing, it is not known whether these representations include missing information of dynamically transforming objects. Long-range apparent motion (AM) provides a unique test case because objects in AM can undergo changes both in position and in features. Using fMRI and encoding methods, we found that the “intermediate” orientation of an apparently rotating grating, never presented in the retinal input but interpolated during AM, is reconstructed in population-level, feature-selective tuning responses in the region of early visual cortex (V1) that corresponds to the retinotopic location of the AM path. This neural representation is absent when AM inducers are presented simultaneously and when AM is visually imagined. Our results demonstrate dynamic filling-in in V1 for object features that are interpolated during kinetic transformations. PMID:26712004

  3. Model based control of dynamic atomic force microscope

    SciTech Connect

    Lee, Chibum; Salapaka, Srinivasa M.

    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.

  4. Model based control of dynamic atomic force microscope.

    PubMed

    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.

  5. Dynamics of intermittent force fluctuations in vesicular nanotubulation

    NASA Astrophysics Data System (ADS)

    Ashok, B.; Ananthakrishna, G.

    2014-11-01

    Irregular force fluctuations are seen in most nanotubulation experiments. The dynamics behind their presence has, however, been neither commented upon nor modeled. A simple estimate of the mean energy dissipated in force drops turns out to be several times the thermal energy. This coupled with the rate dependent nature of the deformation reported in several experiments point to a dynamical origin of the serrations. We simplify the whole process of tether formation through a three-stage model of successive deformations of sphere to ellipsoid, neck-formation, and tubule birth and extension. Based on this, we envisage a rate-softening frictional force at the neck that must be overcome before a nanotube can be pulled out. Our minimal model includes elastic and visco-elastic deformation of the vesicle, and has built-in dependence on pull velocity, vesicle radius, and other material parameters, enabling us to capture various kinds of serrated force-extension curves for different parameter choices. Serrations are predicted in the nanotubulation region. Other features of force-extension plots reported in the literature such as a plateauing serrated region beyond a force drop, serrated flow region with a small positive slope, an increase in the elastic threshold with pull velocity, force-extension curves for vesicles with larger radius lying lower than those for smaller radius, are all also predicted by the model. A toy model is introduced to demonstrate that the role of the friction law is limited to inducing stick-slip oscillations in the force, and all other qualitative and quantitative features emerging from the model can only be attributed to other physical mechanisms included in the deformation dynamics of the vesicle.

  6. Dynamic adhesion forces between microparticles and substrates in water.

    PubMed

    Xu, Quan; Li, Mingtao; Zhang, Lipeng; Niu, Jianbing; Xia, Zhenhai

    2014-09-23

    The interactions between micrometer-sized particles and substrates in aqueous environment are fundamental to numerous natural phenomena and industrial processes. Here we report a dynamically induced enhancement in adhesion interactions between microparticles and substrates immerged in water, air, and hexane. The dynamic adhesion force was measured by pulling microsized spheres off various substrate (hydrophilic/hydrophobic) surfaces at different retracting velocities. It was observed that when the pull-off velocity varies from 0.02 to 1500 μm/s, there is 100-200% increase in adhesion force in water while it has a 100% increase in nitrogen and hexane. The dynamic adhesion enhancement reduces with increasing effective contact angle defined by the average cosine of wetting angles of the substrates and the particles, and approaches the values measured in dry nitrogen and hexane as the effective contact angle is larger than 90(o). A dynamic model was developed to predict the adhesion forces resulting from this dynamic effect, and the predictions correlate well with the experimental results. The stronger dynamic adhesion enhancement in water is mainly attributed to electrical double layers and the restructuring of water in the contact area between particles and substrates. PMID:25162139

  7. Influence of impeller shroud forces on turbopump rotor dynamics

    NASA Technical Reports Server (NTRS)

    Williams, J. P.; Childs, Dara W.

    1993-01-01

    The shrouded-impeller leakage path forces calculated by Childs have been analyzed to answer two questions. First, because of certain characteristics or the results of Childs, the forces could not be modeled with traditional approaches. Therefore, an approach has been devised to include the forces in conventional rotordynamic analyses. The forces were found to be well-modeled with this approach. Finally, the effect these forces had on a simple rotor-bearing system was analyzed, and, therefore, they, in addition to seal forces, were applied to a Jeffcott rotor. The traditional methods of dynamic system analysis were modified to incorporate the impeller forces and yielded results for the eigenproblem, frequency response, critical speed, transient response, and an iterative technique for finding the frequency of free vibration as well as system stability. All results lead to the conclusion that the forces have little influence on natural frequency but can have appreciable effects on system stability. Specifically, at higher values of fluid swirl at the leakage path entrance, relative stability is reduced. The only unexpected response characteristics that occurred are attributed to the nonlinearity of the model.

  8. Monitoring dynamic loads on wind tunnel force balances

    NASA Technical Reports Server (NTRS)

    Ferris, Alice T.; White, William C.

    1989-01-01

    Two devices have been developed at NASA Langley to monitor the dynamic loads incurred during wind-tunnel testing. The Balance Dynamic Display Unit (BDDU), displays and monitors the combined static and dynamic forces and moments in the orthogonal axes. The Balance Critical Point Analyzer scales and sums each normalized signal from the BDDU to obtain combined dynamic and static signals that represent the dynamic loads at predefined high-stress points. The display of each instrument is a multiplex of six analog signals in a way that each channel is displayed sequentially as one-sixth of the horizontal axis on a single oscilloscope trace. Thus this display format permits the operator to quickly and easily monitor the combined static and dynamic level of up to six channels at the same time.

  9. An implicit divalent counterion force field for RNA molecular dynamics

    NASA Astrophysics Data System (ADS)

    Henke, Paul S.; Mak, Chi H.

    2016-03-01

    How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg2+ screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grained models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.

  10. Dynamic Electrode Forces in Gas Metal Arc Welding.

    NASA Astrophysics Data System (ADS)

    Jones, Lawrence Anthony

    In gas metal arc welding, a low-voltage electric -arc plasma is maintained between a work-piece and a wire electrode, both of which are melted by the arc. This thesis examines the dynamic forces that affect the detachment of molten metal drops from the consumable wire electrode. Unlike drops falling from a water faucet, the drops in gas metal arc welding experience strong magnetic forces generated by the interaction of the welding current with its own magnetic field. An extensive set of clear high-speed motion images of metal drops detaching from a welding electrode was collected under a wide variety of conditions. The images are used to measure the surface tension of steel as it is found in a gas metal arc welding plasma. Impulse-response oscillations of pendent molten steel drops are also measured. A derivation of the magnetic forces acting on necking drops is performed. Numerical computations of these forces are performed by using shapes fitted to high -speed images of molten steel drops as they are ejected from the electrode by magnetic forces during short-duty -cycle current pulsing. A dynamic model of drop detachment is developed and used to study the competition between the retaining surface tension force and other forces (magnetic, gravitational, and inertial). Simulations performed with this model are compared with extensive measurements of constant-current welding images and with limited measurements of pulsed -current welding images. The comparisons indicate that the experimental magnetic forces are much less potent than the calculated magnetic forces when welding-current transients are not present. A hypothesis is advanced that internal flows are able to develop under the relatively quiescent conditions that exist during drop development in constant -current welding. An apparatus was constructed to axially vibrate the electrode as it is consumed. Experiments using inertial forces to induce drop detachment are shown. Comparisons of experimental

  11. Static and dynamic buckling of reconstructions at triple steps on Si(111) surfaces

    NASA Astrophysics Data System (ADS)

    Zhachuk, R.; Teys, S.; Coutinho, J.; Rayson, M. J.; Briddon, P. R.

    2014-10-01

    Triple steps on Si(111) surfaces are popular building blocks for bottom-up nanostructure assembly, conferring size uniformity and precise positioning of growing nanostructures. In this work, we employ the Si(7 7 10) regular stepped surface as model system to study the triple steps by scanning tunneling microscopy (STM) and large-scale first-principles calculations. We find a surprising cohabitation of reconstruction elements at the step edge that either buckles statically or dynamically at room temperature. The driving force for the observed sequence of buckling patterns is traced back to Coulomb interactions involving charged adatoms and rest-atoms lying on a mini-terrace. These results reconcile the Si(111) triple step model with the experimental STM data.

  12. Static and dynamic buckling of reconstructions at triple steps on Si(111) surfaces

    SciTech Connect

    Zhachuk, R. Teys, S.; Coutinho, J.; Rayson, M. J.; Briddon, P. R.

    2014-10-27

    Triple steps on Si(111) surfaces are popular building blocks for bottom-up nanostructure assembly, conferring size uniformity and precise positioning of growing nanostructures. In this work, we employ the Si(7 7 10) regular stepped surface as model system to study the triple steps by scanning tunneling microscopy (STM) and large-scale first-principles calculations. We find a surprising cohabitation of reconstruction elements at the step edge that either buckles statically or dynamically at room temperature. The driving force for the observed sequence of buckling patterns is traced back to Coulomb interactions involving charged adatoms and rest-atoms lying on a mini-terrace. These results reconcile the Si(111) triple step model with the experimental STM data.

  13. Molecular dynamics simulations of methane hydrate using polarizable force fields

    SciTech Connect

    Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

    2007-06-14

    Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are found between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane onl

  14. Realizing nonholonomic dynamics as limit of friction forces

    NASA Astrophysics Data System (ADS)

    Eldering, Jaap

    2016-07-01

    The classical question whether nonholonomic dynamics is realized as limit of friction forces was first posed by Carathéodory. It is known that, indeed, when friction forces are scaled to infinity, then nonholonomic dynamics is obtained as a singular limit. Our results are twofold. First, we formulate the problem in a differential geometric context. Using modern geometric singular perturbation theory in our proof, we then obtain a sharp statement on the convergence of solutions on infinite time intervals. Secondly, we set up an explicit scheme to approximate systems with large friction by a perturbation of the nonholonomic dynamics. The theory is illustrated in detail by studying analytically and numerically the Chaplygin sleigh as an example. This approximation scheme offers a reduction in dimension and has potential use in applications.

  15. Are current molecular dynamics force fields too helical?

    PubMed

    Best, Robert B; Buchete, Nicolae-Viorel; Hummer, Gerhard

    2008-07-01

    Accurate force fields are essential for the success of molecular dynamics simulations. In apparent contrast to the conformational preferences of most force fields, recent NMR experiments suggest that short polyalanine peptides in water populate the polyproline II structure almost exclusively. To investigate this apparent contradiction, with its ramifications for the assessment of molecular force fields and the structure of unfolded proteins, we performed extensive simulations of Ala(5) in water ( approximately 5 micros total time), using twelve different force fields and three different peptide terminal groups. Using either empirical or density-functional-based Karplus relations for the J-couplings, we find that most current force fields do overpopulate the alpha-region, with quantitative results depending on the choice of Karplus relation and on the peptide termini. Even after reweighting to match experiment, we find that Ala(5) retains significant alpha- and beta-populations. In fact, several force fields match the experimental data well before reweighting and have a significant helical population. We conclude that radical changes to the best current force fields are not necessary, based on the NMR data. Nevertheless, experiments on short peptides open the way toward the systematic improvement of current simulation models.

  16. High-Resolution Force Balance Analyses of Tidewater Glacier Dynamics

    NASA Astrophysics Data System (ADS)

    Enderlin, E. M.; Hamilton, G. S.; O'Neel, S.

    2015-12-01

    Changes in glacier velocity, thickness, and terminus position have been used to infer the dynamic response of tidewater glaciers to environmental perturbations, yet few analyses have attempted to quantify the associated variations in the glacier force balance. Where repeat high-resolution ice thickness and velocity estimates are available, force balance time series can be constructed to investigate the redistribution of driving and resistive forces associated with changes in terminus position. Comparative force balance analyses may, therefore, help us understand the variable dynamic response observed for glaciers in close proximity to each other. Here we construct force balance time series for Helheim Glacier, SE Greenland, and Columbia Glacier, SE Alaska, to investigate differences in dynamic sensitivity to terminus position change. The analysis relies on in situ and remotely sensed observations of ice thickness, velocity, and terminus position. Ice thickness time series are obtained from stereo satellite image-derived surface elevation and continuity-derived bed elevations that are constrained by airborne radar observations. Surface velocity time series are obtained from interferometric synthetic aperture radar (InSAR) observations. Approximately daily terminus positions are from a combination of satellite images and terrestrial time-lapse photographs. Helheim and Columbia glaciers are two of the best-studied Arctic tidewater glaciers with comprehensive high-resolution observational time series, yet we find that bed elevation uncertainties and poorly-constrained stress-coupling length estimates still hinder the analysis of spatial and temporal force balance variations. Here we use a new observationally-based method to estimate the stress-coupling length which successfully reduces noise in the derived force balance but preserves spatial variations that can be over-smoothed when estimating the stress-coupling length as a scalar function of the ice thickness

  17. Mean and covariance properties of dynamic PET reconstructions from list-mode data.

    PubMed

    Asma, Evren; Leahy, Richard M

    2006-01-01

    We derive computationally efficient methods for the estimation of the mean and variance properties of penalized likelihood dynamic positron emission tomography (PET) images. This allows us to predict the accuracy of reconstructed activity estimates and to compare reconstruction algorithms theoretically. We combine a bin-mode approach in which data is modeled as a collection of independent Poisson random variables at each spatiotemporal bin with the space-time separabilities in the imaging equation and penalties to derive rapidly computable analytic mean and variance approximations. We use these approximations to compare bias/variance properties of our dynamic PET image reconstruction algorithm with those of multiframe static PET reconstructions.

  18. Ares I-X First Stage Separation Loads and Dynamics Reconstruction

    NASA Technical Reports Server (NTRS)

    Demory, Lee; Rooker, BIll; Jarmulowicz, Marc; Glaese, John

    2011-01-01

    The Ares I-X flight test provided NASA with the opportunity to test hardware and gather critical data to ensure the success of future Ares I flights. One of the primary test flight objectives was to evaluate the environment during First Stage separation to better understand the conditions that the J-2X second stage engine will experience at ignition [1]. A secondary objective was to evaluate the effectiveness of the stage separation motors. The Ares I-X flight test vehicle was successfully launched on October 29, 2009, achieving most of its primary and secondary test objectives. Ground based video camera recordings of the separation event appeared to show recontact of the First Stage and the Upper Stage Simulator followed by an unconventional tumbling of the Upper Stage Simulator. Closer inspection of the videos and flight test data showed that recontact did not occur. Also, the motion during staging was as predicted through CFD analysis performed during the Ares I-X development. This paper describes the efforts to reconstruct the vehicle dynamics and loads through the staging event by means of a time integrated simulation developed in TREETOPS, a multi-body dynamics software tool developed at NASA [2]. The simulation was built around vehicle mass and geometry properties at the time of staging and thrust profiles for the first stage solid rocket motor as well as for the booster deceleration motors and booster tumble motors. Aerodynamic forces were determined by models created from a combination of wind tunnel testing and CFD. The initial conditions such as position, velocity, and attitude were obtained from the Best Estimated Trajectory (BET), which is compiled from multiple ground based and vehicle mounted instruments. Dynamic loads were calculated by subtracting the inertial forces from the applied forces. The simulation results were compared to the Best Estimated Trajectory, accelerometer flight data, and to ground based video.

  19. Reconstruction of principal dynamical modes from climatic variability: nonlinear approach

    NASA Astrophysics Data System (ADS)

    Mukhin, Dmitry; Gavrilov, Andrey; Loskutov, Evgeny; Feigin, Alexander; Kurths, Juergen

    2015-04-01

    Analysis of multivariate time-series produced by complex systems requires efficient tools for reduction of data dimension. We consider this problem in relation to empirical modeling of climate, which implies an analysis of spatial-distributed time-series. The main goal is to establish the number of principal modes which have key contribution to data and actually governs the observed variability. Currently, the number of widely used linear methods based on PCA and factor analysis exists, which yield different data decompositions taking into consideration simultanious/time-lag correlations between spatial grid points. However, the question about possibility of improving the decomposition by taking into account nonlinear couplings between variables often remains untouched. In the report the method for constructing principal dynamic modes on the basis of low-dimensional nonlinear parametric representation of observed multivariate time-series is suggested. It is aimed to extracting the set of latent modes that both explains an essential part of variability, and obeys the simplest evolution law. Thus, this approach can be used for optimal reconstruction of the phase space for empirical prognostic modeling of observed dynamics. The evidence of nonlinear couplings in SST space-distributed data covering the Globe is investigated by the proposed approach. It is demonstrated that the obtained principal modes capture more part of SST variability than principal components (PCs) constructed by either EOF decomposition or its spatio-temporal extension. Relation of these modes to various climate phenomena is shown and discussed in the report. The application of the approach to data-driven forecast of climate bahavior is also discussed.

  20. Forced vibration of flexible body systems. A dynamic stiffness method

    NASA Astrophysics Data System (ADS)

    Liu, T. S.; Lin, J. C.

    1993-10-01

    Due to the development of high speed machinery, robots, and aerospace structures, the research of flexible body systems undergoing both gross motion and elastic deformation has seen increasing importance. The finite element method and modal analysis are often used in formulating equations of motion for dynamic analysis of the systems which entail time domain, forced vibration analysis. This study develops a new method based on dynamic stiffness to investigate forced vibration of flexible body systems. In contrast to the conventional finite element method, shape functions and stiffness matrices used in this study are derived from equations of motion for continuum beams. Hence, the resulting shape functions are named as dynamic shape functions. By applying the dynamic shape functions, the mass and stiffness matrices of a beam element are derived. The virtual work principle is employed to formulate equations of motion. Not only the coupling of gross motion and elastic deformation, but also the stiffening effect of axial forces is taken into account. Simulation results of a cantilever beam, a rotating beam, and a slider crank mechanism are compared with the literature to verify the proposed method.

  1. Comparing molecular dynamics force fields in the essential subspace.

    PubMed

    Martín-García, Fernando; Papaleo, Elena; Gomez-Puertas, Paulino; Boomsma, Wouter; Lindorff-Larsen, Kresten

    2015-01-01

    The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their "unbalanced" counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements.

  2. Comparing molecular dynamics force fields in the essential subspace.

    PubMed

    Martín-García, Fernando; Papaleo, Elena; Gomez-Puertas, Paulino; Boomsma, Wouter; Lindorff-Larsen, Kresten

    2015-01-01

    The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their "unbalanced" counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements. PMID:25811178

  3. Direct observation of dynamic force propagation between focal adhesions of cells on microposts by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Okada, Akinori; Mizutani, Yusuke; Subagyo, Agus; Hosoi, Hirotaka; Nakamura, Motonori; Sueoka, Kazuhisa; Kawahara, Koichi; Okajima, Takaharu

    2011-12-01

    We investigated dynamic force propagation between focal adhesions of fibroblast cells cultured on polydimethylsiloxane micropost substrates, by atomic force microscopy. Live cells were mechanically modulated by the atomic force microscopy probe bound to cell apical surfaces at 0.01-0.5 Hz, while microposts served as a force sensor at basal surfaces. We observed that cells exhibited rheological behavior at the apical surface but had no apparent out-of-phase response at the basal surface, indicating that the dynamic force propagating through cytoskeletal filaments behaves in an elastic manner. Moreover, the direction of the propagated force was observed to be intimately associated with the prestress.

  4. Protein displacements under external forces: An atomistic Langevin dynamics approach

    NASA Astrophysics Data System (ADS)

    Gnandt, David; Utz, Nadine; Blumen, Alexander; Koslowski, Thorsten

    2009-02-01

    We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply this scheme to identify polymorphs of model proteins by their mechanical response fingerprint, and we relate the averaged dynamics of proteins to their biological functionality, with the ion channel gramicidin A, a phosphorylase, and neuropeptide Y as examples. In an environment akin to dilute solutions, even small proteins show relaxation times up to 50 ns. Atomically resolved Langevin dynamics computations have been performed for the stretched gramicidin A ion channel.

  5. Dynamic stability of repulsive-force maglev suspension systems

    SciTech Connect

    Cai, Y.; Rote, D.M.; Mulcahy, T.M.; Wang, Z.

    1996-11-01

    This report summarizes the research performed on maglev vehicle dynamic stability at Argonne National Laboratory during the past few years. It also documents both measured and calculated magnetic-force data. Because dynamic instability is not acceptable for any commercial maglev system, it is important to consider this phenomenon in the development of all maglev systems. This report presents dynamic stability experiments on maglev systems and compares the results with predictions calculated by a nonlinear-dynamics computer code. Instabilities of an electrodynamic-suspension system type vehicle model were obtained by experimental observation and computer simulation of a five-degree-of-freedom maglev vehicle moving on a guideway that consists of a pair of L-shaped aluminum conductors attached to a rotating wheel. The experimental and theoretical analyses developed in this study identify basic stability characteristics and future research needs of maglev systems.

  6. A robust state-space kinetics-guided framework for dynamic PET image reconstruction.

    PubMed

    Tong, S; Alessio, A M; Kinahan, P E; Liu, H; Shi, P

    2011-04-21

    Dynamic PET image reconstruction is a challenging issue due to the low SNR and the large quantity of spatio-temporal data. We propose a robust state-space image reconstruction (SSIR) framework for activity reconstruction in dynamic PET. Unlike statistically-based frame-by-frame methods, tracer kinetic modeling is incorporated to provide physiological guidance for the reconstruction, harnessing the temporal information of the dynamic data. Dynamic reconstruction is formulated in a state-space representation, where a compartmental model describes the kinetic processes in a continuous-time system equation, and the imaging data are expressed in a discrete measurement equation. Tracer activity concentrations are treated as the state variables, and are estimated from the dynamic data. Sampled-data H(∞) filtering is adopted for robust estimation. H(∞) filtering makes no assumptions on the system and measurement statistics, and guarantees bounded estimation error for finite-energy disturbances, leading to robust performance for dynamic data with low SNR and/or errors. This alternative reconstruction approach could help us to deal with unpredictable situations in imaging (e.g. data corruption from failed detector blocks) or inaccurate noise models. Experiments on synthetic phantom and patient PET data are performed to demonstrate feasibility of the SSIR framework, and to explore its potential advantages over frame-by-frame statistical reconstruction approaches.

  7. Dynamic Force Balances and Cell Shape Changes during Cytokinesis

    NASA Astrophysics Data System (ADS)

    Sain, Anirban; Inamdar, Mandar M.; Jülicher, Frank

    2015-01-01

    During the division of animal cells, an actomyosin ring is formed in the cell cortex. The contraction of this ring induces shape changes of the cell and the formation of a cytokinesis furrow. In many cases, a cell-cell interface forms that separates the two new cells. Here we present a simple physical description of the cell shape changes and the dynamics of the interface closure, based on force balances involving active stresses and viscous friction. We discuss conditions in which the interface closure is either axially symmetric or asymmetric. We show that our model can account for the observed dynamics of ring contraction and interface closure in the C. elegans embryo.

  8. Dynamic force balances and cell shape changes during cytokinesis.

    PubMed

    Sain, Anirban; Inamdar, Mandar M; Jülicher, Frank

    2015-01-30

    During the division of animal cells, an actomyosin ring is formed in the cell cortex. The contraction of this ring induces shape changes of the cell and the formation of a cytokinesis furrow. In many cases, a cell-cell interface forms that separates the two new cells. Here we present a simple physical description of the cell shape changes and the dynamics of the interface closure, based on force balances involving active stresses and viscous friction. We discuss conditions in which the interface closure is either axially symmetric or asymmetric. We show that our model can account for the observed dynamics of ring contraction and interface closure in the C. elegans embryo.

  9. Forced dynamic position control of PMSM with DTC utilization

    NASA Astrophysics Data System (ADS)

    Malek, Michal

    2012-11-01

    Almost one and a half century after the publication of Maxwell’s On Governors, feedback theory with PID controllers in cascade structure is still an essential part of control structures of most controlled electric drives. There are a few control strategies which are “ready” to replace it but they usually miss one of the essential fundamentals of every successful approach - simplicity hand in hand with lucidity. But there is one close relative which is simple and powerful at the same time, is not excessively abstract and without complicated mathematics. The name of this technique is Forced Dynamic Control. In this paper forced dynamic control is presented together with direct torque controlled PMSM drive as unique combination of simple algorithms for inner and outer loop of cascade structure.

  10. Holocene carbon dynamics and climate forcing of two subarctic minerotrophic fens

    NASA Astrophysics Data System (ADS)

    Mathijssen, P.; Aurela, M.; Blaauw, M.; Juutinen, S.; Lohila, A.; Niemelä, E.; Tuittila, E.; Tuovinen, J.; Väliranta, M.

    2013-12-01

    Historical data on three dimensional peatland development patterns, carbon (C) dynamics and radiative forcing may aid us to understand peatland - climate-related feedback mechanisms. We investigated vertical and horizontal peat growth patterns of two subarctic fens, Lompolonjänkkä (Western Finnish Lapland) and Kiposuo (Eastern Finnish Lapland). We calculated C accumulation rates and, based on these and modern gas measurements, we estimated historical CO2 and CH4 fluxes. Past C budgets and radiative forcing were reconstructed. The C accumulation rates of Lompolojänkkä fen and Kiposuo fen varied between ranges 3 - 47 and 2 - 27 g C m-2 a-1, respectively. Plant macrofossil analyses suggest that fen plant communities have changed only a little throughout the Holocene and accordingly we assume only minor variation in CH4 emissions. However, C uptake rates varied and showed extended periods of low C uptake between 8 and 2 kcal BP in Lompolojänkkä and between 9 and 4 kcal BP in Kiposuo. These periods of low C uptake coincide with warm and dry climate conditions. Lateral expansion of Lompolojänkkä was fast after peatland initiation, which happened through infilling, and during the last two millennia, but expansion was slow between 6 and 3 kcal BP. Kiposuo started to initiate simultaneously over a large area mainly on mineral soil. Subsequent lateral expansion has been negligible. In conclusion the reconstructed C dynamics suggest that the mid Holocene dry and warm conditions slowed down peat growth and C accumulation. This was especially striking in Lompolonjänkkä. Both fens had a positive radiative forcing (RF) effect to the atmosphere after the peat initiation. The RF turned negative after c. 700 years from the initiation in Lompolonjänkkä and after c. 1500 years in Kiposuo. Afterwards the radiative forcing continued to decrease until the present, reaching current radiative forcing of -1.33 x 10-8 W m-2 (Lompolonjänkkä) and -0.77 x 10-8 W m-2 (Kiposuo

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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 the 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 force-based model which produces realistic jam dynamics without the appearance of unrealistic negative speeds for empirical desired walking speeds.

  12. Subharmonic Oscillations and Chaos in Dynamic Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Cantrell, John H.; Cantrell, Sean A.

    2015-01-01

    The increasing use of dynamic atomic force microscopy (d-AFM) for nanoscale materials characterization calls for a deeper understanding of the cantilever dynamics influencing scan stability, predictability, and image quality. Model development is critical to such understanding. Renormalization of the equations governing d- AFM provides a simple interpretation of cantilever dynamics as a single spring and mass system with frequency dependent cantilever stiffness and damping parameters. The renormalized model is sufficiently robust to predict the experimentally observed splitting of the free-space cantilever resonance into multiple resonances upon cantilever-sample contact. Central to the model is the representation of the cantilever sample interaction force as a polynomial expansion with coefficients F(sub ij) (i,j = 0, 1, 2) that account for the effective interaction stiffness parameter, the cantilever-to-sample energy transfer, and the amplitude of cantilever oscillation. Application of the Melnikov method to the model equation is shown to predict a homoclinic bifurcation of the Smale horseshoe type leading to a cascade of period doublings with increasing drive displacement amplitude culminating in chaos and loss of image quality. The threshold value of the drive displacement amplitude necessary to initiate subharmonic generation depends on the acoustic drive frequency, the effective damping coefficient, and the nonlinearity of the cantilever-sample interaction force. For parameter values leading to displacement amplitudes below threshold for homoclinic bifurcation other bifurcation scenarios can occur, some of which lead to chaos.

  13. Configurational forces and variational mesh adaptation in solid dynamics

    NASA Astrophysics Data System (ADS)

    Zielonka, Matias G.

    This thesis is concerned with the exploration and development of a variational finite element mesh adaption framework for non-linear solid dynamics and its conceptual links with the theory of dynamic configurational forces. The distinctive attribute of this methodology is that the underlying variational principle of the problem under study is used to supply both the discretized fields and the mesh on which the discretization is supported. To this end a mixed-multifield version of Hamilton's principle of stationary action and Lagrange-d'Alembert, principle is proposed, a fresh perspective on the theory of dynamic configurational forces is presented, and a unifying variational formulation that generalizes the framework to systems with general dissipative behavior is developed. A mixed finite element formulation with independent spatial interpolations for deformations and velocities and a mixed variational integrator with independent time interpolations for the resulting nodal parameters is constructed. This discretization is supported on a continuously deforming mesh that is not prescribed at the outset but computed as part of the solution. The resulting space-time discretization satisfies exact discrete configurational force balance and exhibits excellent long term global energy stability behavior. The robustness of the mesh adaption framework is assessed and demonstrated with a set of examples and convergence tests.

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

    PubMed

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

    2015-10-01

    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 the 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 force-based model which produces realistic jam dynamics without the appearance of unrealistic negative speeds for empirical desired walking speeds. PMID:26565291

  15. Langevin Dynamics with Space-Time Periodic Nonequilibrium Forcing

    NASA Astrophysics Data System (ADS)

    Joubaud, R.; Pavliotis, G. A.; Stoltz, G.

    2015-01-01

    We present results on the ballistic and diffusive behavior of the Langevin dynamics in a periodic potential that is driven away from equilibrium by a space-time periodic driving force, extending some of the results obtained by Collet and Martinez in (J Math Biol, 56(6):765-792 2008). In the hyperbolic scaling, a nontrivial average velocity can be observed even if the external forcing vanishes in average. More surprisingly, an average velocity in the direction opposite to the forcing may develop at the linear response level—a phenomenon called negative mobility. The diffusive limit of the non-equilibrium Langevin dynamics is also studied using the general methodology of central limit theorems for additive functionals of Markov processes. To apply this methodology, which is based on the study of appropriate Poisson equations, we extend recent results on pointwise estimates of the resolvent of the generator associated with the Langevin dynamics. Our theoretical results are illustrated by numerical simulations of a two-dimensional system.

  16. Dynamics of living phytoplankton: Implications for paleoenvironmental reconstructions

    NASA Astrophysics Data System (ADS)

    Barbosa, A. B.

    2009-01-01

    Phytoplankton is the dominant primary producer in aquatic ecosystems and is considered a gauge of ecological condition and change. Some phytoplankton groups, namely diatoms, dinoflagellates, and coccolithophores, produce morphological or chemical fossils that can be used for paleoenvironmental reconstruction. This study aims to review the processes that regulate dynamics in living phytoplankton and to highlight how this knowledge is used in paleoecological studies. The distribution patterns of phytoplankton in present-day aquatic ecosystems are shaped by the interplay between processes that regulate cell growth and cell death. Cell growth and cell death are regulated by the internal environment of phytoplankton (e.g., specific environmental tolerances, resource uptake properties, cell size, density and morphology, alternative nutritional strategies such as mixotrophy or N2 uptake, motility, intracellular storage capacities, grazing resistance properties), and by its external environment. The external environment includes variables dependent on the availability of resources (e.g., light intensity, concentration of CO2 and dissolved inorganic macronutrients and micronutrients, availability of living prey in case of mixotrophs) and variables independent of resources (e.g., temperature, salinity, turbulence, ultraviolet radiation, bioactive compounds, activity of grazers, viruses, and eukaryotic parasites). The importance of recently described loss processes, such as grazing by phagotrophic protists, viral lyses, and programmed cell death, is discussed in the context of its potential impact upon phytoplankton vertical fluxes. Examples of the use of different phytoplankton metrics (e.g. abundance, species composition, species morphology, and elemental composition) to infer contemporaneous as well as past environmental and ecological conditions are critically evaluated.

  17. Satellite Dynamic Damping via Active Force Control Augmentation

    NASA Astrophysics Data System (ADS)

    Varatharajoo, Renuganth

    2012-07-01

    An approach that incorporates the Active Force Control (AFC) technique into a conventional Proportional-Derivative (PD) controller is proposed for a satellite active dynamic damping towards a full attitude control. The AFC method has been established to facilitate a robust motion control of dynamical systems in the presence of disturbances, parametric uncertainties and changes that are commonly prevalent in the real-world environment. The usefulness of the method can be extended by introducing intelligent mechanisms to approximate the mass or inertia matrix of the dynamic system to trigger the compensation effect of the controller. AFC is a technique that relies on the appropriate estimation of the inertial or mass parameters of the dynamic system and the measurements of the acceleration and force signals induced by the system if practical implementation is ever considered. In AFC, it is shown that the system subjected to a number of disturbances remains stable and robust via the compensating action of the control strategy. We demonstrate that it is possible to design a spacecraft attitude feedback controller that will ensure the system dynamics set point remains unchanged even in the presence of the disturbances provided that the actual disturbances can be modeled effectively. In order to further facilitate this analysis, a combined energy and attitude control system (CEACS) is proposed as a model satellite attitude control actuator. All the governing equations are established and the proposed satellite attitude control architecture is made amenable to numerical treatments. The results show that the PD-AFC attitude damping performances are superiorly better than that of the solely PD type. It is also shown that the tunings of the AFC system gains are crucial to ensure a better attitude damping performance and this process is mandatory for AFC systems. Finally, the results demonstrate an important satellite dynamic damping enhancement capability using the AFC

  18. Correlation of Force Production with Apoptosis in Tissue Dynamics

    NASA Astrophysics Data System (ADS)

    Toyama, Yusuke; Peralta, Xomalin; Venakides, Stephanos; Kiehart, Daniel; Edwards, Glenn

    2007-03-01

    To understand embryo morphogenesis, it is necessary to know the force distribution in the various tissues. Since cells are largely inaccessible to mechanical probes in vivo, measurements of the net forces exerted by cells are challenging. The combination of experimental and theoretical approaches has proven to improve our understanding of these forces. A steerable UV-laser microbeam was used to probe the forces and the resulting kinematics were monitored with confocal microscopy. Dorsal closure is a developmental stage in Drosophila embryogenesis, where the dynamics are a consequence of four biological processes [1]. During this stage, cells that have outlived their usefulness undergo apoptosis, a biological process also known as programmed cell death for cells. Apoptotic events were decreased with genetic techniques or increased by irradiation with a UV-C lamp. We present experimental evidence for force generation correlating with apoptosis. This research has been supported by the NIH (GM33830 and GM61240). [1] M. S. Hutson, et al. Science, 300, 145 (2003).

  19. Dynamic force spectroscopy of parallel individual mucin1-antibody bonds

    SciTech Connect

    Sulchek, T A; Friddle, R W; Langry, K; Lau, E; Albrecht, H; Ratto, T; DeNardo, S; Colvin, M E; Noy, A

    2005-05-02

    We used atomic force microscopy (AFM) to measure the binding forces between Mucin1 (MUC1) peptide and a single chain antibody fragment (scFv) selected from a scFv library screened against MUC1. This binding interaction is central to the design of the molecules for targeted delivery of radioimmunotherapeutic agents for prostate and breast cancer treatment. Our experiments separated the specific binding interaction from non-specific interactions by tethering the antibody and MUC1 molecules to the AFM tip and sample surface with flexible polymer spacers. Rupture force magnitude and elastic characteristics of the spacers allowed identification of the bond rupture events corresponding to different number of interacting proteins. We used dynamic force spectroscopy to estimate the intermolecular potential widths and equivalent thermodynamic off rates for mono-, bi-, and tri-valent interactions. Measured interaction potential parameters agree with the results of molecular docking simulation. Our results demonstrate that an increase of the interaction valency leads to a precipitous decline in the dissociation rate. Binding forces measured for mono and multivalent interactions match the predictions of a Markovian model for the strength of multiple uncorrelated bonds in parallel configuration. Our approach is promising for comparison of the specific effects of molecular modifications as well as for determination of the best configuration of antibody-based multivalent targeting agents.

  20. Frequency adaptation for enhanced radiation force amplitude in dynamic elastography.

    PubMed

    Ouared, Abderrahmane; Montagnon, Emmanuel; Kazemirad, Siavash; Gaboury, Louis; Robidoux, André; Cloutier, Guy

    2015-08-01

    In remote dynamic elastography, the amplitude of the generated displacement field is directly related to the amplitude of the radiation force. Therefore, displacement improvement for better tissue characterization requires the optimization of the radiation force amplitude by increasing the push duration and/or the excitation amplitude applied on the transducer. The main problem of these approaches is that the Food and Drug Administration (FDA) thresholds for medical applications and transducer limitations may be easily exceeded. In the present study, the effect of the frequency used for the generation of the radiation force on the amplitude of the displacement field was investigated. We found that amplitudes of displacements generated by adapted radiation force sequences were greater than those generated by standard nonadapted ones (i.e., single push acoustic radiation force impulse and supersonic shear imaging). Gains in magnitude were between 20 to 158% for in vitro measurements on agar-gelatin phantoms, and 170 to 336% for ex vivo measurements on a human breast sample, depending on focus depths and attenuations of tested samples. The signal-to-noise ratio was also improved more than 4-fold with adapted sequences. We conclude that frequency adaptation is a complementary technique that is efficient for the optimization of displacement amplitudes. This technique can be used safely to optimize the deposited local acoustic energy without increasing the risk of damaging tissues and transducer elements.

  1. On the dynamics of a response to volume flux forcing

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Koehl, Armin; Stammer, Detlef

    2015-04-01

    The dynamical impact of surface volume flux forcing on the global oceans circulation is investigated for the period 1949-2011. As part of the study an ocean circulation model is forced in two ways using NCEP surface freshwater forcing: a virtual salt flux version and a volume flux version. The resulting differences in the circulation can be described by the Goldsbrough-Stommel circulation. This barotropic circulation is on the order of 1 Sv, weakens the mean flow of the world oceans and changes the sea level. The meridional freshwater and heat transport differences between these two versions are about 5% of the mean transports. Decomposing these transports into overturning and gyre components, reveals that it is the overturning component that dominates the transport differences that are caused by the volume flux forcing. The overturning freshwater and heat transports induced by the volume flux weaken the mean overturning related transports of the world oceans expect for the southern Pacific-Indian oceans. Furthermore, the volume flux also has impact on the meridional overturning circulation. The overturning transport differences are on the order of 0.1 Sv, which at the surface are described by the volume transports of the volume flux forcing.

  2. Dynamic calibration of higher eigenmode parameters of a cantilever in atomic force microscopy by using tip–surface interactions

    DOE PAGES

    Borysov, Stanislav S.; Forchheimer, Daniel; Haviland, David B.

    2014-10-29

    Here we present a theoretical framework for the dynamic calibration of the higher eigenmode parameters (stiffness and optical lever inverse responsivity) of a cantilever. The method is based on the tip–surface force reconstruction technique and does not require any prior knowledge of the eigenmode shape or the particular form of the tip–surface interaction. The calibration method proposed requires a single-point force measurement by using a multimodal drive and its accuracy is independent of the unknown physical amplitude of a higher eigenmode.

  3. MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions.

    PubMed

    Novosad, Philip; Reader, Andrew J

    2016-06-21

    Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [(18)F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral

  4. MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions

    NASA Astrophysics Data System (ADS)

    Novosad, Philip; Reader, Andrew J.

    2016-06-01

    Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [18F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral

  5. Guided crowd dynamics via modified social force model

    NASA Astrophysics Data System (ADS)

    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.

  6. Dynamic mechanoelectrochemistry of polypyrrole membranes via shear-force tracking.

    PubMed

    Northcutt, Robert G; Heinemann, Christian; Sundaresan, Vishnu Baba

    2016-07-14

    Mechanoelectrochemistry is the study of elastic and plastic deformation of materials during reversible reduction and oxidation processes. In this article, we introduce shear-force tracking as a method to dynamically measure mechanical (strain), chemical (ion transport), and electrical (applied redox potentials) responses of the conducting polymer polypyrrole (PPy) during redox reactions. This tracking technique uses a control algorithm to maintain a set distance between a ultramicroelectrode (UME) tip and a surface via shear-force regulation. Due to the sensitivity of shear-force signals in the near field of substrate surfaces, a significantly improved signal to noise ratio (20 : 1) is possible and allows for nanoscale measurement of redox events. Chemomechanical coupling (the ratio of ion transport to resultant extensional actuation) is calculated for PPy-based membranes of various thicknesses based on a mechanistic interpretation of charge storage in redox active conducting polymers. The measured dynamic response demonstrates that chemomechanical coupling is not a constant, as assumed in literature, but is dependent on the polymers state of charge and the direction (ingress/egress) of ion transport. PMID:27263628

  7. Dynamic disorder in receptor-ligand forced dissociation experiments

    NASA Astrophysics Data System (ADS)

    Liu, Fei; Ou-Yang, Zhong-Can; Iwamoto, Mitsumasa

    2006-01-01

    Recently experiments showed that some biological noncovalent bonds increase their lifetimes when they are stretched by an external force, and their lifetimes will decrease when the force increases further. Several specific quantitative models have been proposed to explain the intriguing transitions from the “catch bond” to the “slip bond.” In this work we propose that the dynamic disorder of the force-dependent dissociation rate can account for the counterintuitive behaviors of the bonds. A Gaussian stochastic rate model is used to quantitatively describe the transitions observed recently in the single bond P-selctin glycoprotein ligand 1-P-selectin force rupture experiment [Marshall , Nature 423, 190 (2003)]. Our model agrees well with the experimental data. We conclude that the catch bonds could arise from the stronger positive correlation between the height of the intrinsic energy barrier and the distance from the bound state to the barrier; classical pathway scenario or a priori catch bond assumption is not essential.

  8. Dynamics of Bond Breaking Studied by Chemical Force Microscopy

    NASA Astrophysics Data System (ADS)

    Noy, Aleksandr; Zepeda, Salvador; Orme, Chris; Yeh, Yin; Deyoreo, Jim

    2000-03-01

    Intermolecular forces underline a variety of phenomena in chemical and in biological systems, such as cell adhesion, protein folding and molecular recognition in ligand-receptor pairs. Understanding the dynamics of these interactions is critical for modeling and controlling these processes. The advent of ultra-sensitive force measurement techniques has enabled direct measurement of the bond strength on the relevant length scales. Recent measurements have pointed out the importance of kinetic factors in bond strength and pointed out the necessity to explore the whole energy landscape of a chemical bond. Still, little is known about the response of the bond strength to the environmental variables such as temperature. The analysis of this response provides a way to determine thermodynamic characteristics of the binding interaction. We used chemical force microscopy to measure the temperature dependence of the interaction forces in a well-defined system presenting a finite number of identical bonds. The tip of the scanning probe microscope was modified with distinct chemical functionalities to give rise to the well-defined and uniform interactions with the sample surface. We will discuss the theoretical framework for interpretation of such measurements, as well as the relative importance of thermodynamic and kinetic factors affecting the bond strength in the presence of solvent medium. We also point out the differences in kinetics of bond breaking in single bond systems vs. multiple bond systems.

  9. An improved technique for the reconstruction of former glacier mass-balance and dynamics

    NASA Astrophysics Data System (ADS)

    Carr, Simon; Coleman, Christopher

    2007-11-01

    The recognition of past glacier extent and dynamics is a fundamental aspect of investigations of the climatic sensitivity of glaciers, especially when examining short-lived climate events such as the Younger Dryas or Little Ice Age. Existing approaches to the reconstruction of glacier form and dynamics depend on speculative reasoning of key glacier dynamic parameters, including the role of basal slip and subglacial deformation in glacier mass-transfer. This study reviews approaches to glacier reconstruction, derivation of former glacier equilibrium line altitudes (ELA's) and estimation of mass-balance and dynamics, concluding that most reconstructions of glacier mass-balance are compromised by a lack of glaciological considerations. An alternative approach to glacier reconstruction is presented, demonstrated and discussed, by which an empirical relationship between ablation gradient and mass loss at the ELA is used to derive mass-balance, mass-flux through the ELA and average balance velocity at the ELA. This 'glaciological' approach is applied to four reconstructed glaciers to test previous interpretations that each reflects Younger Dryas glaciation in the UK. The study concludes that this approach provides a more robust technique for reconstructing former glacier dynamics, and may be applied to test geomorphological interpretations of former mountain glaciation.

  10. Local viscoelastic properties of live cells investigated using dynamic and quasi-static atomic force microscopy methods.

    PubMed

    Cartagena, Alexander; Raman, Arvind

    2014-03-01

    The measurement of viscoelasticity of cells in physiological environments with high spatio-temporal resolution is a key goal in cell mechanobiology. Traditionally only the elastic properties have been measured from quasi-static force-distance curves using the atomic force microscope (AFM). Recently, dynamic AFM-based methods have been proposed to map the local in vitro viscoelastic properties of living cells with nanoscale resolution. However, the differences in viscoelastic properties estimated from such dynamic and traditional quasi-static techniques are poorly understood. In this work we quantitatively reconstruct the local force and dissipation gradients (viscoelasticity) on live fibroblast cells in buffer solutions using Lorentz force excited cantilevers and present a careful comparison between mechanical properties (local stiffness and damping) extracted using dynamic and quasi-static force spectroscopy methods. The results highlight the dependence of measured viscoelastic properties on both the frequency at which the chosen technique operates as well as the interactions with subcellular components beyond certain indentation depth, both of which are responsible for differences between the viscoelasticity property maps acquired using the dynamic AFM method against the quasi-static measurements.

  11. Microcantilevers with embedded accelerometers for dynamic atomic force microscopy

    SciTech Connect

    Shaik, Nurul Huda; Raman, Arvind; Reifenberger, Ronald G.

    2014-02-24

    The measurement of the intermittent interaction between an oscillating nanotip and the sample surface is a key challenge in dynamic Atomic Force Microscopy (AFM). Accelerometers integrated onto AFM cantilevers can directly measure this interaction with minimal cantilever modification but have been difficult to realize. Here, we design and fabricate high frequency bandwidth accelerometers on AFM cantilevers to directly measure the tip acceleration in commercial AFM systems. We demonstrate a simple way of calibrating such accelerometers and present experiments using amplitude modulated AFM on freshly cleaved mica samples in water to study the response of the accelerometer.

  12. Holocene carbon dynamics and radiative forcing of three different types of peatlands in Finland

    NASA Astrophysics Data System (ADS)

    Mathijssen, Paul; Väliranta, Minna; Lohila, Annalea; Minkkinen, Kari; Tuittila, Eeva-Stiina; Tuovinen, Juha-Pekka; Korrensalo, Aino

    2016-04-01

    Peatlands contain approximately a third of all soil carbon globally and as they exchange carbon dioxide (CO2) and methane (CH4) copiously with the atmosphere, changes in peatland carbon budgets have a large impact on the global carbon balance and the concentration of greenhouse gasses in the atmosphere. There has been a growing interest in reconstructing and linking peatland carbon dynamics to past climate variations, because quantitative reconstructions can be used as a basis for future carbon balance predictions. In order to increase our understanding on peatland development and response patterns we quantitatively reconstructed Holocene carbon dynamics of three different peatlands in Finland: a subarctic fen, a boreal peatland complex and a boreal managed pine bog. Several cores from each peatland were investigated. The peatlands showed distinct successional pathways, which were sometimes triggered by fires. Successional stages were partly reflected in carbon accumulation patterns. Sometimes variations in carbon accumulation rates coincided with autogenic changes in peat type and vegetation, but accumulation rates were also related to the large-scale Holocene climate phases. However, Holocene climate changes as such did not seem to result in changes in the peat plant species composition. The mid-Holocene warm and dry climate conditions reduced the carbon accumulation in the subarctic fen and in the fen part of the boreal peatland complex, but when the peatland was in bog phase this effect was not visible. Some bog cores showed a clear increase in carbon accumulation after fen-bog transition, but the pattern was not unanimous. In addition to carbon accumulation, we estimated past CH4 emissions for each peatland respectively by applying different methods and by utilising the established current vegetation-CH4 emission relationship. The reconstructions showed that CH4 emissions always decreased during bog stages, but that the CH4 emissions played a major role in the

  13. Replicator dynamics with alternate growth functions, delay, and quasiperiodic forcing

    NASA Astrophysics Data System (ADS)

    Wesson, Elizabeth Nicholas

    Evolutionary dynamics combines game theory and nonlinear dynamics to model competition in biological and social situations. The replicator equation is a standard paradigm in evolutionary dynamics. The growth rate of each strategy is its excess fitness: the deviation of its fitness from the average. The gametheoretic aspect of the model lies in the choice of fitness function, which is determined by a payoff matrix. Two well-known replicator systems are the threestrategy Rock-Paper-Scissors game and the two-strategy Hawk-Dove game. In this work, we analyze the dynamics of replicator systems with three different types of modifications. The first generalization of the replicator model is given by considering alternate growth functions. We find that in the Rock-Paper-Scissors game with a logistic growth function, there are several fixed points that do not exist in the standard replicator model. The system exhibits both periodic motion and convergence to attractors. We also analyze replicator systems with delayed interactions between strategies. We consider a symmetric delay model, in which the fitness of each strategy is its expected payoff delayed by a time interval; and an asymmetric model, in which same-strategy terms appearing in the fitness of a given strategy are not delayed. In both cases, limit cycles arise that cannot occur in the usual replicator model. Finally, we examine Rock-Paper-Scissors systems with quasiperiodic forcing of the payoff coefficients. This model may represent systems in which the competition is affected by cyclical processes on different time-scales. We find that the stability of the equilibrium state depends sensitively on the two forcing frequencies; in fact, the region of stability has fractal boundary.

  14. A CLASS OF RECONSTRUCTED DISCONTINUOUS GALERKIN METHODS IN COMPUTATIONAL FLUID DYNAMICS

    SciTech Connect

    Hong Luo; Yidong Xia; Robert Nourgaliev

    2011-05-01

    A class of reconstructed discontinuous Galerkin (DG) methods is presented to solve compressible flow problems on arbitrary grids. The idea is to combine the efficiency of the reconstruction methods in finite volume methods and the accuracy of the DG methods to obtain a better numerical algorithm in computational fluid dynamics. The beauty of the resulting reconstructed discontinuous Galerkin (RDG) methods is that they provide a unified formulation for both finite volume and DG methods, and contain both classical finite volume and standard DG methods as two special cases of the RDG methods, and thus allow for a direct efficiency comparison. Both Green-Gauss and least-squares reconstruction methods and a least-squares recovery method are presented to obtain a quadratic polynomial representation of the underlying linear discontinuous Galerkin solution on each cell via a so-called in-cell reconstruction process. The devised in-cell reconstruction is aimed to augment the accuracy of the discontinuous Galerkin method by increasing the order of the underlying polynomial solution. These three reconstructed discontinuous Galerkin methods are used to compute a variety of compressible flow problems on arbitrary meshes to assess their accuracy. The numerical experiments demonstrate that all three reconstructed discontinuous Galerkin methods can significantly improve the accuracy of the underlying second-order DG method, although the least-squares reconstructed DG method provides the best performance in terms of both accuracy, efficiency, and robustness.

  15. Dynamic performance assessment of selected sport shoes on impact forces.

    PubMed

    Dufek, J S; Bates, B T; Davis, H P; Malone, L A

    1991-09-01

    Few investigators have evaluated the performance characteristics of non-running sport shoes. The purpose of this study was to assess the dynamic performance characteristics of four different shoe models during landings. Five male subjects performed 25 voluntary hanging drop landings (60 cm) onto a force platform (1000 Hz) for each of four shoe conditions (C1 and C2 = basketball shoe, C3 = running shoe, C4 = volleyball shoe). Ground reaction force data were evaluated for maximum forefoot (F1) and rearfoot (F2) impact forces as well as the respective times of occurrence of these events (T1, T2). Results of the group data analysis indicated a preferential performance rank order of C1, C3, C4, C2 although significant interaction effects were observed, indicating a need for single-subject analyses. Three techniques were incorporated to assess individual subject condition differences, all of which elicited unique rank orders for the shoes although each identified C1 as the "best" shoe condition. The results of the study support the necessity for within-subject analyses conducted with an adequate number of trials when attempting to detect subtle performance differences that may exist between various sport shoes. Whether the observed statistically significant differences are biomechanically meaningful remains an important unanswered question.

  16. Force Generation, Polymerization Dynamics and Nucleation of Actin Filaments

    NASA Astrophysics Data System (ADS)

    Wang, Ruizhe

    We study force generation and actin filament dynamics using stochastic and deterministic methods. First, we treat force generation of bundled actin filaments by polymerization via molecular-level stochastic simulations. In the widely-used Brownian Ratchet model, actin filaments grow freely whenever the tip-obstacle gap created by thermal fluctuation exceeds the monomer size. We name this model the Perfect Brownian Ratchet (PBR) model. In the PBR model, actin monomer diffusion is treated implicitly. We perform a series of simulations based on the PBR, in which obstacle motion is treated explicitly; in most previous studies, obstacle motion has been treated implicitly. We find that the cooperativity of filaments is generally weak in the PBR model, meaning that more filaments would grow more slowly given the same force per filament. Closed-form formulas are also developed, which match the simulation results. These portable and accurate formulas provide guidance for experiments and upper and lower bounds for theoretical analyses. We also studied a variation of the PBR, called the Diffusing Brownian Ratchet (DBR) model, in which both actin monomer and obstacle diffusion are treated explicitly. We find that the growth rate of multiple filaments is even lower, compared with that in PBR. This finding challenges the widely-accepted PBR assumption and suggests that pushing the study of actin dynamics down to the sub-nanometer level yields new insights. We subsequently used a rate equation approach to model the effect of local depletion of actin monomers on the nucleation of actin filaments on biomimetic beads, and how the effect is regulated by capping protein (CP). We find that near the bead surface, a higher CP concentration increases local actin concentration, which leads to an enhanced activities of actin filaments' nucleation. Our model analysis matches the experimental results and lends support to an important but undervalued hypothesis proposed by Carlier and

  17. Multiscale Dynamics of ENSO Impacts on Coral Proxy Environments: Towards Improving Reconstruction Accuracy

    NASA Astrophysics Data System (ADS)

    Stevenson, Samantha; Powell, Brian; Merrifield, Mark; Cobb, Kim; Noone, David; Nusbaumer, Jesse

    2015-04-01

    Oxygen isotope (δ18O) records from tropical coral skeletons are widely used for reconstructing the El Niño/ Southern Oscillation (ENSO). However, data limitations have prevented detailed investigation of the dynamical connection between ENSO variability and δ18O anomalies near sites used for reconstructions, potentially creating large uncertainties. To address this issue, a new, isotope-enabled version of the Regional Ocean Modeling System ("isoROMS") has been developed to simulate seawater oxygen isotope anomalies during historical El Niño and La Niña events at a variety of spatial scales. isoROMS is forced with 20th century (1979-2009) boundary conditions and surface fluxes, in addition to precipitation δ18O from the newly developed isotope-enabled Community Atmosphere Model (iCAM5); it thus functions as an approximate 'reanalysis' of seawater δ18O over the satellite era. The balance of surface and advective/diffusive processes during central and eastern Pacific El Niño events is investigated at sites throughout the tropical Pacific, in order to understand the mechanisms governing the magnitude of individual δ18O excursions in existing proxy records. Budget analysis shows that in many cases impacts on δ18O take place primarily through advective changes, rather than surface fluxes as previously thought. Additionally, mesoscale processes such as tropical instability waves significantly affect temperature and δ18O in some locations, and their importance varies with ENSO phase; this suggests that rectification of such high-frequency variability into the proxy signal may affect estimates of overall ENSO variance. Implications for ENSO estimates using 'pseudoproxy' conversions from instrumental data are discussed.

  18. Dynamic medial patellofemoral ligament reconstruction in recurrent patellar instability: A surgical technique

    PubMed Central

    Kiran, Kopuri Ravi; Srikanth, I Muni; Chinnusamy, Lenin; Deepti, K

    2015-01-01

    The medial patellofemoral ligament (MPFL) is the primary stabilizer of the patellofemoral joint; its reconstruction has been recommended in adults over the past decade after recurrent patellar instability. However, there has been no standardized technique for reconstruction, therefore, ideal graft and technique for reconstruction are yet undetermined. However, dynamic MPFL reconstruction studies claim to be superior to other procedures as it is more anatomical. This preliminary study aims at assessing the outcomes of MPFL reconstruction in a dynamic pattern using hamstring graft. We performed this procedure in four consecutive patients with chronic patellar instability following trauma. MPFL reconstruction was done with hamstring tendons detached distally and secured to patellar periosteum after being passed through a bony tunnel in the patella without an implant and using the medial collateral ligament as a pulley. In all 4 knees, the MPFL reconstruction was isolated and was not associated with any other realignment procedures. No recurrent episodes of dislocation or subluxation were reported at 24 months followup. PMID:26806970

  19. Reconstruction of dynamical pulse trains via time-resolved multiheterodyne detection.

    PubMed

    Butler, T; Tykalewicz, B; Goulding, D; Kelleher, B; Huyet, G; Hegarty, S P

    2013-12-01

    A multiheterodyne technique is presented which can accurately measure the complex spectrum and temporally reconstruct certain dynamic pulse trains. This technique is applied to periodic pulses formed in a LiNb0₃ Mach Zehnder modulator. The spectral amplitude and phase of 20 GHz 66% return-to-zero (RZ) pulses and 10 GHz 50% RZ pulses are measured, and compared to independent measurements from a high resolution optical spectrum analyser. The temporal pulse shape and phase is reconstructed and compared to high speed sampling oscilloscope measurements. This technique is applied to sections of a large single acquisition, allowing the reconstruction of frequency and amplitude modulated pulse trains. PMID:24514462

  20. Solar forcing and climate variability in the North Atlantic during the last millennium: comparison between models and reconstructions

    NASA Astrophysics Data System (ADS)

    Servonnat, J.; Khodri, M.; Yiou, P.; Guiot, J.; Denvil, S.

    2009-04-01

    Studying the climate of the last millennium allows replacing the present climate change in a long term context. Since it is a relatively well-documented period, it provides an interesting base to assess the secular variability of the climate, free of anthropogenic greenhouse gas influence. Considering this, the climate of the last millennium is likely to have been driven by natural forcings, such as major volcanic eruptions or solar variability. We present here the results of the simulations performed with the IPSLCM4v2 climate model for the French ANR ESCARSEL project (reconstruction of the climate of the last millennium). In order to understand the role of the solar variability during this period, we have forced the model with a reconstruction of the Total Solar Irradiance since 1000AD (Crowley et al., 2000). The results are compared with various reconstructions based on proxy data, from the hemispheric to the continental scale. A new reconstruction of the temperature in Europe since 600AD (annual April to September mean, based on tree rings data) has been achieved within the ESCARSEL project. This dataset provides the possibility to compare the spatial response of the model to the solar forcing with the corresponding temperature patterns recorded in the proxys. As a first step we present the results on the long term variability, before focusing on selected periods to assess the spatial behaviour of the model to different value of the total solar irradiance. Crowley et al. 2000, Causes of climate change over the past 1000yrs, Science 289, 270

  1. The effect of graft strength on knee laxity and graft in-situ forces after posterior cruciate ligament reconstruction.

    PubMed

    Lai, Yu-Shu; Chen, Wen-Chuan; Huang, Chang-Hung; Cheng, Cheng-Kung; Chan, Kam-Kong; Chang, Ting-Kuo

    2015-01-01

    Surgical reconstruction is generally recommended for posterior cruciate ligament (PCL) injuries; however, the use of grafts is still a controversial problem. In this study, a three-dimensional finite element model of the human tibiofemoral joint with articular cartilage layers, menisci, and four main ligaments was constructed to investigate the effects of graft strengths on knee kinematics and in-situ forces of PCL grafts. Nine different graft strengths with stiffness ranging from 0% (PCL rupture) to 200%, in increments of 25%, of an intact PCL's strength were used to simulate the PCL reconstruction. A 100 N posterior tibial drawer load was applied to the knee joint at full extension. Results revealed that the maximum posterior translation of the PCL rupture model (0% stiffness) was 6.77 mm in the medial compartment, which resulted in tibial internal rotation of about 3.01°. After PCL reconstruction with any graft strength, the laxity of the medial tibial compartment was noticeably improved. Tibial translation and rotation were similar to the intact knee after PCL reconstruction with graft strengths ranging from 75% to 125% of an intact PCL. When the graft's strength surpassed 150%, the medial tibia moved forward and external tibial rotation greatly increased. The in-situ forces generated in the PCL grafts ranged from 13.15 N to 75.82 N, depending on the stiffness. In conclusion, the strength of PCL grafts have has a noticeable effect on anterior-posterior translation of the medial tibial compartment and its in-situ force. Similar kinematic response may happen in the models when the PCL graft's strength lies between 75% and 125% of an intact PCL.

  2. The effect of graft strength on knee laxity and graft in-situ forces after posterior cruciate ligament reconstruction.

    PubMed

    Lai, Yu-Shu; Chen, Wen-Chuan; Huang, Chang-Hung; Cheng, Cheng-Kung; Chan, Kam-Kong; Chang, Ting-Kuo

    2015-01-01

    Surgical reconstruction is generally recommended for posterior cruciate ligament (PCL) injuries; however, the use of grafts is still a controversial problem. In this study, a three-dimensional finite element model of the human tibiofemoral joint with articular cartilage layers, menisci, and four main ligaments was constructed to investigate the effects of graft strengths on knee kinematics and in-situ forces of PCL grafts. Nine different graft strengths with stiffness ranging from 0% (PCL rupture) to 200%, in increments of 25%, of an intact PCL's strength were used to simulate the PCL reconstruction. A 100 N posterior tibial drawer load was applied to the knee joint at full extension. Results revealed that the maximum posterior translation of the PCL rupture model (0% stiffness) was 6.77 mm in the medial compartment, which resulted in tibial internal rotation of about 3.01°. After PCL reconstruction with any graft strength, the laxity of the medial tibial compartment was noticeably improved. Tibial translation and rotation were similar to the intact knee after PCL reconstruction with graft strengths ranging from 75% to 125% of an intact PCL. When the graft's strength surpassed 150%, the medial tibia moved forward and external tibial rotation greatly increased. The in-situ forces generated in the PCL grafts ranged from 13.15 N to 75.82 N, depending on the stiffness. In conclusion, the strength of PCL grafts have has a noticeable effect on anterior-posterior translation of the medial tibial compartment and its in-situ force. Similar kinematic response may happen in the models when the PCL graft's strength lies between 75% and 125% of an intact PCL. PMID:26001045

  3. The Effect of Graft Strength on Knee Laxity and Graft In-Situ Forces after Posterior Cruciate Ligament Reconstruction

    PubMed Central

    Lai, Yu-Shu; Chen, Wen-Chuan; Huang, Chang-Hung; Cheng, Cheng-Kung; Chan, Kam-Kong; Chang, Ting-Kuo

    2015-01-01

    Surgical reconstruction is generally recommended for posterior cruciate ligament (PCL) injuries; however, the use of grafts is still a controversial problem. In this study, a three-dimensional finite element model of the human tibiofemoral joint with articular cartilage layers, menisci, and four main ligaments was constructed to investigate the effects of graft strengths on knee kinematics and in-situ forces of PCL grafts. Nine different graft strengths with stiffness ranging from 0% (PCL rupture) to 200%, in increments of 25%, of an intact PCL’s strength were used to simulate the PCL reconstruction. A 100 N posterior tibial drawer load was applied to the knee joint at full extension. Results revealed that the maximum posterior translation of the PCL rupture model (0% stiffness) was 6.77 mm in the medial compartment, which resulted in tibial internal rotation of about 3.01°. After PCL reconstruction with any graft strength, the laxity of the medial tibial compartment was noticeably improved. Tibial translation and rotation were similar to the intact knee after PCL reconstruction with graft strengths ranging from 75% to 125% of an intact PCL. When the graft’s strength surpassed 150%, the medial tibia moved forward and external tibial rotation greatly increased. The in-situ forces generated in the PCL grafts ranged from 13.15 N to 75.82 N, depending on the stiffness. In conclusion, the strength of PCL grafts have has a noticeable effect on anterior-posterior translation of the medial tibial compartment and its in-situ force. Similar kinematic response may happen in the models when the PCL graft’s strength lies between 75% and 125% of an intact PCL. PMID:26001045

  4. Modelled vs. reconstructed past fire dynamics - how can we compare?

    NASA Astrophysics Data System (ADS)

    Brücher, Tim; Brovkin, Victor; Kloster, Silvia; Marlon, Jennifer R.; Power, Mitch J.

    2015-04-01

    Fire is an important process that affects climate through changes in CO2 emissions, albedo, and aerosols (Ward et al. 2012). Fire-history reconstructions from charcoal accumulations in sediment indicate that biomass burning has increased since the Last Glacial Maximum (Power et al. 2008; Marlon et al. 2013). Recent comparisons with transient climate model output suggest that this increase in global ?re activity is linked primarily to variations in temperature and secondarily to variations in precipitation (Daniau et al. 2012). In this study, we discuss the best way to compare global ?re model output with charcoal records. Fire models generate quantitative output for burned area and fire-related emissions of CO2, whereas charcoal data indicate relative changes in biomass burning for specific regions and time periods only. However, models can be used to relate trends in charcoal data to trends in quantitative changes in burned area or fire carbon emissions. Charcoal records are often reported as Z-scores (Power et al. 2008). Since Z-scores are non-linear power transformations of charcoal influxes, we must evaluate if, for example, a two-fold increase in the standardized charcoal reconstruction corresponds to a 2- or 200-fold increase in the area burned. In our study we apply the Z-score metric to the model output. This allows us to test how well the model can quantitatively reproduce the charcoal-based reconstructions and how Z-score metrics affect the statistics of model output. The Global Charcoal Database (GCD version 2.5; www.gpwg.org/gpwgdb.html) is used to determine regional and global paleofire trends from 218 sedimentary charcoal records covering part or all of the last 8 ka BP. To retrieve regional and global composites of changes in fire activity over the Holocene the time series of Z-scores are linearly averaged to achieve regional composites. A coupled climate-carbon cycle model, CLIMBA (Brücher et al. 2014), is used for this study. It consists of the

  5. Charge-state dynamics in electrostatic force spectroscopy

    NASA Astrophysics Data System (ADS)

    Ondráček, Martin; Hapala, Prokop; Jelínek, Pavel

    2016-07-01

    We present a numerical model that allows us to study the response of an oscillating probe in electrostatic force spectroscopy to charge switching in quantum dots at various time scales. The model provides more insight into the behavior of frequency shift and dissipated energy under different scanning conditions when measuring a temporarily charged quantum dot on a surface. Namely, we analyze the dependence of the frequency shift, the dissipated energy, and their fluctuations on the resonance frequency of the tip and on the electron tunneling rates across the tip-quantum dot and quantum dot-sample junctions. We discuss two complementary approaches to simulating the charge dynamics, a stochastic and a deterministic one. In addition, we derive analytic formulas valid for small amplitudes, describing relations between the frequency shift, dissipated energy, and the characteristic rates driving the charging and discharging processes.

  6. Molecular dynamics simulations of methane hydrate using polarizable force fields

    SciTech Connect

    Jiang, H.N.; Jordan, K.D.; Taylor, C.E.

    2007-03-01

    Molecular dynamics simulations of methane hydrate have been carried out using the AMOEBA and COS/G2 polarizable force fields. Properties examined include the temperature dependence of the lattice constant, the OC and OO radial distribution functions and the vibrational spectra. Both the AMOEBA and COS/G2 models are found to successfully account for the available experimental data, with overall slightly better agreement with experiment being found for the AMOEBA model. Several properties calculated using the AMOEBA and COS/G2 models differ appreciable from the corresponding results obtained previously using the polarizable TIP4P-FQ model. This appears to be due to the inadequacy of the treatment of polarization, especially, the restriction of polarization to in-plane only, in the TIP4P-FQ model.

  7. Classical and quantum dynamics of the Faraday lines of force

    SciTech Connect

    Frittelli, S.; Koshti, S.; Newman, E.T.; Rovelli, C. )

    1994-06-15

    We study the vacuum Maxwell theory by expressing the electric field in terms of its Faraday lines of force. This representation allows us to capture the two physical degrees of freedom of the electric field by means of two scalar fields. The corresponding classical canonical theory is constructed in terms of four scalar fields, is fully gauge invariant, has an attractive kinematics, but a rather complicated dynamics. The corresponding quantum theory can be constructed in a well-defined functional representation, which we refer to as the Euler representation. This representation turns out to be related to the loop representation. The resulting quantization scheme is, perhaps, of relevance for non-Abelian theories and for gravity.

  8. Molecular dynamics simulation of amplitude modulation atomic force microscopy.

    PubMed

    Hu, Xiaoli; Egberts, Philip; Dong, Yalin; Martini, Ashlie

    2015-06-12

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip-substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip-sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement.

  9. Laser Actuation of Cantilevers for Picometre Amplitude Dynamic Force Microscopy

    PubMed Central

    Evans, Drew R.; Tayati, Ponlawat; An, Hongjie; Lam, Ping Koy; Craig, Vincent S. J.; Senden, Tim J.

    2014-01-01

    As nanoscale and molecular devices become reality, the ability to probe materials on these scales is increasing in importance. To address this, we have developed a dynamic force microscopy technique where the flexure of the microcantilever is excited using an intensity modulated laser beam to achieve modulation on the picoscale. The flexure arises from thermally induced bending through differential expansion and the conservation of momentum when the photons are reflected and absorbed by the cantilever. In this study, we investigated the photothermal and photon pressure responses of monolithic and layered cantilevers using a modulated laser in air and immersed in water. The developed photon actuation technique is applied to the stretching of single polymer chains. PMID:24993548

  10. Dynamical degrees of freedom and correlations in isometric finger force production.

    PubMed

    James, Eric G

    2012-12-01

    Prior research has concluded that the correlations of isometric finger forces represent the extent to which the fingers are controlled as a single unit. If this is the case, finger force correlations should be consistent with estimates of the controlled (dynamical) degrees of freedom in finger forces. The present study examined the finger force correlations and the dynamical degrees of freedom in four isometric force tasks. The tasks were to produce a preferred level of force with the (a) Index, (b) Ring, (c) Both fingers and also to (d) Rest the fingers on the load cells. Dynamical degrees of freedom in finger forces were lowest in the Both finger force task and progressively higher in the Ring, Index and Resting finger force tasks. The finger force correlations were highest in the Resting and lowest in the Index and Ring finger tasks. The results for the dynamical degrees of freedom in finger forces were consistent with a reduction in degrees of freedom in response to the degrees of freedom problem and the task constraints. The results for the finger force correlations were inconsistent with a reduction in the dynamical degrees of freedom. These findings indicate that finger force correlations do not necessarily reflect the coupling of finger forces. The findings also highlight the value of time-domain analyses to reveal the organization of control in isometric finger forces.

  11. Force regulated dynamics of RPA on a DNA fork

    PubMed Central

    Kemmerich, Felix E.; Daldrop, Peter; Pinto, Cosimo; Levikova, Maryna; Cejka, Petr; Seidel, Ralf

    2016-01-01

    Replication protein A (RPA) is a single-stranded DNA binding protein, involved in most aspects of eukaryotic DNA metabolism. Here, we study the behavior of RPA on a DNA substrate that mimics a replication fork. Using magnetic tweezers we show that both yeast and human RPA can open forked DNA when sufficient external tension is applied. In contrast, at low force, RPA becomes rapidly displaced by the rehybridization of the DNA fork. This process appears to be governed by the binding or the release of an RPA microdomain (toehold) of only few base-pairs length. This gives rise to an extremely rapid exchange dynamics of RPA at the fork. Fork rezipping rates reach up to hundreds of base-pairs per second, being orders of magnitude faster than RPA dissociation from ssDNA alone. Additionally, we show that RPA undergoes diffusive motion on ssDNA, such that it can be pushed over long distances by a rezipping fork. Generally the behavior of both human and yeast RPA homologs is very similar. However, in contrast to yeast RPA, the dissociation of human RPA from ssDNA is greatly reduced at low Mg2+ concentrations, such that human RPA can melt DNA in absence of force. PMID:27016742

  12. Force regulated dynamics of RPA on a DNA fork.

    PubMed

    Kemmerich, Felix E; Daldrop, Peter; Pinto, Cosimo; Levikova, Maryna; Cejka, Petr; Seidel, Ralf

    2016-07-01

    Replication protein A (RPA) is a single-stranded DNA binding protein, involved in most aspects of eukaryotic DNA metabolism. Here, we study the behavior of RPA on a DNA substrate that mimics a replication fork. Using magnetic tweezers we show that both yeast and human RPA can open forked DNA when sufficient external tension is applied. In contrast, at low force, RPA becomes rapidly displaced by the rehybridization of the DNA fork. This process appears to be governed by the binding or the release of an RPA microdomain (toehold) of only few base-pairs length. This gives rise to an extremely rapid exchange dynamics of RPA at the fork. Fork rezipping rates reach up to hundreds of base-pairs per second, being orders of magnitude faster than RPA dissociation from ssDNA alone. Additionally, we show that RPA undergoes diffusive motion on ssDNA, such that it can be pushed over long distances by a rezipping fork. Generally the behavior of both human and yeast RPA homologs is very similar. However, in contrast to yeast RPA, the dissociation of human RPA from ssDNA is greatly reduced at low Mg(2+) concentrations, such that human RPA can melt DNA in absence of force.

  13. Automated Reconstruction of Three-Dimensional Fish Motion, Forces, and Torques

    PubMed Central

    Voesenek, Cees J.; Pieters, Remco P. M.; van Leeuwen, Johan L.

    2016-01-01

    Fish can move freely through the water column and make complex three-dimensional motions to explore their environment, escape or feed. Nevertheless, the majority of swimming studies is currently limited to two-dimensional analyses. Accurate experimental quantification of changes in body shape, position and orientation (swimming kinematics) in three dimensions is therefore essential to advance biomechanical research of fish swimming. Here, we present a validated method that automatically tracks a swimming fish in three dimensions from multi-camera high-speed video. We use an optimisation procedure to fit a parameterised, morphology-based fish model to each set of video images. This results in a time sequence of position, orientation and body curvature. We post-process this data to derive additional kinematic parameters (e.g. velocities, accelerations) and propose an inverse-dynamics method to compute the resultant forces and torques during swimming. The presented method for quantifying 3D fish motion paves the way for future analyses of swimming biomechanics. PMID:26752597

  14. Reconstruction of dark energy and expansion dynamics using Gaussian processes

    SciTech Connect

    Seikel, Marina; Clarkson, Chris; Smith, Mathew E-mail: chris.clarkson@uct.ac.za

    2012-06-01

    An important issue in cosmology is reconstructing the effective dark energy equation of state directly from observations. With few physically motivated models, future dark energy studies cannot only be based on constraining a dark energy parameter space, as the errors found depend strongly on the parametrisation considered. We present a new non-parametric approach to reconstructing the history of the expansion rate and dark energy using Gaussian Processes, which is a fully Bayesian approach for smoothing data. We present a pedagogical introduction to Gaussian Processes, and discuss how it can be used to robustly differentiate data in a suitable way. Using this method we show that the Dark Energy Survey - Supernova Survey (DES) can accurately recover a slowly evolving equation of state to σ{sub w} = ±0.05 (95% CL) at z = 0 and ±0.25 at z = 0.7, with a minimum error of ±0.025 at the sweet-spot at z ∼ 0.16, provided the other parameters of the model are known. Errors on the expansion history are an order of magnitude smaller, yet make no assumptions about dark energy whatsoever. A code for calculating functions and their first three derivatives using Gaussian processes has been developed and is available for download.

  15. Current Status of Protein Force Fields for Molecular Dynamics

    PubMed Central

    Lopes, Pedro E.M.; Guvench, Olgun

    2015-01-01

    Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958

  16. Current status of protein force fields for molecular dynamics simulations.

    PubMed

    Lopes, Pedro E M; Guvench, Olgun; MacKerell, Alexander D

    2015-01-01

    The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.

  17. Single-molecule studies of DNA dynamics and intermolecular forces

    NASA Astrophysics Data System (ADS)

    Robertson, Rae Marie

    DNA molecules were used as a model system to investigate fundamental problems in polymer physics; namely, how molecular length, topology and concentration influence the dynamical properties of polymers. A set of DNA molecules suitable for polymer studies was prepared using molecular biology techniques. Video fluorescence microscopy and single-molecule tracking were used to determine self-diffusion coefficients of DNA molecules. Optical tweezers were used to measure the intermolecular forces confining entangled DNA molecules. Scaling of diffusion with molecular length was in agreement with the Zimm model for dilute solutions of linear and circular DNA, indicating that excluded volume effects are appreciable for both topologies. Scaling of diffusion with concentration was also determined for the four possible topological combinations of linear and circular molecules: linear DNA diffusing in a solution of linear DNA, linear DNA in circular DNA, circular in circular, and circular in linear. For lower concentrations molecular topology had little effect and scaling was in agreement with that of the Rouse model. As concentration was increased topology played a much larger role and scaling crossed over to that of the reptation model, predicted to describe the dynamics of entangled polymers. The notable exception was the strongly hindered diffusion observed for a circular molecule diffusing in an entangled linear solution, suggesting the importance of constraint release. Using a new experimental approach with optical tweezers, a tube-like field confining a single entangled molecule was measured, in accord with the key assumption of the reptation model. A time-dependent harmonic potential opposed displacement transverse to the molecular contour, and the force relaxations following displacement were composed of three distinct modes. A characteristic tube radius of the entangled solution was also determined, close to the classically predicted value. The dependence of the above

  18. eVolv2k: A new ice core-based volcanic forcing reconstruction for the past 2000 years

    NASA Astrophysics Data System (ADS)

    Toohey, Matthew; Sigl, Michael

    2016-04-01

    Radiative forcing resulting from stratospheric aerosols produced by major volcanic eruptions is a dominant driver of climate variability in the Earth's past. The ability of climate model simulations to accurately recreate past climate is tied directly to the accuracy of the volcanic forcing timeseries used in the simulations. We present here a new volcanic forcing reconstruction, based on newly updated ice core composites from Antarctica and Greenland. Ice core records are translated into stratospheric aerosol properties for use in climate models through the Easy Volcanic Aerosol (EVA) module, which provides an analytic representation of volcanic stratospheric aerosol forcing based on available observations and aerosol model results, prescribing the aerosol's radiative properties and primary modes of spatial and temporal variability. The evolv2k volcanic forcing dataset covers the past 2000 years, and has been provided for use in the Paleo-Modeling Intercomparison Project (PMIP), and VolMIP experiments within CMIP6. Here, we describe the construction of the eVolv2k data set, compare with prior forcing sets, and show initial simulation results.

  19. A New Forced Oscillation Capability for the Transonic Dynamics Tunnel

    NASA Technical Reports Server (NTRS)

    Piatak, David J.; Cleckner, Craig S.

    2002-01-01

    A new forced oscillation system has been installed and tested at NASA Langley Research Center's Transonic Dynamics Tunnel (TDT). The system is known as the Oscillating Turntable (OTT) and has been designed for the purpose of oscillating, large semispan models in pitch at frequencies up to 40 Hz to acquire high-quality unsteady pressure and loads data. Precisely controlled motions of a wind-tunnel model on the OTT can yield unsteady aerodynamic phenomena associated with flutter, limit cycle oscillations, shock dynamics, and non-linear aerodynamic effects on many vehicle configurations. This paper will discuss general design and components of the OTT and will present test data from performance testing and from research tests on two rigid semispan wind-tunnel models. The research tests were designed to challenge the OTT over a wide range of operating conditions while acquiring unsteady pressure data on a small rectangular supercritical wing and a large supersonic transport wing. These results will be presented to illustrate the performance capabilities, consistency of oscillations, and usefulness of the OTT as a research tool.

  20. Knee Contact Force Asymmetries in Patients Who Failed Return-to-Sport Readiness Criteria 6 Months After Anterior Cruciate Ligament Reconstruction

    PubMed Central

    Gardinier, Emily S.; Di Stasi, Stephanie; Manal, Kurt; Buchanan, Thomas S.; Snyder-Mackler, Lynn

    2015-01-01

    Background After anterior cruciate ligament (ACL) injury, contact forces are decreased in the injured knee when compared with the uninjured knee. The persistence of contact force asymmetries after ACL reconstruction may increase the risk of reinjury and may play an important role in the development of knee osteoarthritis in these patients. Functional performance may also be useful in identifying patients who demonstrate potentially harmful joint contact force asymmetries after ACL reconstruction. Hypothesis Knee joint contact force asymmetries would be present during gait after ACL reconstruction, and performance on a specific set of validated return-to-sport (RTS) readiness criteria would discriminate between those who demonstrated contact force asymmetries and those who did not. Study Design Descriptive laboratory study. Methods A total of 29 patients with ACL ruptures participated in gait analysis and RTS readiness testing 6 months after reconstruction. Muscle and joint contact forces were estimated using an electromyography (EMG)–driven musculoskeletal model of the knee. The magnitude of typical limb asymmetry in uninjured controls was used to define limits of meaningful limb asymmetry in patients after ACL reconstruction. The RTS testing included isometric quadriceps strength testing, 4 unilateral hop tests, and 2 self-report questionnaires. Paired t tests were used to assess limb symmetry for peak medial and tibiofemoral contact forces in all patients, and a mixed-design analysis of variance was used to analyze the effect of passing or failing RTS testing on contact force asymmetry. Results Among all patients, neither statistically significant nor meaningful contact force asymmetries were identified. However, patients who failed RTS testing exhibited meaningful contact force asymmetries, with tibiofemoral contact force being significantly lower for the involved knee. Conversely, patients who passed RTS testing exhibited neither significant nor meaningful

  1. Interface dynamics of a two-component Bose-Einstein condensate driven by an external force

    SciTech Connect

    Kobyakov, D.; Bychkov, V.; Lundh, E.; Bezett, A.; Marklund, M.; Akkerman, V.

    2011-04-15

    The dynamics of an interface in a two-component Bose-Einstein condensate driven by a spatially uniform time-dependent force is studied. Starting from the Gross-Pitaevskii Lagrangian, the dispersion relation for linear waves and instabilities at the interface is derived by means of a variational approach. A number of diverse dynamical effects for different types of driving force is demonstrated, which includes the Rayleigh-Taylor instability for a constant force, the Richtmyer-Meshkov instability for a pulse force, dynamic stabilization of the Rayleigh-Taylor instability and onset of the parametric instability for an oscillating force. Gaussian Markovian and non-Markovian stochastic forces are also considered. It is found that the Markovian stochastic force does not produce any average effect on the dynamics of the interface, while the non-Markovian force leads to exponential perturbation growth.

  2. HYPR: constrained reconstruction for enhanced SNR in dynamic medical imaging

    NASA Astrophysics Data System (ADS)

    Mistretta, C.; Wieben, O.; Velikina, J.; Wu, Y.; Johnson, K.; Korosec, F.; Unal, O.; Chen, G.; Fain, S.; Christian, B.; Nalcioglu, O.; Kruger, R. A.; Block, W.; Samsonov, A.; Speidel, M.; Van Lysel, M.; Rowley, H.; Supanich, M.; Turski, P.; Wu, Yan; Holmes, J.; Kecskemeti, S.; Moran, C.; O'Halloran, R.; Keith, L.; Alexander, A.; Brodsky, E.; Lee, J. E.; Hall, T.; Zagzebski, J.

    2008-03-01

    During the last eight years our group has developed radial acquisitions with angular undersampling factors of several hundred that accelerate MRI in selected applications. As with all previous acceleration techniques, SNR typically falls as least as fast as the inverse square root of the undersampling factor. This limits the SNR available to support the small voxels that these methods can image over short time intervals in applications like time-resolved contrast-enhanced MR angiography (CE-MRA). Instead of processing each time interval independently, we have developed constrained reconstruction methods that exploit the significant correlation between temporal sampling points. A broad class of methods, termed HighlY Constrained Back PRojection (HYPR), generalizes this concept to other modalities and sampling dimensions.

  3. Dynamic Data-Driven Event Reconstruction for Atmospheric Releases

    SciTech Connect

    Sugiyama, G; Kosovic, B; Hanley, W; Johannesson, G; Larsen, S; Loosmore, G; Lundquist, J; Mirin, A; Nitao, J; Serban, R; Dyer, K

    2004-10-13

    For atmospheric releases, event reconstruction answers the critical questions - How much material was released? When? Where? and What are the potential consequences? Inaccurate estimation of the source term can lead to gross errors, time delays during a crisis, and even fatalities. We are developing a capability that seamlessly integrates observational data streams with predictive models in order to provide the best possible estimates of unknown source term parameters, as well as optimal and timely situation analyses consistent with both models and data. Our approach utilizes Bayesian inference and stochastic sampling methods (Markov Chain and Sequential Monte Carlo) to reformulate the inverse problem into a solution based on efficient sampling of an ensemble of predictive simulations, guided by statistical comparisons with data.

  4. The static force from lattice QCD with two dynamical quarks

    SciTech Connect

    Leder, B.; Knechtli, F.

    2011-05-23

    We report on the measurement of the static force from HYP-smeared Wilson loops in two flavour QCD. We analyse the quark mass dependence of the force at three lattice spacings. The QCD static force around distance r{sub 0} is compared with the force obtained from pure gauge theory, potential models and perturbation theory.

  5. Force and Moment Approach for Achievable Dynamics Using Nonlinear Dynamic Inversion

    NASA Technical Reports Server (NTRS)

    Ostroff, Aaron J.; Bacon, Barton J.

    1999-01-01

    This paper describes a general form of nonlinear dynamic inversion control for use in a generic nonlinear simulation to evaluate candidate augmented aircraft dynamics. The implementation is specifically tailored to the task of quickly assessing an aircraft's control power requirements and defining the achievable dynamic set. The achievable set is evaluated while undergoing complex mission maneuvers, and perfect tracking will be accomplished when the desired dynamics are achievable. Variables are extracted directly from the simulation model each iteration, so robustness is not an issue. Included in this paper is a description of the implementation of the forces and moments from simulation variables, the calculation of control effectiveness coefficients, methods for implementing different types of aerodynamic and thrust vectoring controls, adjustments for control effector failures, and the allocation approach used. A few examples illustrate the perfect tracking results obtained.

  6. Bayer patterned high dynamic range image reconstruction using adaptive weighting function

    NASA Astrophysics Data System (ADS)

    Kang, Hee; Lee, Suk Ho; Song, Ki Sun; Kang, Moon Gi

    2014-12-01

    It is not easy to acquire a desired high dynamic range (HDR) image directly from a camera due to the limited dynamic range of most image sensors. Therefore, generally, a post-process called HDR image reconstruction is used, which reconstructs an HDR image from a set of differently exposed images to overcome the limited dynamic range. However, conventional HDR image reconstruction methods suffer from noise factors and ghost artifacts. This is due to the fact that the input images taken with a short exposure time contain much noise in the dark regions, which contributes to increased noise in the corresponding dark regions of the reconstructed HDR image. Furthermore, since input images are acquired at different times, the images contain different motion information, which results in ghost artifacts. In this paper, we propose an HDR image reconstruction method which reduces the impact of the noise factors and prevents ghost artifacts. To reduce the influence of the noise factors, the weighting function, which determines the contribution of a certain input image to the reconstructed HDR image, is designed to adapt to the exposure time and local motions. Furthermore, the weighting function is designed to exclude ghosting regions by considering the differences of the luminance and the chrominance values between several input images. Unlike conventional methods, which generally work on a color image processed by the image processing module (IPM), the proposed method works directly on the Bayer raw image. This allows for a linear camera response function and also improves the efficiency in hardware implementation. Experimental results show that the proposed method can reconstruct high-quality Bayer patterned HDR images while being robust against ghost artifacts and noise factors.

  7. Lacustrine 87Sr/86Sr as a tracer to reconstruct Milankovitch forcing of the Eocene hydrologic cycle

    NASA Astrophysics Data System (ADS)

    Baddouh, M'bark; Meyers, Stephen R.; Carroll, Alan R.; Beard, Brian L.; Johnson, Clark M.

    2016-08-01

    The Green River Formation (GRF) provides one of the premier paleoclimate archives of the Early Eocene Climatic Optimum (∼50 Ma), representing the apex of the early Cenozoic greenhouse climate. Rhythmic lake-level variability expressed in the GRF has inspired numerous hypotheses for the behavior of the Eocene hydrologic cycle, including its linkage to astronomical forcing, solar variability, and the El Niño Southern Oscillation (ENSO). However, the lack of sufficient proxy data to document atmospheric water-mass transport and the geographic pattern of evaporation/precipitation/runoff has made it difficult to discriminate between different models for astronomical forcing. Variable 87Sr/86Sr ratios of bedrock that encompass the GRF provide an opportunity to reconstruct the spatial expression of the Eocene hydrologic cycle and its linkage to lake level. Here Sr isotope data from the Wilkins Peak Member, a rhythmic succession that has been demonstrated to record Milankovitch forcing of lake levels, indicate that high lake levels reflect an increased proportion of runoff from less radiogenic rocks west of the basin, eliminating a number of the existing astronomical-forcing hypotheses. The 87Sr/86Sr variability is consistent with a change in mean ENSO state, which is predicted by climate models to be linked to orbital-insolation. Thus, the 87Sr/86Sr data reveal a coupling of high frequency (ENSO) and low frequency (astronomical) climate variability, and also predict the existence of sizable astronomically-forced alpine snowpack during the last greenhouse climate. More broadly, this study demonstrates the utility of 87Sr/86Sr as a powerful tool for reconstructing the deep-time hydrologic cycle.

  8. Adaptive pulsed laser line extraction for terrain reconstruction using a dynamic vision sensor.

    PubMed

    Brandli, Christian; Mantel, Thomas A; Hutter, Marco; Höpflinger, Markus A; Berner, Raphael; Siegwart, Roland; Delbruck, Tobi

    2013-01-01

    Mobile robots need to know the terrain in which they are moving for path planning and obstacle avoidance. This paper proposes the combination of a bio-inspired, redundancy-suppressing dynamic vision sensor (DVS) with a pulsed line laser to allow fast terrain reconstruction. A stable laser stripe extraction is achieved by exploiting the sensor's ability to capture the temporal dynamics in a scene. An adaptive temporal filter for the sensor output allows a reliable reconstruction of 3D terrain surfaces. Laser stripe extractions up to pulsing frequencies of 500 Hz were achieved using a line laser of 3 mW at a distance of 45 cm using an event-based algorithm that exploits the sparseness of the sensor output. As a proof of concept, unstructured rapid prototype terrain samples have been successfully reconstructed with an accuracy of 2 mm. PMID:24478619

  9. Adaptive pulsed laser line extraction for terrain reconstruction using a dynamic vision sensor.

    PubMed

    Brandli, Christian; Mantel, Thomas A; Hutter, Marco; Höpflinger, Markus A; Berner, Raphael; Siegwart, Roland; Delbruck, Tobi

    2013-01-01

    Mobile robots need to know the terrain in which they are moving for path planning and obstacle avoidance. This paper proposes the combination of a bio-inspired, redundancy-suppressing dynamic vision sensor (DVS) with a pulsed line laser to allow fast terrain reconstruction. A stable laser stripe extraction is achieved by exploiting the sensor's ability to capture the temporal dynamics in a scene. An adaptive temporal filter for the sensor output allows a reliable reconstruction of 3D terrain surfaces. Laser stripe extractions up to pulsing frequencies of 500 Hz were achieved using a line laser of 3 mW at a distance of 45 cm using an event-based algorithm that exploits the sparseness of the sensor output. As a proof of concept, unstructured rapid prototype terrain samples have been successfully reconstructed with an accuracy of 2 mm.

  10. Adaptive pulsed laser line extraction for terrain reconstruction using a dynamic vision sensor

    PubMed Central

    Brandli, Christian; Mantel, Thomas A.; Hutter, Marco; Höpflinger, Markus A.; Berner, Raphael; Siegwart, Roland; Delbruck, Tobi

    2014-01-01

    Mobile robots need to know the terrain in which they are moving for path planning and obstacle avoidance. This paper proposes the combination of a bio-inspired, redundancy-suppressing dynamic vision sensor (DVS) with a pulsed line laser to allow fast terrain reconstruction. A stable laser stripe extraction is achieved by exploiting the sensor's ability to capture the temporal dynamics in a scene. An adaptive temporal filter for the sensor output allows a reliable reconstruction of 3D terrain surfaces. Laser stripe extractions up to pulsing frequencies of 500 Hz were achieved using a line laser of 3 mW at a distance of 45 cm using an event-based algorithm that exploits the sparseness of the sensor output. As a proof of concept, unstructured rapid prototype terrain samples have been successfully reconstructed with an accuracy of 2 mm. PMID:24478619

  11. Theoretical Analysis of Penalized Maximum-Likelihood Patlak Parametric Image Reconstruction in Dynamic PET for Lesion Detection.

    PubMed

    Yang, Li; Wang, Guobao; Qi, Jinyi

    2016-04-01

    Detecting cancerous lesions is a major clinical application of emission tomography. In a previous work, we studied penalized maximum-likelihood (PML) image reconstruction for lesion detection in static PET. Here we extend our theoretical analysis of static PET reconstruction to dynamic PET. We study both the conventional indirect reconstruction and direct reconstruction for Patlak parametric image estimation. In indirect reconstruction, Patlak parametric images are generated by first reconstructing a sequence of dynamic PET images, and then performing Patlak analysis on the time activity curves (TACs) pixel-by-pixel. In direct reconstruction, Patlak parametric images are estimated directly from raw sinogram data by incorporating the Patlak model into the image reconstruction procedure. PML reconstruction is used in both the indirect and direct reconstruction methods. We use a channelized Hotelling observer (CHO) to assess lesion detectability in Patlak parametric images. Simplified expressions for evaluating the lesion detectability have been derived and applied to the selection of the regularization parameter value to maximize detection performance. The proposed method is validated using computer-based Monte Carlo simulations. Good agreements between the theoretical predictions and the Monte Carlo results are observed. Both theoretical predictions and Monte Carlo simulation results show the benefit of the indirect and direct methods under optimized regularization parameters in dynamic PET reconstruction for lesion detection, when compared with the conventional static PET reconstruction.

  12. Comparison study of temporal regularization methods for fully 5D reconstruction of cardiac gated dynamic SPECT

    NASA Astrophysics Data System (ADS)

    Niu, Xiaofeng; Yang, Yongyi; King, Michael A.

    2012-09-01

    Temporal regularization plays a critical role in cardiac gated dynamic SPECT reconstruction, of which the goal is to obtain an image sequence from a single acquisition which simultaneously shows both cardiac motion and tracer distribution change over the course of imaging (termed 5D). In our recent work, we explored two different approaches for temporal regularization of the dynamic activities in gated dynamic reconstruction without the use of fast camera rotation: one is the dynamic EM (dEM) approach which is imposed on the temporal trend of the time activity of each voxel, and the other is a B-spline modeling approach in which the time activity is regulated by a set of B-spline basis functions. In this work, we extend the B-spline approach to fully 5D reconstruction and conduct a thorough quantitative comparison with the dEM approach. In the evaluation of the reconstruction results, we apply a number of quantitative measures on two major aspects of the reconstructed dynamic images: (1) the accuracy of the reconstructed activity distribution in the myocardium and (2) the ability of the reconstructed dynamic activities to differentiate perfusion defects from normal myocardial wall uptake. These measures include the mean square error (MSE), bias-variance analysis, accuracy of time-activity curves (TAC), contrast-to-noise ratio of a defect, composite kinetic map of the left ventricle wall and perfusion defect detectability with channelized Hotelling observer. In experiments, we simulated cardiac gated imaging with the NURBS-based cardiac-torso phantom and Tc99m-Teboroxime as the imaging agent, where acquisition with the equivalent of only three full camera rotations was used during the imaging period. The results show that both dEM and B-spline 5D could achieve similar overall accuracy in the myocardium in terms of MSE. However, compared to dEM 5D, the B-spline approach could achieve a more accurate reconstruction of the voxel TACs; in particular, B-spline 5D could

  13. Forcing of stratospheric chemistry and dynamics during the Dalton Minimum

    NASA Astrophysics Data System (ADS)

    Anet, J. G.; Muthers, S.; Rozanov, E.; Raible, C. C.; Peter, T.; Stenke, A.; Shapiro, A. I.; Beer, J.; Steinhilber, F.; Brönnimann, S.; Arfeuille, F.; Brugnara, Y.; Schmutz, W.

    2013-11-01

    when all forcing factors are applied during the Dalton Minimum (DM) - this effect is especially well visible for NOx/NOy. Thus, this study also shows the non-linear behaviour of the coupled chemistry-climate system. Finally, we conclude that especially UV and volcanic eruptions dominate the changes in the ozone, temperature and dynamics while the NOx field is dominated by the energetic particle precipitation. Visible radiation changes have only very minor effects on both stratospheric dynamics and chemistry.

  14. The Effects of Balance Training on Static and Dynamic Postural Stability Indices After Acute ACL Reconstruction

    PubMed Central

    Akbari, Asghar; Ghiasi, Fateme; Mir, Mohsen; Hosseinifar, Mohammad

    2016-01-01

    Background: Proprioception and postural stability play an important role in knee movements. However, there are controversies about the overall recovery time of proprioception following knee surgery and onset of balance and neuromuscular training after ACL reconstruction. Therefore, it is necessary to evaluate the effect of balance training in early stage of knee rehabilitation after anterior cruciate ligament (ACL) reconstruction. The purpose of this study was to evaluate the effect of balance exercises on postural stability indices in subjects with anterior cruciate ligament (ACL) reconstruction. Methods: The study was a controlled randomized trial study. Twenty four patients who had ACL reconstructed (balance training group) and twenty four healthy adults without any knee injury (control group) were recruited in the study. The balance exercises group performed balance exercises for 2 weeks. Before and after the interventions, overall, anteroposterior, and mediolateral stability indices were measured with a Biodex Balance System in bilateral and unilateral stance positions with the eyes open and closed. T-tests were used for statistical analysis (p<0.05). Results: Results showed that amount of static stability indices did not change after training and there were not significant differences in static stability indices before and after balance training (p>0.05). Although amount of dynamic stability indices decreased, there were not significant differences in dynamic stability indices before and after balance training (p>0.05). Amount of dynamic stability indices were decreased in balance training group, however, there were not significant differences between groups (p>0.05). Conclusion: These results support that balance exercise could partially improved dynamic stability indices in early stage of ACL reconstruction rehabilitation. The results of this study suggest that balance exercises should be part of the rehabilitation program following ACL reconstruction. PMID

  15. Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

    SciTech Connect

    Davtyan, Aram; Dama, James F.; Voth, Gregory A.; Andersen, Hans C.

    2015-04-21

    Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that

  16. Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

    NASA Astrophysics Data System (ADS)

    Davtyan, Aram; Dama, James F.; Voth, Gregory A.; Andersen, Hans C.

    2015-04-01

    Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that

  17. Rapid 3D dynamic arterial spin labeling with a sparse model-based image reconstruction.

    PubMed

    Zhao, Li; Fielden, Samuel W; Feng, Xue; Wintermark, Max; Mugler, John P; Meyer, Craig H

    2015-11-01

    Dynamic arterial spin labeling (ASL) MRI measures the perfusion bolus at multiple observation times and yields accurate estimates of cerebral blood flow in the presence of variations in arterial transit time. ASL has intrinsically low signal-to-noise ratio (SNR) and is sensitive to motion, so that extensive signal averaging is typically required, leading to long scan times for dynamic ASL. The goal of this study was to develop an accelerated dynamic ASL method with improved SNR and robustness to motion using a model-based image reconstruction that exploits the inherent sparsity of dynamic ASL data. The first component of this method is a single-shot 3D turbo spin echo spiral pulse sequence accelerated using a combination of parallel imaging and compressed sensing. This pulse sequence was then incorporated into a dynamic pseudo continuous ASL acquisition acquired at multiple observation times, and the resulting images were jointly reconstructed enforcing a model of potential perfusion time courses. Performance of the technique was verified using a numerical phantom and it was validated on normal volunteers on a 3-Tesla scanner. In simulation, a spatial sparsity constraint improved SNR and reduced estimation errors. Combined with a model-based sparsity constraint, the proposed method further improved SNR, reduced estimation error and suppressed motion artifacts. Experimentally, the proposed method resulted in significant improvements, with scan times as short as 20s per time point. These results suggest that the model-based image reconstruction enables rapid dynamic ASL with improved accuracy and robustness.

  18. New SSI and TSI reconstruction suggests large value of the radiative solar forcing

    NASA Astrophysics Data System (ADS)

    Shapiro, A.; Schmutz, W. K.; Thuillier, G.; Rozanov, E.; Haberreiter, M.; Schoell, M.; Shapiro, A.; Nyeki, S.

    2010-12-01

    We have developed and published the COde for Solar Irradiance (COSI) which allows us to calculate the entire solar spectrum. COSI reproduces the spectral irradiance measured by SOLSTICE (up to 320 nm) and SIM (from 320 nm onward) onboard the SORCE satellite during the 2008 solar minimum as well as SOLSPEC during the ATLAS 3 mission in 1994 with high accuracy. COSI is also used as a tool for modeling the variability of the solar irradiance. In our new reconstruction we represent the quiet Sun as a combination of two components. The first corresponds to the least active areas of the Sun as presently observed, while the second component is responsible for the magnetic activity of the quiet Sun. The time-dependent filling factors of these components are calculated based on the solar activity as derived from cosmogenic isotope concentrations in natural archieves. This allows us to obtain a time-dependent reconstructed solar spectrum from 7000 BC to the present with a temporal resolution of 22 years. From 1610 onward we have additional information from sunspot numbers, which allows the reconstruction of the spectral solar irradiance with a yearly resolution. These basic assumptions lead to a total and spectral solar irradiance that was substantially lower during the Maunder minimum than observed today. The difference is remarkably larger than other estimations published in the recent literature. Using our reconstruction as an input to a chemistry-climate model we show that the enhanced UV variability results in significant variations of stratospheric ozone and temperature.

  19. Traction force dynamics predict gap formation in activated endothelium.

    PubMed

    Valent, Erik T; van Nieuw Amerongen, Geerten P; van Hinsbergh, Victor W M; Hordijk, Peter L

    2016-09-10

    In many pathological conditions the endothelium becomes activated and dysfunctional, resulting in hyperpermeability and plasma leakage. No specific therapies are available yet to control endothelial barrier function, which is regulated by inter-endothelial junctions and the generation of acto-myosin-based contractile forces in the context of cell-cell and cell-matrix interactions. However, the spatiotemporal distribution and stimulus-induced reorganization of these integral forces remain largely unknown. Traction force microscopy of human endothelial monolayers was used to visualize contractile forces in resting cells and during thrombin-induced hyperpermeability. Simultaneously, information about endothelial monolayer integrity, adherens junctions and cytoskeletal proteins (F-actin) were captured. This revealed a heterogeneous distribution of traction forces, with nuclear areas showing lower and cell-cell junctions higher traction forces than the whole-monolayer average. Moreover, junctional forces were asymmetrically distributed among neighboring cells. Force vector orientation analysis showed a good correlation with the alignment of F-actin and revealed contractile forces in newly formed filopodia and lamellipodia-like protrusions within the monolayer. Finally, unstable areas, showing high force fluctuations within the monolayer were prone to form inter-endothelial gaps upon stimulation with thrombin. To conclude, contractile traction forces are heterogeneously distributed within endothelial monolayers and force instability, rather than force magnitude, predicts the stimulus-induced formation of intercellular gaps. PMID:27498166

  20. Dynamic Data-Driven Event Reconstruction for Atmospheric Releases

    SciTech Connect

    Mirin, A; Serban, R; Kosovic, B

    2005-03-14

    This is a collaborative LDRD Exploratory Research project involving four directorates--Energy & Environment, Engineering, NAI and Computation. The project seeks to answer the following critical questions regarding atmospheric releases--''How much material was released? When? Where? and What are the potential consequences?'' Inaccurate estimation of the source term can lead to gross errors, time delays during a crisis, and even fatalities. We are developing a capability that seamlessly integrates observational data streams with predictive models in order to provide the best possible estimates of unknown source term parameters, as well as optimal and timely situation analyses consistent with both models and data. Our approach utilizes Bayesian inference and stochastic sampling methods (Markov Chain and Sequential Monte Carlo) to reformulate the inverse problem into a solution based on efficient sampling of an ensemble of predictive simulations, guided by statistical comparisons with data. We are developing a flexible and adaptable data-driven event-reconstruction capability for atmospheric releases that provides (1) quantitative probabilistic estimates of the principal source-term parameters (e.g., the time-varying release rate and location); (2) predictions of increasing fidelity as an event progresses and additional data become available; and (3) analysis tools for sensor network design and uncertainty studies. Our computational framework incorporates multiple stochastic algorithms, operates with a range and variety of atmospheric models, and runs on multiple computer platforms, from workstations to large-scale computing resources. Our final goal is a multi-resolution capability for both real-time operational response and high fidelity multi-scale applications.

  1. Reconstructing ancient river dynamics from the stratigraphic record: can lessons from the past inform our future?

    NASA Astrophysics Data System (ADS)

    Hajek, E. A.; Chamberlin, E.; Baisden, T.

    2014-12-01

    The richness of the deep-time record and its potential for revealing important characteristics of ancient fluvial landscapes has been demonstrated time and again, including compelling examples of rivers altering their behavior in response to changes in vegetation patterns or abrupt shifts in water and sediment discharge. At present, reconstructions of ancient river and floodplain dynamics are commonly qualitative, and when quantitative metrics are used, it is often for comparison among ancient deposits. Without being able to reconstruct, more comprehensively, important aspects of ancient river and floodplains dynamics, this information has only anecdotal relevance for evaluating and managing present-day landscapes. While methods for reconstructing hydrodynamic and morphodynamic aspects of ancient rivers and floodplains are useful, uncertainties associated with these snapshots complicate the ability to translate observations from geologic to engineering scales, thereby limiting the utility of insight from Earth's past in decision-making and development of sustainable landscape-management practices for modern fluvial landscapes. Here, we explore the degree to which paleomorphodynamic reconstructions from ancient channel and floodplain deposits can be used to make specific, quantitative inferences about ancient river dynamics. We compare a suite of paleoenvironmental measurements from a variety of ancient fluvial deposits (including reconstructions of paleoflow depth, paleoslope, paleo-channel mobility, the caliber of paleo-sediment load, and paleo-floodplain heterogeneity) in an effort to evaluate sampling and empirical uncertainties associated with these methods and identify promising avenues for developing more detailed landscape reconstructions. This work is aimed at helping to develop strategies for extracting practicable information from the stratigraphic record that is relevant for sustainably managing and predicting changes in today's environments.

  2. Solar forcing and atmospheric control of paleoflood dynamics in the Bernese Alps, Switzerland

    NASA Astrophysics Data System (ADS)

    Schulte, Lothar; Peña, Juan Carlos; Burjachs, Francesc; Carvalho, Filipe; Llorca, Jaime; Julià, Ramon; Lomax, Johanna; Schmidt, Thomas; Rubio, Patricio; Losada, Justino; Veit, Heinz

    2014-05-01

    A multidisciplinary approach provides data from natural, historical, and instrumental time series, for the study of potential effects of climatic changes on alpine floods outside the known range of extreme events. The research focuses on the densely populated Bernese Alps, which are a true "hot spot" of hydrological risk. For the reconstruction of climate variability and floods, interdecadal-resolution alluvial delta plain records were examined. The multi-proxy approach affords insight into alpine flood dynamics of mid-scale catchments during the last three millennia. Spectral analysis of the geochemical and pollen time series records and climate proxies (δ14C, δ18O isotopes from the Greenland ice, NAO) evidence similar periodicities of 60, 85, 105 and 200 yrs. Thus, the mechanisms of the flood processes are strongly influenced by the North Atlantic dynamics and solar activity. The proxies indicate that cooler climate pulses and transitions from cool to warm climate pulses were an important external driving force of floods. This hypothesis is supported by the reconstructed floods of the Aare and Lütschine rivers from local documentary sources during the last 500 yrs. Flood periods inferred from sedimentary archives (flood layers, geochemical proxies and shifts of river channel) were calibrated by local documentary flood records and compared with the pattern of settlement on flood prone landforms. The generated data series shows also a good correlation with climate proxies, such as the annual temperatures of Europe (Luterbacher et al., 2004), tree ring based summer temperatures of Central Europe (Büntgen et al., 2011) and total solar irradiance according to the model of Steinhilber et al. (2009). With regard to the last two centuries flood magnitude and frequencies (exact dating) as well as driving mechanisms were reconstructed with more precision. Furthermore, a summer flood index of Switzerland (INU) based on damages recorded from 1800 to 2008 AD was performed

  3. High-Dynamic-Range CT Reconstruction Based on Varying Tube-Voltage Imaging

    PubMed Central

    2015-01-01

    For complicated structural components characterized by wide X-ray attenuation ranges, the conventional computed tomography (CT) imaging using a single tube-voltage at each rotation angle cannot obtain all structural information. This limitation results in a shortage of CT information, because the effective thickness of the components along the direction of X-ray penetration exceeds the limitation of the dynamic range of the X-ray imaging system. To address this problem, high-dynamic-range CT (HDR-CT) reconstruction is proposed. For this new method, the tube’s voltage is adjusted several times to match the corresponding effective thickness about the local information from an object. Then, HDR fusion and HDR-CT are applied to obtain the full reconstruction information. An accompanying experiment demonstrates that this new technology can extend the dynamic range of X-ray imaging systems and provide the complete internal structures of complicated structural components. PMID:26544723

  4. Dynamic force microscopy simulator (dForce): A tool for planning and understanding tapping and bimodal AFM experiments

    PubMed Central

    Guzman, Horacio V; Garcia, Pablo D

    2015-01-01

    Summary We present a simulation environment, dForce, which can be used for a better understanding of dynamic force microscopy experiments. The simulator presents the cantilever–tip dynamics for two dynamic AFM methods, tapping mode AFM and bimodal AFM. It can be applied for a wide variety of experimental situations in air or liquid. The code provides all the variables and parameters relevant in those modes, for example, the instantaneous deflection and tip–surface force, velocity, virial, dissipated energy, sample deformation and peak force as a function of time or distance. The simulator includes a variety of interactions and contact mechanics models to describe AFM experiments including: van der Waals, Hertz, DMT, JKR, bottom effect cone correction, linear viscoelastic forces or the standard linear solid viscoelastic model. We have compared two numerical integration methods to select the one that offers optimal accuracy and speed. The graphical user interface has been designed to facilitate the navigation of non-experts in simulations. Finally, the accuracy of dForce has been tested against numerical simulations performed during the last 18 years. PMID:25821676

  5. Force.

    ERIC Educational Resources Information Center

    Gamble, Reed

    1989-01-01

    Discusses pupil misconceptions concerning forces. Summarizes some of Assessment of Performance Unit's findings on meaning of (1) force, (2) force and motion in one dimension and two dimensions, and (3) Newton's second law. (YP)

  6. Reconstructing Source-Sink Dynamics in a Population with a Pelagic Dispersal Phase

    PubMed Central

    Chen, Kun; Ciannelli, Lorenzo; Decker, Mary Beth; Ladd, Carol; Cheng, Wei; Zhou, Ziqian; Chan, Kung-Sik

    2014-01-01

    For many organisms, the reconstruction of source-sink dynamics is hampered by limited knowledge of the spatial assemblage of either the source or sink components or lack of information on the strength of the linkage for any source-sink pair. In the case of marine species with a pelagic dispersal phase, these problems may be mitigated through the use of particle drift simulations based on an ocean circulation model. However, when simulated particle trajectories do not intersect sampling sites, the corroboration of model drift simulations with field data is hampered. Here, we apply a new statistical approach for reconstructing source-sink dynamics that overcomes the aforementioned problems. Our research is motivated by the need for understanding observed changes in jellyfish distributions in the eastern Bering Sea since 1990. By contrasting the source-sink dynamics reconstructed with data from the pre-1990 period with that from the post-1990 period, it appears that changes in jellyfish distribution resulted from the combined effects of higher jellyfish productivity and longer dispersal of jellyfish resulting from a shift in the ocean circulation starting in 1991. A sensitivity analysis suggests that the source-sink reconstruction is robust to typical systematic and random errors in the ocean circulation model driving the particle drift simulations. The jellyfish analysis illustrates that new insights can be gained by studying structural changes in source-sink dynamics. The proposed approach is applicable for the spatial source-sink reconstruction of other species and even abiotic processes, such as sediment transport. PMID:24835251

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

    PubMed

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

    2016-04-19

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

  8. Forcing of stratospheric chemistry and dynamics during the Dalton Minimum

    NASA Astrophysics Data System (ADS)

    Anet, J. G.; Muthers, S.; Rozanov, E.; Raible, C. C.; Peter, T.; Stenke, A.; Shapiro, A. I.; Beer, J.; Steinhilber, F.; Brönnimann, S.; Arfeuille, F.; Brugnara, Y.; Schmutz, W.

    2013-06-01

    The response of atmospheric chemistry and climate to volcanic eruptions and a decrease in solar activity during the Dalton Minimum is investigated with the fully coupled atmosphere-ocean-chemistry general circulation model SOCOL-MPIOM covering the time period 1780 to 1840 AD. We carried out several sensitivity ensemble experiments to separate the effects of (i) reduced solar ultra-violet (UV) irradiance, (ii) reduced solar visible and near infrared irradiance, (iii) enhanced galactic cosmic ray intensity as well as less intensive solar energetic proton events and auroral electron precipitation, and (iv) volcanic aerosols. The introduced changes of UV irradiance and volcanic aerosols significantly influence stratospheric climate in the early 19th century, whereas changes in the visible part of the spectrum and energetic particles have smaller effects. A reduction of UV irradiance by 15% causes global ozone decrease below the stratopause reaching 8% in the midlatitudes at 5 hPa and a significant stratospheric cooling of up to 2 °C in the midstratosphere and to 6 °C in the lower mesosphere. Changes in energetic particle precipitation lead only to minor changes in the yearly averaged temperature fields in the stratosphere. Volcanic aerosols heat the tropical lower stratosphere allowing more water vapor to enter the tropical stratosphere, which, via HOx reactions, decreases upper stratospheric and mesospheric ozone by roughly 4%. Conversely, heterogeneous chemistry on aerosols reduces stratospheric NOx leading to a 12% ozone increase in the tropics, whereas a decrease in ozone of up to 5% is found over Antarctica in boreal winter. The linear superposition of the different contributions is not equivalent to the response obtained in a simulation when all forcing factors are applied during the DM - this effect is especially well visible for NOx/NOy. Thus, this study highlights the non-linear behavior of the coupled chemistry-climate system. Finally, we conclude that

  9. Dynamic nuclear polarization in a magnetic resonance force microscope experiment.

    PubMed

    Issac, Corinne E; Gleave, Christine M; Nasr, Paméla T; Nguyen, Hoang L; Curley, Elizabeth A; Yoder, Jonilyn L; Moore, Eric W; Chen, Lei; Marohn, John A

    2016-04-01

    We report achieving enhanced nuclear magnetization in a magnetic resonance force microscope experiment at 0.6 tesla and 4.2 kelvin using the dynamic nuclear polarization (DNP) effect. In our experiments a microwire coplanar waveguide delivered radiowaves to excite nuclear spins and microwaves to excite electron spins in a 250 nm thick nitroxide-doped polystyrene sample. Both electron and proton spin resonance were observed as a change in the mechanical resonance frequency of a nearby cantilever having a micron-scale nickel tip. NMR signal, not observable from Curie-law magnetization at 0.6 T, became observable when microwave irradiation was applied to saturate the electron spins. The resulting NMR signal's size, buildup time, dependence on microwave power, and dependence on irradiation frequency was consistent with a transfer of magnetization from electron spins to nuclear spins. Due to the presence of an inhomogeneous magnetic field introduced by the cantilever's magnetic tip, the electron spins in the sample were saturated in a microwave-resonant slice 10's of nm thick. The spatial distribution of the nuclear polarization enhancement factor ε was mapped by varying the frequency of the applied radiowaves. The observed enhancement factor was zero for spins in the center of the resonant slice, was ε = +10 to +20 for spins proximal to the magnet, and was ε = -10 to -20 for spins distal to the magnet. We show that this bipolar nuclear magnetization profile is consistent with cross-effect DNP in a ∼10(5) T m(-1) magnetic field gradient. Potential challenges associated with generating and using DNP-enhanced nuclear magnetization in a nanometer-resolution magnetic resonance imaging experiment are elucidated and discussed. PMID:26964007

  10. Dynamic nuclear polarization in a magnetic resonance force microscope experiment.

    PubMed

    Issac, Corinne E; Gleave, Christine M; Nasr, Paméla T; Nguyen, Hoang L; Curley, Elizabeth A; Yoder, Jonilyn L; Moore, Eric W; Chen, Lei; Marohn, John A

    2016-04-01

    We report achieving enhanced nuclear magnetization in a magnetic resonance force microscope experiment at 0.6 tesla and 4.2 kelvin using the dynamic nuclear polarization (DNP) effect. In our experiments a microwire coplanar waveguide delivered radiowaves to excite nuclear spins and microwaves to excite electron spins in a 250 nm thick nitroxide-doped polystyrene sample. Both electron and proton spin resonance were observed as a change in the mechanical resonance frequency of a nearby cantilever having a micron-scale nickel tip. NMR signal, not observable from Curie-law magnetization at 0.6 T, became observable when microwave irradiation was applied to saturate the electron spins. The resulting NMR signal's size, buildup time, dependence on microwave power, and dependence on irradiation frequency was consistent with a transfer of magnetization from electron spins to nuclear spins. Due to the presence of an inhomogeneous magnetic field introduced by the cantilever's magnetic tip, the electron spins in the sample were saturated in a microwave-resonant slice 10's of nm thick. The spatial distribution of the nuclear polarization enhancement factor ε was mapped by varying the frequency of the applied radiowaves. The observed enhancement factor was zero for spins in the center of the resonant slice, was ε = +10 to +20 for spins proximal to the magnet, and was ε = -10 to -20 for spins distal to the magnet. We show that this bipolar nuclear magnetization profile is consistent with cross-effect DNP in a ∼10(5) T m(-1) magnetic field gradient. Potential challenges associated with generating and using DNP-enhanced nuclear magnetization in a nanometer-resolution magnetic resonance imaging experiment are elucidated and discussed.

  11. Dynamic-Feature Extraction, Attribution and Reconstruction (DEAR) Method for Power System Model Reduction

    SciTech Connect

    Wang, Shaobu; Lu, Shuai; Zhou, Ning; Lin, Guang; Elizondo, Marcelo A.; Pai, M. A.

    2014-09-04

    In interconnected power systems, dynamic model reduction can be applied on generators outside the area of interest to mitigate the computational cost with transient stability studies. This paper presents an approach of deriving the reduced dynamic model of the external area based on dynamic response measurements, which comprises of three steps, dynamic-feature extraction, attribution and reconstruction (DEAR). In the DEAR approach, a feature extraction technique, such as singular value decomposition (SVD), is applied to the measured generator dynamics after a disturbance. Characteristic generators are then identified in the feature attribution step for matching the extracted dynamic features with the highest similarity, forming a suboptimal ‘basis’ of system dynamics. In the reconstruction step, generator state variables such as rotor angles and voltage magnitudes are approximated with a linear combination of the characteristic generators, resulting in a quasi-nonlinear reduced model of the original external system. Network model is un-changed in the DEAR method. Tests on several IEEE standard systems show that the proposed method gets better reduction ratio and response errors than the traditional coherency aggregation methods.

  12. Fast direct reconstruction strategy of dynamic fluorescence molecular tomography using graphics processing units

    NASA Astrophysics Data System (ADS)

    Chen, Maomao; Zhang, Jiulou; Cai, Chuangjian; Gao, Yang; Luo, Jianwen

    2016-06-01

    Dynamic fluorescence molecular tomography (DFMT) is a valuable method to evaluate the metabolic process of contrast agents in different organs in vivo, and direct reconstruction methods can improve the temporal resolution of DFMT. However, challenges still remain due to the large time consumption of the direct reconstruction methods. An acceleration strategy using graphics processing units (GPU) is presented. The procedure of conjugate gradient optimization in the direct reconstruction method is programmed using the compute unified device architecture and then accelerated on GPU. Numerical simulations and in vivo experiments are performed to validate the feasibility of the strategy. The results demonstrate that, compared with the traditional method, the proposed strategy can reduce the time consumption by ˜90% without a degradation of quality.

  13. Dynamics and stability of mechanical systems with follower forces

    NASA Technical Reports Server (NTRS)

    Herrmann, G.

    1971-01-01

    A monograph on problems of stability of equilibrium of mechanical systems with follower forces is presented. Concepts of stability and criteria of stability are reviewed briefly, together with means of analytical specification of follower forces. Nondissipative systems with two degrees of freedom are discussed, and destabilizing effects due to various types of dissipative forces both in discrete and continuous systems, are treated. The analyses are accompanied by some quantative experiments and observations on demonstrational laboratory models.

  14. Dynamic Simulation of the Effects of Graft Fixation Errors During Medial Patellofemoral Ligament Reconstruction

    PubMed Central

    Elias, John J.; Kelly, Michael J.; Smith, Kathryn E.; Gall, Kenneth A.; Farr, Jack

    2016-01-01

    Background: Medial patellofemoral ligament (MPFL) reconstruction is performed to prevent recurrent instability, but errors in femoral fixation can elevate graft tension. Hypothesis: Errors related to femoral fixation will overconstrain the patella and increase medial patellofemoral pressures. Study Design: Controlled laboratory study. Methods: Five knees with patellar instability were represented with computational models. Kinematics during knee extension were characterized from computational reconstruction of motion performed within a dynamic computed tomography (CT) scanner. Multibody dynamic simulation of knee extension, with discrete element analysis used to quantify contact pressures, was performed for the preoperative condition and after MPFL reconstruction. A standard femoral attachment and graft resting length were set for each knee. The resting length was decreased by 2 mm, and the femoral attachment was shifted 5 mm posteriorly. The simulated errors were also combined. Root-mean-square errors were quantified for the comparison of preoperative patellar lateral shift and tilt between computationally reconstructed motion and dynamic simulation. Simulation output was compared between the preoperative and MPFL reconstruction conditions with repeated-measures Friedman tests and Dunnett comparisons against a control, which was the standard MPFL condition, with statistical significance set at P < .05. Results: Root-mean-square errors for simulated patellar tilt and shift were 5.8° and 3.3 mm, respectively. Patellar lateral tracking for the preoperative condition was significantly larger near full extension compared with the standard MPFL reconstruction (mean differences of 8 mm and 13° for shift and tilt, respectively, at 0°), and lateral tracking was significantly smaller for a posterior femoral attachment (mean differences of 3 mm and 4° for shift and tilt, respectively, at 0°). The maximum medial pressure was also larger for the short graft with a

  15. Protein adhesion force dynamics and single adhesion events.

    PubMed Central

    Sagvolden, G

    1999-01-01

    Using the manipulation force microscope, a novel atomic force microscope, the adhesion forces of bovine serum albumin, myoglobin, ferritin, and lysozyme proteins to glass and polystyrene substrates were characterized by following the force necessary to displace an adsorbed protein-covered microsphere over several orders of magnitude in time. This force was consistent with a power law with exponent a = 0.37 +/- 0.03 on polystyrene, indicating that there is no typical time scale for adhesion on this substrate. On glass, the rate of adhesion depended strongly on protein charge. Forces corresponding to single protein adhesion events were identified. The typical rupture force of a single lysozyme, ferritin, bovine serum albumin, and myoglobin protein adhering to glass was estimated to be 90 +/- 10 pN, 115 +/- 13 pN, 277 +/- 44 pN, and 277 +/- 44 pN, respectively, using a model of the experimental system. These forces, as well as the force amplitudes on hydrophobic polystyrene, correlate with protein stiffness. PMID:10388777

  16. Reconstructing three-dimensional reentrant cardiac electrical wave dynamics using data assimilation.

    PubMed

    Hoffman, M J; LaVigne, N S; Scorse, S T; Fenton, F H; Cherry, E M

    2016-01-01

    For many years, reentrant scroll waves have been predicted and studied as an underlying mechanism for cardiac arrhythmias using numerical techniques, and high-resolution mapping studies using fluorescence recordings from the surfaces of cardiac tissue preparations have confirmed the presence of visible spiral waves. However, assessing the three-dimensional dynamics of these reentrant waves using experimental techniques has been limited to verifying stable scroll-wave dynamics in relatively thin preparations. We propose a different approach to recovering the three-dimensional dynamics of reentrant waves in the heart. By applying techniques commonly used in weather forecasting, we combine dual-surface observations from a particular experiment with predictions from a numerical model to reconstruct the full three-dimensional time series of the experiment. Here, we use model-generated surrogate observations from a numerical experiment to evaluate the performance of the ensemble Kalman filter in reconstructing such time series for a discordant alternans state in one spatial dimension and for scroll waves in three dimensions. We show that our approach is able to recover time series of both observed and unobserved variables matching the truth. Where nearby observations are available, the error is reduced below the synthetic observation error, with a smaller reduction with increased distance from observations. Our findings demonstrate that state reconstruction for spatiotemporally complex cardiac electrical dynamics is possible and will lead naturally to applications using real experimental data. PMID:26826859

  17. Stochastic approach to reconstruction of dynamical systems: optimal model selection criterion

    NASA Astrophysics Data System (ADS)

    Gavrilov, A.; Mukhin, D.; Loskutov, E. M.; Feigin, A. M.

    2011-12-01

    Most of known observable systems are complex and high-dimensional that doesn't allow to make the exact long-term forecast of their behavior. The stochastic approach to reconstruction of such systems gives a hope to describe important qualitative features of their behavior in a low-dimensional way while all other dynamics is modelled as stochastic disturbance. This report is devoted to application of Bayesian evidence for optimal stochastic model selection when reconstructing the evolution operator of observable system. The idea of Bayesian evidence is to find compromise between the model predictiveness and quality of fitting the model into the data. We represent the evolution operator of investigated system in a form of random dynamic system including deterministic and stochastic parts, both parameterized by artificial neural network. Then we use Bayesian evidence criterion to estimate optimal complexity of the model, i.e. both number of parameters and dimension corresponding to most probable model given the data. We demonstrate on the number of model examples that the model with non-uniformly distributed stochastic part (which corresponds to non-Gaussian perturbations of evolution operator) is optimal in general case. Further, we show that simple stochastic model can be the most preferred for reconstruction of the evolution operator underlying complex observed dynamics even in a case of deterministic high-dimensional system. Workability of suggested approach for modeling and prognosis of real-measured geophysical dynamics is investigated.

  18. Force modulating dynamic disorder: A physical model of catch-slip bond transitions in receptor-ligand forced dissociation experiments

    NASA Astrophysics Data System (ADS)

    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.

  19. Force feedback coupling with dynamics for physical simulation of product assembly and operation performance

    NASA Astrophysics Data System (ADS)

    Liu, Zhenyu; Tan, Jianrong; Duan, Guifang; Fu, Yun

    2015-01-01

    Most existing force feedback methods are still difficult to meet the requirements of real-time force calculation in virtual assembly and operation with complex objects. In addition, there is often an assumption that the controlled objects are completely free and the target object is only completely fixed or free, thus, the dynamics of the kinematic chain where the controlled objects are located are neglected during the physical simulation of the product manipulation with force feedback interaction. This paper proposes a physical simulation method of product assembly and operation manipulation based on statistically learned contact force prediction model and the coupling of force feedback and dynamics. In the proposed method, based on hidden Markov model (HMM) and local weighting learning (LWL), contact force prediction model is constructed, which can estimate the contact force in real time during interaction. Based on computational load balance model, the computing resources are dynamically assigned and the dynamics integral step is optimized. In addition, smoothing process is performed to the force feedback on the synchronization points. Consequently, we can solve the coupling and synchronization problems of high-frequency feedback force servo, low-frequency dynamics solver servo and scene rendering servo, and realize highly stable and accurate force feedback in the physical simulation of product assembly and operation manipulation. This research proposes a physical simulation method of product assembly and operation manipulation.

  20. Drivers of drift sand dynamics; a reconstruction for the Wekeromse Zand, the Netherlands

    NASA Astrophysics Data System (ADS)

    Hendriks, Chantal; Sonneveld, Marthijn; Wallinga, Jakob

    2013-04-01

    Inland active drift sand landscapes are regarded as unique ecosystems of great historical and geomorphological value. Recent studies have highlighted the role of multiple factors in the initiation and stabilization of drift sand landscapes. To unravel the importance of different forcings (e.g. agricultural practices, climate) and their interplay, insight in the chronology of drift sand dynamics is essential. In this study, we aimed to reconstruct the dynamics of the drift sand landscape of the Wekeromse Zand (central Netherlands) and to develop a conceptual model to understand the processes involved. The Wekeromse Zand study area (370 ha) is located on the border of a central push moraine and is characterised by open active drift sands (14 ha) and vegetated hills and valleys. The surroundings are dominated by modern agricultural practices, and remnants from ancient iron age Celtic Field systems showing that the area has been in agricultural use since at least the Iron Age. For the study area we: i) analysed historical maps going back to the early 19th century, ii) performed a field survey to map the palaeolandscape (before drift sand activation) and iii) employed optically stimulated luminescence (OSL) dating of drift sand deposits on 11 samples from two locations to determine the timing of drift sand deposition. Analysis of the available topographic maps showed no substantial aeolean activity of the area outside its morphological boundaries. OSL dating revealed that two drift sand layers were deposited between 1373 and 1462 AD and between 1680 and 1780 AD. A layer with a higher organic matter content was found at one of the sites. This suggests that the Wekeromse Zand has known three relatively stable periods: i) a period between the start of the Holocene to the Late Medieval Period, ii) in between the Medieval climatic optimum and the climatic Maunder minimum, and iii) current situation. Despite the fact that agricultural activities occurred in this area from the

  1. A dynamic test of lower extremity function following anterior cruciate ligament reconstruction and rehabilitation.

    PubMed

    Juris, P M; Phillips, E M; Dalpe, C; Edwards, C; Gotlin, R S; Kane, D J

    1997-10-01

    It is essential to assess the functional status of patients with surgically reconstructed and rehabilitated anterior cruciate ligaments prior to discharge. This study established a testing paradigm for functional force production and absorption. Data were obtained from 100 healthy subjects for maximal hops, controlled leaps, and hopping and leaping symmetry. Only 10% of symptomatic patients met maximal hopping criteria, while 15% achieved controlled leaping norms. Ninety-five percent of these patients failed to reach both hopping and leaping symmetry norms. Asymptomatic patients were 63% successful in meeting hopping criteria, and 57% were successful in meeting leaping criteria. Hop symmetry and leap symmetry were achieved at rates of 70% and 60%, respectively. The performance of both groups fell significantly below that of normal subjects (p < .05). Data suggest that this protocol does accurately assess functional and dysfunctional knees, and that force absorption may be more critical than force production in the determination of functional capacity.

  2. Lower Limb Kinematics and Dynamic Postural Stability in Anterior Cruciate Ligament-Reconstructed Female Athletes

    PubMed Central

    Delahunt, Eamonn; Chawke, Mark; Kelleher, Judy; Murphy, Katie; Prendiville, Anna; Sweeny, Lauren; Patterson, Matt

    2013-01-01

    Context: Deficits in lower limb kinematics and postural stability are predisposing factors to the development of knee ligamentous injury. The extent to which these deficits are present after anterior cruciate ligament (ACL) reconstruction is still largely unknown. The primary hypothesis of the present study was that female athletes who have undergone ACL reconstruction and who have returned to sport participation would exhibit deficits in dynamic postural stability as well as deficiencies in hip- and knee-joint kinematics when compared with an age-, activity-, and sex-matched uninjured control group. Objective: To investigate dynamic postural stability as quantified by the Star Excursion Balance Test (SEBT) and simultaneous hip- and knee-joint kinematic profiles in female athletes who have undergone ACL reconstruction. Design: Descriptive laboratory study. Setting: University motion-analysis laboratory. Patients or Other Participants: Fourteen female athletes who had previously undergone ACL reconstruction (ACL-R) and 17 age- and sex-matched uninjured controls. Intervention(s): Each participant performed 3 trials of the anterior, posterior-medial, and posterior-lateral directional components of the SEBT. Main Outcome Measure(s): Reach distances for each directional component were quantified and expressed as a percentage of leg length. Simultaneous hip- and knee-joint kinematic profiles were recorded using a motion-analysis system. Results: The ACL-R group had decreased reach distances on the posterior-medial (P < .01) and posterior-lateral (P < .01) directional components of the SEBT. During performance of the directional components of the SEBT, ACL-R participants demonstrated altered hip-joint frontal-, sagittal-, and transverse-plane kinematic profiles (P < .05), as well as altered knee-joint sagittal-plane kinematic profiles (P < .05). Conclusions: Deficits in dynamic postural stability and concomitant altered hip- and knee-joint kinematics are present after ACL

  3. Force Generation and Dynamics of Individual Cilia under External Loading

    PubMed Central

    Hill, David B.; Swaminathan, Vinay; Estes, Ashley; Cribb, Jeremy; O'Brien, E. Timothy; Davis, C. William; Superfine, R.

    2010-01-01

    Abstract Motile cilia are unique multimotor systems that display coordination and periodicity while imparting forces to biological fluids. They play important roles in normal physiology, and ciliopathies are implicated in a growing number of human diseases. In this work we measure the response of individual human airway cilia to calibrated forces transmitted via spot-labeled magnetic microbeads. Cilia respond to applied forces by 1), a reduction in beat amplitude (up to an 85% reduction by 160–170 pN of force); 2), a decreased tip velocity proportionate to applied force; and 3), no significant change in beat frequency. Tip velocity reduction occurred in each beat direction, independently of the direction of applied force, indicating that the cilium is “driven” in both directions at all times. By applying a quasistatic force model, we deduce that axoneme stiffness is dominated by the rigidity of the microtubules, and that cilia can exert 62 ± 18 pN of force at the tip via the generation of 5.6 ± 1.6 pN/dynein head. PMID:20085719

  4. Towards myocardial contraction force image reconstruction for heart disease assessment and intervention planning

    NASA Astrophysics Data System (ADS)

    Haddad, Seyyed M. H.; Drangova, Maria; White, James A.; Samani, Abbas

    2015-03-01

    It is clinically vital to devise a technique to evaluate regional functionality of the myocardium in order to determine the extent and intensity of local damage to the cardiac tissue caused by ischemic injuries. Such a technique can potentially enable cardiologists to discriminate between reversible and irreversible ischemic injuries and to devise appropriate revascularization therapy in case of reversible lesions. The technique is founded on the premise that sufficient contraction force generated by the cardiac tissue can be regarded as a direct and reliable criterion for regional analysis of tissue healthy functionality. To this end, a number of imaging techniques have been developed and, to our knowledge, none of them assess regional cardiac functionality based on a straightforward mechanical measure such as local cardiac contraction forces. . As such, a novel imaging technique is being developed on the basis of quantification and visualisation of local myocardial contraction forces. In this technique, cardiac contraction force distribution is attained through solving an inverse problem within an optimization framework which uses iterative forward mechanical modelling of the myocardium. Hence, a forward mechanical model of the myocardium which is computationally efficient, robust, and adaptable to diverse pathophysiological conditions is necessary for this development. As such, this paper is geared towards developing a novel mechanical model of the healthy and pathological myocardium which considers all aspects of the myocardial mechanics including hyperelasticity, anisotropy, and active contraction force. In this investigation, two major parts, including background tissue and reinforcement bars (fibers) have been considered for modelling the myocardium. The model was implemented using finite element (FE) approach and demonstrated very good performance in simulating normal and infarcted left ventricle (LV) contractile function.

  5. Sharpening our Understanding but Blurring the Boundaries: Dynamic Observations of Surface Reconstruction

    SciTech Connect

    Baer, Donald R.

    2003-08-20

    Every now and then, reading a specific paper stimulates--in my mind at least--a variety of associations and connections that highlight advances that have been made and suggests links between areas that I may not have previously connected. The recent series of papers by McCarty and Bartelt (and co-workers) using low energy electron microscopy (LEEM) to study the dynamics of surface reconstruction of TiO2 , and NiAl sent my thinking in a variety loosely connected directions. Paraphrasing the response of one of my colleagues - the work causes us to think dynamically where we have often thought statically about what happens when surfaces reconstruct. The measurements also highlight the importance of newer techniques to help us visualize and understand phenomena that may have puzzled us for years. The dynamic interactions between surface structure and both the defect structure (and history) of the substrate and the nature of the environment of the specimen highlight an aspect of phenomena that drive surface reconstruction not normally considered and suggests additional and delightful challenges we face in understanding the bulk stability and surface structures of nano-sized objects. Since the physical arrangement of the atoms controls every aspect of the physics and chemistry of a surface or interface, the atomic geometry is a fundamental defining characteristic of a surface. , Details of the structure of a surface, including altered atomic positions, the presence of steps and various types of defects can significantly change the chemistry of a surface and impact processes ranging from the formation of interfaces in electronic components to the efficiency of a catalyst. Because of its importance there has been considerable effort devoted to understanding and predicting surface structures. However, dynamical aspects of surface reconstruction and the significance of material defects in the process have not been part of the standard picture.

  6. Reconstructing local population dynamics in noisy metapopulations--the role of random catastrophes and Allee effects.

    PubMed

    Hart, Edmund M; Avilés, Leticia

    2014-01-01

    Reconstructing the dynamics of populations is complicated by the different types of stochasticity experienced by populations, in particular if some forms of stochasticity introduce bias in parameter estimation in addition to error. Identification of systematic biases is critical when determining whether the intrinsic dynamics of populations are stable or unstable and whether or not populations exhibit an Allee effect, i.e., a minimum size below which deterministic extinction should follow. Using a simulation model that allows for Allee effects and a range of intrinsic dynamics, we investigated how three types of stochasticity--demographic, environmental, and random catastrophes--affect our ability to reconstruct the intrinsic dynamics of populations. Demographic stochasticity aside, which is only problematic in small populations, we find that environmental stochasticity--positive and negative environmental fluctuations--caused increased error in parameter estimation, but bias was rarely problematic, except at the highest levels of noise. Random catastrophes, events causing large-scale mortality and likely to be more common than usually recognized, caused immediate bias in parameter estimates, in particular when Allee effects were large. In the latter case, population stability was predicted when endogenous dynamics were actually unstable and the minimum viable population size was overestimated in populations with small or non-existent Allee effects. Catastrophes also generally increased extinction risk, in particular when endogenous Allee effects were large. We propose a method for identifying data points likely resulting from catastrophic events when such events have not been recorded. Using social spider colonies (Anelosimus spp.) as models for populations, we show that after known or suspected catastrophes are accounted for, reconstructed growth parameters are consistent with intrinsic dynamical instability and substantial Allee effects. Our results are

  7. Reconstructing Local Population Dynamics in Noisy Metapopulations—The Role of Random Catastrophes and Allee Effects

    PubMed Central

    Hart, Edmund M.; Avilés, Leticia

    2014-01-01

    Reconstructing the dynamics of populations is complicated by the different types of stochasticity experienced by populations, in particular if some forms of stochasticity introduce bias in parameter estimation in addition to error. Identification of systematic biases is critical when determining whether the intrinsic dynamics of populations are stable or unstable and whether or not populations exhibit an Allee effect, i.e., a minimum size below which deterministic extinction should follow. Using a simulation model that allows for Allee effects and a range of intrinsic dynamics, we investigated how three types of stochasticity—demographic, environmental, and random catastrophes— affect our ability to reconstruct the intrinsic dynamics of populations. Demographic stochasticity aside, which is only problematic in small populations, we find that environmental stochasticity—positive and negative environmental fluctuations—caused increased error in parameter estimation, but bias was rarely problematic, except at the highest levels of noise. Random catastrophes, events causing large-scale mortality and likely to be more common than usually recognized, caused immediate bias in parameter estimates, in particular when Allee effects were large. In the latter case, population stability was predicted when endogenous dynamics were actually unstable and the minimum viable population size was overestimated in populations with small or non-existent Allee effects. Catastrophes also generally increased extinction risk, in particular when endogenous Allee effects were large. We propose a method for identifying data points likely resulting from catastrophic events when such events have not been recorded. Using social spider colonies (Anelosimus spp.) as models for populations, we show that after known or suspected catastrophes are accounted for, reconstructed growth parameters are consistent with intrinsic dynamical instability and substantial Allee effects. Our results are

  8. Cohesive suction-cup force in cell separation dynamics

    NASA Astrophysics Data System (ADS)

    Vasseur, H.

    2010-07-01

    When an external pulling force is applied onto a cell stuck to its substrate, a reacting "suction-cup" force, due to the slow penetration of the surrounding fluid between the cell and the substrate, opposes to the separation. It can overcome other known adhesive forces when the process is sufficiently violent (typically 105 N/m2). The physical origin of this effect may be compared with that leaning a suction-cup against a bathroom wall. We address the consequences of this effect on i) the separation energy, ii) the fluid motion surrounding the cell, and iii) the inhibition of cell motion.

  9. Synchronous monitoring of muscle dynamics and muscle force for maximum isometric tetanus

    NASA Astrophysics Data System (ADS)

    Zakir Hossain, M.; Grill, Wolfgang

    2010-03-01

    Skeletal muscle is a classic example of a biological soft matter . At both macro and microscopic levels, skeletal muscle is exquisitely oriented for force generation and movement. In addition to the dynamics of contracting and relaxing muscle which can be monitored with ultrasound, variations in the muscle force are also expected to be monitored. To observe such force and sideways expansion variations synchronously for the skeletal muscle a novel detection scheme has been developed. As already introduced for the detection of sideways expansion variations of the muscle, ultrasonic transducers are mounted sideways on opposing positions of the monitored muscle. To detect variations of the muscle force, angle of pull of the monitored muscle has been restricted by the mechanical pull of the sonic force sensor. Under this condition, any variation in the time-of-flight (TOF) of the transmitted ultrasonic signals can be introduced by the variation of the path length between the transducers. The observed variations of the TOF are compared to the signals obtained by ultrasound monitoring for the muscle dynamics. The general behavior of the muscle dynamics and muscle force shows almost an identical concept. Since muscle force also relates the psychological boosting-up effects, the influence of boosting-up on muscle force and muscle dynamics can also be quantified form this study. Length-tension or force-length and force-velocity relationship can also be derived quantitatively with such monitoring.

  10. Modeling Multibody Stage Separation Dynamics Using Constraint Force Equation Methodology

    NASA Technical Reports Server (NTRS)

    Tartabini, Paul V.; Roithmayr, Carlos M.; Toniolo, Matthew D.; Karlgaard, Christopher D.; Pamadi, Bandu N.

    2011-01-01

    This paper discusses the application of the constraint force equation methodology and its implementation for multibody separation problems using three specially designed test cases. The first test case involves two rigid bodies connected by a fixed joint, the second case involves two rigid bodies connected with a universal joint, and the third test case is that of Mach 7 separation of the X-43A vehicle. For the first two cases, the solutions obtained using the constraint force equation method compare well with those obtained using industry- standard benchmark codes. For the X-43A case, the constraint force equation solutions show reasonable agreement with the flight-test data. Use of the constraint force equation method facilitates the analysis of stage separation in end-to-end simulations of launch vehicle trajectories

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

    SciTech Connect

    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.

  12. Rank-sparsity constrained, spectro-temporal reconstruction for retrospectively gated, dynamic CT

    NASA Astrophysics Data System (ADS)

    Clark, D. P.; Lee, C. L.; Kirsch, D. G.; Badea, C. T.

    2015-03-01

    Relative to prospective projection gating, retrospective projection gating for dynamic CT applications allows fast imaging times, minimizing the potential for physiological and anatomic variability. Preclinically, fast imaging is attractive due to the rapid clearance of low molecular weight contrast agents and the rapid heart rate of rodents. Clinically, retrospective gating is relevant for intraoperative C-arm CT. More generally, retrospective sampling provides an opportunity for significant reduction in x-ray dose within the framework of compressive sensing theory and sparsity-constrained iterative reconstruction. Even so, CT reconstruction from projections with random temporal sampling is a very poorly conditioned inverse problem, requiring high fidelity regularization to minimize variability in the reconstructed results. Here, we introduce a highly novel data acquisition and regularization strategy for spectro-temporal (5D) CT reconstruction from retrospectively gated projections. We show that by taking advantage of the rank-sparse structure and separability of the temporal and spectral reconstruction sub-problems, being able to solve each sub-problem independently effectively guarantees that we can solve both problems together. In this paper, we show 4D simulation results (2D + 2 energies + time) using the proposed technique and compare them with two competing techniques— spatio-temporal total variation minimization and prior image constrained compressed sensing. We also show in vivo, 5D (3D + 2 energies + time) myocardial injury data acquired in a mouse, reconstructing 20 data sets (10 phases, 2 energies) and performing material decomposition from data acquired over a single rotation (360°, dose: ~60 mGy).

  13. Three Dimensional Dynamic Model Based Wind Field Reconstruction from Lidar Data

    NASA Astrophysics Data System (ADS)

    Raach, Steffen; Schlipf, David; Haizmann, Florian; Cheng, Po Wen

    2014-06-01

    Using the inflowing horizontal and vertical wind shears for individual pitch controller is a promising method if blade bending measurements are not available. Due to the limited information provided by a lidar system the reconstruction of shears in real-time is a challenging task especially for the horizontal shear in the presence of changing wind direction. The internal model principle has shown to be a promising approach to estimate the shears and directions in 10 minutes averages with real measurement data. The static model based wind vector field reconstruction is extended in this work taking into account a dynamic reconstruction model based on Taylor's Frozen Turbulence Hypothesis. The presented method provides time series over several seconds of the wind speed, shears and direction, which can be directly used in advanced optimal preview control. Therefore, this work is an important step towards the application of preview individual blade pitch control under realistic wind conditions. The method is tested using a turbulent wind field and a detailed lidar simulator. For the simulation, the turbulent wind field structure is flowing towards the lidar system and is continuously misaligned with respect to the horizontal axis of the wind turbine. Taylor's Frozen Turbulence Hypothesis is taken into account to model the wind evolution. For the reconstruction, the structure is discretized into several stages where each stage is reduced to an effective wind speed, superposed with a linear horizontal and vertical wind shear. Previous lidar measurements are shifted using again Taylor's Hypothesis. The wind field reconstruction problem is then formulated as a nonlinear optimization problem, which minimizes the residual between the assumed wind model and the lidar measurements to obtain the misalignment angle and the effective wind speed and the wind shears for each stage. This method shows good results in reconstructing the wind characteristics of a three dimensional

  14. Dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modelling language (VRML).

    PubMed

    Yu, Zheng-yang; Zheng, Shu-sen; Chen, Lei-ting; He, Xiao-qian; Wang, Jian-jun

    2005-07-01

    This research studies the process of 3D reconstruction and dynamic concision based on 2D medical digital images using virtual reality modelling language (VRML) and JavaScript language, with a focus on how to realize the dynamic concision of 3D medical model with script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be built with such high quality that they are better than those obtained from the traditional methods. With the function of dynamic concision, the VRML browser can offer better windows for man-computer interaction in real-time environment than ever before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and have a promising prospect in the fields of medical imaging.

  15. The main factor causing prolonged reaction time on force producing process following anterior cruciate ligament reconstruction.

    PubMed

    Kaneko, F; Onari, K; Kawaguchi, K; Tsukisaka, K

    2000-12-01

    This study investigated the electromechanical properties of atrophied human quadriceps femoris muscle during a voluntarily elicited maximal isometric contraction (MVC) and a peripherally stimulated twitch contraction. Nineteen patients were recruited 2-3 months following a unilateral anterior cruciate ligament (ACL) reconstruction. Both the involved leg as well as the uninvolved leg were studied. Maximal twitch response was elicited and surface electromyograms (EMG) were recorded from the vastus lateralis. Total reaction time (TRT) for both MVC and twitch on involved leg was prolonged (251.47 msec, 26.01 msec). This prolongation suggests an extended lag in avoiding injury such as during sports. Pre-motor time during both MVC and twitch (PMTmvc, PMTtwitch) did not differ between both groups. Electromechanical delay during MVC (EMDmvc) was prolonged on involved leg (53.42 msec), and also evoked twitch EMD (EMDtwitch) (20.04 msec) as compared to the opposite side. Prolonged EMDtwitch may be due to a decrease in stiffness of the series elastic component, changes of peripheral muscle composition to containing more slow type muscle fibers, or a decrease in function of the excitation-contraction (E-C) coupling process. A prolonged EMDtwitch can also explain the prolonged EMDmvc. These findings also suggested that prolonged TRTmvc to visual stimulus during MVC in atrophied human quadriceps femoris muscle after disuse was principally due to prolongation of EMDmvc. Prolonged EMDmvc may have resulted from decreased muscle stiffness, which was evident in the prolongation of the EMDtwitch.

  16. Refolding dynamics of stretched biopolymers upon force quench

    PubMed Central

    Hyeon, Changbong; Morrison, Greg; Pincus, David L.; Thirumalai, D.

    2009-01-01

    Single-molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse of RNA and proteins upon force quench by using simulations of an RNA hairpin and theory based on the de Gennes model for homopolymer collapse. The folding time, τF, depends asymmetrically on δfS = f S − f m and δf Q = f m − f Q where f S (f Q) is the stretch (quench) force and f m is the transition midforce of the RNA hairpin. In accord with experiments, the relaxation kinetics of the molecular extension, R(t), occurs in three stages: A rapid initial decrease in the extension is followed by a plateau and finally, an abrupt reduction in R(t) occurs as the native state is approached. The duration of the plateau increases as λ = τ Q/τ F decreases (where τ Q is the time in which the force is reduced from f S to f Q). Variations in the mechanisms of force-quench relaxation as λ is altered are reflected in the experimentally measurable time-dependent entropy, which is computed directly from the folding trajectories. An analytical solution of the de Gennes model under tension reproduces the multistage stage kinetics in R(t). The prediction that the initial stages of collapse should also be a generic feature of polymers is validated by simulation of the kinetics of toroid (globule) formation in semiflexible (flexible) homopolymers in poor solvents upon quenching the force from a fully stretched state. Our findings give a unified explanation for multiple disparate experimental observations of protein folding. PMID:19915145

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

    NASA Technical Reports Server (NTRS)

    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.

  18. Segregated and overlapping neural circuits exist for the production of static and dynamic precision grip force.

    PubMed

    Neely, Kristina A; Coombes, Stephen A; Planetta, Peggy J; Vaillancourt, David E

    2013-03-01

    A central topic in sensorimotor neuroscience is the static-dynamic dichotomy that exists throughout the nervous system. Previous work examining motor unit synchronization reports that the activation strategy and timing of motor units differ for static and dynamic tasks. However, it remains unclear whether segregated or overlapping blood-oxygen-level-dependent (BOLD) activity exists in the brain for static and dynamic motor control. This study compared the neural circuits associated with the production of static force to those associated with the production of dynamic force pulses. To that end, healthy young adults (n = 17) completed static and dynamic precision grip force tasks during functional magnetic resonance imaging (fMRI). Both tasks activated core regions within the visuomotor network, including primary and sensory motor cortices, premotor cortices, multiple visual areas, putamen, and cerebellum. Static force was associated with unique activity in a right-lateralized cortical network including inferior parietal lobe, ventral premotor cortex, and dorsolateral prefrontal cortex. In contrast, dynamic force was associated with unique activity in left-lateralized and midline cortical regions, including supplementary motor area, superior parietal lobe, fusiform gyrus, and visual area V3. These findings provide the first neuroimaging evidence supporting a lateralized pattern of brain activity for the production of static and dynamic precision grip force.

  19. Force models for particle-dynamics simulations of granular materials

    SciTech Connect

    Walton, O.R.

    1994-12-01

    Engineering-mechanics contact models are utilized to describe the inelastic, frictional interparticle forces acting in dry granular systems. Simple analyses based on one-dimensional chains are utilized to illustrate wave propagation phenomena in dense and dilute discrete particulates. The variation of restitution coefficient with impact velocity is illustrated for a variety of viscous and hysteretic normal force models. The effects of interparticle friction on material strength in discrete-particle simulations are much closer to measured values than are theories that do not allow article rotations.

  20. Dynamically adaptive mesh refinement technique for image reconstruction in optical tomography.

    PubMed

    Soloviev, Vadim Y; Krasnosselskaia, Lada V

    2006-04-20

    A novel adaptive mesh technique is introduced for problems of image reconstruction in luminescence optical tomography. A dynamical adaptation of the three-dimensional scheme based on the finite-volume formulation reduces computational time and balances the ill-posed nature of the inverse problem. The arbitrary shape of the bounding surface is handled by an additional refinement of computational cells on the boundary. Dynamical shrinking of the search volume is introduced to improve computational performance and accuracy while locating the luminescence target. Light propagation in the medium is modeled by the telegraph equation, and the image-reconstruction algorithm is derived from the Fredholm integral equation of the first kind. Stability and computational efficiency of the introduced method are demonstrated for image reconstruction of one and two spherical luminescent objects embedded within a breastlike tissue phantom. Experimental measurements are simulated by the solution of the forward problem on a grid of 5x5 light guides attached to the surface of the phantom.

  1. Analysis of limit forces on the vehicle wheels using an algorithm of Dynamic Square Method

    NASA Astrophysics Data System (ADS)

    Brukalski, M.

    2016-09-01

    This article presents a method named as Dynamic Square Method (DSM) used for dynamic analysis of a vehicle equipped with a four wheel drive system. This method allows determination of maximum (limit) forces acting on the wheels. Here, the maximum longitudinal forces acting on the wheels are assumed and then used to predict whether they can be achieved by a specific dynamic motion or whether the actual friction forces under a given wheel is large enough to transfer lateral forces. For the analysis of DSM a four wheel vehicle model is used. On the basis of this characteristic it is possible to determine the maximum longitudinal force acting on the wheels of the given axle depending on the lateral acceleration of the vehicle. The results of this analysis may be useful in the development of a control algorithm used for example in active differentials.

  2. Superadiabatic forces in the dynamics of the one-dimensional Gaussian core model

    NASA Astrophysics Data System (ADS)

    Bernreuther, Elias; Schmidt, Matthias

    2016-08-01

    Using Brownian dynamics computer simulations we investigate the dynamics of the one-body density and one-body current in a one-dimensional system of particles that interact with a repulsive Gaussian pair potential. We systematically split the internal force distribution into an adiabatic part, which originates from the equilibrium free energy, and a superadiabatic contribution, which is neglected in dynamical density functional theory. We find a strong dependence of the magnitude and phase of the superadiabatic force distribution on the initial state of the system. While the magnitude of the superadiabatic force is small if the system evolves from an equilibrium state inside of a parabolic external potential, it is large for particles with equidistant initial separations at high temperature. We analyze these findings in the light of the known mean-field behavior of Gaussian core particles and discuss a multi-occupancy mechanism which generates superadiabatic forces that are out of phase with respect to the adiabatic force.

  3. Dynamical Casimir–Polder force on a partially dressed atom in a cavity comprising a dielectric

    SciTech Connect

    Yang, H.; Zheng, T.Y. Zhang, X.; Shao, X.Q.; Pan, S.M.

    2014-05-15

    We put a two-level atom into a cavity comprising a dielectric with output coupling. An analytical expression of the dynamical Casimir–Polder force in such a system is obtained when the system starts from a partially dressed state. And the effects of several relevant parameters of the system on the time-dependent force are also discussed. -- Highlights: •We get the dynamical CP force on a partially dressed atom in a dielectric cavity. •The force in this cavity is larger than that in infinite dielectric space. •The force is not symmetric with respect to the center of the cavity. •The oscillating time of the force increases with the cavity size.

  4. WearDY: Wearable dynamics. A prototype for human whole-body force and motion estimation

    NASA Astrophysics Data System (ADS)

    Latella, Claudia; Kuppuswamy, Naveen; Nori, Francesco

    2016-06-01

    Motion capture is a powerful tool used in a large range of applications towards human movement analysis. Although it is a well-established technique, its main limitation is the lack of dynamic information such as forces and torques during the motion capture. In this paper, we present a novel approach for human wearable dynamic (WearDY) motion capture for the simultaneous estimation of whole-body forces along with the motion. Our conceptual framework encompasses traditional passive markers based methods, inertial and contact force sensor modalities and harnesses a probabilistic computational framework for estimating dynamic quantities originally proposed in the domain of humanoid robot control. We present preliminary experimental analysis of our framework on subjects performing a two Degrees-of-Freedom bowing task and we estimate the motion and dynamic quantities. We discuss the implication of our proposal towards the design of a novel wearable force and motion capture suit and its applications.

  5. Sliding mode-based lateral vehicle dynamics control using tyre force measurements

    NASA Astrophysics Data System (ADS)

    Kunnappillil Madhusudhanan, Anil; Corno, Matteo; Holweg, Edward

    2015-11-01

    In this work, a lateral vehicle dynamics control based on tyre force measurements is proposed. Most of the lateral vehicle dynamics control schemes are based on yaw rate whereas tyre forces are the most important variables in vehicle dynamics as tyres are the only contact points between the vehicle and road. In the proposed method, active front steering is employed to uniformly distribute the required lateral force among the front left and right tyres. The force distribution is quantified through the tyre utilisation coefficients. In order to address the nonlinearities and uncertainties of the vehicle model, a gain scheduling sliding-mode control technique is used. In addition to stabilising the lateral dynamics, the proposed controller is able to maintain maximum lateral acceleration. The proposed method is tested and validated on a multi-body vehicle simulator.

  6. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.

    PubMed

    Vitalini, F; Noé, F; Keller, B G

    2016-06-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8].

  7. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.

    PubMed

    Vitalini, F; Noé, F; Keller, B G

    2016-06-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161

  8. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields

    PubMed Central

    Vitalini, F.; Noé, F.; Keller, B.G.

    2016-01-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161

  9. Improved dynamic MRI reconstruction by exploiting sparsity and rank-deficiency.

    PubMed

    Majumdar, Angshul

    2013-06-01

    In this paper we address the problem of dynamic MRI reconstruction from partially sampled K-space data. Our work is motivated by previous studies in this area that proposed exploiting the spatiotemporal correlation of the dynamic MRI sequence by posing the reconstruction problem as a least squares minimization regularized by sparsity and low-rank penalties. Ideally the sparsity and low-rank penalties should be represented by the l(0)-norm and the rank of a matrix; however both are NP hard penalties. The previous studies used the convex l(1)-norm as a surrogate for the l(0)-norm and the non-convex Schatten-q norm (0reconstruct the dynamic MRI sequence by solving a least squares minimization problem regularized by l(p)-norm as the sparsity penalty and Schatten-q norm as the low-rank penalty. There are no efficient algorithms to solve the said problems. In this paper, we derive efficient algorithms to solve them. The experiments have been carried out on Dynamic Contrast Enhanced (DCE) MRI datasets. Both quantitative and qualitative analysis indicates the superiority of our proposed improvement over the existing methods.

  10. New jacking system resolves dynamic forces in 400-ft jack up

    SciTech Connect

    Chevallier, J.; Turner, L.

    1984-08-27

    This article describes the design and operation of Trident IX a successfully applied jack up system. A summary of Trident IX's two years of operation in the Arabian Gulf and offshore West Africa is presented. The system is compared to conventional jacking systems in terms of design, operation, costs and safety. Dynamic forces at 400 ft. water depths are summarized, and design of the legs to withstand these dynamic forces and accomodate the new system are explained. Features are listed.

  11. Structure and Dynamics of Dinucleosomes Assessed by Atomic Force Microscopy

    DOE PAGES

    Filenko, Nina A.; Palets, Dmytro B.; Lyubchenko, Yuri L.

    2012-01-01

    Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their populationmore » was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.« less

  12. Recording the dynamic endocytosis of single gold nanoparticles by AFM-based force tracing.

    PubMed

    Ding, Bohua; Tian, Yongmei; Pan, Yangang; Shan, Yuping; Cai, Mingjun; Xu, Haijiao; Sun, Yingchun; Wang, Hongda

    2015-05-01

    We utilized force tracing to directly record the endocytosis of single gold nanoparticles (Au NPs) with different sizes, revealing the size-dependent endocytosis dynamics and the crucial role of membrane cholesterol. The force, duration and velocity of Au NP invagination are accurately determined at the single-particle and microsecond level unprecedentedly. PMID:25864702

  13. Dynamic Image Forces Near a Metal Surface and the Point-Charge Motion

    ERIC Educational Resources Information Center

    Gabovich, A. M.; Voitenko, A. I.

    2012-01-01

    The problem of charge motion governed by image force attraction near a plane metal surface is considered and solved self-consistently. The temporal dispersion of metal dielectric permittivity makes the image forces dynamic and, hence, finite, contrary to the results of the conventional approach. Therefore, the maximal attainable velocity turns out…

  14. Theoretical reconstruction of realistic dynamics of highly coarse-grained cis-1,4-polybutadiene melts

    NASA Astrophysics Data System (ADS)

    Lyubimov, I. Y.; Guenza, M. G.

    2013-03-01

    The theory to reconstruct the atomistic-level chain diffusion from the accelerated dynamics that is measured in mesoscale simulations of the coarse-grained system, is applied here to the dynamics of cis-1,4-polybutadiene melts where each chain is described as a soft interacting colloidal particle. The rescaling formalism accounts for the corrections in the dynamics due to the change in entropy and the change in friction that are a consequence of the coarse-graining procedure. By including these two corrections the dynamics is rescaled to reproduce the realistic dynamics of the system described at the atomistic level. The rescaled diffusion coefficient obtained from mesoscale simulations of coarse-grained cis-1,4-polybutadiene melts shows good agreement with data from united atom simulations performed by Tsolou et al. [Macromolecules 38, 1478 (2005)], 10.1021/ma0491210. The derived monomer friction coefficient is used as an input to the theory for cooperative dynamics that describes the internal dynamics of a polymer moving in a transient regions of slow cooperative motion in a liquid of macromolecules. Theoretically predicted time correlation functions show good agreement with simulations in the whole range of length and time scales in which data are available.

  15. Theoretical reconstruction of realistic dynamics of highly coarse-grained cis-1,4-polybutadiene melts.

    PubMed

    Lyubimov, I Y; Guenza, M G

    2013-03-28

    The theory to reconstruct the atomistic-level chain diffusion from the accelerated dynamics that is measured in mesoscale simulations of the coarse-grained system, is applied here to the dynamics of cis-1,4-polybutadiene melts where each chain is described as a soft interacting colloidal particle. The rescaling formalism accounts for the corrections in the dynamics due to the change in entropy and the change in friction that are a consequence of the coarse-graining procedure. By including these two corrections the dynamics is rescaled to reproduce the realistic dynamics of the system described at the atomistic level. The rescaled diffusion coefficient obtained from mesoscale simulations of coarse-grained cis-1,4-polybutadiene melts shows good agreement with data from united atom simulations performed by Tsolou et al. [Macromolecules 38, 1478 (2005)]. The derived monomer friction coefficient is used as an input to the theory for cooperative dynamics that describes the internal dynamics of a polymer moving in a transient regions of slow cooperative motion in a liquid of macromolecules. Theoretically predicted time correlation functions show good agreement with simulations in the whole range of length and time scales in which data are available. PMID:23556797

  16. Low dose dynamic CT myocardial perfusion imaging using a statistical iterative reconstruction method

    SciTech Connect

    Tao, Yinghua; Chen, Guang-Hong; Hacker, Timothy A.; Raval, Amish N.; Van Lysel, Michael S.; Speidel, Michael A.

    2014-07-15

    Purpose: Dynamic CT myocardial perfusion imaging has the potential to provide both functional and anatomical information regarding coronary artery stenosis. However, radiation dose can be potentially high due to repeated scanning of the same region. The purpose of this study is to investigate the use of statistical iterative reconstruction to improve parametric maps of myocardial perfusion derived from a low tube current dynamic CT acquisition. Methods: Four pigs underwent high (500 mA) and low (25 mA) dose dynamic CT myocardial perfusion scans with and without coronary occlusion. To delineate the affected myocardial territory, an N-13 ammonia PET perfusion scan was performed for each animal in each occlusion state. Filtered backprojection (FBP) reconstruction was first applied to all CT data sets. Then, a statistical iterative reconstruction (SIR) method was applied to data sets acquired at low dose. Image voxel noise was matched between the low dose SIR and high dose FBP reconstructions. CT perfusion maps were compared among the low dose FBP, low dose SIR and high dose FBP reconstructions. Numerical simulations of a dynamic CT scan at high and low dose (20:1 ratio) were performed to quantitatively evaluate SIR and FBP performance in terms of flow map accuracy, precision, dose efficiency, and spatial resolution. Results: Forin vivo studies, the 500 mA FBP maps gave −88.4%, −96.0%, −76.7%, and −65.8% flow change in the occluded anterior region compared to the open-coronary scans (four animals). The percent changes in the 25 mA SIR maps were in good agreement, measuring −94.7%, −81.6%, −84.0%, and −72.2%. The 25 mA FBP maps gave unreliable flow measurements due to streaks caused by photon starvation (percent changes of +137.4%, +71.0%, −11.8%, and −3.5%). Agreement between 25 mA SIR and 500 mA FBP global flow was −9.7%, 8.8%, −3.1%, and 26.4%. The average variability of flow measurements in a nonoccluded region was 16.3%, 24.1%, and 937

  17. Forces and Motion: Dynamics of the Tethered Satellite

    NASA Technical Reports Server (NTRS)

    1994-01-01

    In this 'Lift off to Learning' series, Loren Shriver, commander of STS 46, and the other members of the mission (Claude Nicollier, Marsha Ivins, Andrew Allen, Jeffrey Hoffman, Franklin Chiang-Diaz, and Franco Maerba) use computer graphics, and physical experiments to explain how the tethered satellite to be deployed during their mission will be raised, how it works, the influence of the Shuttle on the satellite and the satellite's influence on the Shuttle's orbit, the gravitational effects, and other effects concerning the Theoretical Physics used to plan this mission (gravity gradient force, center of mass, angular momentum, centrifugal force, and coriolis effect). This video ends with a discussion of the technology transfer and utilization of this tethered satellite concept and design.

  18. The Role of Forcing and Internal Dynamics in explaining the 'Medieval Climate Anomaly'

    NASA Technical Reports Server (NTRS)

    Goossee, Hugues; Crespin, Elisabeth; Dubinkina, Svetlana; Loutre, Marie-France; Mann, Michael E.; Renssen, Hans; Shindell, Drew

    2012-01-01

    Proxy reconstructions suggest that peak global temperature during the past warm interval known as the Medieval Climate Anomaly (MCA, roughly 950-1250 AD) has been exceeded only during the most recent decades. To better understand the origin of this warm period, we use model simulations constrained by data assimilation establishing the spatial pattern of temperature changes that is most consistent with forcing estimates, model physics and the empirical information contained in paleoclimate proxy records. These numerical experiments demonstrate that the reconstructed spatial temperature pattern of the MCA can be explained by a simple thermodynamical response of the climate system to relatively weak changes in radiative forcing combined with a modification of the atmospheric circulation, displaying some similarities with the positive phase of the so-called Arctic Oscillation, and with northward shifts in the position of the Gulf Stream and Kuroshio currents. The mechanisms underlying the MCA are thus quite different from anthropogenic mechanisms responsible for modern global warming.

  19. Critical correlations and dynamics of force networks in a model of jammed granular solids

    NASA Astrophysics Data System (ADS)

    Turitsyn, Konstantin; Gruzberg, Ilya; Stern, Julie; Nienhuis, Bernard

    2010-03-01

    Distribution and correlations of contact forces in two-dimensional static granular packings is studied within a framework of (Edwards) Force Network Ensemble. A two-dimensional ``snooker'' model without friction is shown to be critical. An explicit expression for the force correlation function is derived using Bethe Ansatz. The force correlation function decays algebraically with universal exponent -2. This result implies that the system satisfies (extended) Harris criterion, and that the scale invariant force networks (studied by Ostojic et. al. Nature, 439, 2006) belong to the universality class of the usual percolation transition. These analytical results are confirmed by direct numerical sampling from the ensemble. It is also shown that the microscopic dynamics of forces experiences critical slowdown: the force network relaxation time grows like the sixth power of the system size. This result explains the slow convergence of standard Monte Carlo algorithms, and suggests novel approaches for studying the model.

  20. Exploring the Contribution of Collective Motions to the Dynamics of Forced-Unfolding in Tubulin

    PubMed Central

    Joshi, Harshad; Momin, Farhana; Haines, Kelly E.; Dima, Ruxandra I.

    2010-01-01

    Abstract Decomposition of the intrinsic dynamics of proteins into collective motions among distant regions of the protein structure provides a physically appealing approach that couples the dynamics of the system with its functional role. The cellular functions of microtubules (an essential component of the cytoskeleton in all eukaryotic cells) depend on their dynamic instability, which is altered by various factors among which applied forces are central. To shed light on the coupling between forces and the dynamic instability of microtubules, we focus on the investigation of the response of the microtubule subunits (tubulin) to applied forces. We address this point by adapting an approach designed to survey correlations for the equilibrium dynamics of proteins to the case of correlations for proteins forced-dynamics. The resulting collective motions in tubulin have a number of functional implications, such as the identification of long-range couplings with a role in blocking the dynamic instability of microtubules. A fundamental implication of our study for the life of a cell is that, to increase the likelihood of unraveling of large cytoskeletal filaments under physiological forces, molecular motors must use a combination of pulling and torsion rather than just pulling. PMID:20159162

  1. Rapid dynamic radial MRI via reference image enforced histogram constrained reconstruction

    NASA Astrophysics Data System (ADS)

    Gaass, Thomas; Bauman, Grzegorz; Potdevin, Guillaume; Noël, Peter B.; Haase, Axel

    2014-03-01

    Exploiting spatio-temporal redundancies in sub-Nyquist sampled dynamic MRI for the suppression of undersampling artifacts was shown to be of great success. However, temporally averaged and blurred structures in image space composite data poses the risk of false information in the reconstruction. Within this work we assess the possibility of employing the composite image histogram as a measure of undersampling artifacts and as basis of their suppression. The proposed algorithm utilizes a histogram, computed from a composite image within a dynamically acquired interleaved radial MRI measurement as reference to compensate for the impact of undersampling in temporally resolved data without the incorporation of temporal averaging. In addition an image space regularization utilizing a single frame low-resolution reconstruction is implemented to enforce overall contrast fidelity. The performance of the approach was evaluated on a simulated radial dynamic MRI acquisition and on two functional in vivo radial cardiac acquisitions. Results demonstrate that the algorithm maintained contrast properties, details and temporal resolution in the images, while effectively suppressing undersampling artifacts.

  2. Patient-adaptive reconstruction and acquisition in dynamic imaging with sensitivity encoding (PARADISE).

    PubMed

    Sharif, Behzad; Derbyshire, J Andrew; Faranesh, Anthony Z; Bresler, Yoram

    2010-08-01

    MRI of the human heart without explicit cardiac synchronization promises to extend the applicability of cardiac MR to a larger patient population and potentially expand its diagnostic capabilities. However, conventional nongated imaging techniques typically suffer from low image quality or inadequate spatio-temporal resolution and fidelity. Patient-Adaptive Reconstruction and Acquisition in Dynamic Imaging with Sensitivity Encoding (PARADISE) is a highly accelerated nongated dynamic imaging method that enables artifact-free imaging with high spatio-temporal resolutions by utilizing novel computational techniques to optimize the imaging process. In addition to using parallel imaging, the method gains acceleration from a physiologically driven spatio-temporal support model; hence, it is doubly accelerated. The support model is patient adaptive, i.e., its geometry depends on dynamics of the imaged slice, e.g., subject's heart rate and heart location within the slice. The proposed method is also doubly adaptive as it adapts both the acquisition and reconstruction schemes. Based on the theory of time-sequential sampling, the proposed framework explicitly accounts for speed limitations of gradient encoding and provides performance guarantees on achievable image quality. The presented in-vivo results demonstrate the effectiveness and feasibility of the PARADISE method for high-resolution nongated cardiac MRI during short breath-hold. PMID:20665794

  3. Contact force history and dynamic response due to the impact of a soft projectile

    NASA Technical Reports Server (NTRS)

    Grady, J. E.

    1988-01-01

    A series of ballistic impact tests on several different instrumented targets was performed to characterize the dynamic contact force history resulting from the impact of a compliant projectile. The results show that the variation of contact force history with impact velocity does not follow the trends predicted by classical impact models. An empirical model was therefore developed to describe this behavior. This model was then used in a finite-element analysis to estimate the force history and calculate the resulting dynamic strain response in a transversely impacted composite laminate.

  4. Estimation of changes in dynamic hydraulic force in a magnetically suspended centrifugal blood pump with transient computational fluid dynamics analysis.

    PubMed

    Masuzawa, Toru; Ohta, Akiko; Tanaka, Nobuatu; Qian, Yi; Tsukiya, Tomonori

    2009-01-01

    The effect of the hydraulic force on magnetically levitated (maglev) pumps should be studied carefully to improve the suspension performance and the reliability of the pumps. A maglev centrifugal pump, developed at Ibaraki University, was modeled with 926 376 hexahedral elements for computational fluid dynamics (CFD) analyses. The pump has a fully open six-vane impeller with a diameter of 72.5 mm. A self-bearing motor suspends the impeller in the radial direction. The maximum pressure head and flow rate were 250 mmHg and 14 l/min, respectively. First, a steady-state analysis was performed using commercial code STAR-CD to confirm the model's suitability by comparing the results with the real pump performance. Second, transient analysis was performed to estimate the hydraulic force on the levitated impeller. The impeller was rotated in steps of 1 degrees using a sliding mesh. The force around the impeller was integrated at every step. The transient analysis revealed that the direction of the radial force changed dynamically as the vane's position changed relative to the outlet port during one circulation, and the magnitude of this force was about 1 N. The current maglev pump has sufficient performance to counteract this hydraulic force. Transient CFD analysis is not only useful for observing dynamic flow conditions in a centrifugal pump but is also effective for obtaining information about the levitation dynamics of a maglev pump. PMID:19894088

  5. Estimation of changes in dynamic hydraulic force in a magnetically suspended centrifugal blood pump with transient computational fluid dynamics analysis.

    PubMed

    Masuzawa, Toru; Ohta, Akiko; Tanaka, Nobuatu; Qian, Yi; Tsukiya, Tomonori

    2009-01-01

    The effect of the hydraulic force on magnetically levitated (maglev) pumps should be studied carefully to improve the suspension performance and the reliability of the pumps. A maglev centrifugal pump, developed at Ibaraki University, was modeled with 926 376 hexahedral elements for computational fluid dynamics (CFD) analyses. The pump has a fully open six-vane impeller with a diameter of 72.5 mm. A self-bearing motor suspends the impeller in the radial direction. The maximum pressure head and flow rate were 250 mmHg and 14 l/min, respectively. First, a steady-state analysis was performed using commercial code STAR-CD to confirm the model's suitability by comparing the results with the real pump performance. Second, transient analysis was performed to estimate the hydraulic force on the levitated impeller. The impeller was rotated in steps of 1 degrees using a sliding mesh. The force around the impeller was integrated at every step. The transient analysis revealed that the direction of the radial force changed dynamically as the vane's position changed relative to the outlet port during one circulation, and the magnitude of this force was about 1 N. The current maglev pump has sufficient performance to counteract this hydraulic force. Transient CFD analysis is not only useful for observing dynamic flow conditions in a centrifugal pump but is also effective for obtaining information about the levitation dynamics of a maglev pump.

  6. Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields.

    PubMed

    Meher, Biswa Ranjan; Kumar, Mattaparthi Venkata Satish; Sharma, Smriti; Bandyopadhyay, Pradipta

    2012-12-01

    Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree reasonably well with the NMR S2 values, whereas ff99 calculated values deviate most from the NMR order parameters. Stereochemical geometry of protein models from each force field also agrees well with the remarks from NMR S2 values. However, between ff99SB and ff03, there are several differences, most notably in the loop regions. It is found that these loops are, in general, more flexible in the ff03 force field. This results in a larger active site cavity in the simulation with the ff03 force field. The effect of this difference in computer-aided drug design against flexible receptors is discussed.

  7. DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.

    PubMed

    Symonova, Olga; Topp, Christopher N; Edelsbrunner, Herbert

    2015-01-01

    We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.

  8. Absence of gamma-range corticomuscular coherence during dynamic force in a deafferented patient.

    PubMed

    Patino, Luis; Omlor, Wolfgang; Chakarov, Vihren; Hepp-Reymond, Marie-Claude; Kristeva, Rumyana

    2008-04-01

    Recently, we studied corticomuscular coherence (CMC) in a visuomotor task and showed for the first time gamma-range (30-45 Hz) CMC during isometric compensation of a periodically modulated dynamic force. We speculated that for the control of such forces, the sensorimotor system resonates at gamma-range frequencies to rapidly integrate the visual and proprioceptive information and produce the appropriate motor command. In this study, we tested the role of the proprioceptive afferent feedback on gamma-range CMC by comparing the deafferented patient GL to six age- and sex-matched subjects during the performance of a visuomotor force task consisting of isometric compensation of static and dynamic forces applied on the finger. Patient GL presented no significant gamma-band CMC during dynamic force. Instead, she had only beta-range CMC as in the static force condition; concurrently, her performance was significantly worse than that of the controls in both conditions. This gives support to the conclusions of our previous paper and suggests that proprioceptive information is mandatory in the genesis of gamma-band CMC during the generation and control of dynamic forces.

  9. Tidal dynamics: Coastal flooding and cycles of gravitational force

    SciTech Connect

    Wood, F.J.

    1986-01-01

    This book deals with the dynamic properties of perigean (and proxigean) spring tides and their special vulnerability to coastal flooding when impelled by strong onshore winds. A 400-year computer printout of the discrete astronomical circumstances producing such tides has been closely correlated with outstanding cases of tidal flooding from 1635 to the present.

  10. Dynamic Topography and Sea Level Change Inferred from Dipole and Quadrupole Moments of Plate Tectonic Reconstructions

    NASA Astrophysics Data System (ADS)

    Conrad, C. P.; Steinberger, B. M.; Torsvik, T. H.

    2014-12-01

    Although constraints on the history of mantle flow are difficult to obtain, tectonic reconstructions contain information about the longest wavelength patterns of mantle flow that drove plate motions in the past. To examine the influence of this long-wavelength flow on global geodynamics, we computed the dipole and quadrupole moments (harmonic degrees 1 and 2) of the spherical vector fields associated with tectonic reconstructions of plate motions back to 250 Ma. Areas of dipole or quadrupole divergence lie above regions of major mantle upwelling, and convergence regions reside atop major mantle downwellings. To constrain the time-dependence of dynamic topography associated with these upwellings and downwellings, we used a numerical model of present-day mantle flow to relate degree-1 and degree-2 patterns of dynamic topography to the orientations and amplitudes of the dipole and quadrupole moments of present-day plate motions. We then apply this relationship to the dipole and quadrupole moments of past plate motions to compute the long-wavelength components of dynamic topography for the Mesozoic and Cenozoic. Continental motions over this time-evolving dynamic topography predict patterns of continental uplift and subsidence that can be related to geological observations of continental surfaces relative to sea level. Net uplift or subsidence of the global seafloor can also induce eustatic sea level changes. We infer that dispersal of the Pangean supercontinent away from upwelling beneath Africa may have exposed the seafloor to an increasingly larger area of positive dynamic topography since the early Mesozoic that has caused up to 100 m of sea level rise during this time period. This component of sea level change helps to balance observations of Cretaceous and Cenozoic sea level change with an estimated total sea level budget that includes concurrent tectonic and climatic influences that produce sea level drop of up to ~250 m.

  11. Theoretical Analysis of Shear Wave Interference Patterns by Means of Dynamic Acoustic Radiation Forces.

    PubMed

    Hoyt, Kenneth

    2011-03-01

    Acoustic radiation forces associated with high intensity focused ultrasound stimulate shear wave propagation allowing shear wave speed and shear viscosity estimation of tissue structures. As wave speeds are meters per second, real time displacement tracking over an extend field-of-view using ultrasound is problematic due to very high frame rate requirements. However, two spatially separated dynamic external sources can stimulate shear wave motion leading to shear wave interference patterns. Advantages are shear waves can be imaged at lower frame rates and local interference pattern spatial properties reflect tissue's viscoelastic properties. Here a theoretical analysis of shear wave interference patterns by means of dynamic acoustic radiation forces is detailed. Using a viscoelastic Green's function analysis, tissue motion due to a pair of focused ultrasound beams and associated radiation forces are presented. Overall, this paper theoretically demonstrates shear wave interference patterns can be stimulated using dynamic acoustic radiation forces and tracked using conventional ultrasound imaging.

  12. Identification of nanoscale dissipation processes by dynamic atomic force microscopy.

    PubMed

    Garcia, R; Gómez, C J; Martinez, N F; Patil, S; Dietz, C; Magerle, R

    2006-07-01

    Identification of energy-dissipation processes at the nanoscale is demonstrated by using amplitude-modulation atomic force microscopy. The variation of the energy dissipated on a surface by a vibrating tip as a function of its oscillation amplitude has a shape that singles out the dissipative process occurring at the surface. The method is illustrated by calculating the energy-dissipation curves for surface energy hysteresis, long-range interfacial interactions and viscoelasticity. The method remains valid with independency of the amount of dissipated energy per cycle, from 0.1 to 50 eV. The agreement obtained between theory and experiments performed on silicon and polystyrene validates the method.

  13. Optimized molecular reconstruction procedure combining hybrid reverse Monte Carlo and molecular dynamics

    SciTech Connect

    Bousige, Colin; Boţan, Alexandru; Coasne, Benoît; Ulm, Franz-Josef; Pellenq, Roland J.-M.

    2015-03-21

    We report an efficient atom-scale reconstruction method that consists of combining the Hybrid Reverse Monte Carlo algorithm (HRMC) with Molecular Dynamics (MD) in the framework of a simulated annealing technique. In the spirit of the experimentally constrained molecular relaxation technique [Biswas et al., Phys. Rev. B 69, 195207 (2004)], this modified procedure offers a refined strategy in the field of reconstruction techniques, with special interest for heterogeneous and disordered solids such as amorphous porous materials. While the HRMC method generates physical structures, thanks to the use of energy penalties, the combination with MD makes the method at least one order of magnitude faster than HRMC simulations to obtain structures of similar quality. Furthermore, in order to ensure the transferability of this technique, we provide rational arguments to select the various input parameters such as the relative weight ω of the energy penalty with respect to the structure optimization. By applying the method to disordered porous carbons, we show that adsorption properties provide data to test the global texture of the reconstructed sample but are only weakly sensitive to the presence of defects. In contrast, the vibrational properties such as the phonon density of states are found to be very sensitive to the local structure of the sample.

  14. Blood flow dynamics and sensitivity in breasts after reconstruction with DIEP-flap.

    PubMed

    Klasson, Stina; Svensson, Karin; Wollmer, Per; Velander, Patrik; Svensson, Henry

    2014-12-01

    A method of breast reconstruction is based on the Deep Inferior Epigastric Perforator (DIEP) technique. Skin and fat are transplanted from the abdomen to the chest; blood vessels are reconnected through microsurgery. Nerves are, however, left unconnected. This study aims to evaluate the blood flow and reinnervation of blood vessels and skin in breasts reconstructed by DIEP flaps without neural repair. In all, DIEP flaps of 10 patients were tested at an average of 16.3 months postoperatively. Blood flow was assessed by PeriScan PIM II System, both before and after indirect heating. Tactile perception threshold was assessed by Semmes-Weinstein monofilament and thermal sensibility by SENSELab MSA Thermotest. The patients' contralateral breasts were used as controls. The blood flow of the flaps was statistically significantly lower than in the control breasts, both before and after indirect heating. The change in blood flow after indirect heating did, however, not significantly differ when comparing the breasts. All flaps regained deep pressure sensibility in all four quadrants. Five patients regained even better sensibility in one of their quadrants. Seven patients regained perception of cold stimuli, five perceived warmth. This study has shown that skin blood flow regulation is present in DIEP flaps 1 year after reconstruction. Blood flow dynamics are very similar to those in the normal breast. There is also a recovery of tactile and thermal sensibility, but this study has not shown any clear parallels between recovery blood flow, tactile sensibility and thermal sensibility.

  15. Blood flow dynamics and sensitivity in breasts after reconstruction with DIEP-flap.

    PubMed

    Klasson, Stina; Svensson, Karin; Wollmer, Per; Velander, Patrik; Svensson, Henry

    2014-12-01

    A method of breast reconstruction is based on the Deep Inferior Epigastric Perforator (DIEP) technique. Skin and fat are transplanted from the abdomen to the chest; blood vessels are reconnected through microsurgery. Nerves are, however, left unconnected. This study aims to evaluate the blood flow and reinnervation of blood vessels and skin in breasts reconstructed by DIEP flaps without neural repair. In all, DIEP flaps of 10 patients were tested at an average of 16.3 months postoperatively. Blood flow was assessed by PeriScan PIM II System, both before and after indirect heating. Tactile perception threshold was assessed by Semmes-Weinstein monofilament and thermal sensibility by SENSELab MSA Thermotest. The patients' contralateral breasts were used as controls. The blood flow of the flaps was statistically significantly lower than in the control breasts, both before and after indirect heating. The change in blood flow after indirect heating did, however, not significantly differ when comparing the breasts. All flaps regained deep pressure sensibility in all four quadrants. Five patients regained even better sensibility in one of their quadrants. Seven patients regained perception of cold stimuli, five perceived warmth. This study has shown that skin blood flow regulation is present in DIEP flaps 1 year after reconstruction. Blood flow dynamics are very similar to those in the normal breast. There is also a recovery of tactile and thermal sensibility, but this study has not shown any clear parallels between recovery blood flow, tactile sensibility and thermal sensibility. PMID:24693867

  16. Optimized molecular reconstruction procedure combining hybrid reverse Monte Carlo and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bousige, Colin; BoÅ£an, Alexandru; Ulm, Franz-Josef; Pellenq, Roland J.-M.; Coasne, Benoît

    2015-03-01

    We report an efficient atom-scale reconstruction method that consists of combining the Hybrid Reverse Monte Carlo algorithm (HRMC) with Molecular Dynamics (MD) in the framework of a simulated annealing technique. In the spirit of the experimentally constrained molecular relaxation technique [Biswas et al., Phys. Rev. B 69, 195207 (2004)], this modified procedure offers a refined strategy in the field of reconstruction techniques, with special interest for heterogeneous and disordered solids such as amorphous porous materials. While the HRMC method generates physical structures, thanks to the use of energy penalties, the combination with MD makes the method at least one order of magnitude faster than HRMC simulations to obtain structures of similar quality. Furthermore, in order to ensure the transferability of this technique, we provide rational arguments to select the various input parameters such as the relative weight ω of the energy penalty with respect to the structure optimization. By applying the method to disordered porous carbons, we show that adsorption properties provide data to test the global texture of the reconstructed sample but are only weakly sensitive to the presence of defects. In contrast, the vibrational properties such as the phonon density of states are found to be very sensitive to the local structure of the sample.

  17. Dynamics of Oscillatory Vortex Multipoles Generated by Electromagnetic Forcing

    NASA Astrophysics Data System (ADS)

    Figueroa, Aldo; Cuevas, Sergio; Ramos, Eduardo

    2010-11-01

    Vortices formed by the concurrent effect on a localized magnetic field distribution and two alternate electric currents perpendicular to each other in a shallow (4mm) layer of an electrolyte are analyzed. Alternate currents with frequencies and amplitude in the range of 1-500 mHz and 80 mA, respectively, are explored. For a single dipolar magnetic field and a single electric current, the dominant structure of the flow is a pair of alternating lobes located co-linear with the generated Lorenz force. The flow presents a resonant behavior when the forcing frequency is around 10 mHz. When multipoles are used to generate the magnetic field, more complicated lobe distributions are obtained. The flow patterns were successfully described using a quasi-two-dimensional numerical model. A tridimensional numerical models corroborates the theoretical results. Flow visualization and numerical Lagrangian particle tracking indicate that multipolar flows present symmetries according to the magnetic field distributions. Although in some regions the flow patterns efficiently mix the fluid, the mixing is inhomogeneous due to symmetry conditions of the flows. Mixing is enhanced when symmetries are destroyed by the use of a random array of magnets or by injecting two electric currents.

  18. A comparison of static and dynamic optimization muscle force predictions during wheelchair propulsion.

    PubMed

    Morrow, Melissa M; Rankin, Jeffery W; Neptune, Richard R; Kaufman, Kenton R

    2014-11-01

    The primary purpose of this study was to compare static and dynamic optimization muscle force and work predictions during the push phase of wheelchair propulsion. A secondary purpose was to compare the differences in predicted shoulder and elbow kinetics and kinematics and handrim forces. The forward dynamics simulation minimized differences between simulated and experimental data (obtained from 10 manual wheelchair users) and muscle co-contraction. For direct comparison between models, the shoulder and elbow muscle moment arms and net joint moments from the dynamic optimization were used as inputs into the static optimization routine. RMS errors between model predictions were calculated to quantify model agreement. There was a wide range of individual muscle force agreement that spanned from poor (26.4% Fmax error in the middle deltoid) to good (6.4% Fmax error in the anterior deltoid) in the prime movers of the shoulder. The predicted muscle forces from the static optimization were sufficient to create the appropriate motion and joint moments at the shoulder for the push phase of wheelchair propulsion, but showed deviations in the elbow moment, pronation-supination motion and hand rim forces. These results suggest the static approach does not produce results similar enough to be a replacement for forward dynamics simulations, and care should be taken in choosing the appropriate method for a specific task and set of constraints. Dynamic optimization modeling approaches may be required for motions that are greatly influenced by muscle activation dynamics or that require significant co-contraction. PMID:25282075

  19. A comparison of static and dynamic optimization muscle force predictions during wheelchair propulsion.

    PubMed

    Morrow, Melissa M; Rankin, Jeffery W; Neptune, Richard R; Kaufman, Kenton R

    2014-11-01

    The primary purpose of this study was to compare static and dynamic optimization muscle force and work predictions during the push phase of wheelchair propulsion. A secondary purpose was to compare the differences in predicted shoulder and elbow kinetics and kinematics and handrim forces. The forward dynamics simulation minimized differences between simulated and experimental data (obtained from 10 manual wheelchair users) and muscle co-contraction. For direct comparison between models, the shoulder and elbow muscle moment arms and net joint moments from the dynamic optimization were used as inputs into the static optimization routine. RMS errors between model predictions were calculated to quantify model agreement. There was a wide range of individual muscle force agreement that spanned from poor (26.4% Fmax error in the middle deltoid) to good (6.4% Fmax error in the anterior deltoid) in the prime movers of the shoulder. The predicted muscle forces from the static optimization were sufficient to create the appropriate motion and joint moments at the shoulder for the push phase of wheelchair propulsion, but showed deviations in the elbow moment, pronation-supination motion and hand rim forces. These results suggest the static approach does not produce results similar enough to be a replacement for forward dynamics simulations, and care should be taken in choosing the appropriate method for a specific task and set of constraints. Dynamic optimization modeling approaches may be required for motions that are greatly influenced by muscle activation dynamics or that require significant co-contraction.

  20. Dynamically adjustable foot-ground contact model to estimate ground reaction force during walking and running.

    PubMed

    Jung, Yihwan; Jung, Moonki; Ryu, Jiseon; Yoon, Sukhoon; Park, Sang-Kyoon; Koo, Seungbum

    2016-03-01

    Human dynamic models have been used to estimate joint kinetics during various activities. Kinetics estimation is in demand in sports and clinical applications where data on external forces, such as the ground reaction force (GRF), are not available. The purpose of this study was to estimate the GRF during gait by utilizing distance- and velocity-dependent force models between the foot and ground in an inverse-dynamics-based optimization. Ten males were tested as they walked at four different speeds on a force plate-embedded treadmill system. The full-GRF model whose foot-ground reaction elements were dynamically adjusted according to vertical displacement and anterior-posterior speed between the foot and ground was implemented in a full-body skeletal model. The model estimated the vertical and shear forces of the GRF from body kinematics. The shear-GRF model with dynamically adjustable shear reaction elements according to the input vertical force was also implemented in the foot of a full-body skeletal model. Shear forces of the GRF were estimated from body kinematics, vertical GRF, and center of pressure. The estimated full GRF had the lowest root mean square (RMS) errors at the slow walking speed (1.0m/s) with 4.2, 1.3, and 5.7% BW for anterior-posterior, medial-lateral, and vertical forces, respectively. The estimated shear forces were not significantly different between the full-GRF and shear-GRF models, but the RMS errors of the estimated knee joint kinetics were significantly lower for the shear-GRF model. Providing COP and vertical GRF with sensors, such as an insole-type pressure mat, can help estimate shear forces of the GRF and increase accuracy for estimation of joint kinetics. PMID:26979885

  1. Reconstructing monsoon dynamics on the Tibetan Plateau using ostracod shell chemistry

    NASA Astrophysics Data System (ADS)

    Boerner, N.; De Baere, B.; Yang, Q.; Francois, R. H. G. M.; Jochum, K. P.; Frenzel, P.; Schwalb, A.

    2014-12-01

    Ostracod shells have widely been used as source material for geochemical analysis of stable isotope and trace element composition in paleolimnological reconstruction of lake hydrochemistry and climate as they provide insight into past water balance and solute evolution of lakes. During five fieldtrips to the Tibetan Plateau, taking place between 2008 and 2012, we collected live and sub-recent ostracods from 333 sites. Hydrochemical parameters, such as temperature, electrical conductivity, pH as well as major and minor ion concentrations were measured at each site and show high variability between sites. Adult intact individuals from the most common ostracod taxa were selected and their shell chemistry analyzed. The trace elemental data for the living ostracods compared to the hydrological data provides a calibration dataset for further hydrological and thus climatological reconstruction. Mg/Ca, Sr/Ca and Ba/Ca ratios in ostracod shells provide information about past water temperature and salinity resulting from changes in precipitation vs. evaporation ratios and monsoon activity. Furthermore, Mn/Ca, Fe/Ca and U/Ca ratios are being explored as redox indicators to reconstruct oxygenation cycles. To reconstruct the monsoon dynamics on the Tibetan Plateau, sediment cores from different lakes on an east-west transect were taken: two long sediment cores from lakes Nam Co and Tangra Yumco, covering the past 20,000 years, and a short core from Lake Taro Co. The lakes feature an alkaline environment but show significant differences in their electrical conductivity ranging from 0.99 mS/cm (Taro Co) and 1.8 mS/cm (Nam Co) to 12 mS/cm (Tangra Yumco). The chemical composition of valves of the most common ostracod species in these lakes, Leucocytherella sinensis, was analyzed using laser ablation ICP-MS. The reconstruction provides a more extensive insight in past precipitation - evaporation balance and lake level change and provides clues about the interaction between the

  2. Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

    PubMed Central

    Poon, Art F. Y.; Swenson, Luke C.; Bunnik, Evelien M.; Edo-Matas, Diana; Schuitemaker, Hanneke; van 't Wout, Angélique B.; Harrigan, P. Richard

    2012-01-01

    At the early stage of infection, human immunodeficiency virus (HIV)-1 predominantly uses the CCR5 coreceptor for host cell entry. The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progression to AIDS. The presence of a ‘fitness valley’ separating CCR5- and CXCR4-using genotypes is postulated to be a biological determinant of whether the HIV coreceptor switch occurs. Using phylogenetic methods to reconstruct the evolutionary dynamics of HIV within hosts enables us to discriminate between competing models of this process. We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data. These data were generated by next-generation sequencing of HIV RNA extracted from longitudinal serum samples (median 7 time points) from 8 untreated subjects with chronic HIV infections (Amsterdam Cohort Studies on HIV-1 infection and AIDS). We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days. HIV coreceptor usage was predicted from reconstructed ancestral sequences using the geno2pheno algorithm. We determined that the first mutations contributing to CXCR4 use emerged about 16 (per subject range 4 to 30) months before the earliest predicted CXCR4-using ancestor, which preceded the first positive cell-based assay of CXCR4 usage by 10 (range 5 to 25) months. CXCR4 usage arose in multiple lineages within 5 of 8 subjects, and ancestral lineages following alternate mutational pathways before going extinct were common. We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant. PMID:23133358

  3. Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data.

    PubMed

    Poon, Art F Y; Swenson, Luke C; Bunnik, Evelien M; Edo-Matas, Diana; Schuitemaker, Hanneke; van 't Wout, Angélique B; Harrigan, P Richard

    2012-01-01

    At the early stage of infection, human immunodeficiency virus (HIV)-1 predominantly uses the CCR5 coreceptor for host cell entry. The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progression to AIDS. The presence of a 'fitness valley' separating CCR5- and CXCR4-using genotypes is postulated to be a biological determinant of whether the HIV coreceptor switch occurs. Using phylogenetic methods to reconstruct the evolutionary dynamics of HIV within hosts enables us to discriminate between competing models of this process. We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data. These data were generated by next-generation sequencing of HIV RNA extracted from longitudinal serum samples (median 7 time points) from 8 untreated subjects with chronic HIV infections (Amsterdam Cohort Studies on HIV-1 infection and AIDS). We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days. HIV coreceptor usage was predicted from reconstructed ancestral sequences using the geno2pheno algorithm. We determined that the first mutations contributing to CXCR4 use emerged about 16 (per subject range 4 to 30) months before the earliest predicted CXCR4-using ancestor, which preceded the first positive cell-based assay of CXCR4 usage by 10 (range 5 to 25) months. CXCR4 usage arose in multiple lineages within 5 of 8 subjects, and ancestral lineages following alternate mutational pathways before going extinct were common. We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant.

  4. A twentieth-century reanalysis forced ocean model to reconstruct the North Atlantic climate variation during the 1920s

    NASA Astrophysics Data System (ADS)

    Müller, W. A.; Matei, D.; Bersch, M.; Jungclaus, J. H.; Haak, H.; Lohmann, K.; Compo, G. P.; Sardeshmukh, P. D.; Marotzke, J.

    2015-04-01

    The observed North Atlantic multi-decadal variability for the period 1872-2009 is reconstructed with the Max Planck Institute ocean model, which is forced with an ensemble of the atmospheric twentieth century reanalysis. Special emphasis is put on the early part of the experiments, which includes a prominent climate variation during the 1920s. The experiments are in agreement with selected hydrographic records, indicating a transition from cold and fresh North Atlantic water properties, prior to the 1920 climate variation, towards warm and saline waters afterwards. Examining the variation reveals that sea level pressure (SLP) anomalies prior to the 1900s resemble a negative phase of North Atlantic Oscillation and associated weak winds result in a weak North Atlantic Current (NAC) and sub-polar gyre (SPG). This leads to a reduced transport of warm and saline waters into the higher latitudes. Simultaneously, Arctic freshwater release results in the accumulation of cold and fresh water properties, which cover the upper layers in the Labrador Sea and subsequently suppress convection. From the 1910s, the Arctic freshwater export is reduced, and, NAC and SPG are strengthened as a result of an increased SLP gradient over the North Atlantic. Concurrently, Labrador Sea convection and Atlantic meridional overturning circulation (AMOC) increase. The intensified NAC, SPG, and AMOC redistribute sub-tropical water into the North Atlantic and Nordic Seas, thereby increasing observed and modelled temperature and salinity during the 1920s.

  5. Reconstruction of an input function from a dynamic PET water image using multiple tissue curves

    NASA Astrophysics Data System (ADS)

    Kudomi, Nobuyuki; Maeda, Yukito; Yamamoto, Yuka; Nishiyama, Yoshihiro

    2016-08-01

    Quantification of cerebral blood flow (CBF) is important for the understanding of normal and pathologic brain physiology. When CBF is assessed using PET with {{\\text{H}}2} 15O or C15O2, its calculation requires an arterial input function, which generally requires invasive arterial blood sampling. The aim of the present study was to develop a new technique to reconstruct an image derived input function (IDIF) from a dynamic {{\\text{H}}2} 15O PET image as a completely non-invasive approach. Our technique consisted of using a formula to express the input using tissue curve with rate constant parameter. For multiple tissue curves extracted from the dynamic image, the rate constants were estimated so as to minimize the sum of the differences of the reproduced inputs expressed by the extracted tissue curves. The estimated rates were used to express the inputs and the mean of the estimated inputs was used as an IDIF. The method was tested in human subjects (n  =  29) and was compared to the blood sampling method. Simulation studies were performed to examine the magnitude of potential biases in CBF and to optimize the number of multiple tissue curves used for the input reconstruction. In the PET study, the estimated IDIFs were well reproduced against the measured ones. The difference between the calculated CBF values obtained using the two methods was small as around  <8% and the calculated CBF values showed a tight correlation (r  =  0.97). The simulation showed that errors associated with the assumed parameters were  <10%, and that the optimal number of tissue curves to be used was around 500. Our results demonstrate that IDIF can be reconstructed directly from tissue curves obtained through {{\\text{H}}2} 15O PET imaging. This suggests the possibility of using a completely non-invasive technique to assess CBF in patho-physiological studies.

  6. On the optimal reconstruction and control of adaptive optical systems with mirror dynamics.

    PubMed

    Correia, Carlos; Raynaud, Henri-François; Kulcsár, Caroline; Conan, Jean-Marc

    2010-02-01

    In adaptive optics (AO) the deformable mirror (DM) dynamics are usually neglected because, in general, the DM can be considered infinitely fast. Such assumption may no longer apply for the upcoming Extremely Large Telescopes (ELTs) with DM that are several meters in diameter with slow and/or resonant responses. For such systems an important challenge is to design an optimal regulator minimizing the variance of the residual phase. In this contribution, the general optimal minimum-variance (MV) solution to the full dynamical reconstruction and control problem of AO systems (AOSs) is established. It can be looked upon as the parent solution from which simpler (used hitherto) suboptimal solutions can be derived as special cases. These include either partial DM-dynamics-free solutions or solutions derived from the static minimum-variance reconstruction (where both atmospheric disturbance and DM dynamics are neglected altogether). Based on a continuous stochastic model of the disturbance, a state-space approach is developed that yields a fully optimal MV solution in the form of a discrete-time linear-quadratic-Gaussian (LQG) regulator design. From this LQG standpoint, the control-oriented state-space model allows one to (1) derive the optimal state-feedback linear regulator and (2) evaluate the performance of both the optimal and the sub-optimal solutions. Performance results are given for weakly damped second-order oscillatory DMs with large-amplitude resonant responses, in conditions representative of an ELT AO system. The highly energetic optical disturbance caused on the tip/tilt (TT) modes by the wind buffeting is considered. Results show that resonant responses are correctly handled with the MV regulator developed here. The use of sub-optimal regulators results in prohibitive performance losses in terms of residual variance; in addition, the closed-loop system may become unstable for resonant frequencies in the range of interest. PMID:20126246

  7. Analysis of dynamic cantilever behavior in tapping mode atomic force microscopy.

    PubMed

    Deng, Wenqi; Zhang, Guang-Ming; Murphy, Mark F; Lilley, Francis; Harvey, David M; Burton, David R

    2015-10-01

    Tapping mode atomic force microscopy (AFM) provides phase images in addition to height and amplitude images. Although the behavior of tapping mode AFM has been investigated using mathematical modeling, comprehensive understanding of the behavior of tapping mode AFM still poses a significant challenge to the AFM community, involving issues such as the correct interpretation of the phase images. In this paper, the cantilever's dynamic behavior in tapping mode AFM is studied through a three dimensional finite element method. The cantilever's dynamic displacement responses are firstly obtained via simulation under different tip-sample separations, and for different tip-sample interaction forces, such as elastic force, adhesion force, viscosity force, and the van der Waals force, which correspond to the cantilever's action upon various different representative computer-generated test samples. Simulated results show that the dynamic cantilever displacement response can be divided into three zones: a free vibration zone, a transition zone, and a contact vibration zone. Phase trajectory, phase shift, transition time, pseudo stable amplitude, and frequency changes are then analyzed from the dynamic displacement responses that are obtained. Finally, experiments are carried out on a real AFM system to support the findings of the simulations. PMID:26303510

  8. Integrated dynamic and static tactile sensor: focus on static force sensing

    NASA Astrophysics Data System (ADS)

    Wettels, Nicholas; Pletner, Baruch

    2012-04-01

    Object grasping by robotic hands in unstructured environments demands a sensor that is durable, compliant, and responsive to static and dynamic force conditions. In order for a tactile sensor to be useful for grasp control in these, it should have the following properties: tri-axial force sensing (two shear plus normal component), dynamic event sensing across slip frequencies, compliant surface for grip, wide dynamic range (depending on application), insensitivity to environmental conditions, ability to withstand abuse and good sensing behavior (e.g. low hysteresis, high repeatability). These features can be combined in a novel multimodal tactile sensor. This sensor combines commercial-off-the-shelf MEMS technology with two proprietary force sensors: a high bandwidth device based on PZT technology and low bandwidth device based on elastomers and optics. In this study, we focus on the latter transduction mechanism and the proposed architecture of the completed device. In this study, an embedded LED was utilized to produce a constant light source throughout a layer of silicon rubber which covered a plastic mandrel containing a set of sensitive phototransistors. Features about the contacted object such as center of pressure and force vectors can be extracted from the information in the changing patterns of light. The voltage versus force relationship obtained with this molded humanlike finger had a wide dynamic range that coincided with forces relevant for most human grip tasks.

  9. Control of cell-cell forces and collective cell dynamics by the intercellular adhesome

    PubMed Central

    Bazellières, Elsa; Conte, Vito; Elosegui-Artola, Alberto; Serra-Picamal, Xavier; Bintanel-Morcillo, María; Roca-Cusachs, Pere; Muñoz, José J; Sales-Pardo, Marta; Guimerà, Roger; Trepat, Xavier

    2015-01-01

    Dynamics of epithelial tissues determines key processes in development, tissue healing, and cancer invasion. These processes are critically influenced by cell-cell adhesion forces. However, the identity of the proteins that resist and transmit forces at cell-cell junctions remains unclear, and how these proteins control tissue dynamics is largely unknown. Here we provide a systematic study of the interplay between cell-cell adhesion proteins, intercellular forces, and epithelial tissue dynamics. We show that collective cellular responses to selective perturbations of the intercellular adhesome conform to three mechanical phenotypes. These phenotypes are controlled by different molecular modules and characterized by distinct relationships between cellular kinematics and intercellular forces. We show that these forces and their rates can be predicted by the concentrations of cadherins and catenins. Unexpectedly, we identified different mechanical roles for P-cadherin and E-cadherin; while P-cadherin predicts levels of intercellular force, E-cadherin predicts the rate at which intercellular force builds up. PMID:25812522

  10. Vegetation and soil dynamics under climatic to anthropogenic forcing through the Holocene in Eastern France

    NASA Astrophysics Data System (ADS)

    Doyen, Elise; Vannière, Boris; Gauthier, Emilie; Bichet, Vincent; Berger, Jean-François; Arnaud, Fabien

    2010-05-01

    Small lakes with little catchment areas, and high resolution Holocene sediment infilling, offer the interest to record mainly local perturbation and to study the switch from climatic to anthropogenic forcing. Two cores were extracted from Lake Antre in the Jura Mountains (Eastern France, 798 m a.s.l) and Lake Moras located on a low-elevated plateau from the upper Rhone valley (Eastern France, 304 m a.s.l). Cores taken from the deep zone of the lakes present continuous sedimentary series from the Late-glacial (15 000 cal. BP) for Lake Moras and from the Atlantic chronozone (6000 cal. BP) for Lake Antre. Several archaeological excavations and investigations around Lakes Antre and Moras give evidence of major human occupation during Gallo-roman period, while former settlements are indicating by Pre- and Protohistoric archaeological artifacts. Multi-proxy reconstructions with high temporal resolution were undertaken: vegetation dynamics by pollen analysis, fire history by the quantification of microscopic charcoal and soil erosion by magnetic susceptibility measurements. Before the anthropogenic forcing, during the mid-Holocene environment of both lakes are constituted mainly by a dense mixed oak forest. The first palaeoecological signs of anthropogenic impact on the two sites appear to have been discontinuous and limited. They appear at the early Neolithic (ca 6000 cal .BP) for Lake Moras and during the Bronze Age (4000 to 3000 cal .BP) for Lake Antre. For the both sites, all the proxies indicate an acceleration of human impact around 3000 to 2700 cal. BP i.e. at the transition between the Bronze Age and the beginning of the Iron Age. The dense forest and the Alnus dominated vegetation on borders of lakes are affected by several clearances. The influx of micro-charcoal increases due to the use of the fire for clearing and manage settlements. The development of Poaceae and Anthropogenic Pollen Indicators (API) suggest an expansion of pastures, whereas the farming

  11. The acute effects of dynamic and ballistic stretching on vertical jump height, force, and power.

    PubMed

    Jaggers, Jason R; Swank, Ann M; Frost, Karen L; Lee, Chong D

    2008-11-01

    Stretching before performance is a common practice among athletes in hopes of increasing performance and reducing the risk of injury. However, cumulative results indicate a negative impact of static stretching and proprioceptive neuromuscular facilitation (PNF) on performance; thus, there is a need for evaluating other stretching strategies for effective warm-up. The purpose of this study was to compare the differences between two sets of ballistic stretching and two sets of a dynamic stretching routine on vertical jump performance. Twenty healthy male and female college students between the ages of 22 and 34 (24.8 +/- 3 years) volunteered to participate in this study. All subjects completed three individual testing sessions on three nonconsecutive days. On each day, the subjects completed one of three treatments (no stretch, ballistic stretch, and dynamic stretch). Intraclass reliability was determined using the data obtained from each subject. A paired samples t-test revealed no significant difference in jump height, force, or power when comparing no stretch with ballistic stretch. A significant difference was found on jump power when comparing no stretch with dynamic stretch, but no significant difference was found for jump height or force. Statistics showed a very high reliability when measuring jump height, force, and power using the Kistler Quattro Jump force plate. It seems that neither dynamic stretching nor ballistic stretching will result in an increase in vertical jump height or force. However, dynamic stretching elicited gains in jump power poststretch.

  12. GravitoMagnetic force in modified Newtonian dynamics

    SciTech Connect

    Exirifard, Qasem

    2013-08-01

    We introduce the Gauge Vector-Tensor (GVT) theory by extending the AQUAL's approach to the GravitoElectroMagnetism (GEM) approximation of gravity. GVT is a generally covariant theory of gravity composed of a pseudo Riemannian metric and two U(1) gauge connections that reproduces MOND in the limit of very weak gravitational fields while remains consistent with the Einstein-Hilbert gravity in the limit of strong and Newtonian gravitational fields. GVT also provides a simple framework to study the GEM approximation to gravity. We illustrate that the gravitomagnetic force at the edge of a galaxy can be in accord with either GVT or ΛCDM but not both. We also study the physics of the GVT theory around the gravitational saddle point of the Sun and Jupiter system. We notice that the conclusive refusal of the GVT theory demands measuring either both of the gravitoelectric and gravitomagnetic fields inside the Sun-Jupiter MOND window, or the gravitoelectric field inside two different solar GVT MOND windows. The GVT theory, however, will be favored by observing an anomaly in the gravitoelectric field inside a single MOND window.

  13. Numerical, analytical, experimental study of fluid dynamic forces in seals

    NASA Astrophysics Data System (ADS)

    Shapiro, William; Artiles, Antonio; Aggarwal, Bharat; Walowit, Jed; Athavale, Mahesh M.; Preskwas, Andrzej J.

    1992-04-01

    NASA/Lewis Research Center is sponsoring a program for providing computer codes for analyzing and designing turbomachinery seals for future aerospace and engine systems. The program is made up of three principal components: (1) the development of advanced three dimensional (3-D) computational fluid dynamics codes, (2) the production of simpler two dimensional (2-D) industrial codes, and (3) the development of a knowledge based system (KBS) that contains an expert system to assist in seal selection and design. The first task has been to concentrate on cylindrical geometries with straight, tapered, and stepped bores. Improvements have been made by adoption of a colocated grid formulation, incorporation of higher order, time accurate schemes for transient analysis and high order discretization schemes for spatial derivatives. This report describes the mathematical formulations and presents a variety of 2-D results, including labyrinth and brush seal flows. Extensions of 3-D are presently in progress.

  14. Numerical, analytical, experimental study of fluid dynamic forces in seals

    NASA Technical Reports Server (NTRS)

    Shapiro, William; Artiles, Antonio; Aggarwal, Bharat; Walowit, Jed; Athavale, Mahesh M.; Preskwas, Andrzej J.

    1992-01-01

    NASA/Lewis Research Center is sponsoring a program for providing computer codes for analyzing and designing turbomachinery seals for future aerospace and engine systems. The program is made up of three principal components: (1) the development of advanced three dimensional (3-D) computational fluid dynamics codes, (2) the production of simpler two dimensional (2-D) industrial codes, and (3) the development of a knowledge based system (KBS) that contains an expert system to assist in seal selection and design. The first task has been to concentrate on cylindrical geometries with straight, tapered, and stepped bores. Improvements have been made by adoption of a colocated grid formulation, incorporation of higher order, time accurate schemes for transient analysis and high order discretization schemes for spatial derivatives. This report describes the mathematical formulations and presents a variety of 2-D results, including labyrinth and brush seal flows. Extensions of 3-D are presently in progress.

  15. Recording the dynamic endocytosis of single gold nanoparticles by AFM-based force tracing

    NASA Astrophysics Data System (ADS)

    Ding, Bohua; Tian, Yongmei; Pan, Yangang; Shan, Yuping; Cai, Mingjun; Xu, Haijiao; Sun, Yingchun; Wang, Hongda

    2015-04-01

    We utilized force tracing to directly record the endocytosis of single gold nanoparticles (Au NPs) with different sizes, revealing the size-dependent endocytosis dynamics and the crucial role of membrane cholesterol. The force, duration and velocity of Au NP invagination are accurately determined at the single-particle and microsecond level unprecedentedly.We utilized force tracing to directly record the endocytosis of single gold nanoparticles (Au NPs) with different sizes, revealing the size-dependent endocytosis dynamics and the crucial role of membrane cholesterol. The force, duration and velocity of Au NP invagination are accurately determined at the single-particle and microsecond level unprecedentedly. Electronic supplementary information (ESI) available: Details of the experimental procedures and the results of the control experiments. See DOI: 10.1039/c5nr01020a

  16. Reciprocity-based experimental determination of dynamic forces and moments: A feasibility study

    NASA Technical Reports Server (NTRS)

    Ver, Istvan L.; Howe, Michael S.

    1994-01-01

    BBN Systems and Technologies has been tasked by the Georgia Tech Research Center to carry Task Assignment No. 7 for the NASA Langley Research Center to explore the feasibility of 'In-Situ Experimental Evaluation of the Source Strength of Complex Vibration Sources Utilizing Reciprocity.' The task was carried out under NASA Contract No. NAS1-19061. In flight it is not feasible to connect the vibration sources to their mounting points on the fuselage through force gauges to measure dynamic forces and moments directly. However, it is possible to measure the interior sound field or vibration response caused by these structureborne sound sources at many locations and invoke principle of reciprocity to predict the dynamic forces and moments. The work carried out in the framework of Task 7 was directed to explore the feasibility of reciprocity-based measurements of vibration forces and moments.

  17. Dynamical forcing of sub-seasonal variability in the tropical Brewer-Dobson circulation

    NASA Astrophysics Data System (ADS)

    Abalos, Marta; Randel, William; Serrano, Encarna

    2014-05-01

    Upwelling across the tropical tropopause exhibits strong sub-seasonal variability superimposed on the well-known annual cycle, and these variations directly affect temperature and tracers in the tropical lower stratosphere. The dynamical forcing of tropical upwelling on sub-seasonal timescales is investigated using the ERA-Interim reanalysis for 1979-2011. Momentum balance diagnostics reveal that transience is linked to the effects of extratropical wave forcing, with centers of action in the extratropical winter stratosphere and in the subtropical upper troposphere of both hemispheres. From a diagnostic point of view, the zonal-mean wind transient response is important for communicating the remote wave forcing to the tropical stratosphere. Dynamical patterns reflect distinctive forcing of the shallow versus deep branches of the Brewer-Dobson circulation.

  18. Nonparametric and data-driven data assimilation for the reconstruction of complex geophysical dynamics

    NASA Astrophysics Data System (ADS)

    Tandeo, Pierre; Ailliot, Pierre; Ruiz, Juan; Hannart, Alexis; Chapron, Bertrand; Cuzol, Anne; Monbet, Valérie; Le Goff, Clément; Lguensat, Redouane; Fablet, Ronan

    2015-04-01

    Nowadays, ocean, atmosphere and climate sciences face a deluge of data pouring from space, in situ monitoring as well as numerical simulations. The availability of these different data sources offer new opportunities, still largely underexploited, to improve the understanding, modeling and reconstruction of geophysical dynamics. The classical way to reconstruct the space-time dynamics of a geophysical system from observation series relies on data assimilation methods, which perform multiple runs of the known dynamical model. This classical framework may have severe limitations including its computational cost, the lack of consistency of the model with respect to the observed data, modeling uncertainties. Here, we explore an alternative approach and develop a fully data-driven framework. We assume that a representative catalog of examples of the space-time dynamics of the geophysical system of interest is available. Depending on the case-study, such a catalog may be issued from observations as well as numerical simulations. Based on this catalog, we combine machine learning and statistical sampling to address data assimilation as follows. The key idea is to design a nonparametric sampler of the dynamics of the considered geophysical system from the available catalog. We focus in this work on analog (also referred to as nearest-neighbor) methods. They provide us the mean for sampling forecast members with no online evaluation of the physical model. The combination of these members with the observations resorts to the classical stochastic filtering techniques, such as ensemble Kalman or particle filters and smoothers. As a proof concept, we demonstrate the relevance of the proposed data assimilation method for Lorenz-63 and Lorenz-96 chaotic dynamics. We compare different nonparametric sampling schemes as well as stochastic filters and evaluate how the size of the catalog and the dimensionality of the system affect assimilation performance. We show that our

  19. Dynamic Analysis With Stress Mode Animation by the Integrated Force Method

    NASA Technical Reports Server (NTRS)

    Patnaik, Surya N.; Coroneos, Rula M.; Hopkins, Dale A.

    1997-01-01

    Dynamic animation of stresses and displacements, which complement each other, can be a useful tool in the analysis and design of structural components. At the present time only displacement-mode animation is available through the popular stiffness formulation. This paper attempts to complete this valuable visualization tool by augmenting the existing art with stress mode animation. The reformulated method of forces, which in the literature is known as the integrated force method (IFM), became the analyzer of choice for the development of stress mode animation because stresses are the primary unknowns of its dynamic analysis. Animation of stresses and displacements, which have been developed successfully through the IFM analyzers, is illustrated in several examples along with a brief introduction to IFM dynamic analysis. The usefulness of animation in design optimization is illustrated considering the spacer structure component of the International Space Station as an example. An overview of the integrated force method analysis code (IFM/ANALYZERS) is provided in the appendix.

  20. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields.

    PubMed

    Chen, Wei; Shi, Chuanyin; MacKerell, Alexander D; Shen, Jana

    2015-06-25

    Physics-based force fields are the backbone of molecular dynamics simulations. In recent years, significant progress has been made in the assessment and improvement of commonly used force fields for describing conformational dynamics of folded proteins. However, the accuracy for the unfolded states remains unclear. The latter is however important for detailed studies of protein folding pathways, conformational transitions involving unfolded states, and dynamics of intrinsically disordered proteins. In this work, we compare the three commonly used force fields, AMBER ff99SB-ILDN, CHARMM22/CMAP, and CHARMM36, for modeling the natively unfolded fragment peptides, NTL9(1-22) and NTL9(6-17), using explicit-solvent replica-exchange molecular dynamics simulations. All three simulations show that NTL9(6-17) is completely unstructured, while NTL9(1-22) transiently samples various β-hairpin states, reminiscent of the first β-hairpin in the structure of the intact NTL9 protein. The radius of gyration of the two peptides is force field independent but likely underestimated due to the current deficiency of additive force fields. Compared to the CHARMM force fields, ff99SB-ILDN gives slightly higher β-sheet propensity and more native-like residual structures for NTL9(1-22), which may be attributed to its known β preference. Surprisingly, only two sequence-local pairs of charged residues make appreciable ionic contacts in the simulations of NTL9(1-22), which are sampled slightly more by the CHARMM force fields. Taken together, these data suggest that the current CHARMM and AMBER force fields are globally in agreement in modeling the unfolded states corresponding to β-sheet in the folded structure, while differing in details such as the native-likeness of the residual structures and interactions. PMID:26020564

  1. Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields.

    PubMed

    Chen, Wei; Shi, Chuanyin; MacKerell, Alexander D; Shen, Jana

    2015-06-25

    Physics-based force fields are the backbone of molecular dynamics simulations. In recent years, significant progress has been made in the assessment and improvement of commonly used force fields for describing conformational dynamics of folded proteins. However, the accuracy for the unfolded states remains unclear. The latter is however important for detailed studies of protein folding pathways, conformational transitions involving unfolded states, and dynamics of intrinsically disordered proteins. In this work, we compare the three commonly used force fields, AMBER ff99SB-ILDN, CHARMM22/CMAP, and CHARMM36, for modeling the natively unfolded fragment peptides, NTL9(1-22) and NTL9(6-17), using explicit-solvent replica-exchange molecular dynamics simulations. All three simulations show that NTL9(6-17) is completely unstructured, while NTL9(1-22) transiently samples various β-hairpin states, reminiscent of the first β-hairpin in the structure of the intact NTL9 protein. The radius of gyration of the two peptides is force field independent but likely underestimated due to the current deficiency of additive force fields. Compared to the CHARMM force fields, ff99SB-ILDN gives slightly higher β-sheet propensity and more native-like residual structures for NTL9(1-22), which may be attributed to its known β preference. Surprisingly, only two sequence-local pairs of charged residues make appreciable ionic contacts in the simulations of NTL9(1-22), which are sampled slightly more by the CHARMM force fields. Taken together, these data suggest that the current CHARMM and AMBER force fields are globally in agreement in modeling the unfolded states corresponding to β-sheet in the folded structure, while differing in details such as the native-likeness of the residual structures and interactions.

  2. No effect of dynamic loading on bone graft healing in femoral segmental defect reconstructions in the goat.

    PubMed

    Bullens, Pieter H J; Hannink, Gerjon; Verdonschot, Nico; Buma, Pieter

    2010-12-01

    We studied if a static or dynamic mode of nail fixation influenced the healing of segmental defect reconstructions in long bones. Defects in the femur of goats were reconstructed using a cage filled with firmly impacted morsellised allograft mixed with a hydroxyapatite paste (Ostim). All reconstructions were stabilised with an intramedullary nail. In one group (n=6) the intramedullary nail was statically locked, in the second group (n=6) a dynamic mode of nail fixation was applied. We hypothesised that dynamisation of the nail would load, and by that stimulate the healing of the bone graft. Mechanical torsion strength of the reconstructions of the femur with the static and dynamic mode of nail fixation appeared to be 74.8±17.5% and 73.0±13.4%, respectively as compared with the contralateral femurs after 6 months. In all reconstructions, the grafts united radiographically and histologically to the host bone, and remodelled into a new vital bone structure. No large differences were found between newly formed bone areas inside and outside the mesh of the two groups. The area of callus outside the mesh in the dynamic mode of fixation group was smaller (p=0.042), whilst the percentage of bone outside the mesh was larger (p=0.049), as compared to the static mode of fixation group. The data suggest that healing of these defects with impacted morsellised graft in a cage is not significantly influenced by the mode of fixation of the nail in this model.

  3. DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

    PubMed Central

    2012-01-01

    Background Modeling dynamic regulatory networks is a major challenge since much of the protein-DNA interaction data available is static. The Dynamic Regulatory Events Miner (DREM) uses a Hidden Markov Model-based approach to integrate this static interaction data with time series gene expression leading to models that can determine when transcription factors (TFs) activate genes and what genes they regulate. DREM has been used successfully in diverse areas of biological research. However, several issues were not addressed by the original version. Results DREM 2.0 is a comprehensive software for reconstructing dynamic regulatory networks that supports interactive graphical or batch mode. With version 2.0 a set of new features that are unique in comparison with other softwares are introduced. First, we provide static interaction data for additional species. Second, DREM 2.0 now accepts continuous binding values and we added a new method to utilize TF expression levels when searching for dynamic models. Third, we added support for discriminative motif discovery, which is particularly powerful for species with limited experimental interaction data. Finally, we improved the visualization to support the new features. Combined, these changes improve the ability of DREM 2.0 to accurately recover dynamic regulatory networks and make it much easier to use it for analyzing such networks in several species with varying degrees of interaction information. Conclusions DREM 2.0 provides a unique framework for constructing and visualizing dynamic regulatory networks. DREM 2.0 can be downloaded from: www.sb.cs.cmu.edu/drem. PMID:22897824

  4. Numerical stability in multifluid gas dynamics with implicit drag forces

    NASA Astrophysics Data System (ADS)

    Ramshaw, J. D.; Chang, C. H.

    2015-10-01

    The numerical stability of a conventional explicit numerical scheme for solving the inviscid multifluid dynamical equations describing a multicomponent gas mixture is investigated both analytically and computationally. Although these equations do not explicitly contain diffusion terms, it is well known that they reduce to a single-fluid diffusional description when the drag coefficients in the species momentum equations are large. The question then arises as to whether their numerical solution is subject to a diffusional stability restriction on the time step in addition to the usual Courant sound-speed stability condition. An analytical stability analysis is performed for the special case of a quiescent binary gas mixture with equal sound speeds and temperatures. It is found that the Courant condition is always sufficient to ensure stability, so that no additional diffusional stability restriction arises for any value of the drag coefficient, however large. This result is confirmed by one-dimensional computational results for binary and ternary mixtures with unequal sound speeds, which remain stable even when the time step exceeds the usual diffusional limit by factors of order 100.

  5. Dynamics of the coiled-coil unfolding transition of myosin rod probed by dissipation force spectrum.

    PubMed

    Taniguchi, Yukinori; Khatri, Bhavin S; Brockwell, David J; Paci, Emanuele; Kawakami, Masaru

    2010-07-01

    The motor protein myosin II plays a crucial role in muscle contraction. The mechanical properties of its coiled-coil region, the myosin rod, are important for effective force transduction during muscle function. Previous studies have investigated the static elastic response of the myosin rod. However, analogous to the study of macroscopic complex fluids, how myosin will respond to physiological time-dependent loads can only be understood from its viscoelastic response. Here, we apply atomic force microscopy using a magnetically driven oscillating cantilever to measure the dissipative properties of single myosin rods that provide unique dynamical information about the coiled-coil structure as a function of force. We find that the friction constant of the single myosin rod has a highly nontrivial variation with force; in particular, the single-molecule friction constant is reduced dramatically and increases again as it passes through the coiled-uncoiled transition. This is a direct indication of a large free-energy barrier to uncoiling, which may be related to a fine-tuned dynamic mechanosignaling response to large and unexpected physiological loads. Further, from the critical force at which the minimum in friction occurs we determine the asymmetry of the bistable landscape that controls uncoiling of the coiled coil. This work highlights the sensitivity of the dissipative signal in force unfolding to dynamic molecular structure that is hidden to the elastic signal. PMID:20655854

  6. Haptic perception of force magnitude and its relation to postural arm dynamics in 3D.

    PubMed

    van Beek, Femke E; Bergmann Tiest, Wouter M; Mugge, Winfred; Kappers, Astrid M L

    2015-12-08

    In a previous study, we found the perception of force magnitude to be anisotropic in the horizontal plane. In the current study, we investigated this anisotropy in three dimensional space. In addition, we tested our previous hypothesis that the perceptual anisotropy was directly related to anisotropies in arm dynamics. In experiment 1, static force magnitude perception was studied using a free magnitude estimation paradigm. This experiment revealed a significant and consistent anisotropy in force magnitude perception, with forces exerted perpendicular to the line between hand and shoulder being perceived as 50% larger than forces exerted along this line. In experiment 2, postural arm dynamics were measured using stochastic position perturbations exerted by a haptic device and quantified through system identification. By fitting a mass-damper-spring model to the data, the stiffness, damping and inertia parameters could be characterized in all the directions in which perception was also measured. These results show that none of the arm dynamics parameters were oriented either exactly perpendicular or parallel to the perceptual anisotropy. This means that endpoint stiffness, damping or inertia alone cannot explain the consistent anisotropy in force magnitude perception.

  7. Force field parameters for S-nitrosocysteine and molecular dynamics simulations of S-nitrosated thioredoxin

    SciTech Connect

    Han, Sanghwa

    2008-12-12

    Estimation of structural perturbation induced by S-nitrosation is important to understand the mode of cellular signal transduction mediated by nitric oxide. Crystal structures of S-nitrosated proteins have been solved only for a few cases, however, so that molecular dynamics simulation may provide an alternative tool for probing structural perturbation. In this study AMBER-99 force field parameters for S-nitrosocysteine were developed and applied to molecular dynamics simulations of S-nitrosated thioredoxin. Geometry optimization at the level of HF/6-31G* was followed by a restrained electrostatic potential charge-fitting to obtain the atomic charges of S-nitrosocysteine. Force constants for bonds and angles were obtained from generalized AMBER force field. Torsional force constants for CC-SN and CS-NO were determined by fitting the torsional profiles obtained from geometry optimization with those from molecular mechanical energy minimization. Finally molecular dynamics simulations were performed with theses parameters on oxidized and reduced thioredoxin with and without S-nitrosocysteine. In all cases the root-mean-square deviations of {alpha}-carbons yielded well-behaved trajectories. The CC-SH dihedral angle which fluctuated severely during the simulation became quiet upon S-nitrosation. In conclusion the force field parameters developed in this study for S-nitrosocysteine appear to be suitable for molecular dynamics simulations of S-nitrosated proteins.

  8. Dynamic force measurements for a high bar using 3D motion capturing.

    PubMed

    Cagran, C; Huber, P; Müller, W

    2010-03-01

    The displacement of a calibrated horizontal bar is used as a measure for forces acting on the bar itself during dynamic performances in artistic gymnastics. The high bar is loaded with known forces and the displacement is monitored by means of a Vicon motion capturing system. The calibration results are fitted according to the Euler-Bernoulli beam theory. After calibration, forces can straightforwardly be measured by multiplication of the bar displacement with the determined fit parameter. This approach is also able to account for non-central force application (two hands on the bar) and the effect of the bar's inertia. Uncertainties in measured forces are assessed to be +/-25 N plus an additional 1% for the unknown weight distribution between the two hands. PMID:19906379

  9. An integrated methodology for data processing in dynamic force spectroscopy of ligand-receptor binding.

    PubMed

    Odorico, M; Teulon, J-M; Berthoumieu, O; Chen, S-w W; Parot, P; Pellequer, J-L

    2007-10-01

    Dynamic force spectroscopy (DFS), using atomic force microscopy (AFM), is a powerful tool to study ligand-receptor binding. The interaction mode of two binding partners is investigated by exploring stochastic behaviors of bond rupture events. However, to define a rupture event from force-distance measurements is not conclusive or unique in literature. To reveal the influence of event identification methods, we have developed an efficient protocol to manage tremendous amount of data by implementing different choices of peak selection from the force-distance curve. This data processing software simplifies routinely experimental procedures such as cantilever spring constant and force-distance curve calibrations, statistical treatments of data, and analysis distributions of rupture events. In the present work, we took available experimental data from a complex between a chelate metal compound and a monoclonal antibody as a study system.

  10. Dynamic forces on agglomerated particles caused by high-intensity ultrasound.

    PubMed

    Knoop, Claas; Fritsching, Udo

    2014-03-01

    In this paper the acoustic forces on particles and agglomerates caused by high-intensity ultrasound in gaseous atmosphere are derived by means of computational fluid dynamics (CFD). Sound induced forces cause an oscillating stress scenario where the primary particles of an agglomerate are alternatingly pressed together and torn apart with the frequency of the applied wave. A comparison of the calculated acoustic forces with respect to the inter particle adhesion forces from Van-der-Waals and liquid bridge interactions reveals that the separation forces may reach the same order of magnitude for 80 μm sized SiO2-particles. Hence, with finite probability acoustically agitated gases may de-agglomerate/disperse solid agglomerate structures. This effect is confirmed by dispersion experiments in an acoustic particle levitation setup. PMID:24152872

  11. High velocity properties of the dynamic frictional force between ductile metals

    SciTech Connect

    Hammerberg, James Edward; Hollan, Brad L; Germann, Timothy C; Ravelo, Ramon J

    2010-01-01

    The high velocity properties of the tangential frictional force between ductile metal interfaces seen in large-scale NonEquilibrium Molecular Dynamics (NEMD) simulations are characterized by interesting scaling behavior. In many cases a power law decrease in the frictional force with increasing velocity is observed at high velocities. We discuss the velocity dependence of the high velocity branch of the tangential force in terms of structural transformation and ultimate transition, at the highest velocities, to confined fluid behavior characterized by a critical strain rate. The particular case of an Al/Al interface is discussed.

  12. Influence of materials' optical response on actuation dynamics by Casimir forces.

    PubMed

    Sedighi, M; Broer, W H; Van der Veeke, S; Svetovoy, V B; Palasantzas, G

    2015-06-01

    The dependence of the Casimir force on the frequency-dependent dielectric functions of interacting materials makes it possible to tailor the actuation dynamics of microactuators. The Casimir force is largest for metallic interacting systems due to the high absorption of conduction electrons in the far-infrared range. For less conductive systems, such as phase change materials or conductive silicon carbide, the reduced force offers the advantage of increased stable operation of MEMS devices against pull-in instabilities that lead to unwanted stiction. Bifurcation analysis with phase portraits has been used to compare the sensitivity of a model actuator when the optical properties are altered.

  13. Influence of materials' optical response on actuation dynamics by Casimir forces

    NASA Astrophysics Data System (ADS)

    Sedighi, M.; Broer, W. H.; Van der Veeke, S.; Svetovoy, V. B.; Palasantzas, G.

    2015-06-01

    The dependence of the Casimir force on the frequency-dependent dielectric functions of interacting materials makes it possible to tailor the actuation dynamics of microactuators. The Casimir force is largest for metallic interacting systems due to the high absorption of conduction electrons in the far-infrared range. For less conductive systems, such as phase change materials or conductive silicon carbide, the reduced force offers the advantage of increased stable operation of MEMS devices against pull-in instabilities that lead to unwanted stiction. Bifurcation analysis with phase portraits has been used to compare the sensitivity of a model actuator when the optical properties are altered.

  14. Pathogens trigger top-down climate forcing on ecosystem dynamics.

    PubMed

    Edeline, Eric; Groth, Andreas; Cazelles, Bernard; Claessen, David; Winfield, Ian J; Ohlberger, Jan; Asbjørn Vøllestad, L; Stenseth, Nils C; Ghil, Michael

    2016-06-01

    Evaluating the effects of climate variation on ecosystems is of paramount importance for our ability to forecast and mitigate the consequences of global change. However, the ways in which complex food webs respond to climate variations remain poorly understood. Here, we use long-term time series to investigate the effects of temperature variation on the intraguild-predation (IGP) system of Windermere (UK), a lake where pike (Esox lucius, top predator) feed on small-sized perch (Perca fluviatilis) but compete with large-sized perch for the same food sources. Spectral analyses of time series reveal that pike recruitment dynamics are temperature controlled. In 1976, expansion of a size-truncating perch pathogen into the lake severely impacted large perch and favoured pike as the IGP-dominant species. This pathogen-induced regime shift to a pike-dominated IGP apparently triggered a temperature-controlled trophic cascade passing through pike down to dissolved nutrients. In simple food chains, warming is predicted to strengthen top-down control by accelerating metabolic rates in ectothermic consumers, while pathogens of top consumers are predicted to dampen this top-down control. In contrast, the local IGP structure in Windermere made warming and pathogens synergistic in their top-down effects on ecosystem functioning. More generally, our results point to top predators as major mediators of community response to global change, and show that size-selective agents (e.g. pathogens, fishers or hunters) may change the topological architecture of food webs and alter whole ecosystem sensitivity to climate variation. PMID:26910776

  15. Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

    PubMed Central

    2012-01-01

    Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

  16. Cross talk between matrix elasticity and mechanical force regulates myoblast traction dynamics.

    PubMed

    Al-Rekabi, Zeinab; Pelling, Andrew E

    2013-12-01

    Growing evidence suggests that critical cellular processes are profoundly influenced by the cross talk between extracellular nanomechanical forces and the material properties of the cellular microenvironment. Although many studies have examined either the effect of nanomechanical forces or the material properties of the microenvironment on biological processes, few have investigated the influence of both. Here, we performed simultaneous atomic force microscopy and traction force microscopy to demonstrate that muscle precursor cells (myoblasts) rapidly generate a significant increase in traction when stimulated with a local 10 nN force. Cells were cultured and nanomechanically stimulated on hydrogel substrates with controllable local elastic moduli varying from ~16-89 kPa, as confirmed with atomic force microscopy. Importantly, cellular traction dynamics in response to nanomechanical stimulation only occurred on substrates that were similar to the elasticity of working muscle tissue (~64-89 kPa) as opposed to substrates mimicking resting tissue (~16-51 kPa). The traction response was also transient, occurring within 30 s, and dissipating by 60 s, during constant nanomechanical stimulation. The observed biophysical dynamics are very much dependent on rho-kinase and myosin-II activity and likely contribute to the physiology of these cells. Our results demonstrate the fundamental ability of cells to integrate nanoscale information in the cellular microenvironment, such as nanomechanical forces and substrate mechanics, during the process of mechanotransduction.

  17. Cross talk between matrix elasticity and mechanical force regulates myoblast traction dynamics

    NASA Astrophysics Data System (ADS)

    Al-Rekabi, Zeinab; Pelling, Andrew E.

    2013-12-01

    Growing evidence suggests that critical cellular processes are profoundly influenced by the cross talk between extracellular nanomechanical forces and the material properties of the cellular microenvironment. Although many studies have examined either the effect of nanomechanical forces or the material properties of the microenvironment on biological processes, few have investigated the influence of both. Here, we performed simultaneous atomic force microscopy and traction force microscopy to demonstrate that muscle precursor cells (myoblasts) rapidly generate a significant increase in traction when stimulated with a local 10 nN force. Cells were cultured and nanomechanically stimulated on hydrogel substrates with controllable local elastic moduli varying from ˜16-89 kPa, as confirmed with atomic force microscopy. Importantly, cellular traction dynamics in response to nanomechanical stimulation only occurred on substrates that were similar to the elasticity of working muscle tissue (˜64-89 kPa) as opposed to substrates mimicking resting tissue (˜16-51 kPa). The traction response was also transient, occurring within 30 s, and dissipating by 60 s, during constant nanomechanical stimulation. The observed biophysical dynamics are very much dependent on rho-kinase and myosin-II activity and likely contribute to the physiology of these cells. Our results demonstrate the fundamental ability of cells to integrate nanoscale information in the cellular microenvironment, such as nanomechanical forces and substrate mechanics, during the process of mechanotransduction.

  18. Quantitative reconstruction of thermal and dynamic characteristics of lava flow from surface thermal measurements

    NASA Astrophysics Data System (ADS)

    Korotkii, Alexander; Kovtunov, Dmitry; Ismail-Zadeh, Alik; Tsepelev, Igor; Melnik, Oleg

    2016-06-01

    We study a model of lava flow to determine its thermal and dynamic characteristics from thermal measurements of the lava at its surface. Mathematically this problem is reduced to solving an inverse boundary problem. Namely, using known conditions at one part of the model boundary we determine the missing condition at the remaining part of the boundary. We develop a numerical approach to the mathematical problem in the case of steady-state flow. Assuming that the temperature and the heat flow are prescribed at the upper surface of the model domain, we determine the flow characteristics in the entire model domain using a variational (adjoint) method. We have performed computations of model examples and showed that in the case of smooth input data the lava temperature and the flow velocity can be reconstructed with a high accuracy. As expected, a noise imposed on the smooth input data results in a less accurate solution, but still acceptable below some noise level. Also we analyse the influence of optimization methods on the solution convergence rate. The proposed method for reconstruction of physical parameters of lava flows can also be applied to other problems in geophysical fluid flows.

  19. Inpainting for videos with dynamic objects using texture and structure reconstruction

    NASA Astrophysics Data System (ADS)

    Voronin, V. V.; Marchuk, V. I.; Gapon, N. V.; Zhuravlev, A. V.; Maslennikov, S.; Stradanchenko, S.

    2015-05-01

    This paper describes a novel inpainting approach for removing marked dynamic objects from videos captured with a camera, so long as the objects occlude parts of the scene with a static background. Proposed approach allow to remove objects or restore missing or tainted regions present in a video sequence by utilizing spatial and temporal information from neighboring scenes. The algorithm iteratively performs following operations: achieve frame; update the scene model; update positions of moving objects; replace parts of the frame occupied by the objects marked for remove with use of a background model. In this paper, we extend an image inpainting algorithm based texture and structure reconstruction by incorporating an improved strategy for video. An image inpainting approach based on the construction of a composite curve for the restoration of the edges of objects in a frame using the concepts of parametric and geometric continuity is presented. It is shown that this approach allows to restore the curved edges and provide more flexibility for curve design in damaged frame by interpolating the boundaries of objects by cubic splines. After edge restoration stage, a texture reconstruction using patch-based method is carried out. We demonstrate the performance of a new approach via several examples, showing the effectiveness of our algorithm and compared with state-of-the-art video inpainting methods.

  20. Population genetic dynamics of an invasion reconstructed from the sediment egg bank.

    PubMed

    Möst, Markus; Oexle, Sarah; Marková, Silvia; Aidukaite, Dalia; Baumgartner, Livia; Stich, Hans-Bernd; Wessels, Martin; Martin-Creuzburg, Dominik; Spaak, Piet

    2015-08-01

    Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as 'European D. pulicaria' originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations. PMID:26122166

  1. Population genetic dynamics of an invasion reconstructed from the sediment egg bank.

    PubMed

    Möst, Markus; Oexle, Sarah; Marková, Silvia; Aidukaite, Dalia; Baumgartner, Livia; Stich, Hans-Bernd; Wessels, Martin; Martin-Creuzburg, Dominik; Spaak, Piet

    2015-08-01

    Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as 'European D. pulicaria' originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations.

  2. Analysis of squat and stoop dynamic liftings: muscle forces and internal spinal loads

    PubMed Central

    Bazrgari, Babak; Arjmand, Navid

    2006-01-01

    Despite the well-recognized role of lifting in back injuries, the relative biomechanical merits of squat versus stoop lifting remain controversial. In vivo kinematics measurements and model studies are combined to estimate trunk muscle forces and internal spinal loads under dynamic squat and stoop lifts with and without load in hands. Measurements were performed on healthy subjects to collect segmental rotations during lifts needed as input data in subsequent model studies. The model accounted for nonlinear properties of the ligamentous spine, wrapping of thoracic extensor muscles to take curved paths in flexion and trunk dynamic characteristics (inertia and damping) while subject to measured kinematics and gravity/external loads. A dynamic kinematics-driven approach was employed accounting for the spinal synergy by simultaneous consideration of passive structures and muscle forces under given posture and loads. Results satisfied kinematics and dynamic equilibrium conditions at all levels and directions. Net moments, muscle forces at different levels, passive (muscle or ligamentous) forces and internal compression/shear forces were larger in stoop lifts than in squat ones. These were due to significantly larger thorax, lumbar and pelvis rotations in stoop lifts. For the relatively slow lifting tasks performed in this study with the lowering and lifting phases each lasting ∼2 s, the effect of inertia and damping was not, in general, important. Moreover, posterior shift in the position of the external load in stoop lift reaching the same lever arm with respect to the S1 as that in squat lift did not influence the conclusion of this study on the merits of squat lifts over stoop ones. Results, for the tasks considered, advocate squat lifting over stoop lifting as the technique of choice in reducing net moments, muscle forces and internal spinal loads (i.e., moment, compression and shear force). PMID:17103232

  3. Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins.

    PubMed

    Janovjak, Harald; Müller, Daniel J; Humphris, Andrew D L

    2005-02-01

    Recent advances in atomic force microscopy allowed globular and membrane proteins to be mechanically unfolded on a single-molecule level. Presented is an extension to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins from native purple membranes, small oscillation amplitudes (6-9 nm) were supplied to the vertical displacement of the cantilever at a frequency of 3 kHz. The phase and amplitude response of the cantilever-protein system was converted to reveal the elastic (conservative) and viscous (dissipative) contributions to the unfolding process. The elastic response (stiffness) of the extended parts of the protein were in the range of a few tens pN/nm and could be well described by the derivative of the wormlike chain model. Discrete events in the viscous response coincided with the unfolding of single secondary structure elements and were in the range of 1 microNs/m. In addition, these force modulation spectroscopy experiments revealed novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing force-distance spectra by the integration of amplitude-distance spectra verified their position, offering a novel approach to detect intermediates during the forced unfolding of single proteins. PMID:15574708

  4. [The dynamic concision for three-dimensional reconstruction of human organ built with virtual reality modeling language (VRML)].

    PubMed

    Yu, Zhengyang; Zheng, Shusen; Chen, Huaiqing; Wang, Jianjun; Xiong, Qingwen; Jing, Wanjun; Zeng, Yu

    2006-10-01

    This research studies the process of dynamic concision and 3D reconstruction from medical body data using VRML and JavaScript language, focuses on how to realize the dynamic concision of 3D medical model built with VRML. The 2D medical digital images firstly are modified and manipulated by 2D image software. Then, based on these images, 3D mould is built with VRML and JavaScript language. After programming in JavaScript to control 3D model, the function of dynamic concision realized by Script node and sensor node in VRML. The 3D reconstruction and concision of body internal organs can be formed in high quality near to those got in traditional methods. By this way, with the function of dynamic concision, VRML browser can offer better windows of man-computer interaction in real time environment than before. 3D reconstruction and dynamic concision with VRML can be used to meet the requirement for the medical observation of 3D reconstruction and has a promising prospect in the fields of medical image.

  5. Partial-profilogram reconstruction method to measure the geometric parameters of wheels in dynamic condition

    NASA Astrophysics Data System (ADS)

    Bernal, E. J.; Martinod, R. M.; Betancur, G. R.; Castañeda, L. F.

    2016-05-01

    The present work poses a method for the measurement of geometric parameters of rail wheels in a dynamic condition, by reconstructing the profilogram from a portion of the wheel surface wear with artificial vision. The suggested procedure can work with a two-dimensional laser displacement transducer or by processing a sole image from a single camera with a structured light source. These two procedures require fewer devices and simpler implementation processes and allow the use of mathematical algorithms that demand less information processing, thus generating more accurate results. Railway operators may implement this method to perform predictive maintenance to their rolling stock at a fraction of the regular cost; thus achieving better precision, availability, maintenance performance and improving safety. Results were compared to those given by commercial equipment, showing similar precision but a better cost-benefit relation.

  6. An attempt to bridge muscle architecture dynamics and its instantaneous rate of force development using ultrasonography.

    PubMed

    Li, Jizhou; Zhou, Yongjin; Zheng, Yong-Ping; Li, Guanglin

    2015-08-01

    Muscle force output is an essential index in rehabilitation assessment or physical exams, and could provide considerable insights for various applications such as load monitoring and muscle assessment in sports science or rehabilitation therapy. Besides direct measurement of force output using a dynamometer, electromyography has earlier been used in several studies to quantify muscle force as an indirect means. However, its spatial resolution is easily compromised as a summation of the action potentials from neighboring motor units of electrode site. To explore an alternative method to indirectly estimate the muscle force output, and with better muscle specificity, we started with an investigation on the relationship between architecture dynamics and force output of triceps surae. The muscular architecture dynamics is captured in ultrasonography sequences and estimated using a previously reported motion estimation method. Then an indicator named as the dorsoventrally averaged motion profile (DAMP) is employed. The performance of force output is represented by an instantaneous version of the rate of force development (RFD), namely I-RFD. From experimental results on ten normal subjects, there were significant correlations between the I-RFD and DAMP for triceps surae, both normalized between 0 and 1, with the sum of squares error at 0.0516±0.0224, R-square at 0.7929±0.0931 and root mean squared error at 0.0159±0.0033. The statistical significance results were less than 0.01. The present study suggested that muscle architecture dynamics extracted from ultrasonography during contraction is well correlated to the I-RFD and it can be a promising option for indirect estimation of muscle force output.

  7. 3D Reconstruction of Human Laryngeal Dynamics Based on Endoscopic High-Speed Recordings.

    PubMed

    Semmler, Marion; Kniesburges, Stefan; Birk, Veronika; Ziethe, Anke; Patel, Rita; Dollinger, Michael

    2016-07-01

    Standard laryngoscopic imaging techniques provide only limited two-dimensional insights into the vocal fold vibrations not taking the vertical component into account. However, previous experiments have shown a significant vertical component in the vibration of the vocal folds. We present a 3D reconstruction of the entire superior vocal fold surface from 2D high-speed videoendoscopy via stereo triangulation. In a typical camera-laser set-up the structured laser light pattern is projected on the vocal folds and captured at 4000 fps. The measuring device is suitable for in vivo application since the external dimensions of the miniaturized set-up barely exceed the size of a standard rigid laryngoscope. We provide a conservative estimate on the resulting resolution based on the hardware components and point out the possibilities and limitations of the miniaturized camera-laser set-up. In addition to the 3D vocal fold surface, we extended previous approaches with a G2-continuous model of the vocal fold edge. The clinical applicability was successfully established by the reconstruction of visual data acquired from 2D in vivo high-speed recordings of a female and a male subject. We present extracted dynamic parameters like maximum amplitude and velocity in the vertical direction. The additional vertical component reveals deeper insights into the vibratory dynamics of the vocal folds by means of a non-invasive method. The successful miniaturization allows for in vivo application giving access to the most realistic model available and hence enables a comprehensive understanding of the human phonation process. PMID:26829782

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

    NASA Technical Reports Server (NTRS)

    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.

  9. Dynamical systems analysis of electrostatic and aerodynamic forced vibrations of a thin flexible electrode

    NASA Astrophysics Data System (ADS)

    Madanu, Sushma Bala

    Transverse vibrations of an electrostatically actuated thin flexible cantilever perturbed by low-speed air flow is studied using both experiments and numerical modeling. In the experiments the dynamic characteristics of the cantilever are studied by supplying a DC voltage with an AC component for electrostatic forcing and a constant uniform air flow around the cantilever system for aerodynamic forcing. The maximum voltage applied varies from 1 - 9 kV and air flow speeds range from 0.224 - 3.58 m/s (0.5 - 8 mile/hr). The Reynolds numbers for these speeds lie in the range of 1000 - 20000. A range of control parameters leading to stable vibrations are established using the Strouhal number as the operating parameter whose inverse values change from 100 - 2500. The Numerical results are validated with experimental results. Assuming the amplitude of vibrations are small, then a non-linear dynamic Euler-Bernoulli beam equation with viscous damping and gravitational effects is used to model the vibrations of the dynamical system. Aerodynamic forcing is modeled as a temporally sinusoidal and uniform force acting perpendicular to the beam length. The forcing amplitude is found to be proportional to square of air flow velocity by obtaining relationship between the experimental amplitude of vibrations and air flow velocity. Numerical results strongly agree with those of experiments predicting accurate vibration amplitudes, displacement frequency and quasi-periodic displacements of the cantilever tip.

  10. Superadiabatic forces in the dynamics of the one-dimensional Gaussian core model.

    PubMed

    Bernreuther, Elias; Schmidt, Matthias

    2016-08-01

    Using Brownian dynamics computer simulations we investigate the dynamics of the one-body density and one-body current in a one-dimensional system of particles that interact with a repulsive Gaussian pair potential. We systematically split the internal force distribution into an adiabatic part, which originates from the equilibrium free energy, and a superadiabatic contribution, which is neglected in dynamical density functional theory. We find a strong dependence of the magnitude and phase of the superadiabatic force distribution on the initial state of the system. While the magnitude of the superadiabatic force is small if the system evolves from an equilibrium state inside of a parabolic external potential, it is large for particles with equidistant initial separations at high temperature. We analyze these findings in the light of the known mean-field behavior of Gaussian core particles and discuss a multi-occupancy mechanism which generates superadiabatic forces that are out of phase with respect to the adiabatic force. PMID:27627244

  11. Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations.

    PubMed

    Velazquez, Hector A; Hamelberg, Donald

    2015-02-21

    Cis-trans isomerization of peptidyl-prolyl bonds of the protein backbone plays an important role in numerous biological processes. Cis-trans isomerization can be the rate-limiting step due its extremely slow dynamics, compared to the millisecond time scale of many processes, and is catalyzed by a widely studied family of peptidyl-prolyl cis-trans isomerase enzymes. Also, mechanical forces along the peptide chain can speed up the rate of isomerization, resulting in "mechanical catalysis," and have been used to study peptidyl-prolyl cis-trans isomerization and other mechanical properties of proteins. Here, we use constant force molecular dynamics simulations to study the dynamical effects of phosphorylation on serine/threonine-proline protein motifs that are involved in the function of many proteins and have been implicated in many aberrant biological processes. We show that the rate of cis-trans isomerization is slowed down by phosphorylation, in excellent agreement with experiments. We use a well-grounded theory to describe the force dependent rate of isomerization. The calculated rates at zero force are also in excellent agreement with experimentally measured rates, providing additional validation of the models and force field parameters. Our results suggest that the slowdown in the rate upon phosphorylation is mainly due to an increase in the friction along the peptidyl-prolyl bond angle during isomerization. Our results provide a microscopic description of the dynamical effects of post-translational phosphorylation on cis-trans isomerization and insights into the properties of proteins under tension.

  12. Spatial and Temporal Dynamics in the Ionic Driving Force for GABAA Receptors

    PubMed Central

    Wright, R.; Raimondo, J. V.; Akerman, C. J.

    2011-01-01

    It is becoming increasingly apparent that the strength of GABAergic synaptic transmission is dynamic. One parameter that can establish differences in the actions of GABAergic synapses is the ionic driving force for the chloride-permeable GABAA receptor (GABAAR). Here we review some of the sophisticated ways in which this ionic driving force can vary within neuronal circuits. This driving force for GABAARs is subject to tight spatial control, with the distribution of Cl− transporter proteins and channels generating regional variation in the strength of GABAAR signalling across a single neuron. GABAAR dynamics can result from short-term changes in their driving force, which involve the temporary accumulation or depletion of intracellular Cl−. In addition, activity-dependent changes in the expression and function of Cl− regulating proteins can result in long-term shifts in the driving force for GABAARs. The multifaceted regulation of the ionic driving force for GABAARs has wide ranging implications for mature brain function, neural circuit development, and disease. PMID:21766044

  13. Molecular dynamics simulation study of friction force and torque on a rough spherical particle.

    PubMed

    Kohale, Swapnil C; Khare, Rajesh

    2010-06-21

    Recent developments in techniques of micro- and nanofluidics have led to an increased interest in nanoscale hydrodynamics in confined geometries. In our previous study [S. C. Kohale and R. Khare, J. Chem. Phys. 129, 164706 (2008)], we analyzed the friction force experienced by a smooth spherical particle that is translating in a fluid confined between parallel plates. The magnitude of three effects--velocity slip at particle surface, the presence of confining surfaces, and the cooperative hydrodynamic interactions between periodic images of the moving particle--that determine the friction force was quantified in that work using molecular dynamics simulations. In this work, we have studied the motion of a rough spherical particle in a confined geometry. Specifically, the friction force experienced by a translating particle and the torque experienced by a rotating particle are studied using molecular dynamics simulations. Our results demonstrate that the surface roughness of the particle significantly reduces the slip at the particle surface, thus leading to higher values of the friction force and hence a better agreement with the continuum predictions. The particle size dependence of the friction force and the torque values is shown to be consistent with the expectations from the continuum theory. As was observed for the smooth sphere, the cooperative hydrodynamic interactions between the images of the sphere have a significant effect on the value of the friction force experienced by the translating sphere. On the other hand, the torque experienced by a spherical particle that is rotating at the channel center is insensitive to this effect.

  14. Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

    SciTech Connect

    Smith, Dayle MA; Xiong, Yijia; Straatsma, TP; Rosso, Kevin M.; Squier, Thomas C.

    2012-05-09

    Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexible in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.

  15. Hydrophobic, electrostatic, and dynamic polymer forces at silicone surfaces modified with long-chain bolaform surfactants.

    PubMed

    Rapp, Michael V; Donaldson, Stephen H; Gebbie, Matthew A; Das, Saurabh; Kaufman, Yair; Gizaw, Yonas; Koenig, Peter; Roiter, Yuri; Israelachvili, Jacob N

    2015-05-01

    Surfactant self-assembly on surfaces is an effective way to tailor the complex forces at and between hydrophobic-water interfaces. Here, the range of structures and forces that are possible at surfactant-adsorbed hydrophobic surfaces are demonstrated: certain long-chain bolaform surfactants-containing a polydimethylsiloxane (PDMS) mid-block domain and two cationic α, ω-quarternary ammonium end-groups-readily adsorb onto thin PDMS films and form dynamically fluctuating nanostructures. Through measurements with the surface forces apparatus (SFA), it is found that these soft protruding nanostructures display polymer-like exploration behavior at the PDMS surface and give rise to a long-ranged, temperature- and rate-dependent attractive bridging force (not due to viscous forces) on approach to a hydrophilic bare mica surface. Coulombic interactions between the cationic surfactant end-groups and negatively-charged mica result in a rate-dependent polymer bridging force during separation as the hydrophobic surfactant mid-blocks are pulled out from the PDMS interface, yielding strong adhesion energies. Thus, (i) the versatile array of surfactant structures that may form at hydrophobic surfaces is highlighted, (ii) the need to consider the interaction dynamics of such self-assembled polymer layers is emphasized, and (iii) it is shown that long-chain surfactants can promote robust adhesion in aqueous solutions. PMID:25504803

  16. Diminished sub-maximal quadriceps force control in anterior cruciate ligament reconstructed patients is related to quadriceps and hamstring muscle dyskinesia.

    PubMed

    Telianidis, Stacey; Perraton, Luke; Clark, Ross A; Pua, Yong-Hao; Fortin, Karine; Bryant, Adam L

    2014-08-01

    The aim of this study was to determine the effects of anterior cruciate ligament reconstruction (ACLR) on sub-maximal quadriceps force control with respect to quadriceps and hamstring muscle activity. Thirty ACLR individuals together with 30 healthy individuals participated. With real-time visual feedback of muscle force output and electromyographic electrodes attached to the quadriceps and hamstring muscles, subjects performed an isometric knee extension task where they increased and decreased their muscle force output at 0.128Hz within a range of 5-30% maximum voluntary capacity. The ACLR group completed the task with more error and increased medial hamstring and vastus medialis activation (p<0.05). Moderate negative correlations (p<0.05) were observed between quadriceps force control and medial (Spearman's rho=-0.448, p=0.022) and lateral (Spearman's rho=-0.401, p=0.034) hamstring activation in the ACLR group. Diminished quadriceps sub-maximal force control in ACLR subjects was reflective of medial quadriceps and hamstring dyskinesia (i.e., altered muscle activity patterns and coordination deficits). Within the ACLR group however, augmented hamstring co-activation was associated with better quadriceps force control. Future studies should explore the convergent validity of quadriceps force control in ACLR patients.

  17. Dynamic tunneling force microscopy for characterizing electronic trap states in non-conductive surfaces

    SciTech Connect

    Wang, R.; Williams, C. C.

    2015-09-15

    Dynamic tunneling force microscopy (DTFM) is a scanning probe technique for real space mapping and characterization of individual electronic trap states in non-conductive films with atomic scale spatial resolution. The method is based upon the quantum mechanical tunneling of a single electron back and forth between a metallic atomic force microscopy tip and individual trap states in completely non-conducting surface. This single electron shuttling is measured by detecting the electrostatic force induced on the probe tip at the shuttling frequency. In this paper, the physical basis for the DTFM method is unfolded through a physical model and a derivation of the dynamic tunneling signal as a function of several experimental parameters is shown. Experimental data are compared with the theoretical simulations, showing quantitative consistency and verifying the physical model used. The experimental system is described and representative imaging results are shown.

  18. A method of improving the dynamic response of 3D force/torque sensors

    NASA Astrophysics Data System (ADS)

    Osypiuk, Rafał; Piskorowski, Jacek; Kubus, Daniel

    2016-02-01

    In the paper attention is drawn to adverse dynamic properties of filters implemented in commercial measurement systems, force/torque sensors, which are increasingly used in industrial robotics. To remedy the problem, it has been proposed to employ a time-variant filter with appropriately modulated parameters, owing to which it is possible to suppress the amplitude of the transient response and, at the same time, to increase the pulsation of damped oscillations; this results in the improvement of dynamic properties in terms of reducing the duration of transients. This property plays a key role in force control and in the fundamental problem of the robot establishing contact with rigid environment. The parametric filters have been verified experimentally and compared with filters available for force/torque sensors manufactured by JR3. The obtained results clearly indicate the advantages of the proposed solution, which may be an interesting alternative to the classic methods of filtration.

  19. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  20. Finite element modeling of atomic force microscopy cantilever dynamics during video rate imaging

    SciTech Connect

    Howard-Knight, J. P.; Hobbs, J. K.

    2011-04-01

    A dynamic finite element model has been constructed to simulate the behavior of low spring constant atomic force microscope (AFM) cantilevers used for imaging at high speed without active feedback as in VideoAFM. The model is tested against experimental data collected at 20 frame/s and good agreement is found. The complex dynamics of the cantilever, consisting of traveling waves coming from the tip sample interaction, reflecting off the cantilever-substrate junction, and interfering with new waves created at the tip, are revealed. The construction of the image from this resulting nonequilibrium cantilever deflection is also examined. Transient tip-sample forces are found to reach values up to 260 nN on a calibration grid sample, and the maximum forces do not always correspond to the position of steepest features as a result of energy stored in the cantilever.

  1. Dynamic tunneling force microscopy for characterizing electronic trap states in non-conductive surfaces

    NASA Astrophysics Data System (ADS)

    Wang, R.; Williams, C. C.

    2015-09-01

    Dynamic tunneling force microscopy (DTFM) is a scanning probe technique for real space mapping and characterization of individual electronic trap states in non-conductive films with atomic scale spatial resolution. The method is based upon the quantum mechanical tunneling of a single electron back and forth between a metallic atomic force microscopy tip and individual trap states in completely non-conducting surface. This single electron shuttling is measured by detecting the electrostatic force induced on the probe tip at the shuttling frequency. In this paper, the physical basis for the DTFM method is unfolded through a physical model and a derivation of the dynamic tunneling signal as a function of several experimental parameters is shown. Experimental data are compared with the theoretical simulations, showing quantitative consistency and verifying the physical model used. The experimental system is described and representative imaging results are shown.

  2. Improving synthesis and analysis prior blind compressed sensing with low-rank constraints for dynamic MRI reconstruction.

    PubMed

    Majumdar, Angshul

    2015-01-01

    In blind compressed sensing (BCS), both the sparsifying dictionary and the sparse coefficients are estimated simultaneously during signal recovery. A recent study adopted the BCS framework for recovering dynamic MRI sequences from under-sampled K-space measurements; the results were promising. Previous works in dynamic MRI reconstruction showed that, recovery accuracy can be improved by incorporating low-rank penalties into the standard compressed sensing (CS) optimization framework. Our work is motivated by these studies, and we improve upon the basic BCS framework by incorporating low-rank penalties into the optimization problem. The resulting optimization problem has not been solved before; hence we derive a Split Bregman type technique to solve the same. Experiments were carried out on real dynamic contrast enhanced MRI sequences. Results show that, with our proposed improvement, the reconstruction accuracy is better than BCS and other state-of-the-art dynamic MRI recovery algorithms.

  3. Reconstruction of the Dynamics of Mammoth Tundra-Steppe Ecosystem Productivity

    NASA Astrophysics Data System (ADS)

    Zimov, S. A.; Chapin, F. S.

    2001-12-01

    During periods of glaciation, the mammoth tundra-steppe (MTS) ecosystem was the largest biome.The productivity of this ecosystem is under discussion. During the Pleistocene, a thick layer of frozen loess accumulated on the lowlands of northern Siberia. As loess deposited on the surface, the bottom of the soil profile was incorporated into permafrost. Present-day frozen loess soils of Siberia are cryo-preserved soils of the MTS. These soils have little humus but contain large quantities of grass roots and live Pleistocene microorganisms. As the soil melts, they start to respire actively. Analysis of vertical distribution of respiration in different types of modern soil and permafrost showed that respiration potential of cryo-preserved soil is similar to respiration of low soil horizons. On the basis of the correlation of photosynthesis to respiration, we calculated productivity of the MTS ecosystem and reconstructed its dynamics. Dynamics of MTS productivity was evaluated through the dynamics of the relative quantities of herbivorous animals. We analyzed the distribution of about 600 14C dates of mammoths, bison, and rhinoceroses. An estimate of the absolute density of mammoths in the north of Siberia was calculated on the basis of data collected on the density of skeletons buried in the permafrost. Our investigations showed that vegetation productivity and density of herbivorous animals in the MTS ecosystem varied within a wide range depending on climate. Dynamics of these parameters correlate with data of temperature and atmospheric CH4 obtained from Greenland cores. During periods of climate warming the quantity of mammoths in the north of Siberia was comparable to the quantity of elephants in present-day undisturbed African savanna.

  4. Cascaded spin motive force driven by the dynamics of the skyrmion lattice

    SciTech Connect

    Ohe, Jun-ichiro; Shimada, Yuhki

    2013-12-09

    We numerically investigate the spin motive force (SMF) driven by the dynamics of a Skyrmion lattice. The rotating mode of the Skyrmion core excited by the AC magnetic field induces the large spin-dependent electric field near the core. Due to the collective dynamics of Skyrmion lattice, the measurable voltage is enhanced by the cascade effect of the SMF. The amplitude of the AC voltage is estimated to 30 μV in a macroscopic sample, where 100 Skyrmions exist between two probes. We also investigate the SMF due to the dynamics of the helical magnetic state, where the enhancement of the SMF does not occur.

  5. Dynamically Consistent Shallow-Atmosphere Equations with a Complete Coriolis force

    NASA Astrophysics Data System (ADS)

    Tort, Marine; Dubos, Thomas; Bouchut, François; Zeitlin, Vladimir

    2014-05-01

    Dynamically Consistent Shallow-Atmosphere Equations with a Complete Coriolis force Marine Tort1, Thomas Dubos1, François Bouchut2 & Vladimir Zeitlin1,3 1 Laboratoire of Dynamical Meteorology, Univ. P. and M. Curie, Ecole Normale Supérieure, and Ecole Polytechnique, FRANCE 2 Université Paris-Est, Laboratoire d'Analyse et de Mathématiques Appliquées, FRANCE 3 Institut Universitaire de France Atmospheric and oceanic motion are usually modeled within the shallow-fluid approximation, which simplifies the 3D spherical geometry. For dynamical consistency, i.e. to ensure conservation laws for potential vorticity, energy and angular momentum, the horizontal component of the Coriolis force is neglected. Here new equation sets combining consistently a simplified shallow-fluid geometry with a complete Coriolis force is presented. The derivation invokes Hamilton's principle of least action with an approximate Lagrangian capturing the small increase with height of the solid-body entrainment velocity due to planetary rotation. A three-dimensional compressible model and a one-layer shallow-water model are obtained. The latter extends previous work done on the f-plane and β-plane. Preliminary numerical results confirm the accuracy of the 3D model within the range of parameters for which the equations are relevant. These new models could be useful to incorporate a full Coriolis force into existing numerical models and to disentangle the effects of the shallow-atmosphere approximation from those of the traditional approximation. Related papers: Tort M., Dubos T., Bouchut F. and Zeitlin V. Consistent shallow-water equations on the rotating sphere with complete Coriolis force and topography. J. Fluid Mech. (under revisions) Tort M. and Dubos T. Dynamically consistent shallow-atmosphere equations with a complete Coriolis force. Q.J.R. Meteorol. Soc. (DOI: 10.1002/qj.2274)

  6. Flexible Piezoelectric Tactile Sensor Array for Dynamic Three-Axis Force Measurement.

    PubMed

    Yu, Ping; Liu, Weiting; Gu, Chunxin; Cheng, Xiaoying; Fu, Xin

    2016-06-03

    A new flexible piezoelectric tactile sensor array based on polyvinylidene fluoride (PVDF) film is proposed for measuring three-axis dynamic contact force distribution. The array consists of six tactile units arranged as a 3 × 2 matrix with spacing 8 mm between neighbor units. In each unit, a PVDF film is sandwiched between four square-shaped upper electrodes and one square-shaped lower electrode, forming four piezoelectric capacitors. A truncated pyramid bump is located above the four piezoelectric capacitors to improve force transmission. A three-axis contact force transmitted from the top of the bump will lead to the four piezoelectric capacitors underneath undergoing different charge changes, from which the normal and shear components of the force can be calculated. A series of dynamic tests have been carried out by exerting sinusoidal forces with amplitudes ranging from 0 to 0.5 N in the x-axis, 0 to 0.5 N in the y-axis, and 0 to 1.5 N in the z-axis, separately. The tactile units show good sensitivities with 14.93, 14.92, and 6.62 pC/N in the x-, y-, and z-axes, respectively. They can work with good linearity, relatively low coupling effect, high repeatability, and acceptable frequency response in the range of 5-400 Hz to both normal and shear load. In addition, dynamic three-axis force measurement has been conducted for all of the tactile units. The average errors between the applied and calculated forces are 10.68% ± 6.84%. Furthermore, the sensor array can be easily integrated onto a curved surface, such as robotic and prosthetic hands, due to its excellent flexibility.

  7. Complexity of the tensegrity structure for dynamic energy and force distribution of cytoskeleton during cell spreading.

    PubMed

    Chen, Ting-Jung; Wu, Chia-Ching; Tang, Ming-Jer; Huang, Jong-Shin; Su, Fong-Chin

    2010-01-01

    Cytoskeleton plays important roles in intracellular force equilibrium and extracellular force transmission from/to attaching substrate through focal adhesions (FAs). Numerical simulations of intracellular force distribution to describe dynamic cell behaviors are still limited. The tensegrity structure comprises tension-supporting cables and compression-supporting struts that represent the actin filament and microtubule respectively, and has many features consistent with living cells. To simulate the dynamics of intracellular force distribution and total stored energy during cell spreading, the present study employed different complexities of the tensegrity structures by using octahedron tensegrity (OT) and cuboctahedron tensegrity (COT). The spreading was simulated by assigning specific connection nodes for radial displacement and attachment to substrate to form FAs. The traction force on each FA was estimated by summarizing the force carried in sounding cytoskeletal elements. The OT structure consisted of 24 cables and 6 struts and had limitations soon after the beginning of spreading by declining energy stored in struts indicating the abolishment of compression in microtubules. The COT structure, double the amount of cables and struts than the OT structure, provided sufficient spreading area and expressed similar features with documented cell behaviors. The traction force pointed inward on peripheral FAs in the spread out COT structure. The complex structure in COT provided further investigation of various FA number during different spreading stages. Before the middle phase of spreading (half of maximum spreading area), cell attachment with 8 FAs obtained minimized cytoskeletal energy. The maximum number of 12 FAs in the COT structure was required to achieve further spreading. The stored energy in actin filaments increased as cells spread out, while the energy stored in microtubules increased at initial spreading, peaked in middle phase, and then declined as

  8. Flexible Piezoelectric Tactile Sensor Array for Dynamic Three-Axis Force Measurement.

    PubMed

    Yu, Ping; Liu, Weiting; Gu, Chunxin; Cheng, Xiaoying; Fu, Xin

    2016-01-01

    A new flexible piezoelectric tactile sensor array based on polyvinylidene fluoride (PVDF) film is proposed for measuring three-axis dynamic contact force distribution. The array consists of six tactile units arranged as a 3 × 2 matrix with spacing 8 mm between neighbor units. In each unit, a PVDF film is sandwiched between four square-shaped upper electrodes and one square-shaped lower electrode, forming four piezoelectric capacitors. A truncated pyramid bump is located above the four piezoelectric capacitors to improve force transmission. A three-axis contact force transmitted from the top of the bump will lead to the four piezoelectric capacitors underneath undergoing different charge changes, from which the normal and shear components of the force can be calculated. A series of dynamic tests have been carried out by exerting sinusoidal forces with amplitudes ranging from 0 to 0.5 N in the x-axis, 0 to 0.5 N in the y-axis, and 0 to 1.5 N in the z-axis, separately. The tactile units show good sensitivities with 14.93, 14.92, and 6.62 pC/N in the x-, y-, and z-axes, respectively. They can work with good linearity, relatively low coupling effect, high repeatability, and acceptable frequency response in the range of 5-400 Hz to both normal and shear load. In addition, dynamic three-axis force measurement has been conducted for all of the tactile units. The average errors between the applied and calculated forces are 10.68% ± 6.84%. Furthermore, the sensor array can be easily integrated onto a curved surface, such as robotic and prosthetic hands, due to its excellent flexibility. PMID:27271631

  9. Flexible Piezoelectric Tactile Sensor Array for Dynamic Three-Axis Force Measurement

    PubMed Central

    Yu, Ping; Liu, Weiting; Gu, Chunxin; Cheng, Xiaoying; Fu, Xin

    2016-01-01

    A new flexible piezoelectric tactile sensor array based on polyvinylidene fluoride (PVDF) film is proposed for measuring three-axis dynamic contact force distribution. The array consists of six tactile units arranged as a 3 × 2 matrix with spacing 8 mm between neighbor units. In each unit, a PVDF film is sandwiched between four square-shaped upper electrodes and one square-shaped lower electrode, forming four piezoelectric capacitors. A truncated pyramid bump is located above the four piezoelectric capacitors to improve force transmission. A three-axis contact force transmitted from the top of the bump will lead to the four piezoelectric capacitors underneath undergoing different charge changes, from which the normal and shear components of the force can be calculated. A series of dynamic tests have been carried out by exerting sinusoidal forces with amplitudes ranging from 0 to 0.5 N in the x-axis, 0 to 0.5 N in the y-axis, and 0 to 1.5 N in the z-axis, separately. The tactile units show good sensitivities with 14.93, 14.92, and 6.62 pC/N in the x-, y-, and z-axes, respectively. They can work with good linearity, relatively low coupling effect, high repeatability, and acceptable frequency response in the range of 5–400 Hz to both normal and shear load. In addition, dynamic three-axis force measurement has been conducted for all of the tactile units. The average errors between the applied and calculated forces are 10.68% ± 6.84%. Furthermore, the sensor array can be easily integrated onto a curved surface, such as robotic and prosthetic hands, due to its excellent flexibility. PMID:27271631

  10. WE-G-18C-08: Real Time Tumor Imaging Using a Novel Dynamic Keyhole MRI Reconstruction Technique

    SciTech Connect

    Lee, D; Pollock, S; Whelan, B; Keall, P; Greer, P; Kim, T

    2014-06-15

    Purpose: To test the hypothesis that the novel Dynamic Keyhole MRI reconstruction technique can accelerate image acquisition whilst maintaining high image quality for lung cancer patients. Methods: 18 MRI datasets from 5 lung cancer patients were acquired using a 3T MRI scanner. These datasets were retrospectively reconstructed using (A) The novel Dynamic Keyhole technique, (B) The conventional keyhole technique and (C) the conventional zero filling technique. The dynamic keyhole technique in MRI refers to techniques in which previously acquired k-space data is used to supplement under sampled data obtained in real time. The novel Dynamic Keyhole technique utilizes a previously acquired a library of kspace datasets in conjunction with central k-space datasets acquired in realtime. A simultaneously acquired respiratory signal is utilized to sort, match and combine the two k-space streams with respect to respiratory displacement. Reconstruction performance was quantified by (1) comparing the keyhole size (which corresponds to imaging speed) required to achieve the same image quality, and (2) maintaining a constant keyhole size across the three reconstruction methods to compare the resulting image quality to the ground truth image. Results: (1) The dynamic keyhole method required a mean keyhole size which was 48% smaller than the conventional keyhole technique and 60% smaller than the zero filling technique to achieve the same image quality. This directly corresponds to faster imaging. (2) When a constant keyhole size was utilized, the Dynamic Keyhole technique resulted in the smallest difference of the tumor region compared to the ground truth. Conclusion: The dynamic keyhole is a simple and adaptable technique for clinical applications requiring real-time imaging and tumor monitoring such as MRI guided radiotherapy. Based on the results from this study, the dynamic keyhole method could increase the imaging frequency by a factor of five compared with full k

  11. The validation of a human force model to predict dynamic forces resulting from multi-joint motions

    NASA Technical Reports Server (NTRS)

    Pandya, Abhilash K.; Maida, James C.; Aldridge, Ann M.; Hasson, Scott M.; Woolford, Barbara J.

    1992-01-01

    The development and validation is examined of a dynamic strength model for humans. This model is based on empirical data. The shoulder, elbow, and wrist joints were characterized in terms of maximum isolated torque, or position and velocity, in all rotational planes. This data was reduced by a least squares regression technique into a table of single variable second degree polynomial equations determining torque as a function of position and velocity. The isolated joint torque equations were then used to compute forces resulting from a composite motion, in this case, a ratchet wrench push and pull operation. A comparison of the predicted results of the model with the actual measured values for the composite motion indicates that forces derived from a composite motion of joints (ratcheting) can be predicted from isolated joint measures. Calculated T values comparing model versus measured values for 14 subjects were well within the statistically acceptable limits and regression analysis revealed coefficient of variation between actual and measured to be within 0.72 and 0.80.

  12. Viking Mars lander 1975 dynamic test model/orbiter developmental test model forced vibration test

    NASA Technical Reports Server (NTRS)

    Fortenberry, J.; Brownlee, G. R.

    1974-01-01

    The Viking Mars Lander 1975 dynamic test model and orbiter developmental test model were subjected to forced vibration sine tests. Flight acceptance (FA) and type approval (TA) test levels were applied to the spacecraft structure in a longitudinal test configuration using a 133,440-N (30,000-lb) force shaker. Testing in the two lateral axes (X, Y) was performed at lower levels using four 667-N (150-lb) force shakers. Forced vibration qualification (TA) test levels were successfully imposed on the spacecraft at frequencies down to 10 Hz. Measured responses showed the same character as analytical predictions, and correlation was reasonably good. Because of control system test tolerances, orbiter primary structure generally did not reach the design load limits attained in earlier static testing. A post-test examination of critical orbiter structure disclosed no apparent damage to the structure as a result of the test environment.

  13. Dynamic force spectroscopy of the Helicobacter pylori BabA-Lewis b binding.

    PubMed

    Björnham, Oscar; Bugaytsova, Jeanna; Borén, Thomas; Schedin, Staffan

    2009-07-01

    The binding strength of the Helicobacter pylori adhesin-receptor complex BabA-ABO/Lewis b has been analyzed by means of dynamic force spectroscopy. High-resolution measurements of rupture forces were performed in situ on single bacterial cells, expressing the high-affinity binding BabA adhesin, by the use of force measuring optical tweezers. The resulting force spectra revealed the mechanical properties of a single BabA-Leb bond. It was found that the bond is dominated by one single energy barrier and that it is a slip-bond. The bond length and thermal off-rate were assessed to be 0.86+/-0.07 nm and 0.015+/-0.006 s(-1), respectively.

  14. The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis.

    PubMed

    Yang, Y; Pan, L; Lightstone, F C; Merz, K M

    2016-01-01

    The potential of mean force simulations, widely applied in Monte Carlo or molecular dynamics simulations, are useful tools to examine the free energy variation as a function of one or more specific reaction coordinate(s) for a given system. Implementation of the potential of mean force in the simulations of biological processes, such as enzyme catalysis, can help overcome the difficulties of sampling specific regions on the energy landscape and provide useful insights to understand the catalytic mechanism. The potential of mean force simulations usually require many, possibly parallelizable, short simulations instead of a few extremely long simulations and, therefore, are fairly manageable for most research facilities. In this chapter, we provide detailed protocols for applying the potential of mean force simulations to investigate enzymatic mechanisms for several different enzyme systems. PMID:27498632

  15. Dynamic tensile forces drive collective cell migration through three-dimensional extracellular matrices

    PubMed Central

    Gjorevski, Nikolce; S. Piotrowski, Alexandra; Varner, Victor D.; Nelson, Celeste M.

    2015-01-01

    Collective cell migration drives tissue remodeling during development, wound repair, and metastatic invasion. The physical mechanisms by which cells move cohesively through dense three-dimensional (3D) extracellular matrix (ECM) remain incompletely understood. Here, we show directly that migration of multicellular cohorts through collagenous matrices occurs via a dynamic pulling mechanism, the nature of which had only been inferred previously in 3D. Tensile forces increase at the invasive front of cohorts, serving a physical, propelling role as well as a regulatory one by conditioning the cells and matrix for further extension. These forces elicit mechanosensitive signaling within the leading edge and align the ECM, creating microtracks conducive to further migration. Moreover, cell movements are highly correlated and in phase with ECM deformations. Migrating cohorts use spatially localized, long-range forces and consequent matrix alignment to navigate through the ECM. These results suggest biophysical forces are critical for 3D collective migration. PMID:26165921

  16. Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics.

    PubMed

    Armond, Jonathan W; Harry, Edward F; McAinsh, Andrew D; Burroughs, Nigel J

    2015-11-01

    Kinetochores are multi-protein complexes that mediate the physical coupling of sister chromatids to spindle microtubule bundles (called kinetochore (K)-fibres) from respective poles. These kinetochore-attached K-fibres generate pushing and pulling forces, which combine with polar ejection forces (PEF) and elastic inter-sister chromatin to govern chromosome movements. Classic experiments in meiotic cells using calibrated micro-needles measured an approximate stall force for a chromosome, but methods that allow the systematic determination of forces acting on a kinetochore in living cells are lacking. Here we report the development of mathematical models that can be fitted (reverse engineered) to high-resolution kinetochore tracking data, thereby estimating the model parameters and allowing us to indirectly compute the (relative) force components (K-fibre, spring force and PEF) acting on individual sister kinetochores in vivo. We applied our methodology to thousands of human kinetochore pair trajectories and report distinct signatures in temporal force profiles during directional switches. We found the K-fibre force to be the dominant force throughout oscillations, and the centromeric spring the smallest although it has the strongest directional switching signature. There is also structure throughout the metaphase plate, with a steeper PEF potential well towards the periphery and a concomitant reduction in plate thickness and oscillation amplitude. This data driven reverse engineering approach is sufficiently flexible to allow fitting of more complex mechanistic models; mathematical models of kinetochore dynamics can therefore be thoroughly tested on experimental data for the first time. Future work will now be able to map out how individual proteins contribute to kinetochore-based force generation and sensing.

  17. Wheel-rail dynamic forces induced by random vertical track irregularities

    NASA Astrophysics Data System (ADS)

    Spiroiu, M. A.

    2016-08-01

    The present paper investigates the wheel-rail dynamic forces produced by railway vehicles in motion, which are an important issue especially for the high-speed rail transport from the point of view of traffic safety, ride quality and undesirable effects on vehicles, on track and on the land in the vicinity of railways. The research is carried out on a model which includes track system, vehicle unsprung mass, vehicle primary suspension and the bogie sprung mass. The wheel-rail dynamic overloads are evaluated assuming random vertical irregularities of the track. The estimation of wheel-rail dynamic forces is made for a range of vehicle speeds up to 300 km/h and the influence of track and vehicle various parameters is investigated.

  18. Role of inertial forces on the chaotic dynamics of flexible rotating bodies

    NASA Astrophysics Data System (ADS)

    Calvo, F.

    2013-02-01

    The nonlinear dynamics of isolated flexible but rotating many-body atomic systems is theoretically investigated, following the dependence on initial conditions through Lyapunov exponents. The tangent-space equations of motion that rule the time evolution of such small perturbations are rewritten in the rotating reference frame, and the various contributions of the centrifugal, Coriolis, and Euler forces are determined. Evaluating the largest Lyapunov in the rotating frame under various approximations, we show on the example of Lennard-Jones clusters that the dynamics in phase space is qualitatively at variance with the effective dynamics on the centrifugal energy surface. Coupling terms between positions and momenta in phase space, especially arising from the Coriolis force, are essential to recover the measure of chaos in the fixed reference frame.

  19. Nonlinear dynamics of confined liquid systems with interfaces subject to forced vibrations.

    PubMed

    Higuera, María; Porter, Jeff; Varas, Fernando; Vega, José M

    2014-04-01

    A review is presented of the dynamic behavior of confined fluid systems with interfaces under monochromatic mechanical forcing, emphasizing the associated spatio-temporal structure of the fluid response. At low viscosity, vibrations significantly affect dynamics and always produce viscous mean flows, which are coupled to the primary oscillating flow and evolve on a very slow timescale. Thus, unlike the primary oscillating flow, mean flows may easily interact with the surface rheology, which generates dynamics that usually exhibit a much slower timescale than that of typical gravity-capillary waves. The review is made with an eye to the typical experimental devices used to measure surface properties, which usually consist of periodically forced, symmetric fluid systems with interfaces. The current theoretical description of these systems ignores the fluid mechanics, which could play a larger role than presently assumed. PMID:24315015

  20. The Dynamics of Voluntary Force Production in Afferented Muscle Influence Involuntary Tremor

    PubMed Central

    Laine, Christopher M.; Nagamori, Akira; Valero-Cuevas, Francisco J.

    2016-01-01

    Voluntary control of force is always marked by some degree of error and unsteadiness. Both neural and mechanical factors contribute to these fluctuations, but how they interact to produce them is poorly understood. In this study, we identify and characterize a previously undescribed neuromechanical interaction where the dynamics of voluntary force production suffice to generate involuntary tremor. Specifically, participants were asked to produce isometric force with the index finger and use visual feedback to track a sinusoidal target spanning 5–9% of each individual's maximal voluntary force level. Force fluctuations and EMG activity over the flexor digitorum superficialis (FDS) muscle were recorded and their frequency content was analyzed as a function of target phase. Force variability in either the 1–5 or 6–15 Hz frequency ranges tended to be largest at the peaks and valleys of the target sinusoid. In those same periods, FDS EMG activity was synchronized with force fluctuations. We then constructed a physiologically-realistic computer simulation in which a muscle-tendon complex was set inside of a feedback-driven control loop. Surprisingly, the model sufficed to produce phase-dependent modulation of tremor similar to that observed in humans. Further, the gain of afferent feedback from muscle spindles was critical for appropriately amplifying and shaping this tremor. We suggest that the experimentally-induced tremor may represent the response of a viscoelastic muscle-tendon system to dynamic drive, and therefore does not fall into known categories of tremor generation, such as tremorogenic descending drive, stretch-reflex loop oscillations, motor unit behavior, or mechanical resonance. Our findings motivate future efforts to understand tremor from a perspective that considers neuromechanical coupling within the context of closed-loop control. The strategy of combining experimental recordings with physiologically-sound simulations will enable thorough

  1. The dynamics of two-dimensional turbulence excited at two scales using electromagnetic forces

    NASA Astrophysics Data System (ADS)

    Habchi, Charbel; Antar, Ghassan

    2016-05-01

    Several forcing scales can co-exist in nature leading and affecting turbulent flows. This is not critical in three-dimensional systems where only a direct cascade of energy exists, but it is a concern in two dimensions where the direct and inverse cascades lead to different statistical properties of turbulence. The effect of forcing at two different scales on turbulence is studied here using numerical simulation inspired by a recent experiment [L. M. Moubarak and G. Y. Antar, "Dynamics of a two-dimensional flow subject to steady electromagnetic forces," Exp. Fluids 53, 1627-1636 (2012)] where a thin layer of electrolyte is stirred using electromagnetic forces. The small scale eddies are generated by the Lorentz force near the domain edge while the large scale motion is produced by the magnetic field gradient. We compare the case of one to two forcing scales for steady state turbulence to show that the addition of two forcing scales leads to the onset of turbulence at low Reynolds numbers due to the co-existence and thus the interaction of small and large structures. By determining the k-spectra as well as the energy transfer function, it is established that the dynamics of turbulence change from being dominated by an inverse cascade process, with one forcing scale, to one dominated by a direct cascade process when two scales are present. We believe that these results are important in understanding two- and quasi-two-dimensional turbulence phenomena occurring in nature where several excitation scales co-exist.

  2. Molecular dynamics simulation of hydrated Nafion with a reactive force field for water.

    PubMed

    Hofmann, Detlef W M; Kuleshova, Liudmila; D'Aguanno, Bruno

    2008-03-01

    We apply a newly parameterized central force field to highlight the problem of proton transport in fuel cell membranes and show that central force fields are potential candidates to describe chemical reactions on a classical level. After a short sketch of the parameterization of the force field, we validate the obtained force field for several properties of water. The experimental and simulated radial distribution functions are reproduced very accurately as a consequence of the applied parameterization procedure. Further properties, geometry, coordination, diffusion coefficient and density, are simulated adequately for our purposes. Afterwards we use the new force field for the molecular dynamics simulation of a swollen polyelectrolyte membrane similar to the widespread Nafion 117. We investigate the equilibrated structures, proton transfer, lifetimes of hydronium ions, the diffusion coefficients, and the conductivity in dependence of water content. In a short movie we demonstrate the ability of the obtained force field to describe the bond breaking/formation, and conclude that this force field can be considered as a kind of a reactive force field. The investigations of the lifetimes of hydronium ions give us the information about the kinetics of the proton transfer in a membrane with low water content. We found the evidence for the second order reaction. Finally, we demonstrate that the model is simple enough to handle the large systems sufficient to calculate the conductivity from molecular dynamics simulations. The detailed analysis of the conductivity reveals the importance of the collective moving of hydronium ions in membrane, which might give an interesting encouragement for further development of membranes.

  3. The Dynamics of Voluntary Force Production in Afferented Muscle Influence Involuntary Tremor.

    PubMed

    Laine, Christopher M; Nagamori, Akira; Valero-Cuevas, Francisco J

    2016-01-01

    Voluntary control of force is always marked by some degree of error and unsteadiness. Both neural and mechanical factors contribute to these fluctuations, but how they interact to produce them is poorly understood. In this study, we identify and characterize a previously undescribed neuromechanical interaction where the dynamics of voluntary force production suffice to generate involuntary tremor. Specifically, participants were asked to produce isometric force with the index finger and use visual feedback to track a sinusoidal target spanning 5-9% of each individual's maximal voluntary force level. Force fluctuations and EMG activity over the flexor digitorum superficialis (FDS) muscle were recorded and their frequency content was analyzed as a function of target phase. Force variability in either the 1-5 or 6-15 Hz frequency ranges tended to be largest at the peaks and valleys of the target sinusoid. In those same periods, FDS EMG activity was synchronized with force fluctuations. We then constructed a physiologically-realistic computer simulation in which a muscle-tendon complex was set inside of a feedback-driven control loop. Surprisingly, the model sufficed to produce phase-dependent modulation of tremor similar to that observed in humans. Further, the gain of afferent feedback from muscle spindles was critical for appropriately amplifying and shaping this tremor. We suggest that the experimentally-induced tremor may represent the response of a viscoelastic muscle-tendon system to dynamic drive, and therefore does not fall into known categories of tremor generation, such as tremorogenic descending drive, stretch-reflex loop oscillations, motor unit behavior, or mechanical resonance. Our findings motivate future efforts to understand tremor from a perspective that considers neuromechanical coupling within the context of closed-loop control. The strategy of combining experimental recordings with physiologically-sound simulations will enable thorough exploration

  4. The Dynamics of Voluntary Force Production in Afferented Muscle Influence Involuntary Tremor

    PubMed Central

    Laine, Christopher M.; Nagamori, Akira; Valero-Cuevas, Francisco J.

    2016-01-01

    Voluntary control of force is always marked by some degree of error and unsteadiness. Both neural and mechanical factors contribute to these fluctuations, but how they interact to produce them is poorly understood. In this study, we identify and characterize a previously undescribed neuromechanical interaction where the dynamics of voluntary force production suffice to generate involuntary tremor. Specifically, participants were asked to produce isometric force with the index finger and use visual feedback to track a sinusoidal target spanning 5–9% of each individual's maximal voluntary force level. Force fluctuations and EMG activity over the flexor digitorum superficialis (FDS) muscle were recorded and their frequency content was analyzed as a function of target phase. Force variability in either the 1–5 or 6–15 Hz frequency ranges tended to be largest at the peaks and valleys of the target sinusoid. In those same periods, FDS EMG activity was synchronized with force fluctuations. We then constructed a physiologically-realistic computer simulation in which a muscle-tendon complex was set inside of a feedback-driven control loop. Surprisingly, the model sufficed to produce phase-dependent modulation of tremor similar to that observed in humans. Further, the gain of afferent feedback from muscle spindles was critical for appropriately amplifying and shaping this tremor. We suggest that the experimentally-induced tremor may represent the response of a viscoelastic muscle-tendon system to dynamic drive, and therefore does not fall into known categories of tremor generation, such as tremorogenic descending drive, stretch-reflex loop oscillations, motor unit behavior, or mechanical resonance. Our findings motivate future efforts to understand tremor from a perspective that considers neuromechanical coupling within the context of closed-loop control. The strategy of combining experimental recordings with physiologically-sound simulations will enable thorough

  5. Temperature-resolution anomalies in the reconstruction of time dynamics from energy-loss experiments

    NASA Astrophysics Data System (ADS)

    Kogar, Anshul; Vig, Sean; Gan, Yu; Abbamonte, Peter

    2014-06-01

    Inelastic scattering techniques provide a powerful approach to studying electron and nuclear dynamics, via reconstruction of a propagator that quantifies the time evolution of a system. There is now growing interest in applying such methods to very low energy excitations, such as lattice vibrations, but in this limit the cross section is no longer proportional to a propagator. Significant deviations occur due to the finite temperature Bose statistics of the excitations. Here we consider this issue in the context of high-resolution electron energy-loss experiments on the copper-oxide superconductor Bi2Sr2CaCu2O8. We find that simple division of a Bose factor yields an accurate propagator on energy scales greater than the resolution width. However, at low energy scales, the effects of resolution and finite temperature conspire to create anomalies in the dynamics at long times. We compare two practical ways for dealing with such anomalies, and discuss the range of validity of the technique in light of this comparison.

  6. Dynamic Regulatory Network Reconstruction for Alzheimer's Disease Based on Matrix Decomposition Techniques

    PubMed Central

    Mou, Xiaoyang; Zhi, Xing; Zhang, Xin; Yang, Yang

    2014-01-01

    Alzheimer's disease (AD) is the most common form of dementia and leads to irreversible neurodegenerative damage of the brain. Finding the dynamic responses of genes, signaling proteins, transcription factor (TF) activities, and regulatory networks of the progressively deteriorative progress of AD would represent a significant advance in discovering the pathogenesis of AD. However, the high throughput technologies of measuring TF activities are not yet available on a genome-wide scale. In this study, based on DNA microarray gene expression data and a priori information of TFs, network component analysis (NCA) algorithm is applied to determining the TF activities and regulatory influences on TGs of incipient, moderate, and severe AD. Based on that, the dynamical gene regulatory networks of the deteriorative courses of AD were reconstructed. To select significant genes which are differentially expressed in different courses of AD, independent component analysis (ICA), which is better than the traditional clustering methods and can successfully group one gene in different meaningful biological processes, was used. The molecular biological analysis showed that the changes of TF activities and interactions of signaling proteins in mitosis, cell cycle, immune response, and inflammation play an important role in the deterioration of AD. PMID:25024739

  7. Time-resolved reconstruction of dynamical pulse trains using multiheterodyne detection

    NASA Astrophysics Data System (ADS)

    Butler, T.; Tykalewicz, B.; Goulding, D.; Kelleher, B.; Huyet, Guillaume; Hegarty, S. P.

    2014-05-01

    A technique has been developed for the measurement of pulse trains demonstrating a dynamical behaviour (i.e. not ideally periodic). Existing techniques in this area (e.g. FROG, SPIDER or other heterodyne methods) require very stable pulse trains, or large averaging times, and so are limited when applied to even slowly varying pulse trains. The technique presented involves mixing the comb under test (CUT) with a reference optical frequency comb (OFC) which has a known spectral intensity profile. Mixing these signals on a photodiode results in a series of radio frequency (RF) beat tones. The phase properties of these beat tones can be used to measure the spectral phase between adjacent modes in the CUT, allowing the full complex spectrum of the CUT to be measured simultaneously with one single real time oscilloscope acquisition. With the spectral properties of the comb known, the pulse train can be reconstructed in the temporal domain. By applying this technique to very small sections of the beating signal ( tens of nanoseconds), a time resolved picture of the pulse train behaviour can be obtained. Dynamic signals generated in a LiNbO3 modulator driven by a modulated RF signal have been measured. This technique is well suited to studying the combs produced by mode-locked semiconductor lasers. Quantum dot mode-locked laser combs can be characterised, and pulse train instabilities measured.

  8. The force generated by biological membranes on a polymer rod and its response: Statics and dynamics

    NASA Astrophysics Data System (ADS)

    Daniels, D. R.; Turner, M. S.

    2004-10-01

    We propose a theory for the force exerted by a fluctuating membrane on a polymer rod tip. Using statistical mechanical methods, the expression for the generated force is written in terms of the distance of the rod tip from the membrane "frame." We apply the theory in calculating the stall force and membrane displacement required to cease the growth of a growing fiber induced by membrane fluctuations, as well as the membrane force and membrane displacement required for rod/fiber buckling. We also consider the dynamics of a growing fiber tip under the influence of a fluctuation-induced membrane force. We discuss the importance of our results in various biological contexts. Finally, we present a method to simultaneously extract both the rigidity of the semiflexible rod and the force applied by, e.g., the membrane from the measurements of the bending fluctuations of the rod. Such a measurement of the force would give information about the thermodynamics of the rod polymerization that involves the usual Brownian ratchet mechanism.

  9. Computational Intelligence Based Data Fusion Algorithm for Dynamic sEMG and Skeletal Muscle Force Modelling

    SciTech Connect

    Chandrasekhar Potluri,; Madhavi Anugolu; Marco P. Schoen; D. Subbaram Naidu

    2013-08-01

    In this work, an array of three surface Electrography (sEMG) sensors are used to acquired muscle extension and contraction signals for 18 healthy test subjects. The skeletal muscle force is estimated using the acquired sEMG signals and a Non-linear Wiener Hammerstein model, relating the two signals in a dynamic fashion. The model is obtained from using System Identification (SI) algorithm. The obtained force models for each sensor are fused using a proposed fuzzy logic concept with the intent to improve the force estimation accuracy and resilience to sensor failure or misalignment. For the fuzzy logic inference system, the sEMG entropy, the relative error, and the correlation of the force signals are considered for defining the membership functions. The proposed fusion algorithm yields an average of 92.49% correlation between the actual force and the overall estimated force output. In addition, the proposed fusionbased approach is implemented on a test platform. Experiments indicate an improvement in finger/hand force estimation.

  10. Investigation of the heparin-thrombin interaction by dynamic force spectroscopy

    PubMed Central

    Wang, Congzhou; Jin, Yingzi; Desai, Umesh R.; Yadavalli, Vamsi K.

    2015-01-01

    Background The interaction between heparin and thrombin is a vital step in the blood (anti) coagulation process. Unraveling the molecular basis of the interactions is therefore extremely important for understanding the mechanisms of this complex biological process. Methods In this study, we use a combination of an efficient thiolation chemistry of heparin, a self-assembled monolayer-based single molecule platform, and dynamic force spectroscopy to provide new insights into the heparin-thrombin interaction from an energy viewpoint at the molecular scale. Results Well-separated single molecules of heparin covalently attached to mixed self-assembled monolayers are demonstrated, whereby interaction forces with thrombin can be measured via atomic force microscopy-based spectroscopy. Further these interactions are studied at different loading rates and salt concentrations to directly obtain kinetic parameters. Conclusions An increase in the loading rate shows a higher interaction force between the heparin and thrombin, which can be directly linked to the kinetic dissociation rate constant (koff ). The stability of the heparin/thrombin complex decreased with increasing NaCl concentration such that the off-rate was found to be driven primarily by non-ionic forces. General Significance These results contribute to understanding the role of specific and nonspecific forces that drive heparin-thrombin interactions under applied force or flow conditions. PMID:25647100

  11. Probabilistic information on object weight shapes force dynamics in a grip-lift task.

    PubMed

    Trampenau, Leif; Kuhtz-Buschbeck, Johann P; van Eimeren, Thilo

    2015-06-01

    Advance information, such as object weight, size and texture, modifies predictive scaling of grip forces in a grip-lift task. Here, we examined the influence of probabilistic advance information about object weight. Fifteen healthy volunteers repeatedly grasped and lifted an object equipped with a force transducer between their thumb and index finger. Three clearly distinguishable object weights were used. Prior to each lift, the probabilities for the three object weights were given by a visual cue. We examined the effect of probabilistic pre-cues on grip and lift force dynamics. We expected predictive scaling of grip force parameters to follow predicted values calculated according to probabilistic contingencies of the cues. We observed that probabilistic cues systematically influenced peak grip and load force rates, as an index of predictive motor scaling. However, the effects of probabilistic cues on force rates were nonlinear, and anticipatory adaptations of the motor output generally seemed to overestimate high probabilities and underestimate low probabilities. These findings support the suggestion that anticipatory adaptations and force scaling of the motor system can integrate probabilistic information. However, probabilistic information seems to influence motor programs in a nonlinear fashion.

  12. The Effects of a Constant Bias Force on the Dynamics of a Periodically Forced Spherical Particle in a Newtonian Fluid at Low Reynolds Numbers

    NASA Astrophysics Data System (ADS)

    Madhukar, K.; Ramamohan, T. R.; Shivakumara, I. S.

    2010-09-01

    of both periodic force and the constant bias force. As the Reynolds numbers increases the drift of the particle reduces, which indicates the effects of inertia. We present a preliminary analysis of the dynamics in this paper.

  13. Capillary and van der Waals interactions on CaF2 crystals from amplitude modulation AFM force reconstruction profiles under ambient conditions.

    PubMed

    Calò, Annalisa; Robles, Oriol Vidal; Santos, Sergio; Verdaguer, Albert

    2015-01-01

    There has been much interest in the past two decades to produce experimental force profiles characteristic of the interaction between nanoscale objects or a nanoscale object and a plane. Arguably, the advent of the atomic force microscope AFM was instrumental in driving such efforts because, in principle, force profiles could be recovered directly. Nevertheless, it has taken years before techniques have developed enough as to recover the attractive part of the force with relatively low noise and without missing information on critical ranges, particularly under ambient conditions where capillary interactions are believed to dominate. Thus a systematic study of the different profiles that may arise in such situations is still lacking. Here we employ the surfaces of CaF2, on which nanoscale water films form, to report on the range and force profiles that might originate by dynamic capillary interactions occurring between an AFM tip and nanoscale water patches. Three types of force profiles were observed under ambient conditions. One in which the force decay resembles the well-known inverse-square law typical of van der Waals interactions during the first 0.5-1 nm of decay, a second one in which the force decays almost linearly, in relatively good agreement with capillary force predicted by the constant chemical potential approximation, and a third one in which the attractive force is almost constant, i.e., forms a plateau, up to 3-4 nm above the surface when the formation of a capillary neck dominates the tip-sample interaction.

  14. Reconstruction of dynamic contrast enhanced magnetic resonance imaging of the breast with temporal constraints.

    PubMed

    Chen, Liyong; Schabel, Matthias C; DiBella, Edward V R

    2010-06-01

    A number of methods using temporal and spatial constraints have been proposed for reconstruction of undersampled dynamic magnetic resonance imaging (MRI) data. The complex data can be constrained or regularized in a number of different ways, for example, the time derivative of the magnitude and phase image voxels can be constrained separately or jointly. Intuitively, the performance of different regularizations will depend on both the data and the chosen temporal constraints. Here, a complex temporal total variation (TV) constraint was compared to the use of separate real and imaginary constraints, and to a magnitude constraint alone. Projection onto Convex Sets (POCS) with a gradient descent method was used to implement the diverse temporal constraints in reconstructions of DCE MRI data. For breast DCE data, serial POCS with separate real and imaginary TV constraints was found to give relatively poor results while serial/parallel POCS with a complex temporal TV constraint and serial POCS with a magnitude-only temporal TV constraint performed well with an acceleration factor as large as R=6. In the tumor area, the best method was found to be parallel POCS with complex temporal TV constraint. This method resulted in estimates for the pharmacokinetic parameters that were linearly correlated to those estimated from the fully-sampled data, with K(trans,R=6)=0.97 K(trans,R=1)+0.00 with correlation coefficient r=0.98, k(ep,R=6)=0.95 k(ep,R=1)+0.00 (r=0.85). These results suggest that it is possible to acquire highly undersampled breast DCE-MRI data with improved spatial and/or temporal resolution with minimal loss of image quality.

  15. Pressure Gradient Error of Spectral Element Dynamical Core associated with Topographic Forcing: Comparison with the Spherical Harmonics Dynamical Core

    NASA Astrophysics Data System (ADS)

    Kang, Hyun-Gyu; Cheong, Hyeong-Bin; Jeong, Han-Byeol; Kim, Won-Ho

    2015-04-01

    Response characteristics of the spectral element hydrostatic dynamical core on the cubed sphere to the global topographic forcing are investigated in terms of pressure gradient error, and it is compared with the spherical harmonics hydrostatic dynamical core. The vertical hybrid-pressure coordinate and finite difference method are introduced to both dynamical cores, and explicit and implicit hyper-diffusion schemes are applied to spectral element dynamical core and spherical harmonics dynamical core, respectively. The model atmosphere at initial time is set to the quiescent environment so that the term affecting on the time tendency of the momentum equation at the first time step is the pressure gradient term only which is influenced by the observed surface topography. During 6 days of time integration, the spurious flow is generated due to inaccurate numerical approximations of pressure gradient term for each dynamical core. High zonal wind speed which can be regarded as numerical error is occurred commonly in two dynamical cores around steep topography (e.g., the Tibetan Plateau, the Rocky Mountains, and the Andes Mountains), but the maximum zonal wind speed at day 6 of spectral element dynamical core is 8-9 times larger than that of spherical harmonics dynamical core. The vertically averaged kinetic energy spectrum at day 6 shows very different trend between two dynamical cores. By performing the experiments with the scale-separated topography, it turns out that these kinetic energy spectrum trends are mainly caused by the small-scale topography. A simple change of pressure gradient term into log-pressure form is found to significantly reduce numerical error (up to 63% of maximum wind speed in case of spectral element dynamical core) and noise-like small-scale phenomena.

  16. Dynamic landscapes and human dispersal patterns: tectonics, coastlines, and the reconstruction of human habitats

    NASA Astrophysics Data System (ADS)

    Bailey, Geoffrey N.; King, Geoffrey C. P.

    2011-06-01

    Studies of the impact of physical environment on human evolution usually focus on climate as the main external forcing agent of evolutionary and cultural change. In this paper we focus on changes in the physical character of the landscape driven by geophysical processes as an equally potent factor. Most of the landscapes where finds of early human fossils and artefacts are concentrated are ones that have been subjected to high levels of geological instability, either because of especially active tectonic processes associated with faulting and volcanic activity or because of proximity to coastlines subject to dramatic changes of geographical position and physical character by changes of relative sea level. These processes can have both beneficial effects, creating ecologically attractive conditions for human settlement, and deleterious or disruptive ones, creating barriers to movement, disruption of ecological conditions, or hazards to survival. Both positive and negative factors can have powerful selective effects on human behaviour and patterns of settlement and dispersal. We consider both these aspects of the interaction, develop a framework for the reconstruction and comparison of landscapes and landscape change at a variety of scales, and illustrate this with selected examples drawn from Africa and Arabia.

  17. Dynamics of confined water reconstructed from inelastic x-ray scattering measurements of bulk response functions

    NASA Astrophysics Data System (ADS)

    Coridan, Robert H.; Schmidt, Nathan W.; Lai, Ghee Hwee; Abbamonte, Peter; Wong, Gerard C. L.

    2012-03-01

    Nanoconfined water and surface-structured water impacts a broad range of fields. For water confined between hydrophilic surfaces, measurements and simulations have shown conflicting results ranging from “liquidlike” to “solidlike” behavior, from bulklike water viscosity to viscosity orders of magnitude higher. Here, we investigate how a homogeneous fluid behaves under nanoconfinement using its bulk response function: The Green's function of water extracted from a library of S(q,ω) inelastic x-ray scattering data is used to make femtosecond movies of nanoconfined water. Between two confining surfaces, the structure undergoes drastic changes as a function of surface separation. For surface separations of ≈9 Å, although the surface-associated hydration layers are highly deformed, they are separated by a layer of bulklike water. For separations of ≈6 Å, the two surface-associated hydration layers are forced to reconstruct into a single layer that modulates between localized “frozen’ and delocalized “melted” structures due to interference of density fields. These results potentially reconcile recent conflicting experiments. Importantly, we find a different delocalized wetting regime for nanoconfined water between surfaces with high spatial frequency charge densities, where water is organized into delocalized hydration layers instead of localized hydration shells, and are strongly resistant to `freezing' down to molecular distances (<6 Å).

  18. The effect of tendon on muscle force in dynamic isometric contractions: a simulation study.

    PubMed

    van Soest, A J; Huijing, P A; Solomonow, M

    1995-07-01

    Recently, Baratta and Solomonow J. Biomechanics 24, 109-116 (1991) studied the effect of tendon on muscle-tendon complex behavior in cat tibialis anterior (TA) muscle. This was done by determining the relation between neural stimulation and muscle force in a dynamic isometric experiment, both before and after the removal of the distal tendon. From their results, Baratta and Solomonow concluded that in isometric and concentric contractions at mid-range force levels, tendon behaves as a rigid force conductor. This conclusion is in conflict with literature in which several functions are attributed to the elastic behavior of the series elastic element (SEE), of which tendon is the major part. The present study investigates the expected generalizability of their findings, by simulating the experiments using a straightforward Hill-type muscle model. First, model predictions are shown to be in line with the experimental results on cat TA: in dynamic isometric experiments at mid-range force levels, the effect of SEE removal is indeed negligible. Second, the effect of SEE removal is predicted to vary largely among muscles. Third, the most important determinants of the effect of SEE removal in dynamic isometric contractions are shown to be maximum fiber shortening velocity and the ratio of SEE slack length to fibre optimum length. PMID:7657678

  19. Cooperative dynamics of microtubule ensembles: Polymerization forces and rescue-induced oscillations

    NASA Astrophysics Data System (ADS)

    Zelinski, Björn; Kierfeld, Jan

    2013-01-01

    We investigate the cooperative dynamics of an ensemble of N microtubules growing against an elastic barrier. Microtubules undergo so-called catastrophes, which are abrupt stochastic transitions from a growing to a shrinking state, and rescues, which are transitions back to the growing state. Microtubules can exert pushing or polymerization forces on an obstacle, such as an elastic barrier, if the growing end is in contact with the obstacle. We use dynamical mean-field theory and stochastic simulations to analyze a model where each microtubule undergoes catastrophes and rescues and where microtubules interact by force sharing. For zero rescue rate, cooperative growth terminates in a collective catastrophe. The maximal polymerization force before catastrophes grows linearly with N for small N or a stiff elastic barrier, in agreement with available experimental results, whereas it crosses over to a logarithmic dependence for larger N or a soft elastic barrier. For a nonzero rescue rate and a soft elastic barrier, the dynamics becomes oscillatory with both collective catastrophe and rescue events, which are part of a robust limit cycle. Both the average and maximal polymerization forces then grow linearly with N, and we investigate their dependence on tubulin on-rates and rescue rates, which can be involved in cellular regulation mechanisms. We further investigate the robustness of the collective catastrophe and rescue oscillations with respect to different catastrophe models.

  20. Solvation structure and dynamics of Ni2+(aq) from a polarizable force field

    NASA Astrophysics Data System (ADS)

    Mareš, Jiří; Vaara, Juha

    2014-10-01

    An aqueous solution of Ni2+ has often been used as a prototypic transition-metal system for experimental and theoretical studies in nuclear and electron-spin magnetic resonance (NMR and ESR). Molecular dynamics (MD) simulation of Ni2+(aq) has been a part of many of these studies. As a transition metal complex, its MD simulation is particularly difficult using common force fields. In this work, we parameterize the Ni2+ ion for a simulation of the aqueous solution within the modern polarizable force field AMOEBA. We show that a successful parameterization is possible for this specific case when releasing the physical interpretation of the electrostatic and polarization parameters of the force field. In doing so, particularly the Thole damping parameter and also the ion charge and polarizability were used as fitting parameters. The resulting parameterizations give in a MD simulation good structural and dynamical properties of the [Ni(H2O)6 ] 2 + complex, along with the expected excellent performance of AMOEBA for the water solvent. The presented parameterization is appropriate for high-accuracy simulations of both structural and dynamic properties of Ni2+(aq). This work documents possible approaches of parameterization of a transition metal within the AMOEBA force field.

  1. Molecular dynamics simulations of a new branched antimicrobial peptide: a comparison of force fields.

    PubMed

    Li, Jianguo; Lakshminarayanan, Rajamani; Bai, Yang; Liu, Shouping; Zhou, Lei; Pervushin, Konstantin; Verma, Chandra; Beuerman, Roger W

    2012-12-01

    Branched antimicrobial peptides are promising as a new class of antibiotics displaying high activity and low toxicity and appear to work through a unique mechanism of action. We explore the structural dynamics of a covalently branched 18 amino acid peptide (referred to as B2088) in aqueous and membrane mimicking environments through molecular dynamics (MD) simulations. Towards this, we carry out conventional MD simulations and supplement these with replica exchange simulations. The simulations are carried out using four different force fields that are commonly employed for simulating biomolecular systems. These force fields are GROMOS53a6, CHARMM27 with cMAP, CHARMM27 without cMAP and AMBER99sb. The force fields are benchmarked against experimental data available from circular dichroism and nuclear magnetic resonance spectroscopies, and show that CHARMM27 without cMAP correction is the most successful in reproducing the structural dynamics of B2088 both in water and in the presence of micelles. Although the four force fields predict different structures of B2088, they all show that B2088 stabilizes against the head group of the lipid through hydrogen bonding of its Lys and Arg side chains. This leads us to hypothesize that B2088 is unlikely to penetrate into the hydrophobic region of the membrane owing to the high free energy costs of transfer from water, and possibly acts by carpeting and thus disrupting the membrane.

  2. Mapping the dynamics of force transduction at cell–cell junctions of epithelial clusters

    PubMed Central

    Ng, Mei Rosa; Besser, Achim; Brugge, Joan S; Danuser, Gaudenz

    2014-01-01

    Force transduction at cell-cell adhesions regulates tissue development, maintenance and adaptation. We developed computational and experimental approaches to quantify, with both sub-cellular and multi-cellular resolution, the dynamics of force transmission in cell clusters. Applying this technology to spontaneously-forming adherent epithelial cell clusters, we found that basal force fluctuations were coupled to E-cadherin localization at the level of individual cell-cell junctions. At the multi-cellular scale, cell-cell force exchange depended on the cell position within a cluster, and was adaptive to reconfigurations due to cell divisions or positional rearrangements. Importantly, force transmission through a cell required coordinated modulation of cell-matrix adhesion and actomyosin contractility in the cell and its neighbors. These data provide insights into mechanisms that could control mechanical stress homeostasis in dynamic epithelial tissues, and highlight our methods as a resource for the study of mechanotransduction in cell-cell adhesions. DOI: http://dx.doi.org/10.7554/eLife.03282.001 PMID:25479385

  3. A many-body dissipative particle dynamics study of forced water-oil displacement in capillary.

    PubMed

    Chen, Chen; Zhuang, Lin; Li, Xuefeng; Dong, Jinfeng; Lu, Juntao

    2012-01-17

    The forced water-oil displacement in capillary is a model that has important applications such as the groundwater remediation and the oil recovery. Whereas it is difficult for experimental studies to observe the displacement process in a capillary at nanoscale, the computational simulation is a unique approach in this regard. In the present work, the many-body dissipative particle dynamics (MDPD) method is employed to simulate the process of water-oil displacement in capillary with external force applied by a piston. As the property of all interfaces involved in this system can be manipulated independently, the dynamic displacement process is studied systematically under various conditions of distinct wettability of water in capillary and miscibility between water and oil as well as of different external forces. By analyzing the dependence of the starting force on the properties of water/capillary and water/oil interfaces, we find that there exist two different modes of the water-oil displacement. In the case of stronger water-oil interaction, the water particles cannot displace those oil particles sticking to the capillary wall, leaving a low oil recovery efficiency. To minimize the residual oil content in capillary, enhancing the wettability of water and reducing the external force will be beneficial. This simulation study provides microscopic insights into the water-oil displacement process in capillary and guiding information for relevant applications.

  4. Reconstructing dynamic mental models of facial expressions in prosopagnosia reveals distinct representations for identity and expression.

    PubMed

    Richoz, Anne-Raphaëlle; Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G; Caldara, Roberto

    2015-04-01

    The human face transmits a wealth of signals that readily provide crucial information for social interactions, such as facial identity and emotional expression. Yet, a fundamental question remains unresolved: does the face information for identity and emotional expression categorization tap into common or distinct representational systems? To address this question we tested PS, a pure case of acquired prosopagnosia with bilateral occipitotemporal lesions anatomically sparing the regions that are assumed to contribute to facial expression (de)coding (i.e., the amygdala, the insula and the posterior superior temporal sulcus--pSTS). We previously demonstrated that PS does not use information from the eye region to identify faces, but relies on the suboptimal mouth region. PS's abnormal information use for identity, coupled with her neural dissociation, provides a unique opportunity to probe the existence of a dichotomy in the face representational system. To reconstruct the mental models of the six basic facial expressions of emotion in PS and age-matched healthy observers, we used a novel reverse correlation technique tracking information use on dynamic faces. PS was comparable to controls, using all facial features to (de)code facial expressions with the exception of fear. PS's normal (de)coding of dynamic facial expressions suggests that the face system relies either on distinct representational systems for identity and expression, or dissociable cortical pathways to access them. Interestingly, PS showed a selective impairment for categorizing many static facial expressions, which could be accounted for by her lesion in the right inferior occipital gyrus. PS's advantage for dynamic facial expressions might instead relate to a functionally distinct and sufficient cortical pathway directly connecting the early visual cortex to the spared pSTS. Altogether, our data provide critical insights on the healthy and impaired face systems, question evidence of deficits

  5. Characterization of Probe Dynamic Behaviors in Critical Dimension Atomic Force Microscopy

    PubMed Central

    Feng, Shaw C.; Joung, Che Bong; Vorburger, Theodore V.

    2009-01-01

    This paper describes a detailed computational model of the interaction between an atomic force microscope probe tip and a sample surface. The model provides analyses of dynamic behaviors of the tip to estimate the probe deflections due to surface intermittent contact and the resulting dimensional biases and uncertainties. Probe tip and cantilever beam responses to intermittent contact between the probe tip and sample surface are computed using the finite element method. Intermittent contacts with a wall and a horizontal surface are computed and modeled, respectively. Using a 75 nm Critical Dimension (CD) tip as an example, the responses of the probe to interaction forces between the sample surface and the probe tip are shown in both time and frequency domains. In particular, interaction forces between the tip and both a vertical wall and a horizontal surface of a silicon sample are modeled using Lennard-Jones theory. The Snap-in and Snap-out of the probe tip in surface scanning are calculated and shown in the time domain. Based on the given tip-sample interaction force model, the calculation includes the compliance of the probe and dynamic forces generated by an excitation. Cantilever and probe tip deflections versus interaction forces in the time domain can be derived for both vertical contact with a plateau and horizontal contact with a side wall. Dynamic analysis using the finite element method and Lennard-Jones model provide a unique means to analyze the interaction of the probe and sample, including calculation of the deflection and the gap between the probe tip and the measured sample surface. PMID:27504222

  6. Use of biaxially oriented polypropylene film for evaluating and cleaning contaminated atomic force microscopy probe tips: An application to blind tip reconstruction

    NASA Astrophysics Data System (ADS)

    Nie, H.-Y.; Walzak, M. J.; McIntyre, N. S.

    2002-11-01

    An atomic force microscopy (AFM) image of a surface is basically a convolution of the probe tip geometry and the surface features; it is important to know this tip effect to ensure that an image truly reflects the surface features. We have found that a biaxially oriented polypropylene (BOPP) film is suitable for checking tip performance and for cleaning contaminated tips, thus making it possible to collect images of the same area of a BOPP film surface before and after the tip was cleaned. Therefore, the difference between the two different images is solely due to the contamination of the tip. We took advantage of our ability to collect AFM images of the same area using the same tip, in one instance, contaminated and, in the other, after being cleaned. First we used blind reconstruction on the image collected using the contaminated tip. Blind tip reconstruction allows one to extract the geometry of the tip from a given image. Once we had estimated the geometry of the contaminated tip, we used it to simulate the tip effect using the image collected using the cleaned tip. By comparing the simulation result with the image collected using the contaminated tip we showed that the blind reconstruction routine works well. Prior to this, there was no de facto method for testing blind reconstruction algorithms.

  7. Temporal resolved x-ray penumbral imaging technique using heuristic image reconstruction procedure and wide dynamic range x-ray streak camera

    SciTech Connect

    Fujioka, Shinsuke; Shiraga, Hiroyuki; Azechi, Hiroshi; Nishimura, Hiroaki; Izawa, Yasukazu; Nozaki, Shinya; Chen, Yen-wei

    2004-10-01

    Temporal resolved x-ray penumbral imaging has been developed using an image reconstruction procedure of the heuristic method and a wide dynamic range x-ray streak camera (XSC). Reconstruction procedure of the penumbral imaging is inherently intolerant to noise, a reconstructed image is strongly distorted by artifacts caused by noise in a penumbral image. Statistical fluctuation in the number of detected photon is the dominant source of noise in an x-ray image, however acceptable brightness of an image is limited by dynamic range of an XSC. The wide dynamic range XSC was used to obtain penumbral images bright enough to be reconstructed. Additionally, the heuristic method was introduced in the penumbral image reconstruction procedure. Distortion of reconstructed images is sufficiently suppressed by these improvements. Density profiles of laser driven brominated plastic and tin plasma were measured with this technique.

  8. An Assessment of Molecular Dynamic Force Fields for Silica for Use in Simulating Laser Damage Mitigation

    SciTech Connect

    Soules, T F; Gilmer, G H; Matthews, M J; Stolken, J S; Feit, M D

    2010-10-21

    We compare force fields (FF's) that have been used in molecular dynamic (MD) simulations of silica in order to assess their applicability for use in simulating IR-laser damage mitigation. Although pairwise FF?s obtained by fitting quantum mechanical calculations such as the BKS and CHIK potentials have been shown to reproduce many of the properties of silica including the stability of silica polymorphs and the densification of the liquid, we show that melting temperatures and fictive temperatures are much too high. Softer empirical force fields give liquid and glass properties at experimental temperatures but may not predict all properties important to laser mitigation experiments.

  9. Force-length relations in isolated intact cardiomyocytes subjected to dynamic changes in mechanical load.

    PubMed

    Iribe, Gentaro; Helmes, Michiel; Kohl, Peter

    2007-03-01

    We developed a dynamic force-length (FL) control system for single intact cardiomyocytes that uses a pair of compliant, computer-controlled, and piezo translator (PZT)-positioned carbon fibers (CF). CF are attached to opposite cell ends to afford dynamic and bidirectional control of the cell's mechanical environment. PZT and CF tip positions, as well as sarcomere length (SL), are simultaneously monitored in real time, and passive/active forces are calculated from CF bending. Cell force and length were dynamically adjusted by corresponding changes in PZT position, to achieve isometric, isotonic, or work-loop style contractions. Functionality of the technique was assessed by studying FL behavior of guinea pig intact cardiomyocytes. End-diastolic and end-systolic FL relations, obtained with varying preload and/or afterloads, were near linear, independent of the mode of contraction, and overlapping for the range of end-diastolic SLs tested (1.85-2.05 micro m). Instantaneous elastance curves, obtained from FL relation curves, showed an afterload-dependent decrease in time to peak elastance and slowed relaxation with both increased preload and afterload. The ability of the present system to independently and dynamically control preload, afterload, and transition between end-diastolic and end-systolic FL coordinates provides a valuable extension to the range of tools available for the study of single cardiomyocyte mechanics, to foster its interrelation with whole heart pathophysiology. PMID:17098830

  10. Nonlinear Decomposition of Climate Data: a New Method for Reconstruction of Dynamical Modes

    NASA Astrophysics Data System (ADS)

    Mukhin, D.; Gavrilov, A.; Loskutov, E. M.; Feigin, A. M.

    2014-12-01

    Modeling of multivariate time-series produced by complex systems requires efficient tools for compact data representation. In this report we consider this problem, relating to empirical modeling of climate, which implies an analysis of spatial-distributed time-series. The main goal is to establish the number of principal modes which have key contribution to data and actually governs the observed variability. Currently, the number of widely used methods based on PCA and factor analysis exists, which yield different data decompositions taking into consideration spatial/spatio-temporal correlations in observed dynamics: spatial empirical orthogonal functions, M-SSA, varimax rotation, empirical orthogonal teleconnections, and so on. However, the question about possibility of improving the decomposition by taking into account nonlinear couplings between variables often remains untouched. In the report the method for construction of principal dynamic modes on the basis of low-dimensional nonlinear parametric representation of observed multivariate time-series is suggested. It is aimed to extracting the set of latent modes that both explains an essential part of variability, and obeys the simplest evolution law. Thus, this approach can be used for optimal reconstruction of the phase space for empirical prognostic modeling of observed dynamics. Criterion of evidence of the nonlinearity, which allows estimating optimal parameters of data representation (including the number of parameters in mode definition and the number of principal modes) is proposed. The effectiveness of suggested method is firstly demonstrated on toy model example: two-dimensional strongly nonlinear problem of unknown dynamic mode retrieval from noisy data is considered. Next, the evidence of nonlinear couplings in SST space-distributed data covering the Globe is investigated by the proposed approach. It is demonstrated that the obtained principal modes capture more part of SST variability than

  11. Dynamic topology multi force particle swarm optimization algorithm and its application

    NASA Astrophysics Data System (ADS)

    Chen, Dongning; Zhang, Ruixing; Yao, Chengyu; Zhao, Zheyu

    2016-01-01

    Particle swarm optimization (PSO) algorithm is an effective bio-inspired algorithm but it has shortage of premature convergence. Researchers have made some improvements especially in force rules and population topologies. However, the current algorithms only consider a single kind of force rules and lack consideration of comprehensive improvement in both multi force rules and population topologies. In this paper, a dynamic topology multi force particle swarm optimization (DTMFPSO) algorithm is proposed in order to get better search performance. First of all, the principle of the presented multi force particle swarm optimization (MFPSO) algorithm is that different force rules are used in different search stages, which can balance the ability of global and local search. Secondly, a fitness-driven edge-changing (FE) topology based on the probability selection mechanism of roulette method is designed to cut and add edges between the particles, and the DTMFPSO algorithm is proposed by combining the FE topology with the MFPSO algorithm through concurrent evolution of both algorithm and structure in order to further improve the search accuracy. Thirdly, Benchmark functions are employed to evaluate the performance of the DTMFPSO algorithm, and test results show that the proposed algorithm is better than the well-known PSO algorithms, such as µPSO, MPSO, and EPSO algorithms. Finally, the proposed algorithm is applied to optimize the process parameters for ultrasonic vibration cutting on SiC wafer, and the surface quality of the SiC wafer is improved by 12.8% compared with the PSO algorithm in Ref. [25]. This research proposes a DTMFPSO algorithm with multi force rules and dynamic population topologies evolved simultaneously, and it has better search performance.

  12. Mechanical dynamics in live cells and fluorescence-based force/tension sensors

    PubMed Central

    Yang, Chao; Zhang, Xiaohan; Guo, Yichen; Meng, Fanjie; Sachs, Frederick; Guo, Jun

    2016-01-01

    Three signaling systems play the fundamental roles in modulating cell activities: chemical, electrical, and mechanical. While the former two are well studied, the mechanical signaling system is still elusive because of the lack of methods to measure structural forces in real time at cellular and subcellular levels. Indeed, almost all biological processes are responsive to modulation by mechanical forces that trigger dispersive downstream electrical and biochemical pathways. Communication among the three systems is essential to make cells and tissues receptive to environmental changes. Cells have evolved many sophisticated mechanisms for the generation, perception and transduction of mechanical forces, including motor proteins and mechanosensors. In this review, we introduce some background information about mechanical dynamics in live cells, including the ubiquitous mechanical activity, various types of mechanical stimuli exerted on cells and the different mechanosensors. We also summarize recent results obtained using genetically encoded FRET (fluorescence resonance energy transfer)-based force/tension sensors; a new technique used to measure mechanical forces in structural proteins. The sensors have been incorporated into many specific structural proteins and have measured the force gradients in real time within live cells, tissues, and animals. PMID:25958335

  13. Mechanical dynamics in live cells and fluorescence-based force/tension sensors.

    PubMed

    Yang, Chao; Zhang, Xiaohan; Guo, Yichen; Meng, Fanjie; Sachs, Frederick; Guo, Jun

    2015-08-01

    Three signaling systems play the fundamental roles in modulating cell activities: chemical, electrical, and mechanical. While the former two are well studied, the mechanical signaling system is still elusive because of the lack of methods to measure structural forces in real time at cellular and subcellular levels. Indeed, almost all biological processes are responsive to modulation by mechanical forces that trigger dispersive downstream electrical and biochemical pathways. Communication among the three systems is essential to make cells and tissues receptive to environmental changes. Cells have evolved many sophisticated mechanisms for the generation, perception and transduction of mechanical forces, including motor proteins and mechanosensors. In this review, we introduce some background information about mechanical dynamics in live cells, including the ubiquitous mechanical activity, various types of mechanical stimuli exerted on cells and the different mechanosensors. We also summarize recent results obtained using genetically encoded FRET (fluorescence resonance energy transfer)-based force/tension sensors; a new technique used to measure mechanical forces in structural proteins. The sensors have been incorporated into many specific structural proteins and have measured the force gradients in real time within live cells, tissues, and animals.

  14. Force, velocity and energy dynamics of nine load-moving muscles.

    PubMed

    Baratta, R V; Solomonow, M; Best, R; D'Ambrosia, R

    1997-01-01

    Nine architecturally different muscles of the cat's hindlimb were investigated with respect to the kinetic energy, the potential energy, and the force variations associated with shortening contractions against gravitational loads. Insight about the energy dynamics of contractile muscle can provide a unifying concept for models of muscle performance capability. In this study, it was found that as contractions shortened from passive equilibrium against a constant mass load, acceleration and deceleration phases appeared. These phase were associated with muscular force variations of up to 25% of the mass weight in fast twitch muscles at low loads. In contrast, slow twitch muscles were associated with less than 10% force variations when shortening against a gravitational load. It also was found that optimal loads exist which maximize each muscle's ability to impart kinetic and potential energy, these optimal loads tend to be in the mid-force range for highly pennate muscle and in the low-force range for justform muscles. It was concluded that the kinetic energy provided by each muscle is a small percentage of that calculated from its length-force relationship, especially at low loads. This study confirms that the efficiency of kinetic energy conversion is very low at low loads (gradually improving as the loads increase) and thereby substantiates early experiments with heat and metabolic energy.

  15. Investigations of the intermolecular forces between RDX and polyethylene by force-distance spectroscopy and molecular dynamics simulations.

    PubMed

    Taylor, D E; Strawhecker, K E; Shanholtz, E R; Sorescu, D C; Sausa, R C

    2014-07-10

    The development of novel nanoenergetic materials with enhanced bulk properties requires an understanding of the intermolecular interactions occurring between molecular components. We investigate the surface interactions between 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) and polyethylene (PE) crystals on the basis of combined use of molecular dynamics (MD) simulations and force-distance spectroscopy, in conjunction with Lifshitz macroscopic theory of van der Waals forces between continuous materials. The binding energy in the RDX-PE system depends both on the degree of PE crystallinity and on the RDX crystal face. Our MD simulations yield binding energies of approximately 132 and 120 mJ/m(2) for 100% amorphous and 100% crystalline PE on RDX (210), respectively. The average value is about 36% greater than our experimental value of 81 ± 15 mJ/m(2) for PE (∼48% amorphous) on RDX (210). By comparison, Liftshitz theory predicts a value of about 79 mJ/m(2) for PE interacting with RDX. Our MD simulations also predict larger binding energies for both amorphous and crystalline PE on RDX (210) compared to the RDX (001) surface. Analysis of the interaction potential indicates that about 60% of the binding energy in the PE-RDX system is due to attractive interactions between HPE-ORDX and CPE-NRDX pairs of atoms. Further, amorphous PE shows a much longer interaction distance than crystalline PE with the (210) and (001) RDX surfaces due to the possibility of larger polymer elongations in the case of amorphous PE as strain is applied. Also, we report estimates of the binding energies of energetic materials RDX and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) with PE, propylene, polystyrene, and several fluorine-containing polymers using Lifshitz theory and compare these with reported MD calculations.

  16. Reconstruction of Rayleigh-Lamb dispersion spectrum based on noise obtained from an air-jet forcing.

    PubMed

    Larose, Eric; Roux, Philippe; Campillo, Michel

    2007-12-01

    The time-domain cross correlation of incoherent and random noise recorded by a series of passive sensors contains the impulse response of the medium between these sensors. By using noise generated by a can of compressed air sprayed on the surface of a plexiglass plate, we are able to reconstruct not only the time of flight but the whole wave forms between the sensors. From the reconstruction of the direct A(0) and S(0) waves, we derive the dispersion curves of the flexural waves, thus estimating the mechanical properties of the material without a conventional electromechanical source. The dense array of receivers employed here allow a precise frequency-wavenumber study of flexural waves, along with a thorough evaluation of the rate of convergence of the correlation with respect to the record length, the frequency, and the distance between the receivers. The reconstruction of the actual amplitude and attenuation of the impulse response is also addressed in this paper.

  17. Capillary climb dynamics in the limits of prevailing capillary and gravity force.

    PubMed

    Bijeljic, B; Markicevic, B; Navaz, H K

    2011-05-01

    The dynamics of capillary climb of a wetting liquid into a porous medium that is opposed by gravity force is studied numerically. We use the capillary network model, in which an actual porous medium is represented as a network of pores and throats, each following a predefined size distribution function. The liquid potential in the pores along the liquid interface within the network is calculated as a result of capillary and gravity forces. The solution is general, and accounts for changes in the climbing height and climbing velocity. The numerical results for the capillary climb reveal that there are at least two distinct flow mechanisms. Initially, the flow is characterized by high climbing velocity, in which the capillary force is higher than the gravity force, and the flow is the viscous force dominated. For this single-phase flow, the Washburn equation can be used to predict the changes of climbing height over time. Later, for longer times and larger climbing height, the capillary and gravity forces become comparable, and one observes a slower increase in the climbing height as a function of time. Due to the two forces being comparable, the gas-liquid sharp interface transforms into flow front, where the multiphase flow develops. The numerical results from this study, expressed as the climbing height as a power law function of time, indicate that the two powers, which correspond to the two distinct mechanisms, differ significantly. The comparison of the powers with experimental data indicates good agreement. Furthermore, the power value from the Washburn solution is also analyzed, where it should be equal to 1/2 for purely viscous force driven flow. This is in contrast to the power value of ∼0.43 that is found experimentally. We show from the numerical solution that this discrepancy is due to the momentum dissipation on the liquid interface.

  18. Dissolution study of active pharmaceutical ingredients using molecular dynamics simulations with classical force fields

    NASA Astrophysics Data System (ADS)

    Greiner, Maximilian; Elts, Ekaterina; Schneider, Julian; Reuter, Karsten; Briesen, Heiko

    2014-11-01

    The CHARMM, general Amber and OPLS force fields are evaluated for their suitability in simulating the molecular dynamics of the dissolution of the hydrophobic, small-molecule active pharmaceutical ingredients aspirin, ibuprofen, and paracetamol in aqueous media. The force fields are evaluated by comparison with quantum chemical simulations or experimental references on the basis of the following capabilities: accurately representing intra- and intermolecular interactions, appropriately reproducing crystal lattice parameters, adequately describing thermodynamic properties, and the qualitative description of the dissolution behavior. To make this approach easily accessible for evaluating the dissolution properties of novel drug candidates in the early stage of drug development, the force field parameter files are generated using online resources such as the SWISS PARAM servers, and the software packages ACPYPE and Maestro. All force fields are found to reproduce the intermolecular interactions with a reasonable degree of accuracy, with the general Amber and CHARMM force fields showing the best agreement with quantum mechanical calculations. A stable crystal bulk structure is obtained for all model substances, except for ibuprofen, where the reproductions of the lattice parameters and observed crystal stability are considerably poor for all force fields. The heat of solution used to evaluate the solid-to-solution phase transitions is found to be in qualitative agreement with the experimental data for all combinations tested, with the results being quantitatively optimum for the general Amber and CHARMM force fields. For aspirin and paracetamol, stable crystal-water interfaces were obtained. The (100), (110), (011) and (001) interfaces of aspirin or paracetamol and water were simulated for each force field for 30 ns. Although generally expected as a rare event, in some of the simulations, dissolution is observed at 310 K and ambient pressure conditions.

  19. Contact stiffness and damping of liquid films in dynamic atomic force microscope

    NASA Astrophysics Data System (ADS)

    Xu, Rong-Guang; Leng, Yongsheng

    2016-04-01

    The mechanical properties and dissipation behaviors of nanometers confined liquid films have been long-standing interests in surface force measurements. The correlation between the contact stiffness and damping of the nanoconfined film is still not well understood. We establish a novel computational framework through molecular dynamics (MD) simulation for the first time to study small-amplitude dynamic atomic force microscopy (dynamic AFM) in a simple nonpolar liquid. Through introducing a tip driven dynamics to mimic the mechanical oscillations of the dynamic AFM tip-cantilever assembly, we find that the contact stiffness and damping of the confined film exhibit distinct oscillations within 6-7 monolayer distances, and they are generally out-of-phase. For the solid-like film with integer monolayer thickness, further compression of the film before layering transition leads to higher stiffness and lower damping, while much lower stiffness and higher damping occur at non-integer monolayer distances. These two alternating mechanisms dominate the mechanical properties and dissipation behaviors of simple liquid films under cyclic elastic compression and inelastic squeeze-out. Our MD simulations provide a direct picture of correlations between the structural property, mechanical stiffness, and dissipation behavior of the nanoconfined film.

  20. Contact stiffness and damping of liquid films in dynamic atomic force microscope.

    PubMed

    Xu, Rong-Guang; Leng, Yongsheng

    2016-04-21

    The mechanical properties and dissipation behaviors of nanometers confined liquid films have been long-standing interests in surface force measurements. The correlation between the contact stiffness and damping of the nanoconfined film is still not well understood. We establish a novel computational framework through molecular dynamics (MD) simulation for the first time to study small-amplitude dynamic atomic force microscopy (dynamic AFM) in a simple nonpolar liquid. Through introducing a tip driven dynamics to mimic the mechanical oscillations of the dynamic AFM tip-cantilever assembly, we find that the contact stiffness and damping of the confined film exhibit distinct oscillations within 6-7 monolayer distances, and they are generally out-of-phase. For the solid-like film with integer monolayer thickness, further compression of the film before layering transition leads to higher stiffness and lower damping, while much lower stiffness and higher damping occur at non-integer monolayer distances. These two alternating mechanisms dominate the mechanical properties and dissipation behaviors of simple liquid films under cyclic elastic compression and inelastic squeeze-out. Our MD simulations provide a direct picture of correlations between the structural property, mechanical stiffness, and dissipation behavior of the nanoconfined film. PMID:27389229

  1. A review of dynamic stability of repulsive-force maglev suspension systems

    SciTech Connect

    Cai, Y.; Rote, D.M.

    1998-07-01

    Vehicle dynamics and the need to satisfy ride quality requirements have long been recognized as crucial to the commercial success of passenger-carrying transportation systems. Design concepts for maglev systems are no exception. Early maglev investigators and designers were well aware of the importance of ride quality and took care to ensure that their designs would meet acceptable ride quality standards. In contrast, the dynamic stability of electrodynamic suspension (EDS) systems, which has obvious implications for system safety and cost as well as for ride quality, has not received nearly as much attention. Because of the well-known under-damped nature of EDS suspension systems and the observation of instabilities in laboratory-scale model systems, it is prudent to develop a better understanding of vehicle stability characteristics. The work reported in this was undertaken with the intention of summarizing information that has been accumulated worldwide and that is relevant to dynamic stability of repulsive-force maglev suspension systems, assimilating that information, and gaining an understanding of the factors that influence that stability. Included in the paper is a discussion and comparison of results acquired from some representative tests of large-scale vehicles on linear test tracks, together with analytical and laboratory-scale investigations of stability and dynamics of EDS systems. This paper will also summarize the R and D activities at Argonne National Laboratory (ANL) since 1991 to study the nature of the forces that are operative in an EDS system and the dynamic stability of such systems.

  2. Ab initio based force field and molecular dynamics simulations of crystalline TATB.

    PubMed

    Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E

    2004-04-15

    An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608

  3. Parameter estimation of social forces in pedestrian dynamics models via a probabilistic method.

    PubMed

    Corbetta, Alessandro; Muntean, Adrian; Vafayi, Kiamars

    2015-04-01

    Focusing on a specific crowd dynamics situation, including real life experiments and measurements, our paper targets a twofold aim: (1) we present a Bayesian probabilistic method to estimate the value and the uncertainty (in the form of a probability density function) of parameters in crowd dynamic models from the experimental data; and (2) we introduce a fitness measure for the models to classify a couple of model structures (forces) according to their fitness to the experimental data, preparing the stage for a more general model-selection and validation strategy inspired by probabilistic data analysis. Finally, we review the essential aspects of our experimental setup and measurement technique.

  4. Pairwise Force Smoothed Particle Hydrodynamics model for multiphase flow: Surface tension and contact line dynamics

    NASA Astrophysics Data System (ADS)

    Tartakovsky, Alexandre M.; Panchenko, Alexander

    2016-01-01

    We present a novel formulation of the Pairwise Force Smoothed Particle Hydrodynamics (PF-SPH) model and use it to simulate two- and three-phase flows in bounded domains. In the PF-SPH model, the Navier-Stokes equations are discretized with the Smoothed Particle Hydrodynamics (SPH) method, and the Young-Laplace boundary condition at the fluid-fluid interface and the Young boundary condition at the fluid-fluid-solid interface are replaced with pairwise forces added into the Navier-Stokes equations. We derive a relationship between the parameters in the pairwise forces and the surface tension and static contact angle. Next, we demonstrate the model's accuracy under static and dynamic conditions. Finally, we use the Pf-SPH model to simulate three phase flow in a porous medium.

  5. Dynamical relations for left ventricular ejection - Flow rate, momentum, force and impulse

    NASA Technical Reports Server (NTRS)

    Back, L. H.; Selzer, R. H.; Gordon, D. G.; Ledbetter, D. C.; Crawford, D. W.

    1984-01-01

    An investigation was carried out to quantitatively evaluate left ventricular volume flow rate, momentum, force and impulse derived from application of conservation principles for mass and momentum of blood within the ventricle during the ejection phase. An automated digital image processing system was developed and applied to left ventricular angiograms which are computer processed and analyzed frame by frame to determine the dynamical relations by numerical methods. The initial experience with force and impulse has indicated that neither quantity seemed to be a sensitive indicator of coronary artery disease as evaluated by qualitative angiography for the particular patient group studied. Utilization of the dynamical relations in evaluating human left ventricular performance requires improved means of measurement and interpretation of clinical studies.

  6. Non-Synchronous Whirling Due to Fluid-Dynamic Forces in Axial Turbo-Machinery Rotors

    NASA Technical Reports Server (NTRS)

    Shen, S. F.; Mengle, V. G.

    1980-01-01

    The role of fluid forces acting on the blades of an axial turborotor with regards to whirling was analyzed. The dynamic equations were formulated for the coning mode of an overhung rotor. The exciting forces due to the motion were defined through a set of rotor stability derivatives, and analytical expressions of the aerodynamic contributions were found for the case of small mean stream deflection, high solidity and equivalent flat plate cascade. For a typical case, only backward whirl was indicated when the phase shifting of the rotor wake effect was ignored. A parametric study of the dynamic stability boundary reveals that a reduction in blade stagger angle, mass flow rate, fluid density and an increase in stiffness and external damping are all inductive for improved stability.

  7. Lipid Bilayers: The Effect of Force Field on Ordering and Dynamics.

    PubMed

    Poger, David; Mark, Alan E

    2012-11-13

    The sensitivity of the structure and dynamics of a fully hydrated pure bilayer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in molecular dynamics simulations to changes in force-field and simulation parameters has been assessed. Three related force fields (the Gromos 54A7 force field, a Gromos 53A6-derived parameter set and a variant of the Berger parameters) in combination with either particle-mesh Ewald (PME) or a reaction field (RF) were compared. Structural properties such as the area per lipid, carbon-deuterium order parameters, electron density profile and bilayer thicknesses, are reproduced by all the parameter sets within the uncertainty of the available experimental data. However, there are clear differences in the ordering of the glycerol backbone and choline headgroup, and the orientation of the headgroup dipole. In some cases, the degree of ordering was reminiscent of a liquid-ordered phase. It is also shown that, although the lateral diffusion of the lipids in the plane of the bilayer is often used to validate lipid force fields, because of the uncertainty in the experimental measurements and the fact that the lateral diffusion is dependent on the choice of the simulation conditions, it should not be employed as a measure of quality. Finally, the simulations show that the effect of small changes in force-field parameters on the structure and dynamics of a bilayer is more significant than the treatment of the long-range electrostatic interactions using RF or PME. Overall, the Gromos 54A7 best reproduced the range of experimental data examined. PMID:26605633

  8. Hydrographical and dynamical reconstruction of the Warm Core Cyprus Eddy from gliders data

    NASA Astrophysics Data System (ADS)

    Bosse, Anthony; Testor, Pierre; Hayes, Dan; Ruiz, Simon; Mauri, Elena; Charantonis, Anastase; d'Ortenzio, Fabrizio; Mortier, Laurent

    2016-04-01

    In the 80s, the POEM (Physical Oceanography of the Eastern Mediterranean) cruises in the Levantine Basin first revealed the presence of a very pronounced dynamical structure off Cyprus: The Cyprus Warm Core Eddy. Since then, a large amount of data have been collected thanks to the use of autonomous oceanic gliders (+8000 profiles since 2009). Part of those profiles were carried out in the upper layers down to 200 m, and we take benefit of a novel approach named ITCOMP SOM that uses a statistical approach to extend them down to 1000 m (see [1] for more details). This dataset have a particularly good spatio-temporal coverage in 2009 for about a month, thanks to simultaneous deployments of several gliders (up to 6). In this study, we present a set of 3D reconstruction of the dynamical and hydrographical characteristics of the Warm Core Cyprus Eddy between 2009 and 2015. Moreover, chlorophyll-a fluorescence data measured by the gliders give evidence to strong vertical velocities at the edge of the eddy. We discuss possible mechanisms (frontogenesis, symmetric instability) that could generate such signals and provide an assessment of the role of this peculiar circulation feature on the circulation and biogeochemistry of the Levantine basin. Reference: [1] Charantonis, A., P. Testor, L. Mortier, F. D'Ortenzio, S. Thiria (2015): Completion of a sparse GLIDER database using multi-iterative Self-Organizing Maps (ITCOMP SOM), Procedia Computer Science, 51(1):2198-2206. DOI: 10.1016/j.procs.2015.05.496

  9. Reconstruction of stand dynamics over the last 2500 years from spruce remains in a treeline peatland

    SciTech Connect

    Arseneault, D.; Payette, S.

    1995-06-01

    Stem remains of black spruce Picea mariana (Mill. BSP.) buried in a permafrost treeless peatland were used for the reconstruction of the long-term forest dynamics at treeline in northeastern Canada. Because most spruce remains were well preserved, forest development was assessed from stem morphology (growth form) and tree ring patterns. The peatland border was colonized by a spruce forest from at least 500 BC (2500 BP) to 1568 AD. Most spruce individuals showed an erect, monopodial bole with only minor stem damage at the snow-air interface. The forest successfully regenerated after two fire events around 350 BC and 10 AD. The number of damaged stems at the snow-air interface increased after another fire around 700 AD, although faster ring growth occurred between 860 and 1000 AD (Medieval period). The forest shifted to an open krummholz after the last fire in 1568 AD because of reduced postfire regeneration and site opening. Reforestation of the site would necessitate sustained warmer conditions than those presently prevailing there.

  10. THREE-DIMENSIONAL RECONSTRUCTION OF AN ERUPTING FILAMENT WITH SOLAR DYNAMICS OBSERVATORY AND STEREO OBSERVATIONS

    SciTech Connect

    Li Ting; Zhang Jun; Zhang Yuzong; Yang Shuhong E-mail: zjun@nao.cas.cn

    2011-09-20

    On 2010 August 1, a global solar event was launched involving almost the entire Earth-facing side of the Sun. This event mainly consisted of a C3.2 flare, a polar crown filament eruption, and two Earth-directed coronal mass ejections. The observations from the Solar Dynamics Observatory (SDO) and STEREO showed that all the activities were coupled together, suggesting a global character of the magnetic eruption. We reconstruct the three-dimensional geometry of the polar crown filament using observations from three different viewpoints (STEREO A, STEREO B, and SDO) for the first time. The filament undergoes two eruption processes. First, the main body of the filament rises up, while it also moves toward the low-latitude region with a change in inclination by {approx}48{sup 0} and expands only in the altitudinal and latitudinal direction in the field of view of the Atmospheric Imaging Assembly. We investigate the true velocities and accelerations of different locations along the filament and find that the highest location always has the largest acceleration during this eruption process. During the late phase of the first eruption, part of the filament material separates from the eastern leg. This material displays a projectile motion and moves toward the west at a constant velocity of 141.8 km s{sup -1}. This may imply that the polar crown filament consists of at least two groups of magnetic systems.

  11. Dynamic Shape Reconstruction of Three-Dimensional Frame Structures Using the Inverse Finite Element Method

    NASA Technical Reports Server (NTRS)

    Gherlone, Marco; Cerracchio, Priscilla; Mattone, Massimiliano; Di Sciuva, Marco; Tessler, Alexander

    2011-01-01

    A robust and efficient computational method for reconstructing the three-dimensional displacement field of truss, beam, and frame structures, using measured surface-strain data, is presented. Known as shape sensing , this inverse problem has important implications for real-time actuation and control of smart structures, and for monitoring of structural integrity. The present formulation, based on the inverse Finite Element Method (iFEM), uses a least-squares variational principle involving strain measures of Timoshenko theory for stretching, torsion, bending, and transverse shear. Two inverse-frame finite elements are derived using interdependent interpolations whose interior degrees-of-freedom are condensed out at the element level. In addition, relationships between the order of kinematic-element interpolations and the number of required strain gauges are established. As an example problem, a thin-walled, circular cross-section cantilevered beam subjected to harmonic excitations in the presence of structural damping is modeled using iFEM; where, to simulate strain-gauge values and to provide reference displacements, a high-fidelity MSC/NASTRAN shell finite element model is used. Examples of low and high-frequency dynamic motion are analyzed and the solution accuracy examined with respect to various levels of discretization and the number of strain gauges.

  12. An experimental study of dynamic stall on advanced airfoil section. Volume 2: Pressure and force data

    NASA Technical Reports Server (NTRS)

    Mcalister, K. W.; Pucci, S. L.; Mccroskey, W. J.; Carr, L. W.

    1982-01-01

    Experimentally derived force and moment data are presented for eight airfoil sections that were tested at fixed and varying incidence in a subsonic two dimensional stream. Airfoil incidence was varied through sinusoidal oscillations in pitch over a wide range of amplitude and frequency. The surface pressure distribution, as well as the lift, drag, and pitching moment derived therefrom, are displayed in a uniform fashion to delineate the static and dynamic characteristics of each airfoil both in and out of stall.

  13. Dynamic nanoindentation by instrumented nanoindentation and force microscopy: a comparative review

    PubMed Central

    Kalfon-Cohen, Estelle

    2013-01-01

    Summary Viscoelasticity is a complex yet important phenomenon that drives material response at different scales of time and space. Burgeoning interest in nanoscale dynamic material mechanics has driven, and been driven by two key techniques: instrumented nanoindentation and atomic force microscopy. This review provides an overview of fundamental principles in nanoindentation, and compares and contrasts these two techniques as they are used for characterization of viscoelastic processes at the nanoscale. PMID:24367751

  14. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

    PubMed

    Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

    2013-11-12

    The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling.

  15. Force and torque on spherical particles in micro-channel flows using computational fluid dynamics.

    PubMed

    Suo, Jin; Edwards, Erin E; Anilkumar, Ananyaveena; Sulchek, Todd; Giddens, Don P; Thomas, Susan N

    2016-07-01

    To delineate the influence of hemodynamic force on cell adhesion processes, model in vitro fluidic assays that mimic physiological conditions are commonly employed. Herein, we offer a framework for solution of the three-dimensional Navier-Stokes equations using computational fluid dynamics (CFD) to estimate the forces resulting from fluid flow near a plane acting on a sphere that is either stationary or in free flow, and we compare these results to a widely used theoretical model that assumes Stokes flow with a constant shear rate. We find that while the full three-dimensional solutions using a parabolic velocity profile in CFD simulations yield similar translational velocities to those predicted by the theoretical method, the CFD approach results in approximately 50% larger rotational velocities over the wall shear stress range of 0.1-5.0 dynes cm(-2). This leads to an approximately 25% difference in force and torque calculations between the two methods. When compared with experimental measurements of translational and rotational velocities of microspheres or cells perfused in microfluidic channels, the CFD simulations yield significantly less error. We propose that CFD modelling can provide better estimations of hemodynamic force levels acting on perfused microspheres and cells in flow fields through microfluidic devices used for cell adhesion dynamics analysis.

  16. Dynamics of Cell Shape and Forces on Micropatterned Substrates Predicted by a Cellular Potts Model

    PubMed Central

    Albert, Philipp J.; Schwarz, Ulrich S.

    2014-01-01

    Micropatterned substrates are often used to standardize cell experiments and to quantitatively study the relation between cell shape and function. Moreover, they are increasingly used in combination with traction force microscopy on soft elastic substrates. To predict the dynamics and steady states of cell shape and forces without any a priori knowledge of how the cell will spread on a given micropattern, here we extend earlier formulations of the two-dimensional cellular Potts model. The third dimension is treated as an area reservoir for spreading. To account for local contour reinforcement by peripheral bundles, we augment the cellular Potts model by elements of the tension-elasticity model. We first parameterize our model and show that it accounts for momentum conservation. We then demonstrate that it is in good agreement with experimental data for shape, spreading dynamics, and traction force patterns of cells on micropatterned substrates. We finally predict shapes and forces for micropatterns that have not yet been experimentally studied. PMID:24896113

  17. Role of radiation reaction forces in the dynamics of centrifugally accelerated particles

    SciTech Connect

    Dalakishvili, G. T.; Rogava, A. D.; Berezhiani, V. I.

    2007-08-15

    In this paper we study the influence of radiation reaction (RR) forces on the dynamics of centrifugally accelerated particles. It is assumed that the particles move along magnetic field lines anchored in the rotating central object. The common 'bead-on-the-wire' approximation is used. The solutions are found and analyzed for cases when the form of the prescribed trajectory (rigidly rotating field line) is approximated by: (a) straight line, and (b) Archimedes spiral. Dynamics of neutral and charged particles are compared with the emphasis on the role of RR forces in the latter case. It is shown that for charged particles there exist locations of stable equilibrium. It is demonstrated that for particular initial conditions RR forces cause centripetal motion of the particles: their 'falling' on the central rotating object. It is found that in the case of Archimedes spiral both neutral and charged particles can reach infinity where their motion has asymptotically force-free character. The possible importance of these processes for the acceleration of relativistic, charged particles by rotating magnetospheres in the context of the generation of nonthermal, high-energy emission of AGN and pulsars is discussed.

  18. Role of radiation reaction forces in the dynamics of centrifugally accelerated particles

    NASA Astrophysics Data System (ADS)

    Dalakishvili, G. T.; Rogava, A. D.; Berezhiani, V. I.

    2007-08-01

    In this paper we study the influence of radiation reaction (RR) forces on the dynamics of centrifugally accelerated particles. It is assumed that the particles move along magnetic field lines anchored in the rotating central object. The common “bead-on-the-wire” approximation is used. The solutions are found and analyzed for cases when the form of the prescribed trajectory (rigidly rotating field line) is approximated by: (a) straight line, and (b) Archimedes spiral. Dynamics of neutral and charged particles are compared with the emphasis on the role of RR forces in the latter case. It is shown that for charged particles there exist locations of stable equilibrium. It is demonstrated that for particular initial conditions RR forces cause centripetal motion of the particles: their “falling” on the central rotating object. It is found that in the case of Archimedes spiral both neutral and charged particles can reach infinity where their motion has asymptotically force-free character. The possible importance of these processes for the acceleration of relativistic, charged particles by rotating magnetospheres in the context of the generation of nonthermal, high-energy emission of AGN and pulsars is discussed.

  19. Force and torque on spherical particles in micro-channel flows using computational fluid dynamics.

    PubMed

    Suo, Jin; Edwards, Erin E; Anilkumar, Ananyaveena; Sulchek, Todd; Giddens, Don P; Thomas, Susan N

    2016-07-01

    To delineate the influence of hemodynamic force on cell adhesion processes, model in vitro fluidic assays that mimic physiological conditions are commonly employed. Herein, we offer a framework for solution of the three-dimensional Navier-Stokes equations using computational fluid dynamics (CFD) to estimate the forces resulting from fluid flow near a plane acting on a sphere that is either stationary or in free flow, and we compare these results to a widely used theoretical model that assumes Stokes flow with a constant shear rate. We find that while the full three-dimensional solutions using a parabolic velocity profile in CFD simulations yield similar translational velocities to those predicted by the theoretical method, the CFD approach results in approximately 50% larger rotational velocities over the wall shear stress range of 0.1-5.0 dynes cm(-2). This leads to an approximately 25% difference in force and torque calculations between the two methods. When compared with experimental measurements of translational and rotational velocities of microspheres or cells perfused in microfluidic channels, the CFD simulations yield significantly less error. We propose that CFD modelling can provide better estimations of hemodynamic force levels acting on perfused microspheres and cells in flow fields through microfluidic devices used for cell adhesion dynamics analysis. PMID:27493783

  20. Force and torque on spherical particles in micro-channel flows using computational fluid dynamics

    PubMed Central

    Suo, Jin; Edwards, Erin E.; Anilkumar, Ananyaveena; Sulchek, Todd; Giddens, Don P.

    2016-01-01

    To delineate the influence of hemodynamic force on cell adhesion processes, model in vitro fluidic assays that mimic physiological conditions are commonly employed. Herein, we offer a framework for solution of the three-dimensional Navier–Stokes equations using computational fluid dynamics (CFD) to estimate the forces resulting from fluid flow near a plane acting on a sphere that is either stationary or in free flow, and we compare these results to a widely used theoretical model that assumes Stokes flow with a constant shear rate. We find that while the full three-dimensional solutions using a parabolic velocity profile in CFD simulations yield similar translational velocities to those predicted by the theoretical method, the CFD approach results in approximately 50% larger rotational velocities over the wall shear stress range of 0.1–5.0 dynes cm−2. This leads to an approximately 25% difference in force and torque calculations between the two methods. When compared with experimental measurements of translational and rotational velocities of microspheres or cells perfused in microfluidic channels, the CFD simulations yield significantly less error. We propose that CFD modelling can provide better estimations of hemodynamic force levels acting on perfused microspheres and cells in flow fields through microfluidic devices used for cell adhesion dynamics analysis. PMID:27493783

  1. Unraveling the Architecture and Structural Dynamics of Pathogens by High-Resolution in vitro Atomic Force Microscopy

    SciTech Connect

    Malkin, A J; Plomp, M; Leighton, T J; McPherson, A; Wheeler, K E

    2005-04-12

    Progress in structural biology very much depends upon the development of new high-resolution techniques and tools. Despite decades of study of viruses, bacteria and bacterial spores and their pressing importance in human medicine and biodefense, many of their structural properties are poorly understood. Thus, characterization and understanding of the architecture of protein surface and internal structures of pathogens is critical to elucidating mechanisms of disease, immune response, physicochemical properties, environmental resistance and development of countermeasures against bioterrorist agents. Furthermore, even though complete genome sequences are available for various pathogens, the structure-function relationships are not understood. Because of their lack of symmetry and heterogeneity, large human pathogens are often refractory to X-ray crystallographic analysis or reconstruction by cryo-electron microscopy (cryo-EM). An alternative high-resolution method to examine native structure of pathogens is atomic force microscopy (AFM), which allows direct visualization of macromolecular assemblies at near-molecular resolution. The capability to image single pathogen surfaces at nanometer scale in vitro would profoundly impact mechanistic and structural studies of pathogenesis, immunobiology, specific cellular processes, environmental dynamics and biotransformation.

  2. Analysis of Dynamic Stability of Space Launch Vehicles under Aerodynamic Forces Using CFD Derived Data

    NASA Astrophysics Data System (ADS)

    Trikha, M.; Gopalakrishnan, S.; Mahapatra, D. Roy

    2011-09-01

    A computational framework is developed to investigate the dynamic stability of space launch vehicles subjected to aerodynamic forces. A detailed mechanics based mathematical model of a moving flexible vehicle is used. The aerodynamic forces on the vehicle are obtained from simulation using Computational Fluid Dynamics (CFD) package. The objective behind this investigation is to analyze the problem of aeroelastic instability in blunt/conical nose slender space launch vehicles. Coupling among the rigid-body modes, the longitudinal vibration modes, and the transverse vibrational modes are considered. The effect of propulsive thrust as a follower force is also considered. A one-dimensional finite element model is developed to investigate the occurrence of aeroelastic instabilities of various types. Eigenvalues of the vehicle are determined in order to analyze the stable regimes. As a special case, we show numerical simulations by considering a typical vehicle configuration, for a vehicle Mach number of 0.8. Phenomenon of flutter is observed at this Mach number. The proposed analysis is suitable for different launch events such as vehicle take-off, maximum dynamic pressure regime, thrust transients, stage separation etc. The approach developed in this paper can be utilized for preliminary design of launch vehicles and establishing the stability boundaries for different trajectory parameters.

  3. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    PubMed

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost.

  4. Dynamics of regenerative chatter and internal resonance in milling process with structural and cutting force nonlinearities

    NASA Astrophysics Data System (ADS)

    Moradi, Hamed; Movahhedy, Mohammad R.; Vossoughi, Gholamreza

    2012-07-01

    In this paper, internal resonance and nonlinear dynamics of regenerative chatter in milling process is investigated. An extended dynamic model of the peripheral milling process including both structural and cutting force nonlinearities is presented. Closed form expressions for the nonlinear cutting forces are derived through their Fourier series components. In the presence of the large vibration amplitudes, the loss of contact effect is included in this model. Using the multiple-scales approach, analytical approximate response of the delayed nonlinear system is obtained. Considering the internal resonance dynamics (i.e. mode coupling), the energy transfer between the coupled x-y modes is studied. The results show that during regenerative chatter under specific cutting conditions, one mode can decay. Furthermore, it is possible to adjust the rate at which the x-mode (or y-mode) decays by implementation of the internal resonance. Therefore, under both internal resonance and regenerative chatter conditions, it is possible to suppress the undesirable vibration of one mode (direction) in which accurate surface finish is required. Under the steady-state motion, jump phenomenon is investigated for the process with regenerative chatter under various cutting conditions. Moreover, the effects of structural and cutting force nonlinearities on the stability lobes diagram of the process are investigated.

  5. Comparison of Brownian-dynamics-based estimates of polymer tension with direct force measurements.

    PubMed

    Arsenault, Mark E; Purohit, Prashant K; Goldman, Yale E; Shuman, Henry; Bau, Haim H

    2010-11-01

    With the aid of brownian dynamics models, it is possible to estimate polymer tension by monitoring polymers' transverse thermal fluctuations. To assess the precision of the approach, brownian dynamics-based tension estimates were compared with the force applied to rhodamine-phalloidin labeled actin filaments bound to polymer beads and suspended between two optical traps. The transverse thermal fluctuations of each filament were monitored with a CCD camera, and the images were analyzed to obtain the filament's transverse displacement variance as a function of position along the filament, the filament's tension, and the camera's exposure time. A linear Brownian dynamics model was used to estimate the filament's tension. The estimated force was compared and agreed within 30% (when the tension <0.1 pN ) and 70% (when the tension <1 pN ) with the applied trap force. In addition, the paper presents concise asymptotic expressions for the mechanical compliance of a system consisting of a filament attached tangentially to bead handles (dumbbell system). The techniques described here can be used for noncontact estimates of polymers' and fibers' tension.

  6. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.

    PubMed

    Kukic, Predrag; Kannan, Arvind; Dijkstra, Maurits J J; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-10-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a 'tube model' approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

  7. Binaries traveling through a gaseous medium: dynamical drag forces and internal torques

    SciTech Connect

    Sánchez-Salcedo, F. J.; Chametla, Raul O.

    2014-10-20

    Using time-dependent linear theory, we investigate the morphology of the gravitational wake induced by a binary, whose center of mass moves at velocity V{sub cm} against a uniform background of gas. For simplicity, we assume that the components of the binary are on circular orbits about their common center of mass. The consequences of dynamical friction is twofold. First, gas dynamical friction may drag the center of mass of the binary and cause the binary to migrate. Second, drag forces also induce a braking torque, which causes the orbits of the components of the binary to shrink. We compute the drag forces acting on one component of the binary due to the gravitational interaction with its own wake. We show that the dynamical friction force responsible for decelerating the center of mass of the binary is smaller than it is in the point-mass case because of the loss of gravitational focusing. We show that the braking internal torque depends on the Mach numbers of each binary component about their center of mass, and also on the Mach number of the center of mass of the binary. In general, the internal torque decreases with increasing the velocity of the binary relative to the ambient gas cloud. However, this is not always the case. We also mention the relevance of our results to the period distribution of binaries.

  8. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

    PubMed Central

    Dijkstra, Maurits J. J.; Abeln, Sanne; Camilloni, Carlo; Vendruscolo, Michele

    2015-01-01

    It has been recently shown that the coarse-graining of the structures of polypeptide chains as self-avoiding tubes can provide an effective representation of the conformational space of proteins. In order to fully exploit the opportunities offered by such a ‘tube model’ approach, we present here a strategy to combine it with molecular dynamics simulations. This strategy is based on the incorporation of the ‘CamTube’ force field into the Gromacs molecular dynamics package. By considering the case of a 60-residue polyvaline chain, we show that CamTube molecular dynamics simulations can comprehensively explore the conformational space of proteins. We obtain this result by a 20 μs metadynamics simulation of the polyvaline chain that recapitulates the currently known protein fold universe. We further show that, if residue-specific interaction potentials are added to the CamTube force field, it is possible to fold a protein into a topology close to that of its native state. These results illustrate how the CamTube force field can be used to explore efficiently the universe of protein folds with good accuracy and very limited computational cost. PMID:26505754

  9. Modeling economic costs of disasters and recovery involving positive effects of reconstruction: analysis using a dynamic CGE model

    NASA Astrophysics Data System (ADS)

    Xie, W.; Li, N.; Wu, J.-D.; Hao, X.-L.

    2013-11-01

    Disaster damages have negative effects on economy, whereas reconstruction investments have positive effects. The aim of this study is to model economic causes of disasters and recovery involving positive effects of reconstruction activities. Computable general equilibrium (CGE) model is a promising approach because it can incorporate these two kinds of shocks into a unified framework and further avoid double-counting problem. In order to factor both shocks in CGE model, direct loss is set as the amount of capital stock reduced on supply side of economy; A portion of investments restore the capital stock in existing period; An investment-driven dynamic model is formulated due to available reconstruction data, and the rest of a given country's saving is set as an endogenous variable. The 2008 Wenchuan Earthquake is selected as a case study to illustrate the model, and three scenarios are constructed: S0 (no disaster occurs), S1 (disaster occurs with reconstruction investment) and S2 (disaster occurs without reconstruction investment). S0 is taken as business as usual, and the differences between S1 and S0 and that between S2 and S0 can be interpreted as economic losses including reconstruction and excluding reconstruction respectively. The study showed that output from S1 is found to be closer to real data than that from S2. S2 overestimates economic loss by roughly two times that under S1. The gap in economic aggregate between S1 and S0 is reduced to 3% in 2011, a level that should take another four years to achieve under S2.

  10. Image reconstruction in higher dimensions: myocardial perfusion imaging of tracer dynamics with cardiac motion due to deformation and respiration

    NASA Astrophysics Data System (ADS)

    Shrestha, Uttam M.; Seo, Youngho; Botvinick, Elias H.; Gullberg, Grant T.

    2015-11-01

    Myocardial perfusion imaging (MPI) using slow rotating large field of view cameras requires spatiotemporal reconstruction of dynamically acquired data to capture the time variation of the radiotracer concentration. In vivo, MPI contains additional degrees of freedom involving unavoidable motion of the heart due to quasiperiodic beating and the effects of respiration, which can severely degrade the quality of the images. This work develops a technique for a single photon emission computed tomography (SPECT) that reconstructs the distribution of the radiotracer concentration in the myocardium using a tensor product of different sets of basis functions that approximately describe the spatiotemporal variation of the radiotracer concentration and the motion of the heart. In this study the temporal B-spline basis functions are chosen to reflect the dynamics of the radiotracer, while the intrinsic deformation and the extrinsic motion of the heart are described by a product of a discrete set of Gaussian basis functions. Reconstruction results are presented showing the dynamics of the tracer in the myocardium as it deforms due to cardiac beating, and is displaced due to respiratory motion. These results are compared with the conventional 4D-spatiotemporal reconstruction method that models only the temporal changes of the tracer activity. The higher dimensional reconstruction method proposed here improves bias, yet the signal-to-noise ratio (SNR) decreases slightly due to redistribution of the counts over the cardiac-respiratory gates. Additionally, there is a trade-off between the number of gates and the number of projections per gate to achieve high contrast images.

  11. Image Reconstruction in Higher Dimensions: Myocardial Perfusion Imaging of Tracer Dynamics with Cardiac Motion Due to Deformation and Respiration

    PubMed Central

    Shrestha, Uttam M.; Seo, Youngho; Botvinick, Elias H.; Gullberg, Grant T.

    2015-01-01

    Myocardial perfusion imaging (MPI) using slow rotating large field of view cameras requires spatiotemporal reconstruction of dynamically acquired data to capture the time variation of the radiotracer concentration. In vivo, MPI contains additional degrees of freedom involving unavoidable motion of the heart due to quasiperiodic beating and the effects of respiration, which can severely degrade the quality of the images. This work develops a technique for a single photon emission computed tomography (SPECT) that reconstructs the distribution of the radiotracer concentration in the myocardium using a tensor product of different sets of basis functions that approximately describe the spatiotemporal variation of the radiotracer concentration and the motion of the heart. In this study the temporal B-spline basis functions are chosen to reflect the dynamics of the radiotracer, while the intrinsic deformation and the extrinsic motion of the heart are described by a product of a discrete set of Gaussian basis functions. Reconstruction results are presented showing the dynamics of the tracer in the myocardium as it deforms due to cardiac beating, and is displaced due to respiratory motion. These results are compared with the conventional 4D-spatiotemporal reconstruction method that models only the temporal changes of the tracer activity. The higher dimensional reconstruction method proposed here improves bias, yet the signal-to-noise ratio (SNR) decreases due to redistribution of the counts over the cardiac-respiratory gates. However, there is a trade-off between the number of gates and the number of projections per gate to achieve high contrast images. PMID:26450115

  12. Image reconstruction in higher dimensions: myocardial perfusion imaging of tracer dynamics with cardiac motion due to deformation and respiration

    DOE PAGES

    Shrestha, Uttam M.; Seo, Youngho; Botvinick, Elias H.; Gullberg, Grant T.

    2015-10-09

    Myocardial perfusion imaging (MPI) using slow rotating large field of view cameras requires spatiotemporal reconstruction of dynamically acquired data to capture the time variation of the radiotracer concentration. In vivo, MPI contains additional degrees of freedom involving unavoidable motion of the heart due to quasiperiodic beating and the effects of respiration, which can severely degrade the quality of the images. This work develops a technique for a single photon emission computed tomography (SPECT) that reconstructs the distribution of the radiotracer concentration in the myocardium using a tensor product of different sets of basis functions that approximately describe the spatiotemporal variationmore » of the radiotracer concentration and the motion of the heart. In this study the temporal B-spline basis functions are chosen to reflect the dynamics of the radiotracer, while the intrinsic deformation and the extrinsic motion of the heart are described by a product of a discrete set of Gaussian basis functions. Reconstruction results are presented showing the dynamics of the tracer in the myocardium as it deforms due to cardiac beating, and is displaced due to respiratory motion. We find these results are compared with the conventional 4D-spatiotemporal reconstruction method that models only the temporal changes of the tracer activity. The higher dimensional reconstruction method proposed here improves bias, yet the signal-to-noise ratio (SNR) decreases slightly due to redistribution of the counts over the cardiac-respiratory gates. Additionally, there is a trade-off between the number of gates and the number of projections per gate to achieve high contrast images.« less

  13. Image reconstruction in higher dimensions: myocardial perfusion imaging of tracer dynamics with cardiac motion due to deformation and respiration

    SciTech Connect

    Shrestha, Uttam M.; Seo, Youngho; Botvinick, Elias H.; Gullberg, Grant T.

    2015-10-09

    Myocardial perfusion imaging (MPI) using slow rotating large field of view cameras requires spatiotemporal reconstruction of dynamically acquired data to capture the time variation of the radiotracer concentration. In vivo, MPI contains additional degrees of freedom involving unavoidable motion of the heart due to quasiperiodic beating and the effects of respiration, which can severely degrade the quality of the images. This work develops a technique for a single photon emission computed tomography (SPECT) that reconstructs the distribution of the radiotracer concentration in the myocardium using a tensor product of different sets of basis functions that approximately describe the spatiotemporal variation of the radiotracer concentration and the motion of the heart. In this study the temporal B-spline basis functions are chosen to reflect the dynamics of the radiotracer, while the intrinsic deformation and the extrinsic motion of the heart are described by a product of a discrete set of Gaussian basis functions. Reconstruction results are presented showing the dynamics of the tracer in the myocardium as it deforms due to cardiac beating, and is displaced due to respiratory motion. We find these results are compared with the conventional 4D-spatiotemporal reconstruction method that models only the temporal changes of the tracer activity. The higher dimensional reconstruction method proposed here improves bias, yet the signal-to-noise ratio (SNR) decreases slightly due to redistribution of the counts over the cardiac-respiratory gates. Additionally, there is a trade-off between the number of gates and the number of projections per gate to achieve high contrast images.

  14. Image reconstruction in higher dimensions: myocardial perfusion imaging of tracer dynamics with cardiac motion due to deformation and respiration.

    PubMed

    Shrestha, Uttam M; Seo, Youngho; Botvinick, Elias H; Gullberg, Grant T

    2015-11-01

    Myocardial perfusion imaging (MPI) using slow rotating large field of view cameras requires spatiotemporal reconstruction of dynamically acquired data to capture the time variation of the radiotracer concentration. In vivo, MPI contains additional degrees of freedom involving unavoidable motion of the heart due to quasiperiodic beating and the effects of respiration, which can severely degrade the quality of the images. This work develops a technique for a single photon emission computed tomography (SPECT) that reconstructs the distribution of the radiotracer concentration in the myocardium using a tensor product of different sets of basis functions that approximately describe the spatiotemporal variation of the radiotracer concentration and the motion of the heart. In this study the temporal B-spline basis functions are chosen to reflect the dynamics of the radiotracer, while the intrinsic deformation and the extrinsic motion of the heart are described by a product of a discrete set of Gaussian basis functions. Reconstruction results are presented showing the dynamics of the tracer in the myocardium as it deforms due to cardiac beating, and is displaced due to respiratory motion. These results are compared with the conventional 4D-spatiotemporal reconstruction method that models only the temporal changes of the tracer activity. The higher dimensional reconstruction method proposed here improves bias, yet the signal-to-noise ratio (SNR) decreases slightly due to redistribution of the counts over the cardiac-respiratory gates. Additionally, there is a trade-off between the number of gates and the number of projections per gate to achieve high contrast images. PMID:26450115

  15. A new dynamic mode for fast imaging in atomic force microscopes

    NASA Astrophysics Data System (ADS)

    Mohan, Gayathri

    Video-rate imaging and property sensing with nanoscale precision is a subject of immense interest to scientists because it facilitates a deep understanding of processes and sample properties at a molecular level. This dissertation addresses the challenges of high-bandwidth imaging and real-time estimation of sample properties in an atomic force microscope (AFM). Atomic force microscopy has enabled high-resolution nanoscale imaging and manipulation of mechanical, biological and chemical properties of samples at atomic scales. However, current atomic force microscopy techniques suffer from limited imaging bandwidths making them impractical for applications requiring high throughput. A dynamic mode of imaging that achieves high imaging speeds while preserving the properties of high resolution and low forcing on the samples is developed. The proposed imaging scheme is particularly significant with the advent of high-speed nanopositioning stages and electronics. The design is accomplished by model-based force regulation that utilizes the fast cantilever de ection signal instead of its slower derivative signals used in existing methods. The control design uses the vertical and dither (shake) piezo-actuators to make the probe de ection signal track an appropriately designed trajectory. The underlying idea is to treat the nonlinear tip-sample interaction forces as an extraneous disturbance and derive an optimal control design for disturbance rejection with emphasis on robustness. The tracking objective guarantees force regulation between the probe-tip and the sample. Hinfinity stacked sensitivity framework is used to impose the control objectives and the optimal controller is derived through multiobjective optimization. The control design achieves disturbance rejection bandwidths of 0.15 -- 0.20 times the first modal frequency of cantilever used for imaging. Consequently, in the presence of appropriate lateral positioning bandwidth, imaging speeds of the order of 15 -- 20

  16. Inverse dynamics calculations during gait with restricted ground reaction force information from pressure insoles.

    PubMed

    Forner-Cordero, A; Koopman, H J F M; van der Helm, F C T

    2006-02-01

    The number of consecutive strides that can be recorded in measurements of gait have been limited due to the number of force plates and dimensions of the measurement field. In addition, the feet are constrained to land on the force plates. A method to calculate the inverse dynamics from the motion and incomplete information from the ground reaction forces (GRF), vertical component and its application point, is presented and compared to the calculations based on force plate measurements. This method is based on the estimation of the three-dimensional GRF during walking with pressure insoles. RMS errors were lower than 20 W for knee joint power compared to those derived from force plate measurements. The errors were larger during double stance phase due to errors in the application point measured with the insoles. This method, with some technical improvement, could be implemented in new gait analysis protocols measuring several consecutive steps either on a treadmill or over ground, depending on the motion-measurement system, without constraining foot placement.

  17. Free-Standing Kinked Silicon Nanowires for Probing Inter- and Intracellular Force Dynamics.

    PubMed

    Zimmerman, John F; Murray, Graeme F; Wang, Yucai; Jumper, John M; Austin, Jotham R; Tian, Bozhi

    2015-08-12

    Silicon nanowires (SiNWs) have emerged as a new class of materials with important applications in biology and medicine with current efforts having focused primarily on using substrate bound SiNW devices. However, developing devices capable of free-standing inter- and intracellular operation is an important next step in designing new synthetic cellular materials and tools for biophysical characterization. To demonstrate this, here we show that label free SiNWs can be internalized in multiple cell lines, forming robust cytoskeletal interfaces, and when kinked can serve as free-standing inter- and intracellular force probes capable of continuous extended (>1 h) force monitoring. Our results show that intercellular interactions exhibit ratcheting like behavior with force peaks of ∼69.6 pN/SiNW, while intracellular force peaks of ∼116.9 pN/SiNW were recorded during smooth muscle contraction. To accomplish this, we have introduced a simple single-capture dark-field/phase contrast optical imaging modality, scatter enhanced phase contrast (SEPC), which enables the simultaneous visualization of both cellular components and inorganic nanostructures. This approach demonstrates that rationally designed devices capable of substrate-independent operation are achievable, providing a simple and scalable method for continuous inter- and intracellular force dynamics studies.

  18. Whole-Body Human Inverse Dynamics with Distributed Micro-Accelerometers, Gyros and Force Sensing.

    PubMed

    Latella, Claudia; Kuppuswamy, Naveen; Romano, Francesco; Traversaro, Silvio; Nori, Francesco

    2016-01-01

    Human motion tracking is a powerful tool used in a large range of applications that require human movement analysis. Although it is a well-established technique, its main limitation is the lack of estimation of real-time kinetics information such as forces and torques during the motion capture. In this paper, we present a novel approach for a human soft wearable force tracking for the simultaneous estimation of whole-body forces along with the motion. The early stage of our framework encompasses traditional passive marker based methods, inertial and contact force sensor modalities and harnesses a probabilistic computational technique for estimating dynamic quantities, originally proposed in the domain of humanoid robot control. We present experimental analysis on subjects performing a two degrees-of-freedom bowing task, and we estimate the motion and kinetics quantities. The results demonstrate the validity of the proposed method. We discuss the possible use of this technique in the design of a novel soft wearable force tracking device and its potential applications. PMID:27213394

  19. Direct measurement of optical force induced by near-field plasmonic cavity using dynamic mode AFM

    DOE PAGES

    Guan, Dongshi; Hang, Zhi Hong; Marset, Zsolt; Liu, Hui; Kravchenko, Ivan I.; Chan, Ho Bun; Chan, C. T.; Tong, Penger

    2015-11-20

    Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength goldmore » disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550 nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. Lastly, the experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures.« less

  20. Direct measurement of optical force induced by near-field plasmonic cavity using dynamic mode AFM

    SciTech Connect

    Guan, Dongshi; Hang, Zhi Hong; Marset, Zsolt; Liu, Hui; Kravchenko, Ivan I.; Chan, Ho Bun; Chan, C. T.; Tong, Penger

    2015-11-20

    Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength gold disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550 nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. Lastly, the experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures.

  1. Quantification of surface displacements and electromechanical phenomena via dynamic atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Balke, Nina; Jesse, Stephen; Yu, Pu; Carmichael, Ben; Kalinin, Sergei V.; Tselev, Alexander

    2016-10-01

    Detection of dynamic surface displacements associated with local changes in material strain provides access to a number of phenomena and material properties. Contact resonance-enhanced methods of atomic force microscopy (AFM) have been shown capable of detecting ˜1-3 pm-level surface displacements, an approach used in techniques such as piezoresponse force microscopy, atomic force acoustic microscopy, and ultrasonic force microscopy. Here, based on an analytical model of AFM cantilever vibrations, we demonstrate a guideline to quantify surface displacements with high accuracy by taking into account the cantilever shape at the first resonant contact mode, depending on the tip-sample contact stiffness. The approach has been experimentally verified and further developed for piezoresponse force microscopy (PFM) using well-defined ferroelectric materials. These results open up a way to accurate and precise measurements of surface displacement as well as piezoelectric constants at the pm-scale with nanometer spatial resolution and will allow avoiding erroneous data interpretations and measurement artifacts. This analysis is directly applicable to all cantilever-resonance-based scanning probe microscopy (SPM) techniques.

  2. Quantification of surface displacements and electromechanical phenomena via dynamic atomic force microscopy.

    PubMed

    Balke, Nina; Jesse, Stephen; Yu, Pu; Ben Carmichael; Kalinin, Sergei V; Tselev, Alexander

    2016-10-21

    Detection of dynamic surface displacements associated with local changes in material strain provides access to a number of phenomena and material properties. Contact resonance-enhanced methods of atomic force microscopy (AFM) have been shown capable of detecting ∼1-3 pm-level surface displacements, an approach used in techniques such as piezoresponse force microscopy, atomic force acoustic microscopy, and ultrasonic force microscopy. Here, based on an analytical model of AFM cantilever vibrations, we demonstrate a guideline to quantify surface displacements with high accuracy by taking into account the cantilever shape at the first resonant contact mode, depending on the tip-sample contact stiffness. The approach has been experimentally verified and further developed for piezoresponse force microscopy (PFM) using well-defined ferroelectric materials. These results open up a way to accurate and precise measurements of surface displacement as well as piezoelectric constants at the pm-scale with nanometer spatial resolution and will allow avoiding erroneous data interpretations and measurement artifacts. This analysis is directly applicable to all cantilever-resonance-based scanning probe microscopy (SPM) techniques. PMID:27631885

  3. Whole-Body Human Inverse Dynamics with Distributed Micro-Accelerometers, Gyros and Force Sensing †

    PubMed Central

    Latella, Claudia; Kuppuswamy, Naveen; Romano, Francesco; Traversaro, Silvio; Nori, Francesco

    2016-01-01

    Human motion tracking is a powerful tool used in a large range of applications that require human movement analysis. Although it is a well-established technique, its main limitation is the lack of estimation of real-time kinetics information such as forces and torques during the motion capture. In this paper, we present a novel approach for a human soft wearable force tracking for the simultaneous estimation of whole-body forces along with the motion. The early stage of our framework encompasses traditional passive marker based methods, inertial and contact force sensor modalities and harnesses a probabilistic computational technique for estimating dynamic quantities, originally proposed in the domain of humanoid robot control. We present experimental analysis on subjects performing a two degrees-of-freedom bowing task, and we estimate the motion and kinetics quantities. The results demonstrate the validity of the proposed method. We discuss the possible use of this technique in the design of a novel soft wearable force tracking device and its potential applications. PMID:27213394

  4. Paramfit: automated optimization of force field parameters for molecular dynamics simulations.

    PubMed

    Betz, Robin M; Walker, Ross C

    2015-01-15

    The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field. PMID:25413259

  5. Quantification of surface displacements and electromechanical phenomena via dynamic atomic force microscopy.

    PubMed

    Balke, Nina; Jesse, Stephen; Yu, Pu; Ben Carmichael; Kalinin, Sergei V; Tselev, Alexander

    2016-10-21

    Detection of dynamic surface displacements associated with local changes in material strain provides access to a number of phenomena and material properties. Contact resonance-enhanced methods of atomic force microscopy (AFM) have been shown capable of detecting ∼1-3 pm-level surface displacements, an approach used in techniques such as piezoresponse force microscopy, atomic force acoustic microscopy, and ultrasonic force microscopy. Here, based on an analytical model of AFM cantilever vibrations, we demonstrate a guideline to quantify surface displacements with high accuracy by taking into account the cantilever shape at the first resonant contact mode, depending on the tip-sample contact stiffness. The approach has been experimentally verified and further developed for piezoresponse force microscopy (PFM) using well-defined ferroelectric materials. These results open up a way to accurate and precise measurements of surface displacement as well as piezoelectric constants at the pm-scale with nanometer spatial resolution and will allow avoiding erroneous data interpretations and measurement artifacts. This analysis is directly applicable to all cantilever-resonance-based scanning probe microscopy (SPM) techniques.

  6. Direct Measurement of Optical Force Induced by Near-Field Plasmonic Cavity Using Dynamic Mode AFM

    PubMed Central

    Guan, Dongshi; Hang, Zhi Hong; Marcet, Zsolt; Liu, Hui; Kravchenko, I. I.; Chan, C. T.; Chan, H. B.; Tong, Penger

    2015-01-01

    Plasmonic nanostructures have attracted much attention in recent years because of their potential applications in optical manipulation through near-field enhancement. Continuing experimental efforts have been made to develop accurate techniques to directly measure the near-field optical force induced by the plasmonic nanostructures in the visible frequency range. In this work, we report a new application of dynamic mode atomic force microscopy (DM-AFM) in the measurement of the enhanced optical force acting on a nano-structured plasmonic resonant cavity. The plasmonic cavity is made of an upper gold-coated glass sphere and a lower quartz substrate patterned with an array of subwavelength gold disks. In the near-field when the sphere is positioned close to the disk array, plasmonic resonance is excited in the cavity and the induced force by a 1550 nm infrared laser is found to be increased by an order of magnitude compared with the photon pressure generated by the same laser light. The experiment demonstrates that DM-AFM is a powerful tool for the study of light induced forces and their enhancement in plasmonic nanostructures. PMID:26586455

  7. Paramfit: automated optimization of force field parameters for molecular dynamics simulations.

    PubMed

    Betz, Robin M; Walker, Ross C

    2015-01-15

    The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field.

  8. Reconstructing the dynamics of the Greenland ice sheet during the last deglaciation

    NASA Astrophysics Data System (ADS)

    Keisling, Benjamin; DeConto, Robert

    2016-04-01

    Today, some outlet glaciers of the Greenland ice sheet (GrIS) are rapidly retreating and may mobilize large volumes of interior ice in the coming centuries. The last period that saw such dramatic, sustained retreat of the GrIS was the last deglaciation, when the ice sheet retreated from its Last Glacial Maximum (LGM) extent. Previous studies have used relative sea level observations to constrain changes in ice thickness and retreat timing during the deglaciation (e.g. Fleming and Lambert 2004, Simpson et al. 2009, Lecavalier et al. 2014). Here we build on these studies by isolating the drivers of ice-sheet retreat, and their spatial and temporal dynamics, during this period. Inclusion of ice-cliff failure and hydrofracturing parameterizations in our model has resulted in a better fit to paleodata for the Antarctic ice sheet, but this modeling approach has not been applied to the GrIS. Here we use a three-dimensional hybrid SSA/SIA ice-sheet model (Pollard et al. 2015) at 10km resolution over Greenland to simulate the last deglaciation. Boundary conditions for the last glacial maximum produce an LGM ice sheet with 3.81 meters sea level equivalent (m s.l.e.) of additional ice. The LGM ice sheet advances to the shelf-break in west, south, and east Greenland with an expansive ice shelf extending across Davis Strait. Applying modern atmospheric and oceanic forcing to the LGM ice sheet yields 1.25 and 1.09 m s.l.e. of melt, respectively, and 1.72 m s.l.e. for both. Ocean warming initially results in a higher rate and magnitude of retreat, but increased surface evaporation over open water results in additional accumulation that offsets losses in 10 kyr simulations. Here, we test the sensitivity of the magnitude of deglacial ice-sheet retreat to uncertainty in bedrock elevation and basal slding coefficients, the applied climate forcing, and the mass balance scheme (positive degree-day or energy balance). We also implement a deglacial climate forcing based on recently

  9. A feasibility study for experimentally determining dynamic force distribution in a lap joint.

    SciTech Connect

    Mayes, Randall Lee

    2013-11-01

    Developing constitutive models of the physics in mechanical joints is currently stymied by inability to measure forces and displacements within the joint. The current state of the art estimates whole joint stiffness and energy loss per cycle from external measured force input and one or two acceleration responses. To validate constitutive models beyond this state requires a measurement of the distributed forces and displacements at the joint interface. Unfortunately, introducing measurement devices at the interface completely disrupts the desired physics. A feasibility study is presented for a non-intrusive method of solving for the interface dynamic forces from an inverse problem using full field measured responses. The responses come from the viewable surface of a beam. The noise levels associated with digital image correlation and continuous scanning laser Doppler velocimetry are evaluated from typical beam experiments. Two inverse problems are simulated. One utilizes the extended Sum of Weighted Accelerations Technique (SWAT). The second is a new approach dubbed the method of truncated orthogonal forces. These methods are much more robust if the contact patch geometry is well identified. Various approaches to identifying the contact patch are investigated, including ion marker tracking, Prussian blue and ultrasonic measurements. A typical experiment is conceived for a beam which has a lap joint at one end with a single bolt connecting it to another identical beam. In a virtual test using the beam finite element analysis, it appears that the SWAT inverse method requires evaluation of too many coefficients to adequately identify the force distribution to be viable. However, the method of truncated orthogonal forces appears viable with current digital image correlation (and probably other) imaging techniques.

  10. Colloid probes with increased tip height for higher sensitivity in friction force microscopy and less cantilever damping in dynamic force microscopy.

    PubMed

    Schmutz, Jan-Erik; Schäfer, Marcus M; Hölscher, Hendrik

    2008-02-01

    We present a method how to glue small spheres to atomic force microscope cantilevers. In difference to an often used approach where the sphere is glued to a tipless cantilever, we suggest to mount small spheres to a conventional cantilever with integrated tips modified by a focused ion beam. In this way it is possible to manufacture a spherical probe with increased tip height which enhances the sensitivity in friction force microscopy and reduces the cantilever damping in dynamic force microscopy. By milling cavities for the spheres at the tip apex the colloid particles can be attached at defined positions and contamination with glue can be prevented. PMID:18315335

  11. Rapid Evolutionary Dynamics of Structural Disorder as a Potential Driving Force for Biological Divergence in Flaviviruses

    PubMed Central

    Ortiz, Juan F.; MacDonald, Madolyn L.; Masterson, Patrick; Uversky, Vladimir N.; Siltberg-Liberles, Jessica

    2013-01-01

    Protein structure is commonly regarded to be conserved and to dictate function. Most proteins rely on conformational flexibility to some degree. Are regions that convey conformational flexibility conserved over evolutionary time? Can changes in conformational flexibility alter protein function? Here, the evolutionary dynamics of structurally ordered and disordered (flexible) regions are investigated genome-wide in flaviviruses, revealing that the amount and location of structural disorder fluctuates highly among related proteins. Some regions are prone to shift between structured and flexible states. Increased evolutionary dynamics of structural disorder is observed for some lineages but not in others. Lineage-specific transitions of this kind could alter the conformational ensemble accessible to the same protein in different species, causing a functional change, even if the predominant function remains conserved. Thus, rapid evolutionary dynamics of structural disorder is a potential driving force for phenotypic divergence among flaviviruses. PMID:23418179

  12. Strength by atomic force microscopy (AFM): Molecular dynamics of water layer squeezing on magnesium oxide

    NASA Astrophysics Data System (ADS)

    Kendall, K.; Dhir, Aman; Yong, Chin W.

    2010-11-01

    Localised strength testing of materials is often carried out in an atomic force microscope (AFM), as foreseen by Kelly in his book Strong Solids (Clarendon Press, Oxford, 1966). During AFM indentation experiments, contamination can strongly influence the observed strength and theoretical interpretation of the results is a major problem. Here, we use molecular dynamics computer modelling to describe the contact of NaCl and MgO crystal probes onto surfaces, comparable to an AFM experiment. Clean NaCl gave elastic, brittle behaviour in contact simulations at 300 K, whereas MgO was more plastic, leading to increased toughness. This paper also considers the strength of an oxide substrate contaminated by water molecules and tested by indentation with a pyramidal probe of oxide crystal. Recent theory on the effect of liquid contaminant layers on surface strength has been mainly focussed on Lennard Jones (LJ) molecules with some studies on alcohols and water, described by molecular dynamics, which allows the molecules to be squeezed out as the crystal lattice is deformed. In this work, we have focused on water by studying the forces between a magnesium oxide (MgO) atomic force microscope (AFM) probe and an MgO slab. Force versus separation has been plotted as the AFM probe was moved towards and away from the substrate. Simulation results showed that the water layers could be removed in steps, giving up to four force peaks. The last monolayer of water could not be squeezed out, even at pressures where MgO deformed plastically. Interestingly, with water present, strength was reduced, but more in tensile than compressive measurements. In conclusion, water contaminating the oxide surface in AFM strength testing is structured. Water layer squeezing removal can be predicted by molecular modelling, which may be verified by AFM experiments to show that water can influence the strength of perfect crystals at the nanometre scale.

  13. Molecular dynamics simulations of lipid membranes with lateral force: rupture and dynamic properties.

    PubMed

    Xie, Jun Yu; Ding, Guang Hong; Karttunen, Mikko

    2014-03-01

    Membranes' response to lateral tension, and eventual rupture, remains poorly understood. In this study, pure dipalmitoylphosphatidylcholine (DPPC) lipid bilayers, under tension/pressure, were studied using molecular dynamics (MD) simulations. The irreversible membrane breakdown is demonstrated to depend on the amplitude of lateral tension, loading rate, and the size of the bilayer. In all of our simulations, -200bar lateral pressure was found to be enough to rupture lipid membrane regardless of the loading rate or the membrane size. Loading rate and membrane size had a significant impact on rupture. A variety of dynamic properties of lipid molecules, probability distribution of area per lipid particularly, have been determined, and found to be fundamental for describing membrane behavior in detail, thus providing the quantitative description for the requirement of membrane rupture.

  14. Capillary and van der Waals interactions on CaF2 crystals from amplitude modulation AFM force reconstruction profiles under ambient conditions

    PubMed Central

    Calò, Annalisa; Robles, Oriol Vidal; Santos, Sergio

    2015-01-01

    Summary There has been much interest in the past two decades to produce experimental force profiles characteristic of the interaction between nanoscale objects or a nanoscale object and a plane. Arguably, the advent of the atomic force microscope AFM was instrumental in driving such efforts because, in principle, force profiles could be recovered directly. Nevertheless, it has taken years before techniques have developed enough as to recover the attractive part of the force with relatively low noise and without missing information on critical ranges, particularly under ambient conditions where capillary interactions are believed to dominate. Thus a systematic study of the different profiles that may arise in such situations is still lacking. Here we employ the surfaces of CaF2, on which nanoscale water films form, to report on the range and force profiles that might originate by dynamic capillary interactions occurring between an AFM tip and nanoscale water patches. Three types of force profiles were observed under ambient conditions. One in which the force decay resembles the well-known inverse-square law typical of van der Waals interactions during the first 0.5–1 nm of decay, a second one in which the force decays almost linearly, in relatively good agreement with capillary force predicted by the constant chemical potential approximation, and a third one in which the attractive force is almost constant, i.e., forms a plateau, up to 3–4 nm above the surface when the formation of a capillary neck dominates the tip–sample interaction. PMID:25977852

  15. Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

    DOE PAGES

    Borreguero Calvo, Jose M.; Lynch, Vickie E.

    2015-11-23

    Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulationmore » due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.« less

  16. Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

    SciTech Connect

    Borreguero Calvo, Jose M.; Lynch, Vickie E.

    2015-11-23

    Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulation due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.

  17. Estimating dynamic external hand forces during manual materials handling based on ground reaction forces and body segment accelerations.

    PubMed

    Faber, Gert S; Chang, Chien-Chi; Kingma, Idsart; Dennerlein, Jack T

    2013-10-18

    Direct measurement of hand forces during assessment of manual materials handling is infeasible in most field studies and some laboratory studies (e.g., during patient handling). Therefore, this study proposed and evaluated the performance of a novel hand force estimation method based on ground reaction forces (GRFs) and body segment accelerations. Ten male subjects performed a manual lifting/carrying task while an optoelectronic motion tracking system measured 3D full body kinematics, a force plate measured 3D GRFs and an instrumented box measured 3D hand forces. The estimated 3D hand forces were calculated by taking the measured GRF vector and subtracting the force vectors due to weight and acceleration of all body segments. Root-mean-square difference (RMSD) between estimated and measured hand forces ranged from 11 to 27N. When ignoring the segment accelerations (just subtracting body weight from the GRFs), the hand force estimation errors were much higher, with RMSDs ranging from 21 to 101N. Future studies should verify the performance of the proposed hand force estimation method when using an ambulatory field measurement system.

  18. The Study of Biomolecule-Substrate Interactions by Single Molecule Force Spectroscopy and Brownian Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Cook, Sara Iliafar

    T, respectively). In addition to the binding strength of ssDNA nucleotide to surfaces, it is equally as important to understand the dynamics of these interactions. The force response of a simple chain-like polymeric molecule (representative of single stranded DNA) was studied using Brownian dynamics to shed light on these dynamics and the features that may be masked in SMFS experiments. Through simulations at slow peeling rates, our Brownian dynamics model confirmed the predictions of an equilibrium statistical thermodynamic model. Faster removal rates resulted in deviations from equilibrium which were dominated by a combination of Stokes (viscous) drag and a finite desorption rate of the monomeric units. Furthermore, the force probe's thermal fluctuations were shown to be affected by the spring constant of the contact mode AFM cantilever Consequently, this effect provided evidence on the source of disappearance for certain key features such as force spikes, associated with the desorption of individual links and predicted by the statistical thermodynamic model under displacement control, from SMFS experiments. In studying the elastic response of a freely jointed chain stretched in 2D and 3D, we obtained analytical expressions for two modes of stretching: i) when force is applied only to one end of the chain, and ii) when the applied force is distributed uniformly throughout the chain. By comparing, we confirmed that these expressions correctly predict the results obtained from our Brownian dynamics simulations as well as experimental results from the literature.

  19. Reconstruction of the evolutionary dynamics of hepatitis C virus subtypes in Montenegro and the Balkan region.

    PubMed

    Zehender, Gianguglielmo; Sorrentino, Chiara; Lai, Alessia; Ebranati, Erika; Gabanelli, Elena; Lo Presti, Alessandra; Vujoševic, Danijela; Lauševic, Dragan; Terzić, Dragica; Shkjezi, Renata; Bino, Silvia; Vratnica, Zoran; Mugosa, Boban; Galli, Massimo; Ciccozzi, Massimo

    2013-07-01

    More than 20 million hepatitis C virus (HCV) carriers live in the countries of the Eastern Mediterranean. We determined HCV genotype distribution among chronically infected patients in Montenegro and investigated the phylodynamics and phylogeography of the most represented HCV subtypes. The HCV-NS5b sequences of the Montenegrin patients were compared with sequences isolated in different known localities of the Mediterranean area, Europe and Asia. A Bayesian approach was used in order to allow the simultaneous estimate of the evolutionary rate, time-scaled phylogeny, demography and ancestral spatial status. The most frequent HCV subtypes among the Montenegrin patients, were 1b (34.7%) and 3a (24.7%), but there was also a significant prevalence of 1a and 4d (19.5%). Subtype 3a was significantly more frequent among younger patients and intravenous drug users (IDUs), whereas subtype 1b was more frequently associated with iatrogenic exposure and older ages. The spatio-temporal analysis of the epidemic suggested that HCV-1b penetrated Europe at the beginning of the XX century, probably through Greece and Cyprus and in the 1920s reached Montenegro, where there was an exponential increase in the effective number of infections between the 1950s and 1970s. The phylogeographic and phylodynamic analysis of HCV 3a showed that its most probable origin was in the Indian sub-continent (Pakistan in our reconstruction) about 300years ago. The evolutionary dynamics analysis showed that HCV-3a reached Montenegro more recently in the late 1970s and underwent multi-phasic growth still persisting. Our data suggest multiple introduction of HCV subtypes in the area, supported by different causes of dispersion: adverse social conditions and unsafe medical practices for HCV-1b and i.v. drug use for HCV-3a.

  20. Force-Induced Dynamical Properties of Multiple Cytoskeletal Filaments Are Distinct from that of Single Filaments

    PubMed Central

    Das, Dipjyoti; Das, Dibyendu; Padinhateeri, Ranjith

    2014-01-01

    How cytoskeletal filaments collectively undergo growth and shrinkage is an intriguing question. Collective properties of multiple bio-filaments (actin or microtubules) undergoing hydrolysis have not been studied extensively earlier within simple theoretical frameworks. In this paper, we study the collective dynamical properties of multiple filaments under force, and demonstrate the distinct properties of a multi-filament system in comparison to a single filament. Comparing stochastic simulation results with recent experimental data, we show that multi-filament collective catastrophes are slower than catastrophes of single filaments. Our study also shows further distinctions as follows: (i) force-dependence of the cap-size distribution of multiple filaments are quantitatively different from that of single filaments, (ii) the diffusion constant associated with the system length fluctuations is distinct for multiple filaments, and (iii) switching dynamics of multiple filaments between capped and uncapped states and the fluctuations therein are also distinct. We build a unified picture by establishing interconnections among all these collective phenomena. Additionally, we show that the collapse times during catastrophes can be sharp indicators of collective stall forces exceeding the additive contributions of single filaments. PMID:25531397

  1. Molecular dynamics simulation of free and forced BSA adsorption on a hydrophobic graphite surface.

    PubMed

    Mücksch, Christian; Urbassek, Herbert M

    2011-11-01

    The adsorption of bovine serum albumin (BSA) onto a hydrophobic graphite surface is studied using molecular-dynamics simulation. In addition to the free, that is, unsteered, adsorption, we also investigate forced adsorption, in which the action of an AFM tip pushing the protein with constant force to the surface is modeled. Using an implicit inviscid water model, the adsorption dynamics and energetics are monitored for two different initial protein orientations toward the surface. In all cases, we find that the protein partially unfolds and spreads on the surface. The spreading is in agreement with the well-known high biocompatibility of graphite-based implants. The denaturation is, however, greatly enhanced in the case of forced adsorption. We follow the position of the so-called lipid-binding pocket found in subdomain IIIA (Sudlow site II) during adsorption and find that it is tilted and moved toward the graphite surface in all cases, in agreement with its hydrophobic character. The relevance of our findings for the common measurement procedure of studying protein adhesion using AFM experiments is discussed.

  2. Effects of a multichannel dynamic functional electrical stimulation system on hemiplegic gait and muscle forces.

    PubMed

    Qian, Jing-Guang; Rong, Ke; Qian, Zhenyun; Wen, Chen; Zhang, Songning

    2015-11-01

    [Purpose] The purpose of the study was to design and implement a multichannel dynamic functional electrical stimulation system and investigate acute effects of functional electrical stimulation of the tibialis anterior and rectus femoris on ankle and knee sagittal-plane kinematics and related muscle forces of hemiplegic gait. [Subjects and Methods] A multichannel dynamic electrical stimulation system was developed with 8-channel low frequency current generators. Eight male hemiplegic patients were trained for 4 weeks with electric stimulation of the tibia anterior and rectus femoris muscles during walking, which was coupled with active contraction. Kinematic data were collected, and muscle forces of the tibialis anterior and rectus femoris of the affected limbs were analyzed using a musculoskelatal modeling approach before and after training. A paired sample t-test was used to detect the differences between before and after training. [Results] The step length of the affected limb significantly increased after the stimulation was applied. The maximum dorsiflexion angle and maximum knee flexion angle of the affected limb were both increased significantly during stimulation. The maximum muscle forces of both the tibia anterior and rectus femoris increased significantly during stimulation compared with before functional electrical stimulation was applied. [Conclusion] This study established a functional electrical stimulation strategy based on hemiplegic gait analysis and musculoskeletal modeling. The multichannel functional electrical stimulation system successfully corrected foot drop and altered circumduction hemiplegic gait pattern.

  3. A new force field for molecular dynamics studies of Li + and Na +-nafion

    NASA Astrophysics Data System (ADS)

    Soolo, Endel; Liivat, Anti; Kasemägi, Heiki; Tamm, Tarmo; Brandell, Daniel; Aabloo, Alvo

    2008-03-01

    Nafion is widely known as one of the most popular membrane materials for low temperature fuel cell applications. However, the particular exchange membrane material properties make it also valuable for other applications. One of the electroactive polymer (EAP) subclasses, ionic polymer metal composites (IPMC) commonly exploits Nafion as the ion exchange polymer membrane. The ion conducting properties of Nafion are extremely important for IPMCs. Although, ion conductivity depends strongly on the structural properties of the polymer matrix, there has been very little insight at the atomistic level. Molecular dynamics simulations are one of the possibilities to study the ion conduction mechanism at atomistic level. So far, the simulation results have been rather contradictory and very much dependent from the force fields and polymer matrix setup used. In the present work, new force field parameters for Li + and Na + - nafion based on DFT calculations are presented. The developed potentials and the force field were tested by molecular dynamics simulations. It can be concluded that Li + and Na + ions are coordinated to different Nafion side-chain terminal group (SO 3 -) oxygens and to very few water molecules. One cation is coordinated to three different side-chains. Oxygens of SO 3 groups and cations form complicated multi-header systems. In the equilibrium state, no cations dissociated from side chains were found.

  4. Use of computational fluid dynamics to study forces exerted on prey by aquatic suction feeders

    PubMed Central

    Skorczewski, Tyler; Cheer, Angela; Cheung, Samson; Wainwright, Peter C.

    2010-01-01

    Suction feeding is the most commonly used mechanism of prey capture among aquatic vertebrates. Most previous models of the fluid flow caused by suction feeders involve making several untested assumptions. In this paper, a Chimera overset grids approach is used to solve the governing equations of fluid dynamics in order to investigate the assumptions that prey do not interact with the flow and that the flow can be modelled as a one-dimensional flow. Results show that, for small prey, both neglecting the prey and considering prey interaction give similar calculated forces exerted on the prey. However, as the prey item increases in size toward the size of the gape, its effect on the flow becomes more pronounced. This in turn affects both the magnitude of the hydrodynamic forces imparted to the prey and the time when maximum force is delivered. Maximum force is delivered most quickly to intermediate sized prey, about one-third of mouth diameter, and most slowly to prey less than 7 per cent or greater than 67 per cent of mouth diameter. This suggests that the effect of prey size on the timing of suction forces may have substantial consequences for the feeding ecology of suction feeders that are known to prefer prey between 25 and 50 per cent of mouth diameter. Moreover, for a 15 cm fish with a 15 mm gape, assuming a radial one-dimensional flow field can result in underestimating the maximum force exerted on a 5 mm diameter spherical prey 1 gape distance from the mouth by up to 28.7 per cent. PMID:19674998

  5. Use of computational fluid dynamics to study forces exerted on prey by aquatic suction feeders.

    PubMed

    Skorczewski, Tyler; Cheer, Angela; Cheung, Samson; Wainwright, Peter C

    2010-03-01

    Suction feeding is the most commonly used mechanism of prey capture among aquatic vertebrates. Most previous models of the fluid flow caused by suction feeders involve making several untested assumptions. In this paper, a Chimera overset grids approach is used to solve the governing equations of fluid dynamics in order to investigate the assumptions that prey do not interact with the flow and that the flow can be modelled as a one-dimensional flow. Results show that, for small prey, both neglecting the prey and considering prey interaction give similar calculated forces exerted on the prey. However, as the prey item increases in size toward the size of the gape, its effect on the flow becomes more pronounced. This in turn affects both the magnitude of the hydrodynamic forces imparted to the prey and the time when maximum force is delivered. Maximum force is delivered most quickly to intermediate sized prey, about one-third of mouth diameter, and most slowly to prey less than 7 per cent or greater than 67 per cent of mouth diameter. This suggests that the effect of prey size on the timing of suction forces may have substantial consequences for the feeding ecology of suction feeders that are known to prefer prey between 25 and 50 per cent of mouth diameter. Moreover, for a 15 cm fish with a 15 mm gape, assuming a radial one-dimensional flow field can result in underestimating the maximum force exerted on a 5 mm diameter spherical prey 1 gape distance from the mouth by up to 28.7 per cent.

  6. Dynamic Charge Equilibration-Morse stretch force field: application to energetics of pure silica zeolites.

    PubMed

    Sefcik, Jan; Demiralp, Ersan; Cagin, Tahir; Goddard, William A

    2002-12-01

    We present the Dynamic Charge Equilibration (DQEq) method for a self-consistent treatment of charge transfer in force field modeling, where atomic charges are designed to reproduce electrostatic potentials calculated quantum mechanically. Force fields coupled with DQEq allow charges to readjust as geometry changes in classical simulations, using appropriate algorithms for periodic boundary conditions. The full electrostatic energy functional is used to derive the corresponding forces and the second derivatives (hessian) for vibrational calculations. Using DQEq electrostatics, we develop a simple nonbond force field for simulation of silica molecular sieves, where nonelectrostatic interactions are described by two-body Morse stretch terms. Energy minimization calculations with the new force field yield accurate unit cell geometries for siliceous zeolites. Relative enthalpies with respect to quartz and third-law entropies calculated from harmonic vibrational analysis agree very well with available calorimetric data: calculated SiO(2) enthalpies relative to alpha-quartz are within 2 kJ/mol and entropies at 298 K are within 3 J/mol K of the respective experimental values. Contributions from the zero point energy and vibrational degrees of freedom were found to be only about 1 kJ/mol for the free energy of mutual transformations between microporous silica polymorphs. The approach presented here can be applied to interfaces and other oxides as well and it is suitable for development of force fields for accurate modeling of geometry and energetics of microporous and mesoporous materials, while providing a realistic description of electrostatic fields near surfaces and inside pores of adsorbents and catalysts.

  7. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    USGS Publications Warehouse

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  8. Molecular dynamics simulation of tri-n-butyl-phosphate liquid: a force field comparative study.

    PubMed

    Cui, Shengting; de Almeida, Valmor F; Hay, Benjamin P; Ye, Xianggui; Khomami, Bamin

    2012-01-12

    Molecular dynamics (MD) simulations were conducted to compare the performance of four force fields in predicting thermophysical properties of tri-n-butyl-phosphate (TBP) in the liquid phase. The intramolecular force parameters used were from the Assisted Model Building with Energy Refinement (AMBER) force field model. The van der Waals parameters were based on either the AMBER or the Optimized Potential for Liquid Simulation (OPLS) force fields. The atomic partial charges were either assigned by performing quantum chemistry calculations or utilized previously published data, and were scaled to approximate the average experimental value of the electric dipole moment. Canonical ensemble computations based on the aforementioned parameters were performed near atmospheric pressure and temperature to obtain the electric dipole moment, mass density, and self-diffusion coefficient. In addition, the microscopic structure of the liquid was characterized via pair correlation functions between selected atoms. It has been demonstrated that the electric dipole moment can be approximated within 1% of the average experimental value by virtue of scaled atomic partial charges. The liquid mass density can be predicted within 0.5-1% of its experimentally determined value when using the corresponding charge scaling. However, in all cases, the predicted self-diffusion coefficient is significantly smaller than a commonly quoted experimental measurement; this result is qualified by the fact that the uncertainty of the experimental value was not available. PMID:22126596

  9. Translocation dynamics of a short polymer driven by an oscillating force.

    PubMed

    Pizzolato, Nicola; Fiasconaro, Alessandro; Adorno, Dominique Persano; Spagnolo, Bernardo

    2013-02-01

    We study the translocation dynamics of a short polymer moving in a noisy environment and driven by an oscillating force. The dynamics is numerically investigated by solving a Langevin equation in a two-dimensional domain. We consider a phenomenological cubic potential with a metastable state to model the polymer-pore interaction and the entropic free energy barrier characterizing the translocation process. The mean first translocation time of the center of inertia of polymers shows a nonmonotonic behavior, with a minimum, as a function of the number of the monomers. The dependence of the mean translocation time on the polymer chain length shows a monotonically increasing behavior for high values of the number of monomers. Moreover, the translocation time shows a minimum as a function of the frequency of the oscillating forcing field for all the polymer lengths investigated. This finding represents the evidence of the resonant activation phenomenon in the dynamics of polymer translocation, whose occurrence is maintained for different values of the noise intensity.

  10. DYNAMICAL INFERENCE FROM A KINEMATIC SNAPSHOT: THE FORCE LAW IN THE SOLAR SYSTEM

    SciTech Connect

    Bovy, Jo; Hogg, David W.; Murray, Iain

    2010-03-10

    If a dynamical system is long-lived and non-resonant (that is, if there is a set of tracers that have evolved independently through many orbital times), and if the system is observed at any non-special time, it is possible to infer the dynamical properties of the system (such as the gravitational force or acceleration law) from a snapshot of the positions and velocities of the tracer population at a single moment in time. In this paper, we describe a general inference technique that solves this problem while allowing (1) the unknown distribution function of the tracer population to be simultaneously inferred and marginalized over, and (2) prior information about the gravitational field and distribution function to be taken into account. As an example, we consider the simplest problem of this kind: we infer the force law in the solar system using only an instantaneous kinematic snapshot (valid at 2009 April 1.0) for the eight major planets. We consider purely radial acceleration laws of the form a{sub r} = -A [r/r{sub 0}]{sup -a}lpha, where r is the distance from the Sun. Using a probabilistic inference technique, we infer 1.989 < alpha < 2.052 (95% interval), largely independent of any assumptions about the distribution of energies and eccentricities in the system beyond the assumption that the system is phase-mixed. Generalizations of the methods used here will permit, among other things, inference of Milky Way dynamics from Gaia-like observations.

  11. The dynamics of highly excited electronic systems: Applications of the electron force field

    NASA Astrophysics Data System (ADS)

    Su, Julius T.; Goddard, William A.

    2009-12-01

    Highly excited heterogeneous complex materials are essential elements of important processes, ranging from inertial confinement fusion to semiconductor device fabrication. Understanding the dynamics of these systems has been challenging because of the difficulty in extracting mechanistic information from either experiment or theory. We describe here the electron force field (eFF) approximation to quantum mechanics which provides a practical approach to simulating the dynamics of such systems. eFF includes all the normal electrostatic interactions between electrons and nuclei and the normal quantum mechanical description of kinetic energy for the electrons, but contains two severe approximations: first, the individual electrons are represented as floating Gaussian wave packets whose position and size respond instantaneously to various forces during the dynamics; and second, these wave packets are combined into a many-body wave function as a Hartree product without explicit antisymmetrization. The Pauli principle is accounted for by adding an extra spin-dependent term to the Hamiltonian. These approximations are a logical extension of existing approaches to simulate the dynamics of fermions, which we review. In this paper, we discuss the details of the equations of motion and potentials that form eFF, and evaluate the ability of eFF to describe ground-state systems containing covalent, ionic, multicenter, and/or metallic bonds. We also summarize two eFF calculations previously reported on electronically excited systems: (1) the thermodynamics of hydrogen compressed up to ten times liquid density and heated up to 200 000 K; and (2) the dynamics of Auger fragmentation in a diamond nanoparticle, where hundreds of electron volts of excitation energy are dissipated over tens of femtoseconds. These cases represent the first steps toward using eFF to model highly excited electronic processes in complex materials.

  12. Dynamics of dissipative self-assembly of particles interacting through oscillatory forces.

    PubMed

    Tagliazucchi, M; Szleifer, I

    2016-01-01

    Dissipative self-assembly is the formation of ordered structures far from equilibrium, which continuously uptake energy and dissipate it into the environment. Due to its dynamical nature, dissipative self-assembly can lead to new phenomena and possibilities of self-organization that are unavailable to equilibrium systems. Understanding the dynamics of dissipative self-assembly is required in order to direct the assembly to structures of interest. In the present work, Brownian dynamics simulations and analytical theory were used to study the dynamics of self-assembly of a mixture of particles coated with weak acids and bases under continuous oscillations of the pH. The pH of the system modulates the charge of the particles and, therefore, the interparticle forces oscillate in time. This system produces a variety of self-assembled structures, including colloidal molecules, fibers and different types of crystalline lattices. The most important conclusions of our study are: (i) in the limit of fast oscillations, the whole dynamics (and not only those at the non-equilibrium steady state) of a system of particles interacting through time-oscillating interparticle forces can be described by an effective potential that is the time average of the time-dependent potential over one oscillation period; (ii) the oscillation period is critical to determine the order of the system. In some cases the order is favored by very fast oscillations while in others small oscillation frequencies increase the order. In the latter case, it is shown that slow oscillations remove kinetic traps and, thus, allow the system to evolve towards the most stable non-equilibrium steady state.

  13. Reconstruction of glacier variability from lake sediments reveals dynamic Holocene climate in Svalbard

    NASA Astrophysics Data System (ADS)

    van der Bilt, Willem G. M.; Bakke, Jostein; Vasskog, Kristian; D'Andrea, William J.; Bradley, Raymond S.; Ólafsdóttir, Sædis

    2015-10-01

    The Arctic is warming faster than anywhere else on Earth. Holocene proxy time-series are increasingly used to put this amplified response in perspective by understanding Arctic climate processes beyond the instrumental period. However, available datasets are scarce, unevenly distributed and often of coarse resolution. Glaciers are sensitive recorders of climate shifts and variations in rock-flour production transfer this signal to the lacustrine sediment archives of downstream lakes. Here, we present the first full Holocene record of continuous glacier variability on Svalbard from glacier-fed Lake Hajeren. This reconstruction is based on an undisturbed lake sediment core that covers the entire Holocene and resolves variability on centennial scales owing to 26 dating points. A toolbox of physical, geochemical (XRF) and magnetic proxies in combination with multivariate statistics has allowed us to fingerprint glacier activity in addition to other processes affecting the sediment record. Evidence from variations in sediment density, validated by changes in Ti concentrations, reveal glaciers remained present in the catchment following deglaciation prior to 11,300 cal BP, culminating in a Holocene maximum between 9.6 and 9.5 ka cal BP. Correspondence with freshwater pulses from Hudson Strait suggests that Early Holocene glacier advances were driven by the melting Laurentide Ice Sheet (LIS). We find that glaciers disappeared from the catchment between 7.4 and 6.7 ka cal BP, following a late Hypsithermal. Glacier reformation around 4250 cal BP marks the onset of the Neoglacial, supporting previous findings. Between 3380 and 3230 cal BP, we find evidence for a previously unreported centennial-scale glacier advance. Both events are concurrent with well-documented episodes of North Atlantic cooling. We argue that this brief forcing created suitable conditions for glaciers to reform in the catchment against a background of gradual orbital cooling. These findings highlight the

  14. Force-velocity relation for actin-polymerization-driven motility from Brownian dynamics simulations.

    PubMed

    Lee, Kun-Chun; Liu, Andrea J

    2009-09-01

    We report numerical simulation results for the force-velocity relation for actin-polymerization-driven motility. We use Brownian dynamics to solve a physically consistent formulation of the dendritic nucleation model with semiflexible filaments that self-assemble and push a disk. We find that at small loads, the disk speed is independent of load, whereas at high loads, the speed decreases and vanishes at a characteristic stall pressure. Our results demonstrate that at small loads, the velocity is controlled by the reaction rates, whereas at high loads the stall pressure is determined by the mechanical properties of the branched actin network. The behavior is consistent with experiments and with our recently proposed self-diffusiophoretic mechanism for actin-polymerization-driven motility. New in vitro experiments to measure the force-velocity relation are proposed.

  15. Dynamical response of the tropical Pacific Ocean to solar forcing during the early Holocene.

    PubMed

    Marchitto, Thomas M; Muscheler, Raimund; Ortiz, Joseph D; Carriquiry, Jose D; van Geen, Alexander

    2010-12-01

    We present a high-resolution magnesium/calcium proxy record of Holocene sea surface temperature (SST) from off the west coast of Baja California Sur, Mexico, a region where interannual SST variability is dominated today by the influence of the El Niño-Southern Oscillation (ENSO). Temperatures were lowest during the early to middle Holocene, consistent with documented eastern equatorial Pacific cooling and numerical model simulations of orbital forcing into a La Niña-like state at that time. The early Holocene SSTs were also characterized by millennial-scale fluctuations that correlate with cosmogenic nuclide proxies of solar variability, with inferred solar minima corresponding to El Niño-like (warm) conditions, in apparent agreement with the theoretical "ocean dynamical thermostat" response of ENSO to exogenous radiative forcing. PMID:21127251

  16. Dynamical Response of the Tropical Pacific Ocean to Solar Forcing During the Early Holocene

    NASA Astrophysics Data System (ADS)

    Marchitto, Thomas M.; Muscheler, Raimund; Ortiz, Joseph D.; Carriquiry, Jose D.; van Geen, Alexander

    2010-12-01

    We present a high-resolution magnesium/calcium proxy record of Holocene sea surface temperature (SST) from off the west coast of Baja California Sur, Mexico, a region where interannual SST variability is dominated today by the influence of the El Niño-Southern Oscillation (ENSO). Temperatures were lowest during the early to middle Holocene, consistent with documented eastern equatorial Pacific cooling and numerical model simulations of orbital forcing into a La Niña-like state at that time. The early Holocene SSTs were also characterized by millennial-scale fluctuations that correlate with cosmogenic nuclide proxies of solar variability, with inferred solar minima corresponding to El Niño-like (warm) conditions, in apparent agreement with the theoretical “ocean dynamical thermostat” response of ENSO to exogenous radiative forcing.

  17. Dynamics of a disturbed sessile drop measured by atomic force microscopy (AFM).

    PubMed

    McGuiggan, Patricia M; Grave, Daniel A; Wallace, Jay S; Cheng, Shengfeng; Prosperetti, Andrea; Robbins, Mark O

    2011-10-01

    A new method for studying the dynamics of a sessile drop by atomic force microscopy (AFM) is demonstrated. A hydrophobic microsphere (radius, r ∼ 20-30 μm) is brought into contact with a small sessile water drop resting on a polytetrafluoroethylene (PTFE) surface. When the microsphere touches the liquid surface, the meniscus rises onto it because of capillary forces. Although the microsphere volume is 6 orders of magnitude smaller than the drop, it excites the normal resonance modes of the liquid interface. The sphere is pinned at the interface, whose small (<100 nm) oscillations are readily measured with AFM. Resonance oscillation frequencies were measured for drop volumes between 5 and 200 μL. The results for the two lowest normal modes are quantitatively consistent with continuum calculations for the natural frequency of hemispherical drops with no adjustable parameters. The method may enable sensitive measurements of volume, surface tension, and viscosity of small drops.

  18. Dynamic image forces near a metal surface and the point-charge motion

    NASA Astrophysics Data System (ADS)

    Gabovich, A. M.; Voitenko, A. I.

    2012-09-01

    The problem of charge motion governed by image force attraction near a plane metal surface is considered and solved self-consistently. The temporal dispersion of metal dielectric permittivity makes the image forces dynamic and, hence, finite, contrary to the results of the conventional approach. Therefore, the maximal attainable velocity turns out to be also finite and comprises a small portion of light velocity so that there is no need for any relativistic generalization of the problem. The time needed for an electron to achieve the surface from the initial position is calculated. The solution of the problem presented may enable undergraduates and lecturers to perceive the limitations of conventional electrostatics when applied to the surface science of real materials.

  19. A "skin-skull-brain model" for the biomechanical reconstruction of blunt forces to the human head.

    PubMed

    Thali, Michael J; Kneubuehl, Beat P; Dirnhofer, Richard

    2002-02-18

    In order to create and study blunt force wound morphology, a "skin-skull-brain model" had to be designed which would make the laboratory reproduction of a blunt force injury to the head possible. During the evaluation of the "skin-skull-brain model", it was possible to show that injuries inflicted to this model are fully comparable to the morphology of equivalent real blunt forces injuries to humans. Utilization of the "skin-skull-brain model" presents some significant advantages: the model is inexpensive, easy to construct, instantly available for use, and eliminates ethics conflicts. The main advantage of such a model is, in comparison with biological substances, the high reproducibility of experimentally inflicted traumas.

  20. The development of a two-component force dynamometer and tool control system for dynamic machine tool research

    NASA Technical Reports Server (NTRS)

    Sutherland, I. A.

    1973-01-01

    The development is presented of a tooling system that makes a controlled sinusoidal oscillation simulating a dynamic chip removal condition. It also measures the machining forces in two mutually perpendicular directions without any cross sensitivity.

  1. Prediction of dynamic cutting force and regenerative chatter stability in inserted cutters milling

    NASA Astrophysics Data System (ADS)

    Li, Zhongqun; Liu, Qiang; Yuan, Songmei; Huang, Kaisheng

    2013-05-01

    Currently, the modeling of cutting process mainly focuses on two aspects: one is the setup of the universal cutting force model that can be adapted to a broader cutting condition; the other is the setup of the exact cutting force model that can accurately reflect a true cutting process. However, there is little research on the prediction of chatter stablity in milling. Based on the generalized mathematical model of inserted cutters introduced by ENGIN, an improved geometrical, mechanical and dynamic model for the vast variety of inserted cutters widely used in engineering applications is presented, in which the average directional cutting force coefficients are obtained by means of a numerical approach, thus leading to an analytical determination of stability lobes diagram (SLD) on the axial depth of cut. A new kind of SLD on the radial depth of cut is also created to satisfy the special requirement of inserted cutter milling. The corresponding algorithms used for predicting cutting forces, vibrations, dimensional surface finish and stability lobes in inserted cutter milling under different cutting conditions are put forward. Thereafter, a dynamic simulation module of inserted cutter milling is implemented by using hybrid program of Matlab with Visual Basic. Verification tests are conducted on a vertical machine center for Aluminum alloy LC4 by using two different types of inserted cutters, and the effectiveness of the model and the algorithm is verified by the good agreement of simulation result with that of cutting tests under different cutting conditions. The proposed model can predict the cutting process accurately under a variety of cutting conditions, and a high efficient and chatter-free milling operation can be achieved by a cutting condition optimization in industry applications.

  2. Development of a Forced Oscillation System for Measuring Dynamic Derivatives of Fluidic Vehicles

    NASA Technical Reports Server (NTRS)

    Trieu, B. C.; Tyler, T. R.; Stewart, B. K.; Chamock, J. K.; Fisher, D. W.; Heim, E. H.; Brandon, J.; Grafton, S. B.

    2006-01-01

    A new Forced Oscillation System (FOS) has been designed and built at NASA Langley Research Center that provides new capabilities for aerodynamic researchers to investigate the dynamic derivatives of vehicle configurations. Test vehicles may include high performance and general aviation aircraft, re-entry spacecraft, submarines and other fluidic vehicles. The measured data from forced oscillation testing is used in damping characteristic studies and in simulation databases for control algorithm development and performance analyses. The newly developed FOS hardware provides new flexibility for conducting dynamic derivative studies. The design is based on a tracking principle where a desired motion profile is achieved via a fast closed-loop positional controller. The motion profile for the tracking system is numerically generated and thus not limited to sinusoidal motion. This approach permits non-traditional profiles such as constant velocity and Schroeder sweeps. Also, the new system permits changes in profile parameters including nominal offset angle, waveform, and associated parameters such as amplitude and frequency. Most importantly, the changes may be made remotely without halting the FOS and the tunnel. System requirements, system analysis, and the resulting design are addressed for a new FOS in the 12-Foot Low-Speed Wind Tunnel (LSWT). The overall system including mechanical, electrical, and control subsystems is described. The design is complete, and the FOS has been built and installed in the 12-Foot LSWT. System integration and testing have verified design intent and safe operation. Currently it is being validated for wind-tunnel operations and aerodynamic testing. The system is a potential major enhancement to forced oscillation studies. The productivity gain from the motion profile automation will shorten the testing cycles needed for control surface and aircraft control algorithm development. The new motion capabilities also will serve as a test bed for

  3. Energy dissipation and dynamic response of an amplitude-modulation atomic-force microscopy subjected to a tip-sample viscous force.

    PubMed

    Lin, Shueei Muh

    2007-01-01

    In a common environment of atomic force microscopy (AFM), a damping force occurs between a tip and a sample. The influence of damping on the dynamic response of a cantilever must be significant. Moreover, accurate theory is very helpful for the interpretation of a sample's topography and properties. In this study, the effects of damping and nonlinear interatomic tip-sample forces on the dynamic response of an amplitude-formulation AFM are investigated. The damping force is simulated by using the conventional Kelvin-Voigt damping model. The interatomic tip-sample force is the attractive van der Waals force. For consistance with real measurement of a cantilever, the mathematical equations of the beam theory of an AM-AFM are built and its analytical solution is derived. Moreover, an AFM system is also simplified into a mass-spring-damper model. Its exact solution is simple and intuitive. Several relations among the damping ratio, the response ratio, the frequency shift, the energy dissipation and the Q-factor are revealed. It is found that the resonant frequencies and the phase angles determined by the two models are almost same. Significant differences in the resonant quality factors and the response ratios determined by using the two models are also found. Finally, the influences of the variations of several parameters on the error of measuring a sample's topography are investigated. PMID:16982149