Quantum mechanical force field for water with explicit electronic polarization.

PubMed

Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

2013-08-07

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

Demonstration of motion control of ZrO2 microparticles in uniform/non-uniform electric field

NASA Astrophysics Data System (ADS)

Onishi, Genki; Trung, Ngo Nguyen Chi; Matsutani, Naoto; Nakayama, Tadachika; Suzuki, Tsuneo; Suematsu, Hisayuki; Niihara, Koichi

2018-02-01

This study aims to elucidate the mechanism that drives dielectric microparticles under an electric field. The driving of microstructures is affected by various electrical phenomena occurring at the same time such as surface potential, polarization, and electrostatic force. It makes the clarification of the driving mechanism challenging. A simple experimental system was used to observe the behavior of spherical ZrO2 microparticles in a nonaqueous solution under an electric field. The results suggest that the mechanism that drives the ZrO2 microparticles under an electric field involved the combination of an electric image force, a gradient force, and the contact charging phenomenon. A method is proposed to control the motion of micro- and nanostructures in further study and applications.

Systematic and Automated Development of Quantum Mechanically Derived Force Fields: The Challenging Case of Halogenated Hydrocarbons.

PubMed

Prampolini, Giacomo; Campetella, Marco; De Mitri, Nicola; Livotto, Paolo Roberto; Cacelli, Ivo

2016-11-08

A robust and automated protocol for the derivation of sound force field parameters, suitable for condensed-phase classical simulations, is here tested and validated on several halogenated hydrocarbons, a class of compounds for which standard force fields have often been reported to deliver rather inaccurate performances. The major strength of the proposed protocol is that all of the parameters are derived only from first principles because all of the information required is retrieved from quantum mechanical data, purposely computed for the investigated molecule. This a priori parametrization is carried out separately for the intra- and intermolecular contributions to the force fields, respectively exploiting the Joyce and Picky programs, previously developed in our group. To avoid high computational costs, all quantum mechanical calculations were performed exploiting the density functional theory. Because the choice of the functional is known to be crucial for the description of the intermolecular interactions, a specific procedure is proposed, which allows for a reliable benchmark of different functionals against higher-level data. The intramolecular and intermolecular contribution are eventually joined together, and the resulting quantum mechanically derived force field is thereafter employed in lengthy molecular dynamics simulations to compute several thermodynamic properties that characterize the resulting bulk phase. The accuracy of the proposed parametrization protocol is finally validated by comparing the computed macroscopic observables with the available experimental counterparts. It is found that, on average, the proposed approach is capable of yielding a consistent description of the investigated set, often outperforming the literature standard force fields, or at least delivering results of similar accuracy.

Recent Developments and Applications of the CHARMM force fields

PubMed Central

Zhu, Xiao; Lopes, Pedro E.M.; MacKerell, Alexander D.

2011-01-01

Empirical force fields commonly used to describe the condensed phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical (QM) methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds and new theoretical developments (eg. polarizable methods) make force-field development a dynamic domain of research. Accordingly, a number of improvements and extensions of the CHARMM force fields have occurred over the years. The objective of the present review is to provide an up-to-date overview of the CHARMM force fields. A limited presentation on the historical aspects of force fields will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable force fields, including examples of recent applications of those force fields. PMID:23066428

Evaluation of reactive force fields for prediction of the thermo-mechanical properties of cellulose Iâ

Treesearch

Fernando L. Dri; Xiawa Wu; Robert J. Moon; Ashlie Martini; Pablo D. Zavattieri

2015-01-01

Molecular dynamics simulation is commonly used to study the properties of nanocellulose-based materials at the atomic scale. It is well known that the accuracy of these simulations strongly depends on the force field that describes energetic interactions. However, since there is no force field developed specifically for cellulose, researchers utilize models...

The Model of Complex Structure of Quark

NASA Astrophysics Data System (ADS)

Liu, Rongwu

2017-09-01

In Quantum Chromodynamics, quark is known as a kind of point-like fundamental particle which carries mass, charge, color, and flavor, strong interaction takes place between quarks by means of exchanging intermediate particles-gluons. An important consequence of this theory is that, strong interaction is a kind of short-range force, and it has the features of ``asymptotic freedom'' and ``quark confinement''. In order to reveal the nature of strong interaction, the ``bag'' model of vacuum and the ``string'' model of string theory were proposed in the context of quantum mechanics, but neither of them can provide a clear interaction mechanism. This article formulates a new mechanism by proposing a model of complex structure of quark, it can be outlined as follows: (1) Quark (as well as electron, etc) is a kind of complex structure, it is composed of fundamental particle (fundamental matter mass and electricity) and fundamental volume field (fundamental matter flavor and color) which exists in the form of limited volume; fundamental particle lies in the center of fundamental volume field, forms the ``nucleus'' of quark. (2) As static electric force, the color field force between quarks has classical form, it is proportional to the square of the color quantity carried by each color field, and inversely proportional to the area of cross section of overlapping color fields which is along force direction, it has the properties of overlap, saturation, non-central, and constant. (3) Any volume field undergoes deformation when interacting with other volume field, the deformation force follows Hooke's law. (4) The phenomena of ``asymptotic freedom'' and ``quark confinement'' are the result of color field force and deformation force.

Analytic Solution of the Problem of Additive Formation of an Inhomogeneous Elastic Spherical Body in an Arbitrary Nonstationary Central Force Field

NASA Astrophysics Data System (ADS)

Parshin, D. A.

2017-09-01

We study the processes of additive formation of spherically shaped rigid bodies due to the uniform accretion of additional matter to their surface in an arbitrary centrally symmetric force field. A special case of such a field can be the gravitational or electrostatic force field. We consider the elastic deformation of the formed body. The body is assumed to be isotropic with elasticmoduli arbitrarily varying along the radial coordinate.We assume that arbitrary initial circular stresses can arise in the additional material added to the body in the process of its formation. In the framework of linear mechanics of growing bodies, the mathematical model of the processes under study is constructed in the quasistatic approximation. The boundary value problems describing the development of stress-strain state of the object under study before the beginning of the process and during the entire process of its formation are posed. The closed analytic solutions of the posed problems are constructed by quadratures for some general types of material inhomogeneity. Important typical characteristics of the mechanical behavior of spherical bodies additively formed in the central force field are revealed. These characteristics substantially distinguish such bodies from the already completely composed bodies similar in dimensions and properties which are placed in the force field and are described by problems of mechanics of deformable solids in the classical statement disregarding the mechanical aspects of additive processes.

Multiloop atom interferometer measurements of chameleon dark energy in microgravity

NASA Astrophysics Data System (ADS)

Chiow, Sheng-wey; Yu, Nan

2018-02-01

Chameleon field is one of the promising candidates of dark energy scalar fields. As in all viable candidate field theories, a screening mechanism is implemented to be consistent with all existing tests of general relativity. The screening effect in the chameleon theory manifests its influence limited only to the thin outer layer of a bulk object, thus producing extra forces orders of magnitude weaker than that of the gravitational force of the bulk. For pointlike particles such as atoms, the depth of screening is larger than the size of the particle, such that the screening mechanism is ineffective and the chameleon force is fully expressed on the atomic test particles. Extra force measurements using atom interferometry are thus much more sensitive than bulk mass based measurements, and indeed have placed the most stringent constraints on the parameters characterizing chameleon field. In this paper, we present a conceptual measurement approach for chameleon force detection using atom interferometry in microgravity, in which multiloop atom interferometers exploit specially designed periodic modulation of chameleon fields. We show that major systematics of the dark energy force measurements, i.e., effects of gravitational forces and their gradients, can be suppressed below all hypothetical chameleon signals in the parameter space of interest.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene III. 3,3-Dimethyl-1-(trimethylsilyl)cyclopropene

NASA Astrophysics Data System (ADS)

De Maré, G. R.; Panchenko, Yu. N.; Abramenkov, A. V.; Baird, M. S.; Tverezovsky, V. V.; Nizovtsev, A. V.; Bolesov, I. G.

2003-07-01

The experimental Raman and IR vibrational spectra of 3,3-dimethyl-1-(trimethylsilyl)cyclopropene in the liquid phase were recorded. Total geometry optimisation was carried out at the HF/6-31G* level and the HF/6-31G*//HF/6-31G* force field was computed. This force field was corrected by scale factors determined previously (using Pulay's method) for correction of the HF/6-31G*//HF/6-31G* force fields of 3,3-dimethylbutene-1, 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The theoretical vibrational frequencies calculated from the scaled quantum mechanical force field and the theoretical intensities obtained from the quantum mechanical calculation were used to construct predicted spectra and to perform the vibrational analysis of the experimental spectra.

Hierarchical atom type definitions and extensible all-atom force fields.

PubMed

Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

2016-03-15

The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

MMS Multipoint Analysis of the Dynamics, Evolution, and Particle Acceleration Mechanisms Inside FTEs at Earth's Subsolar Magnetopause

NASA Astrophysics Data System (ADS)

Akhavan-Tafti, M.; Slavin, J. A.; Eastwood, J. P.; Cassak, P.; Gershman, D. J.; Zhao, C.

2017-12-01

Flux Transfer Events (FTEs) are transient signatures of magnetic reconnection at the dayside magnetopause and play significant roles in determining the rate of reconnection and accelerating particles. This study investigates the magnetohydrodynamic forces inside and outside FTEs to infer the process through which these structures become force-free and uses electron dynamics to study the mechanisms for particle acceleration within the FTE. Akhavan-Tafti et al. [2017] demonstrated that ion-scale FTEs contain regions of elevated plasma density which greatly contribute to plasma pressure forces inside FTEs. It is shown that as FTEs evolve, the plasma is evacuated as the core magnetic field strengthens, hence becoming more force-free. The neighboring ion-scale FTEs formed at the subsolar magnetopause due to multiple X-line reconnection are forced to interact, and likely coalesce. Entropy is invoked to motivate the discussion on the essential role of coalescence in reconfiguring magnetic fields and current density distributions inside FTEs to allow for the adiabatic growth of these structures. Here, we present observational evidence which shows that, in the absence of coalescence, FTEs can become less force free. Local electron kinematics is studied to compare the contributions of parallel electric field, Fermi acceleration, and betatron acceleration mechanisms to particle heating. Acceleration due to parallel electric fields are shown to be dominant in the vicinity of the reconnection site while betatron acceleration controls perpendicular heating inside the FTE in the presence of magnetic pressure gradients. In the downstream of the reconnection site, the `freshly' reconnected field lines start to straighten due to the magnetic curvature force. Straightening field lines accelerate trapped electrons parallel to the local magnetic field (i.e., first-order Fermi acceleration). These acceleration mechanisms are shown to explain the observed anisotropic pitch angle distributions at the core and at the edges of FTEs. Finally, the forces inside non-flux rope-type FTEs (due to coalescence, expansion, contraction, or division) are shown to contribute to selective plasma heating, hence giving rise to anisotropic plasma temperatures and the subsequent wave activities (e.g. propagation of whistler waves).

Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.

PubMed

Saito, Minoru; Okazaki, Isao

2009-12-01

The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. (c) 2009 Wiley Periodicals, Inc.

Structural learning in feedforward and feedback control.

PubMed

Yousif, Nada; Diedrichsen, Jörn

2012-11-01

For smooth and efficient motor control, the brain needs to make fast corrections during the movement to resist possible perturbations. It also needs to adapt subsequent movements to improve future performance. It is important that both feedback corrections and feedforward adaptation need to be made based on noisy and often ambiguous sensory data. Therefore, the initial response of the motor system, both for online corrections and adaptive responses, is guided by prior assumptions about the likely structure of perturbations. In the context of correcting and adapting movements perturbed by a force field, we asked whether these priors are hard wired or whether they can be modified through repeated exposure to differently shaped force fields. We found that both feedback corrections to unexpected perturbations and feedforward adaptation to a new force field changed, such that they were appropriate to counteract the type of force field that participants had experienced previously. We then investigated whether these changes were driven by a common mechanism or by two separate mechanisms. Participants experienced force fields that were either temporally consistent, causing sustained adaptation, or temporally inconsistent, causing little overall adaptation. We found that the consistent force fields modified both feedback and feedforward responses. In contrast, the inconsistent force field modified the temporal shape of feedback corrections but not of the feedforward adaptive response. These results indicate that responses to force perturbations can be modified in a structural manner and that these modifications are at least partly dissociable for feedback and feedforward control.

Structural learning in feedforward and feedback control

PubMed Central

Diedrichsen, Jörn

2012-01-01

For smooth and efficient motor control, the brain needs to make fast corrections during the movement to resist possible perturbations. It also needs to adapt subsequent movements to improve future performance. It is important that both feedback corrections and feedforward adaptation need to be made based on noisy and often ambiguous sensory data. Therefore, the initial response of the motor system, both for online corrections and adaptive responses, is guided by prior assumptions about the likely structure of perturbations. In the context of correcting and adapting movements perturbed by a force field, we asked whether these priors are hard wired or whether they can be modified through repeated exposure to differently shaped force fields. We found that both feedback corrections to unexpected perturbations and feedforward adaptation to a new force field changed, such that they were appropriate to counteract the type of force field that participants had experienced previously. We then investigated whether these changes were driven by a common mechanism or by two separate mechanisms. Participants experienced force fields that were either temporally consistent, causing sustained adaptation, or temporally inconsistent, causing little overall adaptation. We found that the consistent force fields modified both feedback and feedforward responses. In contrast, the inconsistent force field modified the temporal shape of feedback corrections but not of the feedforward adaptive response. These results indicate that responses to force perturbations can be modified in a structural manner and that these modifications are at least partly dissociable for feedback and feedforward control. PMID:22896725

PRESSURE TRANSDUCER

DOEpatents

Sander, H.H.

1959-10-01

A pressure or mechanical force transducer particularly adaptable to miniature telemetering systems is described. Basically the device consists of a transistor located within a magnetic field adapted to change in response to mechanical force. The conduction characteristics of the transistor in turn vary proportionally with changes in the magnetic flux across the transistor such that the output (either frequency of amplitude) of the transistor circuit is proportional to mechanical force or pressure.

Screening fifth forces in k-essence and DBI models

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

Brax, Philippe; Burrage, Clare; Davis, Anne-Christine, E-mail: Philippe.Brax@cea.fr, E-mail: Clare.Burrage@nottingham.ac.uk, E-mail: A.C.Davis@damtp.cam.ac.uk

New fifth forces have not yet been detected in the laboratory or in the solar system, hence it is typically difficult to introduce new light scalar fields that would mediate such forces. In recent years it has been shown that a number of non-linear scalar field theories allow for a dynamical mechanism, such as the Vainshtein and chameleon ones, that suppresses the strength of the scalar fifth force in experimental environments. This is known as screening, however it is unclear how common screening is within non-linear scalar field theories. k-essence models are commonly studied examples of non-linear models, with DBImore » as the best motivated example, and so we ask whether these non-linearities are able to screen a scalar fifth force. We find that a Vainshtein-like screening mechanism exists for such models although with limited applicability. For instance, we cannot find a screening mechanism for DBI models. On the other hand, we construct a large class of k-essence models which lead to the acceleration of the Universe in the recent past for which the fifth force mediated by the scalar can be screened.« less

Detecting the gravitational sensitivity of Paramecium caudatum using magnetic forces

NASA Astrophysics Data System (ADS)

Guevorkian, Karine; Valles, James M., Jr.

2006-03-01

Under normal conditions, Paramecium cells regulate their swimming speed in response to the pN level mechanical force of gravity. This regulation, known as gravikinesis, is more pronounced when the external force is increased by methods such as centrifugation. Here we present a novel technique that simulates gravity fields using the interactions between strong inhomogeneous magnetic fields and cells. We are able to achieve variable gravities spanning from 10xg to -8xg; where g is earth's gravity. Our experiments show that the swimming speed regulation of Paramecium caudatum to magnetically simulated gravity is a true physiological response. In addition, they reveal a maximum propulsion force for paramecia. This advance establishes a general technique for applying continuously variable forces to cells or cell populations suitable for exploring their force transduction mechanisms.

Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins

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

Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie

2015-08-06

Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna–Matthews–Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbitalmore » (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CHARMM force field together with ZINDO/S or TDDFT always show a wider spread in the energy distribution compared to those using the AMBER force field. High- or low-energy tails in these energy distributions result in larger values for the spectral density at low frequencies. A detailed study on individual BChl a molecules in solution shows that without the environment, the density of states is the same for both force field sets. Including the environmental point charges, however, the excitation energy distribution gets broader and, depending on the applied methods, also asymmetric. The excitation energy distribution predicted using TDDFT together with the AMBER force field shows a symmetric, Gaussian-like distribution.« less

Algorithms to automate gap-dependent integral tuning for the 2.8-meter long horizontal field undulator with a dynamic force compensation mechanism

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

Xu, Joseph Z., E-mail: x@anl.gov; Vasserman, Isaac; Strelnikov, Nikita

2016-07-27

A 2.8-meter long horizontal field prototype undulator with a dynamic force compensation mechanism has been developed and tested at the Advanced Photon Source (APS) at Argonne National Laboratory (Argonne). The magnetic tuning of the undulator integrals has been automated and accomplished by applying magnetic shims. A detailed description of the algorithms and performance is reported.

Development and Comparison of Mechanical Structures for FNAL 15 T Nb$$_3$$Sn Dipole Demonstrator

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

Novitski, I.; Zlobin, A. V.

2016-11-08

Main design challenges for 15 T accelerator magnets are large Lorentz forces at this field level. The large Lorentz forces generate high stresses in the coil and mechanical structure and, thus, need stress control to maintain them at the acceptable level for brittle Nb3Sn coils and other elements of magnet mechanical structure. To provide these conditions and achieve the design field in the FNAL 15 T dipole demonstrator, several mechanical structures have been developed and analysed. The possibilities and limitations of these designs are discussed in this paper

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

PubMed Central

Vanommeslaeghe, K.

2014-01-01

Background Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. Scope of Review As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular bimolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields’ parametrization philosophy and methodology. Major Conclusions Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1 microsecond on proteins, DNA, lipids and carbohydrates. General Significance Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers a model that is an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. PMID:25149274

Experimental studies of protozoan response to intense magnetic fields and forces

NASA Astrophysics Data System (ADS)

Guevorkian, Karine

Intense static magnetic fields of up to 31 Tesla were used as a novel tool to manipulate the swimming mechanics of unicellular organisms. It is shown that homogenous magnetic fields alter the swimming trajectories of the single cell protozoan Paramecium caudatum, by aligning them parallel to the applied field. Immobile neutrally buoyant paramecia also oriented in magnetic fields with similar rates as the motile ones. It was established that the magneto-orientation is mostly due to the magnetic torques acting on rigid structures in the cell body and therefore the response is a non-biological, passive response. From the orientation rate of paramecia in various magnetic field strengths, the average anisotropy of the diamagnetic susceptibility of the cell was estimated. It has also been demonstrated that magnetic forces can be used to create increased, decreased and even inverted simulated gravity environments for the investigation of the gravi-responses of single cells. Since the mechanisms by which Earth's gravity affects cell functioning are still not fully understood, a number of methods to simulate different strength gravity environments, such as centrifugation, have been employed. Exploiting the ability to exert magnetic forces on weakly diamagnetic constituents of the cells, we were able to vary the gravity from -8 g to 10 g, where g is Earth's gravity. Investigations of the swimming response of paramecia in these simulated gravities revealed that they actively regulate their swimming speed to oppose the external force. This result is in agreement with centrifugation experiments, confirming the credibility of the technique. Moreover, the Paramecium's swimming ceased in simulated gravity of 10 g, indicating a maximum possible propulsion force of 0.7 nN. The magnetic force technique to simulate gravity is the only earthbound technique that can create increased and decreased simulated gravities in the same experimental setup. These findings establish a general technique for applying continuously variable forces to cells or cell populations suitable for exploring their force transduction mechanisms.

Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model.

PubMed

Mohebifar, Mohamad; Johnson, Erin R; Rowley, Christopher N

2017-12-12

London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquids-benzene, toluene, cyclohexane, n-pentane, and n-hexane-which resulted in improved accuracy in the computed enthalpies of vaporization despite only having to evaluate a much smaller section of the parameter space.

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

PubMed

Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

2013-09-01

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

Clinical Evidence for the Relationship between Nail Configuration and Mechanical Forces

PubMed Central

Ogawa, Rei

2014-01-01

Summary: Mechanobiology is an emerging field of science that focuses on the way physical forces and changes in cell or tissue mechanics contribute to development, physiology, and disease. As nails are always exposed to physical stimulation, mechanical forces may have a particularly pronounced effect on nail configuration and could be involved in the development of nail deformities. However, the role of mechanobiology in nail configuration and deformities has rarely been assessed. This review describes what is currently understood regarding the effect of mechanical force on nail configuration and deformities. On the basis of these observations, we hypothesize that nails have an automatic curvature function that allows them to adapt to the daily upward mechanical forces. Under normal conditions, the upward daily mechanical force and the automatic curvature force are well balanced. However, an imbalance between these 2 forces may cause nail deformation. For example, pincer nails may be caused by the absence of upward mechanical forces or a genetic propensity increase in the automatic curvature force, whereas koilonychias may occur when the upward mechanical force exceeds the automatic curvature force, thereby causing the nail to curve outward. This hypothesis is a new concept that could aid the development of innovative methods to prevent and treat nail deformities. PMID:25289309

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

PubMed

Vanommeslaeghe, K; MacKerell, A D

2015-05-01

Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular biomolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields' parametrization philosophy and methodology. Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1μs on proteins, DNA, lipids and carbohydrates. Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. This article is part of a Special Issue entitled "Recent developments of molecular dynamics". Copyright © 2014 Elsevier B.V. All rights reserved.

Force Field for Water Based on Neural Network.

PubMed

Wang, Hao; Yang, Weitao

2018-05-18

We developed a novel neural network based force field for water based on training with high level ab initio theory. The force field was built based on electrostatically embedded many-body expansion method truncated at binary interactions. Many-body expansion method is a common strategy to partition the total Hamiltonian of large systems into a hierarchy of few-body terms. Neural networks were trained to represent electrostatically embedded one-body and two-body interactions, which require as input only one and two water molecule calculations at the level of ab initio electronic structure method CCSD/aug-cc-pVDZ embedded in the molecular mechanics water environment, making it efficient as a general force field construction approach. Structural and dynamic properties of liquid water calculated with our force field show good agreement with experimental results. We constructed two sets of neural network based force fields: non-polarizable and polarizable force fields. Simulation results show that the non-polarizable force field using fixed TIP3P charges has already behaved well, since polarization effects and many-body effects are implicitly included due to the electrostatic embedding scheme. Our results demonstrate that the electrostatically embedded many-body expansion combined with neural network provides a promising and systematic way to build the next generation force fields at high accuracy and low computational costs, especially for large systems.

Small strain multiphase-field model accounting for configurational forces and mechanical jump conditions

NASA Astrophysics Data System (ADS)

Schneider, Daniel; Schoof, Ephraim; Tschukin, Oleg; Reiter, Andreas; Herrmann, Christoph; Schwab, Felix; Selzer, Michael; Nestler, Britta

2018-03-01

Computational models based on the phase-field method have become an essential tool in material science and physics in order to investigate materials with complex microstructures. The models typically operate on a mesoscopic length scale resolving structural changes of the material and provide valuable information about the evolution of microstructures and mechanical property relations. For many interesting and important phenomena, such as martensitic phase transformation, mechanical driving forces play an important role in the evolution of microstructures. In order to investigate such physical processes, an accurate calculation of the stresses and the strain energy in the transition region is indispensable. We recall a multiphase-field elasticity model based on the force balance and the Hadamard jump condition at the interface. We show the quantitative characteristics of the model by comparing the stresses, strains and configurational forces with theoretical predictions in two-phase cases and with results from sharp interface calculations in a multiphase case. As an application, we choose the martensitic phase transformation process in multigrain systems and demonstrate the influence of the local homogenization scheme within the transition regions on the resulting microstructures.

Nanofibre optic force transducers with sub-piconewton resolution via near-field plasmon–dielectric interactions

PubMed Central

Huang, Qian; Lee, Joon; Arce, Fernando Teran; Yoon, Ilsun; Angsantikul, Pavimol; Liu, Justin; Shi, Yuesong; Villanueva, Josh; Thamphiwatana, Soracha; Ma, Xuanyi; Zhang, Liangfang; Chen, Shaochen; Lal, Ratnesh; Sirbuly, Donald J.

2018-01-01

Ultrasensitive nanomechanical instruments, including the atomic force microscope (AFM)1–4 and optical and magnetic tweezers5–8, have helped shed new light on the complex mechanical environments of biological processes. However, it is difficult to scale down the size of these instruments due to their feedback mechanisms9, which, if overcome, would enable high-density nanomechanical probing inside materials. A variety of molecular force probes including mechanophores10, quantum dots11, fluorescent pairs12,13 and molecular rotors14–16 have been designed to measure intracellular stresses; however, fluorescence-based techniques can have short operating times due to photo-instability and it is still challenging to quantify the forces with high spatial and mechanical resolution. Here, we develop a compact nanofibre optic force transducer (NOFT) that utilizes strong near-field plasmon–dielectric interactions to measure local forces with a sensitivity of <200 fN. The NOFT system is tested by monitoring bacterial motion and heart-cell beating as well as detecting infrasound power in solution. PMID:29576804

Flexible Force Field Parameterization through Fitting on the Ab Initio-Derived Elastic Tensor

PubMed Central

2017-01-01

Constructing functional forms and their corresponding force field parameters for the metal–linker interface of metal–organic frameworks is challenging. We propose fitting these parameters on the elastic tensor, computed from ab initio density functional theory calculations. The advantage of this top-down approach is that it becomes evident if functional forms are missing when components of the elastic tensor are off. As a proof-of-concept, a new flexible force field for MIL-47(V) is derived. Negative thermal expansion is observed and framework flexibility has a negligible effect on adsorption and transport properties for small guest molecules. We believe that this force field parametrization approach can serve as a useful tool for developing accurate flexible force field models that capture the correct mechanical behavior of the full periodic structure. PMID:28661672

Electrostrictive Mechanism of Nanostructure Formation at Solid Surfaces Irradiated by Femtosecond Laser Pulses.

PubMed

Pavlyniuk, Oleg R; Datsyuk, Vitaly V

2016-12-01

The significance of the mechanical pressure of light in creation of laser-induced periodic surface structures (LIPSSs) is investigated. Distributions of the electrically induced normal pressure and tangential stress at the illuminated solid surface, as well as the field of volume electrostrictive forces, are calculated taking into account surface plasmon polariton (SPP) excitation. Based on these calculations, we predict surface destruction and structure formation due to inelastic deformations during single femtosecond pulses. The calculated fields of the electromagnetic forces are found to agree well with the experimental ripple structures. We thus conclude that the electrostrictive forces can explain the origin of the periodic ripple structures.

Chameleons with field-dependent couplings

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

Brax, Philippe; Bruck, Carsten van de; Mota, David F.

2010-10-15

Certain scalar-tensor theories exhibit the so-called chameleon mechanism, whereby observational signatures of scalar fields are hidden by a combination of self-interactions and interactions with ambient matter. Not all scalar-tensor theories exhibit such a chameleon mechanism, which has been originally found in models with inverse power runaway potentials and field-independent couplings to matter. In this paper we investigate field theories with field-dependent couplings and a power-law potential for the scalar field. We show that the theory indeed is a chameleon field theory. We find the thin-shell solution for a spherical body and investigate the consequences for Eoet-Wash experiments, fifth-force searches andmore » Casimir-force experiments. Requiring that the scalar field evades gravitational tests, we find that the coupling is sensitive to a mass scale which is of order of the Hubble scale today.« less

The mechanisms of the effects of magnetic fields on cells

NASA Astrophysics Data System (ADS)

Kondrachuk, A.

The evolution of organisms in conditions of the Earth magnetism results in close dependence of their functioning on the properties of the Earth magnetic field. The magnetic conditions in space flight differ from those on the Earth (e.g. much smaller values of magnetic filed) that effect various processes in living organisms. Meanwhile the mechanisms of interaction of magnetic fields with cell structures are poorly understood and systemized. The goal of the present work is to analyze and estimate the main established mechanisms of "magnetic fields - cell" interaction. Due to variety and complexity of the effects the analysis is mainly restricted to biological effects of the static magnetic field at a cellular level. 1) Magnetic induction. Static magnetic fields exert forces on moving ions in solution (e.g., electrolytes), giving rise to induced electric fields and currents. This effect may be especially important when the currents changed due to the magnetic field application are participating in some receptor functions of cells (e.g. plant cells). 2) Magneto-mechanical effect of reorientation. Uniform static magnetic fields produce torques on certain molecules with anisotropic magnetic properties, which results in their reorientation and spatial ordering. Since the structures of biological cells are magnetically and mechanically inhomogeneous, the application of a homogeneous magnetic field may cause redistribution of stresses within cells, deformation of intracellular structures, change of membrane permeability, etc. 3) Ponderomotive effects. Spatially non-uniform magnetic field exerts ponderomotive force on magnetically non-uniform cell structures. This force is proportional to the gradient of the square of magnetic field and the difference of magnetic susceptibilities of the component of the cell and its environment. 4) Biomagnetic effects. Magnetic fields can exert torques and translational forces on ferromagnetic structures, such as magnetite and ferritins presented in the cells. 5) Electronic interactions. Static magnetic fields can alter energy levels and spin orientation of electrons. Similar interactions can also occur with nuclear spins, but these are very weak compared to electron interactions. 6) Free radicals. Magnetic fields alter the spin states of the radicals, which, in turn, changes the relative probabilities of recombination and other interactions, possibly with biological consequences. 7) Non-linear effects. A number of non-linear mechanisms of magnetic effects on cells were recently proposed to explain how the cell could extract a weak magnetic signal from noise (e.g. stochastic non-linear resonance, self-tuned Hopf bifurcations). These new models need further experimental testing.

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

PubMed

Yildirim, Ilyas; Stern, Harry A; Kennedy, Scott D; Tubbs, Jason D; Turner, Douglas H

2010-05-11

A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

Elongated Nanoparticle Aggregates in Cancer Cells for Mechanical Destruction with Low Frequency Rotating Magnetic Field.

PubMed

Shen, Yajing; Wu, Congyu; Uyeda, Taro Q P; Plaza, Gustavo R; Liu, Bin; Han, Yu; Lesniak, Maciej S; Cheng, Yu

2017-01-01

Magnetic nanoparticles (MNPs) functionalized with targeting moieties can recognize specific cell components and induce mechanical actuation under magnetic field. Their size is adequate for reaching tumors and targeting cancer cells. However, due to the nanometric size, the force generated by MNPs is smaller than the force required for largely disrupting key components of cells. Here, we show the magnetic assembly process of the nanoparticles inside the cells, to form elongated aggregates with the size required to produce elevated mechanical forces. We synthesized iron oxide nanoparticles doped with zinc, to obtain high magnetization, and functionalized with the epidermal growth factor (EGF) peptide for targeting cancer cells. Under a low frequency rotating magnetic field at 15 Hz and 40 mT, the internalized EGF-MNPs formed elongated aggregates and generated hundreds of pN to dramatically damage the plasma and lysosomal membranes. The physical disruption, including leakage of lysosomal hydrolases into the cytosol, led to programmed cell death and necrosis. Our work provides a novel strategy of designing magnetic nanomedicines for mechanical destruction of cancer cells.

Elongated Nanoparticle Aggregates in Cancer Cells for Mechanical Destruction with Low Frequency Rotating Magnetic Field

PubMed Central

Shen, Yajing; Wu, Congyu; Uyeda, Taro Q. P.; Plaza, Gustavo R.; Liu, Bin; Han, Yu; Lesniak, Maciej S.; Cheng, Yu

2017-01-01

Magnetic nanoparticles (MNPs) functionalized with targeting moieties can recognize specific cell components and induce mechanical actuation under magnetic field. Their size is adequate for reaching tumors and targeting cancer cells. However, due to the nanometric size, the force generated by MNPs is smaller than the force required for largely disrupting key components of cells. Here, we show the magnetic assembly process of the nanoparticles inside the cells, to form elongated aggregates with the size required to produce elevated mechanical forces. We synthesized iron oxide nanoparticles doped with zinc, to obtain high magnetization, and functionalized with the epidermal growth factor (EGF) peptide for targeting cancer cells. Under a low frequency rotating magnetic field at 15 Hz and 40 mT, the internalized EGF-MNPs formed elongated aggregates and generated hundreds of pN to dramatically damage the plasma and lysosomal membranes. The physical disruption, including leakage of lysosomal hydrolases into the cytosol, led to programmed cell death and necrosis. Our work provides a novel strategy of designing magnetic nanomedicines for mechanical destruction of cancer cells. PMID:28529648

Analysis of the mechanical behavior of single wall carbon nanotubes by a modified molecular structural mechanics model incorporating an advanced chemical force field

NASA Astrophysics Data System (ADS)

Eberhardt, Oliver; Wallmersperger, Thomas

2018-03-01

The outstanding properties of carbon nanotubes (CNTs) keep attracting the attention of researchers from different fields. CNTs are promising candidates for applications e.g. in lightweight construction but also in electronics, medicine and many more. The basis for the realization of the manifold applications is a detailed knowledge of the material properties of the carbon nanotubes. In particular for applications in lightweight constructions or in composites, the knowledge of the mechanical behavior of the CNTs is of vital interest. Hence, a lot of effort is put into the experimental and theoretical determination of the mechanical material properties of CNTs. Due to their small size, special techniques have to be applied. In this research, a modified molecular structural mechanics model for the numerical determination of the mechanical behavior of carbon nanotubes is presented. It uses an advanced approach for the geometrical representation of the CNT structure while the covalent bonds in the CNTs are represented by beam elements. Furthermore, the model is specifically designed to overcome major drawbacks in existing molecular structural mechanics models. This includes energetic consistency with the underlying chemical force field. The model is developed further to enable the application of a more advanced chemical force field representation. The developed model is able to predict, inter alia, the lateral and radial stiffness properties of the CNTs. The results for the lateral stiffness are given and discussed in order to emphasize the progress made with the presented approach.

Magnetic Nanotweezers for Interrogating Biological Processes in Space and Time.

PubMed

Kim, Ji-Wook; Jeong, Hee-Kyung; Southard, Kaden M; Jun, Young-Wook; Cheon, Jinwoo

2018-04-17

The ability to sense and manipulate the state of biological systems has been extensively advanced during the past decade with the help of recent developments in physical tools. Unlike standard genetic and pharmacological perturbation techniques-knockdown, overexpression, small molecule inhibition-that provide a basic on/off switching capability, these physical tools provide the capacity to control the spatial, temporal, and mechanical properties of the biological targets. Among the various physical cues, magnetism offers distinct advantages over light or electricity. Magnetic fields freely penetrate biological tissues and are already used for clinical applications. As one of the unique features, magnetic fields can be transformed into mechanical stimuli which can serve as a cue in regulating biological processes. However, their biological applications have been limited due to a lack of high-performance magnetism-to-mechanical force transducers with advanced spatiotemporal capabilities. In this Account, we present recent developments in magnetic nanotweezers (MNTs) as a useful tool for interrogating the spatiotemporal control of cells in living tissue. MNTs are composed of force-generating magnetic nanoparticles and field generators. Through proper design and the integration of individual components, MNTs deliver controlled mechanical stimulation to targeted biomolecules at any desired space and time. We first discuss about MNT configuration with different force-stimulation modes. By modulating geometry of the magnetic field generator, MNTs exert pulling, dipole-dipole attraction, and rotational forces to the target specifically and quantitatively. We discuss the key physical parameters determining force magnitude, which include magnetic field strength, magnetic field gradient, magnetic moment of the magnetic particle, as well as distance between the field generator and the particle. MNTs also can be used over a wide range of biological time scales. By simply adjusting the amplitude and phase of the applied current, MNTs based on electromagnets allow for dynamic control of the magnetic field from microseconds to hours. Chemical design and the nanoscale effects of magnetic particles are also essential for optimizing MNT performance. We discuss key strategies to develop magnetic nanoparticles with improved force-generation capabilities with a particular focus on the effects of size, shape, and composition of the nanoparticles. We then introduce various strategies and design considerations for target-specific biomechanical stimulations with MNTs. One-to-one particle-receptor engagement for delivering a defined force to the targeted receptor and the small size of the nanoparticles are important. Finally, we demonstrate the utility of MNTs for manipulating biological functions and activities with various spatial (single molecule/cell to organisms) and temporal resolution (microseconds to days). MNTs have the potential to be utilized in many exciting applications across diverse biological systems spanning from fundamental biology investigations of spatial and mechanical signaling dynamics at the single-cell and systems levels to in vivo therapeutic applications.

Apparatus having reduced mechanical forces for supporting high magnetic fields

DOEpatents

Prueitt, Melvin L.; Mueller, Fred M.; Smith, James L.

1991-01-01

The present invention identifies several configurations of conducting elements capable of supporting extremely high magnetic fields suitable for plasma confinement, wherein forces experienced by the conducting elements are significantly reduced over those which are present as a result of the generation of such high fields by conventional techniques. It is anticipated that the use of superconducting materials will both permit the attainment of such high fields and further permit such fields to be generated with vastly improved efficiency.

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

PubMed

Cole, Daniel J; Vilseck, Jonah Z; Tirado-Rives, Julian; Payne, Mike C; Jorgensen, William L

2016-05-10

Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme.

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

PubMed Central

Lange, Oliver F.; van der Spoel, David; de Groot, Bert L.

2010-01-01

Abstract Protein dynamics on the atomic level and on the microsecond timescale has recently become accessible from both computation and experiment. To validate molecular dynamics (MD) at the submicrosecond timescale against experiment we present microsecond MD simulations in 10 different force-field configurations for two globular proteins, ubiquitin and the gb3 domain of protein G, for which extensive NMR data is available. We find that the reproduction of the measured NMR data strongly depends on the chosen force field and electrostatics treatment. Generally, particle-mesh Ewald outperforms cut-off and reaction-field approaches. A comparison to measured J-couplings across hydrogen bonds suggests that there is room for improvement in the force-field description of hydrogen bonds in most modern force fields. Our results show that with current force fields, simulations beyond hundreds of nanoseconds run an increased risk of undergoing transitions to nonnative conformational states or will persist within states of high free energy for too long, thus skewing the obtained population frequencies. Only for the AMBER99sb force field have such transitions not been observed. Thus, our results have significance for the interpretation of data obtained with long MD simulations, for the selection of force fields for MD studies and for force-field development. We hope that this comprehensive benchmark based on NMR data applied to many popular MD force fields will serve as a useful resource to the MD community. Finally, we find that for gb3, the force-field AMBER99sb reaches comparable accuracy in back-calculated residual dipolar couplings and J-couplings across hydrogen bonds to ensembles obtained by refinement against NMR data. PMID:20643085

Improved side-chain torsion potentials for the Amber ff99SB protein force field

PubMed Central

Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L; Dror, Ron O; Shaw, David E

2010-01-01

Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20408171

Nature of the electromagnetic force between classical magnetic dipoles

NASA Astrophysics Data System (ADS)

Mansuripur, Masud

2017-09-01

The Lorentz force law of classical electrodynamics states that the force 𝑭𝑭 exerted by the magnetic induction 𝑩𝑩 on a particle of charge 𝑞𝑞 moving with velocity 𝑽𝑽 is given by 𝑭𝑭 = 𝑞𝑞𝑽𝑽 × 𝑩𝑩. Since this force is orthogonal to the direction of motion, the magnetic field is said to be incapable of performing mechanical work. Yet there is no denying that a permanent magnet can readily perform mechanical work by pushing/pulling on another permanent magnet or by attracting pieces of magnetizable material such as scrap iron or iron filings. We explain this apparent contradiction by examining the magnetic Lorentz force acting on an Amperian current loop, which is the model for a magnetic dipole. We then extend the discussion by analyzing the Einstein-Laub model of magnetic dipoles in the presence of external magnetic fields.

Interaction Forces Between Multiple Bodies in a Magnetic Field

NASA Technical Reports Server (NTRS)

Joffe, Benjamin

1996-01-01

Some of the results from experiments to determine the interaction forces between multiple bodies in a magnetic field are presented in this paper. It is shown how the force values and the force directions depend on the configuration of the bodies, their relative positions to each other, and the vector of the primary magnetic field. A number of efficient new automatic loading and assembly machines, as well as manipulators and robots, have been created based on the relationship between bodies and magnetic fields. A few of these patented magnetic devices are presented. The concepts involved open a new way to design universal grippers for robot and other kinds of mechanisms for the manipulation of objects. Some of these concepts can be used for space applications.

Is the 2nd Law of Thermodynamics Conditioned? Separating Heat and Cold by a Magnetic Body Force and the Principle for a Non-Carnot Engine

NASA Astrophysics Data System (ADS)

Luo, Weili

2017-11-01

A new type of heat engine has been proposed in 2005 that defies fundamental thermodynamic law: A specifically designed magnetic body force can reverse heat flow from high temperature to low temperature. This mechanism can drive heat to higher temperature, rendering the possibility to re-use the ``waste heat''. As the result, the efficiency is much higher than that of the Carnot Engine. In a recent paper a realization of this proposed mechanism is reported: by using a specific configuration of temperature and magnetic field gradients, we observed that magnetic body force suppresses the gravito-thermal convective heat when the gradients of temperature and field are anti-parallel to each other. This driving force stops the heat flow of approaching to thermal equilibrium in the system, causing the temperature difference across the sample to increase with applied fields. In this work, I will discuss the driving mechanism for this phenomenon and its application in the proposed engine. This remarkable result suggests that the 2nd law of thermodynamics maybe conditioned and needs to be re-examined.

Mechanisms explaining Coulomb's electric force & Lorentz's magnetic force from a classical perspective

NASA Astrophysics Data System (ADS)

Correnti, Dan S.

2018-06-01

The underlying mechanisms of the fundamental electric and magnetic forces are not clear in current models; they are mainly mathematical constructs. This study examines the underlying physics from a classical viewpoint to explain Coulomb's electric force and Lorentz's magnetic force. This is accomplished by building upon already established physics. Although no new physics is introduced, extension of existing models is made by close examination. We all know that an electron carries a bound cylindrical B-field (CBF) as it translates. Here, we show how the electron CBF plays an intrinsic role in the generation of the electric and magnetic forces.

Functional tooth restoration utilising split germs through re-regionalisation of the tooth-forming field

PubMed Central

Yamamoto, Naomi; Oshima, Masamitsu; Tanaka, Chie; Ogawa, Miho; Nakajima, Kei; Ishida, Kentaro; Moriyama, Keiji; Tsuji, Takashi

2015-01-01

The tooth is an ectodermal organ that arises from a tooth germ under the regulation of reciprocal epithelial-mesenchymal interactions. Tooth morphogenesis occurs in the tooth-forming field as a result of reaction-diffusion waves of specific gene expression patterns. Here, we developed a novel mechanical ligation method for splitting tooth germs to artificially regulate the molecules that control tooth morphology. The split tooth germs successfully developed into multiple correct teeth through the re-regionalisation of the tooth-forming field, which is regulated by reaction-diffusion waves in response to mechanical force. Furthermore, split teeth erupted into the oral cavity and restored physiological tooth function, including mastication, periodontal ligament function and responsiveness to noxious stimuli. Thus, this study presents a novel tooth regenerative technology based on split tooth germs and the re-regionalisation of the tooth-forming field by artificial mechanical force. PMID:26673152

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

PubMed

Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

2011-07-01

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

Dynamics of elastic interactions in soft and biological matter.

PubMed

Yuval, Janni; Safran, Samuel A

2013-04-01

Cells probe their mechanical environment and can change the organization of their cytoskeletons when the elastic and viscous properties of their environment are modified. We use a model in which the forces exerted by small, contractile acto-myosin filaments (e.g., nascent stress fibers in stem cells) on the extracellular matrix are modeled as local force dipoles. In some cases, the strain field caused by these force dipoles propagates quickly enough so that only static elastic interactions need be considered. On the other hand, in the case of significant energy dissipation, strain propagation is slower and may be eliminated completely by the relaxation of the cellular cytoskeleton (e.g., by cross-link dissociation). Here, we consider several dissipative mechanisms that affect the propagation of the strain field in adhered cells and consider these effects on the interaction between force dipoles and their resulting mutual orientations. This is a first step in understanding the development of orientational (nematic) or layering (smectic) order in the cytoskeleton. We use the theory to estimate the propagation time of the strain fields over a cellular distance for different mechanisms and find that in some cases it can be of the order of seconds, thus competing with the cytoskeletal relaxation time. Furthermore, for a simple system of two force dipoles, we predict that in some cases the orientation of force dipoles might change significantly with time, e.g., for short times the dipoles exhibit parallel alignment while for later times they align perpendicularly.

Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

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

Gao, Weimin; Niu, Haitao; Lin, Tong

2014-01-28

The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform externalmore » electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.« less

The essence of the Blandford-Znajek process

NASA Astrophysics Data System (ADS)

Kinoshita, Shunichiro; Igata, Takahisa

2018-03-01

From a spacetime perspective, the dynamics of magnetic field lines of force-free electromagnetic fields can be rewritten into a quite similar form for the dynamics of strings, i.e., dynamics of "field sheets". Using this formalism, we explicitly show that the field sheets of stationary and axisymmetric force-free electromagnetic fields have identical intrinsic properties to the world sheets of rigidly rotating Nambu-Goto strings. Thus, we conclude that the Blandford-Znajek process is kinematically identical to an energy-extraction mechanism by the Nambu-Goto string with an effective magnetic tension.

Euler force actuation mechanism for siphon valving in compact disk-like microfluidic chips.

PubMed

Deng, Yongbo; Fan, Jianhua; Zhou, Song; Zhou, Teng; Wu, Junfeng; Li, Yin; Liu, Zhenyu; Xuan, Ming; Wu, Yihui

2014-03-01

Based on the Euler force induced by the acceleration of compact disk (CD)-like microfluidic chip, this paper presents a novel actuation mechanism for siphon valving. At the preliminary stage of acceleration, the Euler force in the tangential direction of CD-like chip takes the primary place compared with the centrifugal force to function as the actuation of the flow, which fills the siphon and actuates the siphon valving. The Euler force actuation mechanism is demonstrated by the numerical solution of the phase-field based mathematical model for the flow in siphon valve. In addition, experimental validation is implemented in the polymethylmethacrylate-based CD-like microfluidic chip manufactured using CO2 laser engraving technique. To prove the application of the proposed Euler force actuation mechanism, whole blood separation and plasma extraction has been conducted using the Euler force actuated siphon valving. The newly introduced actuation mechanism overcomes the dependence on hydrophilic capillary filling of siphon by avoiding external manipulation or surface treatments of polymeric material. The sacrifice for highly integrated processing in pneumatic pumping technique is also prevented by excluding the volume-occupied compressed air chamber.

Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

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

Wang, Xianwei; State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062; Zhang, John Z. H.

2015-11-14

Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. Inmore » this study, quantum mechanical calculation of protein’s internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.« less

Unsteady hydrodynamic forces acting on a robotic arm and its flow field: application to the crawl stroke.

PubMed

Takagi, Hideki; Nakashima, Motomu; Ozaki, Takashi; Matsuuchi, Kazuo

2014-04-11

This study aims to clarify the mechanisms by which unsteady hydrodynamic forces act on the hand of a swimmer during a crawl stroke. Measurements were performed for a hand attached to a robotic arm with five degrees of freedom independently controlled by a computer. The computer was programmed so the hand and arm mimicked a human performing the stroke. We directly measured forces on the hand and pressure distributions around it at 200 Hz; flow fields underwater near the hand were obtained via 2D particle image velocimetry (PIV). The data revealed two mechanisms that generate unsteady forces during a crawl stroke. One is the unsteady lift force generated when hand movement changes direction during the stroke, leading to vortex shedding and bound vortex created around it. This bound vortex circulation results in a lift that contributes to the thrust. The other occurs when the hand moves linearly with a large angle of attack, creating a Kármán vortex street. This street alternatively sheds clockwise and counterclockwise vortices, resulting in a quasi-steady drag contributing to the thrust. We presume that professional swimmers benefit from both mechanisms. Further studies are necessary in which 3D flow fields are measured using a 3D PIV system and a human swimmer. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments.

PubMed

Rinkevicius, Zilvinas; Li, Xin; Sandberg, Jaime A R; Mikkelsen, Kurt V; Ågren, Hans

2014-03-11

We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

Mechanical properties of biological specimens explored by atomic force microscopy

NASA Astrophysics Data System (ADS)

Kasas, S.; Longo, G.; Dietler, G.

2013-04-01

The atomic force microscope is a widely used surface scanning apparatus capable of reconstructing at a nanometric scale resolution the 3D morphology of biological samples. Due to its unique sensitivity, it is now increasingly used as a force sensor, to characterize the mechanical properties of specimens with a similar lateral resolution. This unique capability has produced, in the last years, a vast increase in the number of groups that have exploited the versatility and sensitivity of the instrument to explore the nanomechanics of various samples in the fields of biology, microbiology and medicine. In this review we outline the state of the art in this field, reporting the most interesting recent works involving the exploration of the nanomechanical properties of various biological samples.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

PubMed Central

Neumann, Marcus A.

2017-01-01

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations. PMID:28250956

Accurate van der Waals force field for gas adsorption in porous materials.

PubMed

Sun, Lei; Yang, Li; Zhang, Ya-Dong; Shi, Qi; Lu, Rui-Feng; Deng, Wei-Qiao

2017-09-05

An accurate van der Waals force field (VDW FF) was derived from highly precise quantum mechanical (QM) calculations. Small molecular clusters were used to explore van der Waals interactions between gas molecules and porous materials. The parameters of the accurate van der Waals force field were determined by QM calculations. To validate the force field, the prediction results from the VDW FF were compared with standard FFs, such as UFF, Dreiding, Pcff, and Compass. The results from the VDW FF were in excellent agreement with the experimental measurements. This force field can be applied to the prediction of the gas density (H 2 , CO 2 , C 2 H 4 , CH 4 , N 2 , O 2 ) and adsorption performance inside porous materials, such as covalent organic frameworks (COFs), zeolites and metal organic frameworks (MOFs), consisting of H, B, N, C, O, S, Si, Al, Zn, Mg, Ni, and Co. This work provides a solid basis for studying gas adsorption in porous materials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Molecular modeling studies of structural properties of polyvinyl alcohol: a comparative study using INTERFACE force field.

PubMed

Radosinski, Lukasz; Labus, Karolina

2017-10-05

Polyvinyl alcohol (PVA) is a material with a variety of applications in separation, biotechnology, and biomedicine. Using combined Monte Carlo and molecular dynamics techniques, we present an extensive comparative study of second- and third-generation force fields Universal, COMPASS, COMPASS II, PCFF, and the newly developed INTERFACE, as applied to this system. In particular, we show that an INTERFACE force field provides a possibility of composing a reliable atomistic model to reproduce density change of PVA matrix in a narrow temperature range (298-348 K) and calculate a thermal expansion coefficient with reasonable accuracy. Thus, the INTERFACE force field may be used to predict mechanical properties of the PVA system, being a scaffold for hydrogels, with much greater accuracy than latter approaches. Graphical abstract Molecular Dynamics and Monte Carlo studies indicate that it is possible to predict properties of the PVA in narrow temperature range by using the INTERFACE force field.

Laser-pulse shape effects on magnetic field generation in underdense plasmas

NASA Astrophysics Data System (ADS)

Gopal, Krishna; Raja, Md. Ali; Gupta, Devki Nandan; Avinash, K.; Sharma, Suresh C.

2018-07-01

Laser pulse shape effect has been considered to estimate the self-generated magnetic field in laser-plasma interaction. A ponderomotive force based physical mechanism has been proposed to investigate the self-generated magnetic field for different spatial profiles of the laser pulse in inhomogeneous plasmas. The spatially inhomogeneous electric field of a laser pulse imparts a stronger ponderomotive force on plasma electrons. Thus, the stronger ponderomotive force associated with the asymmetric laser pulse generates a stronger magnetic field in comparison to the case of a symmetric laser pulse. Scaling laws for magnetic field strength with the laser and plasma parameters for different shape of the pulse have been suggested. Present study might be helpful to understand the plasma dynamics relevant to the particle trapping and injection in laser-plasma accelerators.

Applying the new HIT results to tokamak and solar plasmas

NASA Astrophysics Data System (ADS)

Jarboe, Thomas; Sutherland, Derek; Hossack, Aaron; Nelson, Brian; Morgan, Kyle; Chris, Hansen; Benedett, Thomas; Everson, Chris; Penna, James

2016-10-01

Understanding sustainment of stable equilibria with helicity injection in HIT-SI has led to a simple picture of several tokamak features. Perturbations cause a viscous-like force on the current that flattens the λ profile, which sustains and stabilizes the equilibrium. An explanation of the mechanism is based on two properties of stable, ideal, two-fluid, magnetized plasma. First, the electron fluid is frozen to magnetic fields and, therefore, current flow is also magnetic field flow. Second, for a stable equilibrium the structure perpendicular to the flux surface resists deformation. Thus toroidal current is from electrons frozen in nested, rotating resilient flux surfaces. Only symmetric flux surfaces allow free differential current flow. Perturbations cause interference of the flux surfaces. Thus, perturbations cause forces that oppose differential electron rotation and forced differential flow produces a symmetrizing force against perturbations and instability. This mechanism can explain the level of field error that spoils tokamak performance and the rate of poloidal flux loss in argon-induced disruptions in DIII-D. This new understanding has led to an explanation of the source of the solar magnetic fields and the power source for the chromosphere, solar wind and corona. Please place in spheromak and FRC section with other HIT posters.

Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4+ Interactions.

PubMed

Khan, Hanif M; Grauffel, Cédric; Broer, Ria; MacKerell, Alexander D; Havenith, Remco W A; Reuter, Nathalie

2016-11-08

Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH 3 ) 3 ) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/aug-cc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-π interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-π interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants.

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

PubMed

Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

2010-07-28

Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

An improved DNA force field for ssDNA interactions with gold nanoparticles

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

Jiang, Xiankai; Huai, Ping; Fan, Chunhai

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones “protecting” hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thusmore » the “protection” by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.« less

An improved DNA force field for ssDNA interactions with gold nanoparticles

NASA Astrophysics Data System (ADS)

Jiang, Xiankai; Gao, Jun; Huynh, Tien; Huai, Ping; Fan, Chunhai; Zhou, Ruhong; Song, Bo

2014-06-01

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

An improved DNA force field for ssDNA interactions with gold nanoparticles.

PubMed

Jiang, Xiankai; Gao, Jun; Huynh, Tien; Huai, Ping; Fan, Chunhai; Zhou, Ruhong; Song, Bo

2014-06-21

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

Coherent Two-Mode Dynamics of a Nanowire Force Sensor

NASA Astrophysics Data System (ADS)

Braakman, Floris R.; Rossi, Nicola; Tütüncüoglu, Gözde; Morral, Anna Fontcuberta i.; Poggio, Martino

2018-05-01

Classically coherent dynamics analogous to those of quantum two-level systems are studied in the setting of force sensing. We demonstrate quantitative control over the coupling between two orthogonal mechanical modes of a nanowire cantilever through measurement of avoided crossings as we deterministically position the nanowire inside an electric field. Furthermore, we demonstrate Rabi oscillations between the two mechanical modes in the strong-coupling regime. These results give prospects of implementing coherent two-mode control techniques for force-sensing signal enhancement.

Magnetic domain wall tweezers: a new tool for mechanobiology studies on individual target cells.

PubMed

Monticelli, M; Conca, D V; Albisetti, E; Torti, A; Sharma, P P; Kidiyoor, G; Barozzi, S; Parazzoli, D; Ciarletta, P; Lupi, M; Petti, D; Bertacco, R

2016-08-07

In vitro tests are of fundamental importance for investigating cell mechanisms in response to mechanical stimuli or the impact of the genotype on cell mechanical properties. In particular, the application of controlled forces to activate specific bio-pathways and investigate their effects, mimicking the role of the cellular environment, is becoming a prominent approach in the emerging field of mechanobiology. Here, we present an on-chip device based on magnetic domain wall manipulators, which allows the application of finely controlled and localized forces on target living cells. In particular, we demonstrate the application of a magnetic force in the order of hundreds of pN on the membrane of HeLa cells cultured on-chip, via manipulation of 1 μm superparamagnetic beads. Such a mechanical stimulus produces a sizable local indentation of the cellular membrane of about 2 μm. Upon evaluation of the beads' position within the magnetic field originated by the domain wall, the force applied during the experiments is accurately quantified via micromagnetic simulations. The obtained value is in good agreement with that calculated by the application of an elastic model to the cellular membrane.

A finite element study on the mechanical response of the head-neck interface of hip implants under realistic forces and moments of daily activities: Part 1, level walking.

PubMed

Farhoudi, Hamidreza; Fallahnezhad, Khosro; Oskouei, Reza H; Taylor, Mark

2017-11-01

This paper investigates the mechanical response of a modular head-neck interface of hip joint implants under realistic loads of level walking. The realistic loads of the walking activity consist of three dimensional gait forces and the associated frictional moments. These forces and moments were extracted for a 32mm metal-on-metal bearing couple. A previously reported geometry of a modular CoCr/CoCr head-neck interface with a proximal contact was used for this investigation. An explicit finite element analysis was performed to investigate the interface mechanical responses. To study the level of contribution and also the effect of superposition of the load components, three different scenarios of loading were studied: gait forces only, frictional moments only, and combined gait forces and frictional moments. Stress field, micro-motions, shear stresses and fretting work at the contacting nodes of the interface were analysed. Gait forces only were found to significantly influence the mechanical environment of the head-neck interface by temporarily extending the contacting area (8.43% of initially non-contacting surface nodes temporarily came into contact), and therefore changing the stress field and resultant micro-motions during the gait cycle. The frictional moments only did not cause considerable changes in the mechanical response of the interface (only 0.27% of the non-contacting surface nodes temporarily came into contact). However, when superposed with the gait forces, the mechanical response of the interface, particularly micro-motions and fretting work, changed compared to the forces only case. The normal contact stresses and micro-motions obtained from this realistic load-controlled study were typically in the range of 0-275MPa and 0-38µm, respectively. These ranges were found comparable to previous experimental displacement-controlled pin/cylinder-on-disk fretting corrosion studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantum mechanical/molecular mechanical/continuum style solvation model: second order Møller-Plesset perturbation theory.

PubMed

Thellamurege, Nandun M; Si, Dejun; Cui, Fengchao; Li, Hui

2014-05-07

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.

Using atom interferometry to detect dark energy

NASA Astrophysics Data System (ADS)

Burrage, Clare; Copeland, Edmund J.

2016-04-01

We review the tantalising prospect that the first evidence for the dark energy driving the observed acceleration of the universe on giga-parsec scales may be found through metre scale laboratory-based atom interferometry experiments. To do that, we first introduce the idea that scalar fields could be responsible for dark energy and show that in order to be compatible with fifth force constraints, these fields must have a screening mechanism which hides their effects from us within the solar system. Particular emphasis is placed on one such screening mechanism known as the chameleon effect where the field's mass becomes dependent on the environment. The way the field behaves in the presence of a spherical source is determined and we then go on to show how in the presence of the kind of high vacuum associated with atom interferometry experiments, and when the test particle is an atom, it is possible to use the associated interference pattern to place constraints on the acceleration due to the fifth force of the chameleon field - this has already been used to rule out large regions of the chameleon parameter space and maybe one day will be able to detect the force due to the dark energy field in the laboratory.

Force field dependent solution properties of glycine oligomers

PubMed Central

Drake, Justin A.

2015-01-01

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623

Feedforward compensation for novel dynamics depends on force field orientation but is similar for the left and right arms.

PubMed

Reuter, Eva-Maria; Cunnington, Ross; Mattingley, Jason B; Riek, Stephan; Carroll, Timothy J

2016-11-01

There are well-documented differences in the way that people typically perform identical motor tasks with their dominant and the nondominant arms. According to Yadav and Sainburg's (Neuroscience 196: 153-167, 2011) hybrid-control model, this is because the two arms rely to different degrees on impedance control versus predictive control processes. Here, we assessed whether differences in limb control mechanisms influence the rate of feedforward compensation to a novel dynamic environment. Seventy-five healthy, right-handed participants, divided into four subsamples depending on the arm (left, right) and direction of the force field (ipsilateral, contralateral), reached to central targets in velocity-dependent curl force fields. We assessed the rate at which participants developed predictive compensation for the force field using intermittent error-clamp trials and assessed both kinematic errors and initial aiming angles in the field trials. Participants who were exposed to fields that pushed the limb toward ipsilateral space reduced kinematic errors more slowly, built up less predictive field compensation, and relied more on strategic reaiming than those exposed to contralateral fields. However, there were no significant differences in predictive field compensation or kinematic errors between limbs, suggesting that participants using either the left or the right arm could adapt equally well to novel dynamics. It therefore appears that the distinct preferences in control mechanisms typically observed for the dominant and nondominant arms reflect a default mode that is based on habitual functional requirements rather than an absolute limit in capacity to access the controller specialized for the opposite limb. Copyright © 2016 the American Physiological Society.

Feedforward compensation for novel dynamics depends on force field orientation but is similar for the left and right arms

PubMed Central

Cunnington, Ross; Mattingley, Jason B.; Riek, Stephan; Carroll, Timothy J.

2016-01-01

There are well-documented differences in the way that people typically perform identical motor tasks with their dominant and the nondominant arms. According to Yadav and Sainburg's (Neuroscience 196: 153–167, 2011) hybrid-control model, this is because the two arms rely to different degrees on impedance control versus predictive control processes. Here, we assessed whether differences in limb control mechanisms influence the rate of feedforward compensation to a novel dynamic environment. Seventy-five healthy, right-handed participants, divided into four subsamples depending on the arm (left, right) and direction of the force field (ipsilateral, contralateral), reached to central targets in velocity-dependent curl force fields. We assessed the rate at which participants developed predictive compensation for the force field using intermittent error-clamp trials and assessed both kinematic errors and initial aiming angles in the field trials. Participants who were exposed to fields that pushed the limb toward ipsilateral space reduced kinematic errors more slowly, built up less predictive field compensation, and relied more on strategic reaiming than those exposed to contralateral fields. However, there were no significant differences in predictive field compensation or kinematic errors between limbs, suggesting that participants using either the left or the right arm could adapt equally well to novel dynamics. It therefore appears that the distinct preferences in control mechanisms typically observed for the dominant and nondominant arms reflect a default mode that is based on habitual functional requirements rather than an absolute limit in capacity to access the controller specialized for the opposite limb. PMID:27582293

Molecular Mechanics: Illustrations of Its Application.

ERIC Educational Resources Information Center

Cox, Philip J.

1982-01-01

The application of molecular mechanics (a nonquantum mechanical method for solving problems concerning molecular geometries) to calculate force fields for n-butane and cyclohexane is discussed. Implications regarding the stable conformations of the example molecules are also discussed. (Author/SK)

Possible Potentials Responsible for Stable Circular Relativistic Orbits

ERIC Educational Resources Information Center

Kumar, Prashant; Bhattacharya, Kaushik

2011-01-01

Bertrand's theorem in classical mechanics of the central force fields attracts us because of its predictive power. It categorically proves that there can only be two types of forces which can produce stable, circular orbits. In this paper an attempt has been made to generalize Bertrand's theorem to the central force problem of relativistic…

Mechanism of travelling-wave transport of particles

NASA Astrophysics Data System (ADS)

Kawamoto, Hiroyuki; Seki, Kyogo; Kuromiya, Naoyuki

2006-03-01

Numerical and experimental investigations have been carried out on transport of particles in an electrostatic travelling field. A three-dimensional hard-sphere model of the distinct element method was developed to simulate the dynamics of particles. Forces applied to particles in the model were the Coulomb force, the dielectrophoresis force on polarized dipole particles in a non-uniform field, the image force, gravity and the air drag. Friction and repulsion between particle-particle and particle-conveyer were included in the model to replace initial conditions after mechanical contacts. Two kinds of experiments were performed to confirm the model. One was the measurement of charge of particles that is indispensable to determine the Coulomb force. Charge distribution was measured from the locus of free-fallen particles in a parallel electrostatic field. The averaged charge of the bulk particle was confirmed by measurement with a Faraday cage. The other experiment was measurements of the differential dynamics of particles on a conveyer consisting of parallel electrodes to which a four-phase travelling electrostatic wave was applied. Calculated results agreed with measurements, and the following characteristics were clarified. (1) The Coulomb force is the predominant force to drive particles compared with the other kinds of forces, (2) the direction of particle transport did not always coincide with that of the travelling wave but changed partially. It depended on the frequency of the travelling wave, the particle diameter and the electric field, (3) although some particles overtook the travelling wave at a very low frequency, the motion of particles was almost synchronized with the wave at the low frequency and (4) the transport of some particles was delayed to the wave at medium frequency; the majority of particles were transported backwards at high frequency and particles were not transported but only vibrated at very high frequency.

Research on the porous flow of the mechanism of viscous-elastic fluids displacing residual oil droplets in micro pores

NASA Astrophysics Data System (ADS)

Dong, Guanyu

2018-03-01

In order to analyze the microscopic stress field acting on residual oil droplets in micro pores, calculate its deformation, and explore the hydrodynamic mechanism of viscous-elastic fluids displacing oil droplets, the viscous-elastic fluid flow equations in micro pores are established by choosing the Upper Convected Maxwell constitutive equation; the numerical solutions of the flow field are obtained by volume control and Alternate Direction Implicit methods. From the above, the velocity field and microscopic stress field; the forces acting on residual oil droplets; the deformations of residual oil droplets by various viscous-elastic displacing fluids and at various Wiesenberg numbers are calculated and analyzed. The result demonstrated that both the normal stress and horizontal force acting on the residual oil droplets by viscous-elastic fluids are much larger compared to that of inelastic fluid; the distribution of normal stress changes abruptly; under the condition of the same pressure gradient in the system under investigation, the ratio of the horizontal forces acting on the residual oil droplets by different displacing fluids is about 1:8:20, which means that under the above conditions, the driving force on a oil droplet is 20 times higher for a viscous-elastic fluid compared to that of a Newtonian Fluid. The conclusions are supportive of the mechanism that viscous-elastic driving fluids can increase the Displacement Efficiency. This should be of help in designing new chemicals and selecting Enhanced Oil Recovery systems.

Field enhancement of electronic conductance at ferroelectric domain walls

DOE PAGES

Vasudevan, Rama K.; Cao, Ye; Laanait, Nouamane; ...

2017-11-06

Ferroelectric domain walls have continued to attract widespread attention due to both the novelty of the phenomena observed and the ability to reliably pattern them in nanoscale dimensions. But, the conductivity mechanisms remain in debate, particularly around nominally uncharged walls. Here, we posit a conduction mechanism relying on field-modification effect from polarization re-orientation and the structure of the reverse-domain nucleus. Through conductive atomic force microscopy measurements on an ultra-thin (001) BiFeO 3 thin film, in combination with phase-field simulations, we show that the field-induced twisted domain nucleus formed at domain walls results in local-field enhancement around the region of themore » atomic force microscope tip. In conjunction with slight barrier lowering, these two effects are sufficient to explain the observed emission current distribution. Our results suggest that different electronic properties at domain walls are not necessary to observe localized enhancement in domain wall currents.« less

Euler force actuation mechanism for siphon valving in compact disk-like microfluidic chips

PubMed Central

Deng, Yongbo; Fan, Jianhua; Zhou, Song; Zhou, Teng; Wu, Junfeng; Li, Yin; Liu, Zhenyu; Xuan, Ming; Wu, Yihui

2014-01-01

Based on the Euler force induced by the acceleration of compact disk (CD)-like microfluidic chip, this paper presents a novel actuation mechanism for siphon valving. At the preliminary stage of acceleration, the Euler force in the tangential direction of CD-like chip takes the primary place compared with the centrifugal force to function as the actuation of the flow, which fills the siphon and actuates the siphon valving. The Euler force actuation mechanism is demonstrated by the numerical solution of the phase-field based mathematical model for the flow in siphon valve. In addition, experimental validation is implemented in the polymethylmethacrylate-based CD-like microfluidic chip manufactured using CO2 laser engraving technique. To prove the application of the proposed Euler force actuation mechanism, whole blood separation and plasma extraction has been conducted using the Euler force actuated siphon valving. The newly introduced actuation mechanism overcomes the dependence on hydrophilic capillary filling of siphon by avoiding external manipulation or surface treatments of polymeric material. The sacrifice for highly integrated processing in pneumatic pumping technique is also prevented by excluding the volume-occupied compressed air chamber. PMID:24753736

Apparatus for storing high magnetic fields having reduced mechanical forces and reduced magnetic pollution

DOEpatents

Prueitt, Melvin L.; Mueller, Fred M.; Smith, James L.

1991-01-01

The present invention identifies several configurations of conducting elements capable of storing extremely high magnetic fields for the purpose of energy storage or for other uses, wherein forces experienced by the conducting elements and the magnetic field pollution produced at locations away from the configuration are both significantly reduced over those which are present as a result of the generation of such high fields by currently proposed techniques. It is anticipated that the use of superconducting materials will both permit the attainment of such high fields and further permit such fields to be generated with vastly improved efficiency.

Apparatus for storing high magnetic fields having reduced mechanical forces and reduced magnetic pollution

DOEpatents

Prueitt, M.L.; Mueller, F.M.; Smith, J.L.

1991-04-09

The present invention identifies several configurations of conducting elements capable of storing extremely high magnetic fields for the purpose of energy storage or for other uses, wherein forces experienced by the conducting elements and the magnetic field pollution produced at locations away from the configuration are both significantly reduced over those which are present as a result of the generation of such high fields by currently proposed techniques. It is anticipated that the use of superconducting materials will both permit the attainment of such high fields and further permit such fields to be generated with vastly improved efficiency. 15 figures.

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.

Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

NASA Astrophysics Data System (ADS)

Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

2012-01-01

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

Amino acid analogues bind to carbon nanotube via π-π interactions: comparison of molecular mechanical and quantum mechanical calculations.

PubMed

Yang, Zaixing; Wang, Zhigang; Tian, Xingling; Xiu, Peng; Zhou, Ruhong

2012-01-14

Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the π-π stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated π-π interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in π-π interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of π-π interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to π-π interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the π-π interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments.

The effect of temperature on pinning mechanisms in HTS composites

NASA Astrophysics Data System (ADS)

Sotnikova, A. P.; Rudnev, I. A.

2016-09-01

Pinning mechanism in samples of second generation tapes (2G) of high-temperature superconductors (HTS) was studied The critical current and the pinning force were calculated from the magnetization curves measured in the temperature range of 4.2 - 77 K in magnetic fields up to 14 Tesla using vibration sample magnetometer. To determine the pinning mechanism the dependences of pinning force on magnetic field were constructed according to the Dew-Hughes model and Kramer's rule. The obtained dependences revealed a significant influence of the temperature on effectiveness of different types of pinning. At low temperatures the 2G HTS tapes of different manufacturers demonstrated an equal efficiency of the pinning centers but with temperature increase the differences in pinning mechanisms as well as in properties and effectiveness of the pinning centers become obvious. The influence of the pinning mechanism on the energy losses in HTS tapes was shown.

Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

PubMed

Mörschel, Philipp; Schmidt, Martin U

2015-01-01

A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.

PubMed

Muddana, Hari S; Gilson, Michael K

2012-06-12

The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy function, PM6-DH+, coupled with the COSMO solvation model, to 29 host-guest systems with a wide range of measured binding affinities. After correction for a systematic error, which appears to derive from the treatment of polar solvation, the computed absolute binding affinities agree well with experimental measurements, with a mean error 1.6 kcal/mol and a correlation coefficient of 0.91. These calculations also delineate the contributions of various energy components, including solute energy, configurational entropy, and solvation free energy, to the binding free energies of these host-guest complexes. Comparison with our previous calculations, which used empirical force fields, point to significant differences in both the energetic and entropic components of the binding free energy. The present study demonstrates successful combination of a quantum mechanical Hamiltonian with the M2 affinity method.

A Hitchhiker’s Guide to Mechanobiology

PubMed Central

Eyckmans, Jeroen; Boudou, Thomas; Yu, Xiang; Chen, Christopher S.

2011-01-01

More than a century ago, it was proposed that mechanical forces could drive tissue formation. However, only recently with the advent of enabling biophysical and molecular technologies are we beginning to understand how individual cells transduce mechanical force into biochemical signals. In turn, this knowledge of mechanotransduction at the cellular level is beginning to clarify the role of mechanics in patterning processes during embryonic development. In this perspective, we will discuss current mechanotransduction paradigms, along with the technologies that have shaped the field of mechanobiology. PMID:21763607

Chip Scale, Ultra Sensitive Opto Mechanical Acceleration and Force Sensors

DTIC Science & Technology

2017-12-01

an accelerometer of the same mechanical design as that studied in part A. and shown in Fig. 3. One side of the zipper optical cavity is connected to...Ref. [13]. “Endevco 752A13” is Ref. [30]. “Zipper” is our own work on zipper photonic crystals from Ref. [31]. II Accelerometer Noise and Design ...limit, the shot noise of the light field also imparts a force on , and cause motion of, the mechanical resonator. The acceleration PSD due to back-action

Machine learning of accurate energy-conserving molecular force fields.

PubMed

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof T; Müller, Klaus-Robert

2017-05-01

Using conservation of energy-a fundamental property of closed classical and quantum mechanical systems-we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol -1 for energies and 1 kcal mol -1 Å̊ -1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Machine learning of accurate energy-conserving molecular force fields

PubMed Central

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

2017-01-01

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

Quantum mechanical/molecular mechanical/continuum style solvation model: Second order Møller-Plesset perturbation theory

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

Thellamurege, Nandun M.; Si, Dejun; Cui, Fengchao

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths ofmore » the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.« less

Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.

PubMed

Jasiński, Maciej; Feig, Michael; Trylska, Joanna

2018-06-06

Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.

Parametrization of Stillinger-Weber potential based on valence force field model: application to single-layer MoS2 and black phosphorus

NASA Astrophysics Data System (ADS)

Jiang, Jin-Wu

2015-08-01

We propose parametrizing the Stillinger-Weber potential for covalent materials starting from the valence force-field model. All geometrical parameters in the Stillinger-Weber potential are determined analytically according to the equilibrium condition for each individual potential term, while the energy parameters are derived from the valence force-field model. This parametrization approach transfers the accuracy of the valence force field model to the Stillinger-Weber potential. Furthermore, the resulting Stilliinger-Weber potential supports stable molecular dynamics simulations, as each potential term is at an energy-minimum state separately at the equilibrium configuration. We employ this procedure to parametrize Stillinger-Weber potentials for single-layer MoS2 and black phosphorous. The obtained Stillinger-Weber potentials predict an accurate phonon spectrum and mechanical behaviors. We also provide input scripts of these Stillinger-Weber potentials used by publicly available simulation packages including GULP and LAMMPS.

Parametrization of Stillinger-Weber potential based on valence force field model: application to single-layer MoS2 and black phosphorus.

PubMed

Jiang, Jin-Wu

2015-08-07

We propose parametrizing the Stillinger-Weber potential for covalent materials starting from the valence force-field model. All geometrical parameters in the Stillinger-Weber potential are determined analytically according to the equilibrium condition for each individual potential term, while the energy parameters are derived from the valence force-field model. This parametrization approach transfers the accuracy of the valence force field model to the Stillinger-Weber potential. Furthermore, the resulting Stilliinger-Weber potential supports stable molecular dynamics simulations, as each potential term is at an energy-minimum state separately at the equilibrium configuration. We employ this procedure to parametrize Stillinger-Weber potentials for single-layer MoS2 and black phosphorous. The obtained Stillinger-Weber potentials predict an accurate phonon spectrum and mechanical behaviors. We also provide input scripts of these Stillinger-Weber potentials used by publicly available simulation packages including GULP and LAMMPS.

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water.

PubMed

Mittal, Jeetain; Best, Robert B

2010-08-04

The ability to fold proteins on a computer has highlighted the fact that existing force fields tend to be biased toward a particular type of secondary structure. Consequently, force fields for folding simulations are often chosen according to the native structure, implying that they are not truly "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structures, a simple correction to the backbone potential (ff03( *)) results in an unbiased energy function. We take as examples the 35-residue alpha-helical Villin HP35 and 37 residue beta-sheet Pin WW domains, which had not previously been folded with the same force field. Starting from unfolded configurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A RMSD of the experimental structures. This demonstrates that a simple backbone correction results in a more transferable force field, an important requirement if simulations are to be used to interpret folding mechanism. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Sensitivity of Force Fields on Mechanical Properties of Metals Predicted by Atomistic Simulations

NASA Astrophysics Data System (ADS)

Rassoulinejad-Mousavi, Seyed Moein; Zhang, Yuwen

Increasing number of micro/nanoscale studies for scientific and engineering applications, leads to huge deployment of atomistic simulations such as molecular dynamics and Monte-Carlo simulation. Many complains from users in the simulation community arises for obtaining wrong results notwithstanding of correct simulation procedure and conditions. Improper choice of force field, known as interatomic potential is the likely causes. For the sake of users' assurance, convenience and time saving, several interatomic potentials are evaluated by molecular dynamics. Elastic properties of multiple FCC and BCC pure metallic species are obtained by LAMMPS, using different interatomic potentials designed for pure species and their alloys at different temperatures. The potentials created based on the Embedded Atom Method (EAM), Modified EAM (MEAM) and ReaX force fields, adopted from available open databases. Independent elastic stiffness constants of cubic single crystals for different metals are obtained. The results are compared with the experimental ones available in the literature and deviations for each force field are provided at each temperature. Using current work, users of these force fields can easily judge on the one they are going to designate for their problem.

Efficient solution of the Wigner-Liouville equation using a spectral decomposition of the force field

NASA Astrophysics Data System (ADS)

Van de Put, Maarten L.; Sorée, Bart; Magnus, Wim

2017-12-01

The Wigner-Liouville equation is reformulated using a spectral decomposition of the classical force field instead of the potential energy. The latter is shown to simplify the Wigner-Liouville kernel both conceptually and numerically as the spectral force Wigner-Liouville equation avoids the numerical evaluation of the highly oscillatory Wigner kernel which is nonlocal in both position and momentum. The quantum mechanical evolution is instead governed by a term local in space and non-local in momentum, where the non-locality in momentum has only a limited range. An interpretation of the time evolution in terms of two processes is presented; a classical evolution under the influence of the averaged driving field, and a probability-preserving quantum-mechanical generation and annihilation term. Using the inherent stability and reduced complexity, a direct deterministic numerical implementation using Chebyshev and Fourier pseudo-spectral methods is detailed. For the purpose of illustration, we present results for the time-evolution of a one-dimensional resonant tunneling diode driven out of equilibrium.

Force fields of charged particles in micro-nanofluidic preconcentration systems

NASA Astrophysics Data System (ADS)

Gong, Lingyan; Ouyang, Wei; Li, Zirui; Han, Jongyoon

2017-12-01

Electrokinetic concentration devices based on the ion concentration polarization (ICP) phenomenon have drawn much attention due to their simple setup, high enrichment factor, and easy integration with many subsequent processes, such as separation, reaction, and extraction etc. Despite significant progress in the experimental research, fundamental understanding and detailed modeling of the preconcentration systems is still lacking. The mechanism of the electrokinetic trapping of charged particles is currently limited to the force balance analysis between the electric force and fluid drag force in an over-simplified one-dimensional (1D) model, which misses many signatures of the actual system. This letter studies the particle trapping phenomena that are not explainable in the 1D model through the calculation of the two-dimensional (2D) force fields. The trapping of charged particles is shown to significantly distort the electric field and fluid flow pattern, which in turn leads to the different trapping behaviors of particles of different sizes. The mechanisms behind the protrusions and instability of the focused band, which are important factors determining overall preconcentration efficiency, are revealed through analyzing the rotating fluxes of particles in the vicinity of the ion-selective membrane. The differences in the enrichment factors of differently sized particles are understood through the interplay between the electric force and convective fluid flow. These results provide insights into the electrokinetic concentration effect, which could facilitate the design and optimization of ICP-based preconcentration systems.

Nanosecond pulsed electric field induced changes in cell surface charge density.

PubMed

Dutta, Diganta; Palmer, Xavier-Lewis; Asmar, Anthony; Stacey, Michael; Qian, Shizhi

2017-09-01

This study reports that the surface charge density changes in Jurkat cells with the application of single 60 nanosecond pulse electric fields, using atomic force microscopy. Using an atomic force microscope tip and Jurkat cells on silica in a 0.01M KCl ionic concentration, we were able to measure the interfacial forces, while also predicting surface charge densities of both Jurkat cell and silica surfaces. The most important finding is that the pulsing conditions varyingly reduced the cells' surface charge density. This offers a novel way in which to examine cellular effects of pulsed electric fields that may lead to the identification of unique mechanical responses. Compared to a single low field strength NsPEF (15kV/cm) application, exposure of Jurkat cells to a single high field strength NsPEF (60kV/cm) resulted in a further reduction in charge density and major morphological changes. The structural, physical, and chemical properties of biological cells immensely influence their electrostatic force; we were able to investigate this through the use of atomic force microscopy by measuring the surface forces between the AFM's tip and the Jurkat cells under different pulsing conditions as well as the interfacial forces in ionic concentrations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Interfacing 3D magnetic twisting cytometry with confocal fluorescence microscopy to image force responses in living cells.

PubMed

Zhang, Yuejin; Wei, Fuxiang; Poh, Yeh-Chuin; Jia, Qiong; Chen, Junjian; Chen, Junwei; Luo, Junyu; Yao, Wenting; Zhou, Wenwen; Huang, Wei; Yang, Fang; Zhang, Yao; Wang, Ning

2017-07-01

Cells and tissues can undergo a variety of biological and structural changes in response to mechanical forces. Only a few existing techniques are available for quantification of structural changes at high resolution in response to forces applied along different directions. 3D-magnetic twisting cytometry (3D-MTC) is a technique for applying local mechanical stresses to living cells. Here we describe a protocol for interfacing 3D-MTC with confocal fluorescence microscopy. In 3D-MTC, ferromagnetic beads are bound to the cell surface via surface receptors, followed by their magnetization in any desired direction. A magnetic twisting field in a different direction is then applied to generate rotational shear stresses in any desired direction. This protocol describes how to combine magnetic-field-induced mechanical stimulation with confocal fluorescence microscopy and provides an optional extension for super-resolution imaging using stimulated emission depletion (STED) nanoscopy. This technology allows for rapid real-time acquisition of a living cell's mechanical responses to forces via specific receptors and for quantifying structural and biochemical changes in the same cell using confocal fluorescence microscopy or STED. The integrated 3D-MTC-microscopy platform takes ∼20 d to construct, and the experimental procedures require ∼4 d when carried out by a life sciences graduate student.

Interfacing 3D magnetic twisting cytometry with confocal fluorescence microscopy to image force responses in living cells

PubMed Central

Zhang, Yuejin; Wei, Fuxiang; Poh, Yeh-Chuin; Jia, Qiong; Chen, Junjian; Chen, Junwei; Luo, Junyu; Yao, Wenting; Zhou, Wenwen; Huang, Wei; Yang, Fang; Zhang, Yao; Wang, Ning

2017-01-01

Cells and tissues can undergo a variety of biological and structural changes in response to mechanical forces. Only few existing techniques are available for quantification of structural changes at high resolution in response to forces applied along different directions. Three dimensional-Magnetic Twisting Cytometry (3D-MTC) is a technique for applying local mechanical stresses on living cells. Here we describe a protocol for interfacing 3D-MTC with confocal fluorescence microscopy. In 3D-MTC, ferromagnetic beads are bound to the cell surface via surface receptors followed by their magnetization in any desired direction. A magnetic twisting field in a different direction is then applied to generate rotational shear stresses in any desired direction. This protocol describes how to combine magnetic field-induced mechanical stimulation with confocal fluorescence microscopy and provides an optional extension for super resolution imaging using stimulated emission depletion (STED) nanoscopy. This technology allows for rapid real time acquisition of a living cell’s mechanical responses to forces via specific receptors and for quantifying structural and biochemical changes in the same cell using confocal fluorescence microscopy or STED. The integrated 3D-MTC – microscopy platform takes around 20 days to construct and the experimental procedures require ~4 days when carried out by a life sciences graduate student. PMID:28686583

Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential

PubMed Central

Gao, Ya; Li, Yongxiu; Mou, Lirong; Lin, Bingbing; Zhang, John Z. H.; Mei, Ye

2015-01-01

A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER032D), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER032D force field with the implementation of a polarization scheme (AMBER032Dp). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER032D without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. PMID:26039188

Force fields and scoring functions for carbohydrate simulation.

PubMed

Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye

2015-01-12

Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Perspective: Mechanochemistry of biological and synthetic molecules

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

Makarov, Dmitrii E., E-mail: makarov@cm.utexas.edu

Coupling of mechanical forces and chemical transformations is central to the biophysics of molecular machines, polymer chemistry, fracture mechanics, tribology, and other disciplines. As a consequence, the same physical principles and theoretical models should be applicable in all of those fields; in fact, similar models have been invoked (and often repeatedly reinvented) to describe, for example, cell adhesion, dry and wet friction, propagation of cracks, and action of molecular motors. This perspective offers a unified view of these phenomena, described in terms of chemical kinetics with rates of elementary steps that are force dependent. The central question is then tomore » describe how the rate of a chemical transformation (and its other measurable properties such as the transition path) depends on the applied force. I will describe physical models used to answer this question and compare them with experimental measurements, which employ single-molecule force spectroscopy and which become increasingly common. Multidimensionality of the underlying molecular energy landscapes and the ensuing frequent misalignment between chemical and mechanical coordinates result in a number of distinct scenarios, each showing a nontrivial force dependence of the reaction rate. I will discuss these scenarios, their commonness (or its lack), and the prospects for their experimental validation. Finally, I will discuss open issues in the field.« less

Using Magnetic Forces to Probe the Gravi-response of Swimming Paramecium

NASA Astrophysics Data System (ADS)

Guevorkian, Karine; Valles, James M., Jr.

2004-03-01

Paramecium Caudatum, a single celled ciliate, alters its swimming behavior when subjected to different gravity environments (e.g. centrifugation and micro-gravity). To dissect the mechanisms behind this gravi-response and that of other biological systems, we are developing the use of magnetic body forces as a means of creating a rapidly tunable, simulated variable gravity environment. Since biological materials are weakly diamagnetic, we must subject them to intense inhomogeneous magnetic fields with characteristic field-field gradient products on the order of 16 T^2/cm. We will describe experiments on Paramecium Caudatum in which we adjust their net buoyancy with magnetic forces and measure the resulting changes in their swimming behavior.

An Assessment of Molecular Dynamic Force Fields for Silica for Use in Simulating Laser Damage Mitigation

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

Soules, T F; Gilmer, G H; Matthews, M J

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 tomore » laser mitigation experiments.« less

Impact of inertia, friction, and backlash upon force control in telemanipulation

NASA Technical Reports Server (NTRS)

Duffie, Neil A.; Zik, John J.; Wiker, Steven F.; Gale, Karen L.

1991-01-01

The mechanical behavior of master controllers of telemanipulators has been a concern of both designers and implementors of telerobotic systems. In general, the literature recommends that telemanipulator systems be constructed that minimize inertia, friction, and backlash in an effort to improve telemanipulative performance. For the most part, these recommendations are founded upon theoretical analysis or simply intuition. Although these recommendations are not challenged on their merit, the material results are measured of building and fielding telemanipulators that possess less than ideal mechanical behaviors. Experiments are described in which forces in a mechanical system with human input are evaluated as a function of mechanical characteristics such as inertia, friction, and backlash. Results indicate that the ability of the human to maintain gripping forces was relatively unaffected by dynamic characteristics in the range studied, suggesting that telemanipulator design in this range should be based on task level force control requirements rather than human factors.

Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective.

PubMed

Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

2017-08-30

Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at the atomic and molecular levels. However, there are still some parameters including torsions in amino acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single stranded nucleic acids for which the force fields need further improvement, although there are several workers putting in constant efforts in these directions. The existing force fields are not efficient for studying the crowded environment inside the cells, since these interactions involve multiple factors in real time. Therefore, the improved force fields may provide the opportunities for their wider applications on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental biological and physiological processes at the molecular levels that may be further applied in various fields including biotechnology, fisheries, sustainable agriculture and biomedical research. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate

PubMed Central

2015-01-01

Phosphate groups are commonly observed in biomolecules such as nucleic acids and lipids. Due to their highly charged and polarizable nature, modeling these compounds with classical force fields is challenging. Using quantum mechanical studies and liquid-phase simulations, the AMOEBA force field for dimethyl phosphate (DMP) ion and trimethyl phosphate (TMP) has been developed. On the basis of ab initio calculations, it was found that ion binding and the solution environment significantly impact both the molecular geometry and the energy differences between conformations. Atomic multipole moments are derived from MP2/cc-pVQZ calculations of methyl phosphates at several conformations with their chemical environments taken into account. Many-body polarization is handled via a Thole-style induction model using distributed atomic polarizabilities. van der Waals parameters of phosphate and oxygen atoms are determined by fitting to the quantum mechanical interaction energy curves for water with DMP or TMP. Additional stretch-torsion and angle-torsion coupling terms were introduced in order to capture asymmetry in P–O bond lengths and angles due to the generalized anomeric effect. The resulting force field for DMP and TMP is able to accurately describe both the molecular structure and conformational energy surface, including bond and angle variations with conformation, as well as interaction of both species with water and metal ions. The force field was further validated for TMP in the condensed phase by computing hydration free energy, liquid density, and heat of vaporization. The polarization behavior between liquid TMP and TMP in water is drastically different. PMID:26574325

Cutting Force Predication Based on Integration of Symmetric Fuzzy Number and Finite Element Method

PubMed Central

Wang, Zhanli; Hu, Yanjuan; Wang, Yao; Dong, Chao; Pang, Zaixiang

2014-01-01

In the process of turning, pointing at the uncertain phenomenon of cutting which is caused by the disturbance of random factors, for determining the uncertain scope of cutting force, the integrated symmetric fuzzy number and the finite element method (FEM) are used in the prediction of cutting force. The method used symmetric fuzzy number to establish fuzzy function between cutting force and three factors and obtained the uncertain interval of cutting force by linear programming. At the same time, the change curve of cutting force with time was directly simulated by using thermal-mechanical coupling FEM; also the nonuniform stress field and temperature distribution of workpiece, tool, and chip under the action of thermal-mechanical coupling were simulated. The experimental result shows that the method is effective for the uncertain prediction of cutting force. PMID:24790556

ASTROPHYSICS. Atom-interferometry constraints on dark energy.

PubMed

Hamilton, P; Jaffe, M; Haslinger, P; Simmons, Q; Müller, H; Khoury, J

2015-08-21

If dark energy, which drives the accelerated expansion of the universe, consists of a light scalar field, it might be detectable as a "fifth force" between normal-matter objects, in potential conflict with precision tests of gravity. Chameleon fields and other theories with screening mechanisms, however, can evade these tests by suppressing the forces in regions of high density, such as the laboratory. Using a cesium matter-wave interferometer near a spherical mass in an ultrahigh-vacuum chamber, we reduced the screening mechanism by probing the field with individual atoms rather than with bulk matter. We thereby constrained a wide class of dark energy theories, including a range of chameleon and other theories that reproduce the observed cosmic acceleration. Copyright © 2015, American Association for the Advancement of Science.

Mechanical properties of asthmatic airway smooth muscle.

PubMed

Chin, Leslie Y M; Bossé, Ynuk; Pascoe, Chris; Hackett, Tillie L; Seow, Chun Y; Paré, Peter D

2012-07-01

Airway smooth muscle (ASM) is the major effector of excessive airway narrowing in asthma. Changes in some of the mechanical properties of ASM could contribute to excessive narrowing and have not been systematically studied in human ASM from nonasthmatic and asthmatic subjects. Human ASM strips (eight asthmatic and six nonasthmatic) were studied at in situ length and force was normalised to maximal force induced by electric field stimulation (EFS). Measurements included: passive and active force versus length before and after length adaptation, the force-velocity relationship, maximal shortening and force recovery after length oscillation. Force was converted to stress by dividing by cross-sectional area of muscle. The only functional differences were that the asthmatic tissue was stiffer at longer lengths (p<0.05) and oscillatory strain reduced isometric force in response to EFS by 19% as opposed to 36% in nonasthmatics (p<0.01). The mechanical properties of human ASM from asthmatic and nonasthmatic subjects are comparable except for increased passive stiffness and attenuated decline in force generation after an oscillatory perturbation. These data may relate to reduced bronchodilation induced by a deep inspiration in asthmatic subjects.

Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

PubMed Central

KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

2014-01-01

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

Machine-Thermal Coupling Stresses Analysis of the Fin-Type Structural Thermoelectric Generator

NASA Astrophysics Data System (ADS)

Zhang, Zheng; Yue, Hao; Chen, Dongbo; Qin, Delei; Chen, Zijian

2017-05-01

The design structure and heat-transfer mechanism of a thermoelectric generator (TEG) determine its body temperature state. Thermal stress and thermal deformation generated by the temperature variation directly affect the stress state of thermoelectric modules (TEMs). Therefore, the rated temperature and pressing force of TEMs are important parameters in TEG design. Here, the relationships between structural of a fin-type TEG (FTEG) and these parameters are studied by modeling and "machine-thermal" coupling simulation. An indirect calculation method is adopted in the coupling simulation. First, numerical heat transfer calculations of a three-dimensional FTEG model are conducted according to an orthogonal simulation table. The influences of structural parameters for heat transfer in the channel and outer fin temperature distribution are analyzed. The optimal structural parameters are obtained and used to simulate temperature field of the outer fins. Second, taking the thermal calculation results as the initial condition, the thermal-solid coupling calculation is adopted. The thermal stresses of outer fin, mechanical force of spring-angle pressing mechanism, and clamping force on a TEM are analyzed. The simulation results show that the heat transfer area of the inner fin and the physical parameters of the metal materials are the keys to determining the FTEG temperature field. The pressing mechanism's mechanical force can be reduced by reducing the outer fin angle. In addition, a corrugated cooling water pipe, which has cooling and spring functionality, is conducive to establishing an adaptable clamping force to avoid the TEMs being crushed by the thermal stresses in the body.

Multipolar Ewald methods, 1: theory, accuracy, and performance.

PubMed

Giese, Timothy J; Panteva, Maria T; Chen, Haoyuan; York, Darrin M

2015-02-10

The Ewald, Particle Mesh Ewald (PME), and Fast Fourier–Poisson (FFP) methods are developed for systems composed of spherical multipole moment expansions. A unified set of equations is derived that takes advantage of a spherical tensor gradient operator formalism in both real space and reciprocal space to allow extension to arbitrary multipole order. The implementation of these methods into a novel linear-scaling modified “divide-and-conquer” (mDC) quantum mechanical force field is discussed. The evaluation times and relative force errors are compared between the three methods, as a function of multipole expansion order. Timings and errors are also compared within the context of the quantum mechanical force field, which encounters primary errors related to the quality of reproducing electrostatic forces for a given density matrix and secondary errors resulting from the propagation of the approximate electrostatics into the self-consistent field procedure, which yields a converged, variational, but nonetheless approximate density matrix. Condensed-phase simulations of an mDC water model are performed with the multipolar PME method and compared to an electrostatic cutoff method, which is shown to artificially increase the density of water and heat of vaporization relative to full electrostatic treatment.

An Instructional Manual for the US Air Force New Harvest Eagle Field Feeding System

DTIC Science & Technology

1982-07-01

Continue, on revorao aide if necesaary and Identity by block number) FIELD FEEDING SYSTEIV AIR FORCE PORTABLE EQUIPMENT HEATERS (WATER) FOOD ...The-Job Training Program for Food Service Workers is included as is a set of general guidelines for food service managers. This manual describes the...of Westboro, MA. Mr. Ernest Saab and associates of the Aero-Mechanical Engineering Laboratory (NLABS). Mr. John Perry and associates of the Food

The effects of forcing on a single stream shear layer and its parent boundary layer

NASA Technical Reports Server (NTRS)

Haw, Richard C.; Foss, John F.

1990-01-01

Forcing and its effect on fluid flows has become an accepted tool in the study and control of flow systems. It has been used both as a diagnostic tool, to explore the development and interaction of coherent structures, and as a method of controlling the behavior of the flow. A number of forcing methods have been used in order to provide a perturbation to the flow; among these are the use of an oscillating trailing edge, acoustically driven slots, external acoustic forcing, and mechanical piston methods. The effect of a planar mechanical piston forcing on a single stream shear layer is presented; it can be noted that this is one of the lesser studied free shear layers. The single stream shear layer can be characterized by its primary flow velocity scale and the thickness of the separating boundary layer. The velocity scale is constant over the length of the flow field; theta (x) can be used as a width scale to characterize the unforced shear layer. In the case of the forced shear layer the velocity field is a function of phase time and definition of a width measure becomes somewhat problematic.

Three-dimensional cellular deformation analysis with a two-photon magnetic manipulator workstation.

PubMed

Huang, Hayden; Dong, Chen Y; Kwon, Hyuk-Sang; Sutin, Jason D; Kamm, Roger D; So, Peter T C

2002-04-01

The ability to apply quantifiable mechanical stresses at the microscopic scale is critical for studying cellular responses to mechanical forces. This necessitates the use of force transducers that can apply precisely controlled forces to cells while monitoring the responses noninvasively. This paper describes the development of a micromanipulation workstation integrating two-photon, three-dimensional imaging with a high-force, uniform-gradient magnetic manipulator. The uniform-gradient magnetic field applies nearly uniform forces to a large cell population, permitting statistical quantification of select molecular responses to mechanical stresses. The magnetic transducer design is capable of exerting over 200 pN of force on 4.5-microm-diameter paramagnetic particles and over 800 pN on 5.0-microm ferromagnetic particles. These forces vary within +/-10% over an area 500 x 500 microm2. The compatibility with the use of high numerical aperture (approximately 1.0) objectives is an integral part of the workstation design allowing submicron-resolution, three-dimensional, two-photon imaging. Three-dimensional analyses of cellular deformation under localized mechanical strain are reported. These measurements indicate that the response of cells to large focal stresses may contain three-dimensional global deformations and show the suitability of this workstation to further studying cellular response to mechanical stresses.

Dynamic acoustic radiation force acting on cylindrical shells: theory and simulations.

PubMed

Mitri, F G; Fatemi, M

2005-05-01

An object placed in an acoustic field is known to experience a force due to the transfer of momentum from the wave to the object itself. This force is known to be steady when the incident field is considered to be continuous with constant amplitude. One may define the dynamic (oscillatory) radiation force for a continuous wave-field whose intensity varies slowly with time. This paper extends the theory of the dynamic acoustic radiation force resulting from an amplitude-modulated progressive plane wave-field incident on solid cylinders to the case of solid cylindrical shells with particular emphasis on their thickness and contents of their hollow regions. A new factor corresponding to the dynamic radiation force is defined as Y(d) and stands for the dynamic radiation force per unit energy density and unit cross sectional surface. The results of numerical calculations are presented, indicating the ways in which the form of the dynamic radiation force function curves are affected by variations in the material mechanical parameters and by changes in the interior fluid inside the shell's hollow region. It was shown that the dynamic radiation force function Y(d) deviates from the static radiation force function for progressive waves Y(p) when the modulation frequency increases. These results indicate that the theory presented here is broader than the existing theory on cylinders.

Novel combination of near-field s-SNOM microscopy with peak-force tapping for nano-chemical and nano-mechanical material characterization with sub-20 nm spatial resolution

NASA Astrophysics Data System (ADS)

Wagner, Martin; Carneiro, Karina; Habelitz, Stefan; Mueller, Thomas; BNS Team; UCSF Team

Heterogeneity in material systems requires methods for nanoscale chemical identification. Scattering scanning near-field microscopy (s-SNOM) is chemically sensitive in the infrared fingerprint region while providing down to 10 nm spatial resolution. This technique detects material specific tip-scattering in an atomic force microscope. Here, we present the first combination of s-SNOM with peak-force tapping (PFT), a valuable AFM technique that allows precise force control between tip and sample down to 10s of pN. The latter is essential for imaging fragile samples, but allows also quantitative extraction of nano-mechanical properties, e.g. the modulus. PFT can further be complemented by KPFM or conductive AFM for nano-electrical mapping, allowing access to nanoscale optical, mechanical and electrical information in a single instrument. We will address several questions ranging from graphene plasmonics to material distributions in polymers. We highlight a biological application where dental amelogenin protein was studied via s-SNOM to learn about its self-assembly into nanoribbons. At the same time PFT allows to track crystallization to distinguish protein from apatite crystals for which amelogenin is supposed to act as a template.

Plasmonic Spherical Heterodimers: Reversal of Optical Binding Force Based on the Forced Breaking of Symmetry.

PubMed

Mahdy, M R C; Danesh, Md; Zhang, Tianhang; Ding, Weiqiang; Rivy, Hamim Mahmud; Chowdhury, Ariful Bari; Mehmood, M Q

2018-02-16

The stimulating connection between the reversal of near-field plasmonic binding force and the role of symmetry-breaking has not been investigated comprehensively in the literature. In this work, the symmetry of spherical plasmonic heterodimer-setup is broken forcefully by shining the light from a specific side of the set-up instead of impinging it from the top. We demonstrate that for the forced symmetry-broken spherical heterodimer-configurations: reversal of lateral and longitudinal near-field binding force follow completely distinct mechanisms. Interestingly, the reversal of longitudinal binding force can be easily controlled either by changing the direction of light propagation or by varying their relative orientation. This simple process of controlling binding force may open a novel generic way of optical manipulation even with the heterodimers of other shapes. Though it is commonly believed that the reversal of near-field plasmonic binding force should naturally occur for the presence of bonding and anti-bonding modes or at least for the Fano resonance (and plasmonic forces mostly arise from the surface force), our study based on Lorentz-force dynamics suggests notably opposite proposals for the aforementioned cases. Observations in this article can be very useful for improved sensors, particle clustering and aggregation.

Magnetic field effects on the vestibular system: calculation of the pressure on the cupula due to ionic current-induced Lorentz force

NASA Astrophysics Data System (ADS)

Antunes, A.; Glover, P. M.; Li, Y.; Mian, O. S.; Day, B. L.

2012-07-01

Large static magnetic fields may be employed in magnetic resonance imaging (MRI). At high magnetic field strengths (usually from about 3 T and above) it is possible for humans to perceive a number of effects. One such effect is mild vertigo. Recently, Roberts et al (2011 Current Biology 21 1635-40) proposed a Lorentz-force mechanism resulting from the ionic currents occurring naturally in the endolymph of the vestibular system. In the present work a more detailed calculation of the forces and resulting pressures in the vestibular system is carried out using a numerical model. Firstly, realistic 3D finite element conductivity and fluid maps of the utricle and a single semi-circular canal containing the current sources (dark cells) and sinks (hair cells) of the utricle and ampulla were constructed. Secondly, the electrical current densities in the fluid are calculated. Thirdly, the developed Lorentz force is used directly in the Navier-Stokes equation and the trans-cupular pressure is computed. Since the driving force field is relatively large in comparison with the advective acceleration, we demonstrate that it is possible to perform an approximation in the Navier-Stokes equations that reduces the problem to solving a simpler Poisson equation. This simplification allows rapid and easy calculation for many different directions of applied magnetic field. At 7 T a maximum cupula pressure difference of 1.6 mPa was calculated for the combined ampullar (0.7 µA) and utricular (3.31 µA) distributed current sources, assuming a hair-cell resting current of 100 pA per unit. These pressure values are up to an order of magnitude lower than those proposed by Roberts et al using a simplistic model and calculation, and are in good agreement with the estimated pressure values for nystagmus velocities in caloric experiments. This modeling work supports the hypothesis that the Lorentz force mechanism is a significant contributor to the perception of magnetic field induced vertigo.

Fires. A Joint Professional Bulletin for U.S. Field and Air Defense Artillerymen. September-October 2011

DTIC Science & Technology

2011-10-01

said that security of the LOCs was a constant challenge facing the Soviet forces in Afghanistan. Security of the LOCs determined the amount of forces...resistance forces. The Afghan terrain was not ideal for a mechanized force dependent on fire power, secure LOCs and high-technology. Although the popular...Secure logistics and secure LOCs are essential for the both the guerrilla and non-guerrilla force. Security missions, however, can tie up most

Piezoelectric Composites by Solid Freeform Fabrication: A Nature-Inspired Approach

NASA Astrophysics Data System (ADS)

Safari, A.; Akdoğan, E. K.

Piezoelectrics and electrostrictors are indispensable materials for use in transducer technology, as they inherently possess both direct (sensing) and converse (actuation) effects. A piezoelectric/electrostrictive sensor converts a mechanical input (displacement or force) into a measurable electrical output through piezoelectric/electrostrictive energy conversion. In the case of a piezoelectric, an applied mechanical force (stress) induces a voltage across the terminals of the transducer. On the other hand, an applied mechanical force induces a change in the capacitance of an electrostrictive transducer that could be electrically detected. Hence, the mechanical to electrical energy conversion is accomplished directly when a piezoelectric is used, while the same is obtained indirectly if the electroactive material of choice is an electrostrictor. Conversely, both piezoelectric and electrostrictive materials develop an elastic strain under an applied electric field. The said elastic strain is linearly proportional to the applied field in a piezoelectric, whereas electrostrictive coupling involves the second-order (quadratic) coupling of electric field with elastic strain. While piezoelectricity is possible only in noncentrosymetric point groups, electrostriction is observed in all solids, which make it a much more general solid-state phenomenon. Sensing and actuation functions can coexist in a given transducer by the intelligent use of such materials. Piezoelectrics and electrostrictors, therefore, constitute the backbone of modern transducer technology, as mechanical to electric energy (and vice versa) conversion can be accomplished with great efficiency in a way that is second to none among all phenomena known to date [1,2].

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Embryo mechanics: balancing force production with elastic resistance during morphogenesis.

PubMed

Davidson, Lance A

2011-01-01

Morphogenesis requires the spatial and temporal control of embryo mechanics, including force production and mechanical resistance to those forces, to coordinate tissue deformation and large-scale movements. Thus, biomechanical processes play a key role in directly shaping the embryo. Additional roles for embryo mechanics during development may include the patterning of positional information and to provide feedback to ensure the success of morphogenetic movements in shaping the larval body and organs. To understand the multiple roles of mechanics during development requires familiarity with engineering principles of the mechanics of structures, the viscoelastic properties of biomaterials, and the integration of force and stress within embryonic structures as morphogenesis progresses. In this chapter, we review the basic engineering principles of biomechanics as they relate to morphogenesis, introduce methods for quantifying embryo mechanics and the limitations of these methods, and outline a formalism for investigating the role of embryo mechanics in birth defects. We encourage the nascent field of embryo mechanics to adopt standard engineering terms and test methods so that studies of diverse organisms can be compared and universal biomechanical principles can be revealed. Copyright © 2011 Elsevier Inc. All rights reserved.

Spontaneous polarization induced electric field in zinc oxide nanowires and nanostars

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

Farid, S., E-mail: sfarid3@uic.edu; Choi, M.; Datta, D.

We report on the detection mechanism of spontaneous polarization using electrostatic force microscopy in zinc oxide nanowires and nanostars grown by vapor-liquid-solid technique. Optical and structural properties are investigated in detail to understand the complex ZnO nanostructures comprehensively. Calculations are carried out to estimate the electric field from the change in interleave amplitude induced by the electrostatic force due to the spontaneous polarization effects. Attraction of the probe between the tip and the sample varies for different structures with a stronger attraction for nanostars as compared to nanowires. Strength of electric field is dependent on the orientation of nanowires andmore » nanostars c-axis with measured magnitude of electric field to be ∼10{sup 7 }V/m and 10{sup 8 }V/m respectively. This technique presents a unique detection mechanism of built-in spontaneous polarization and electric field from polar ZnO nanowires with applications in voltage gated ion channels, nano-bio interfaces, optoelectronic and photonic devices.« less

Nonlinear dynamics of a rack-pinion-rack device powered by the Casimir force.

PubMed

Miri, MirFaez; Nekouie, Vahid; Golestanian, Ramin

2010-01-01

Using the lateral Casimir force-a manifestation of the quantum fluctuations of the electromagnetic field between objects with corrugated surfaces-as the main force transduction mechanism, a nanomechanical device with rich dynamical behaviors is proposed. The device is made of two parallel racks that are moving in the same direction and a pinion in the middle that couples with both racks via the noncontact lateral Casimir force. The built-in frustration in the device causes it to be very sensitive and react dramatically to minute changes in the geometrical parameters and initial conditions of the system. The noncontact nature of the proposed device could help with the ubiquitous wear problem in nanoscale mechanical systems.

Magneto-capillary dynamics of amphiphilic Janus particles at curved liquid interfaces.

PubMed

Fei, Wenjie; Driscoll, Michelle M; Chaikin, Paul M; Bishop, Kyle J M

2018-05-11

A homogeneous magnetic field can exert no net force on a colloidal particle. However, by coupling the particle's orientation to its position on a curved interface, even static homogeneous fields can be used to drive rapid particle motions. Here, we demonstrate this effect using magnetic Janus particles with amphiphilic surface chemistry adsorbed at the spherical interface of a water drop in decane. Application of a static homogeneous field drives particle motion to the drop equator where the particle's magnetic moment can align parallel to the field. As explained quantitatively by a simple model, the effective magnetic force on the particle scales linearly with the curvature of the interface. For particles adsorbed on small droplets such as those found in emulsions, these magneto-capillary forces can far exceed those due to magnetic field gradients in both magnitude and range. This mechanism may be useful in creating highly responsive emulsions and foams stabilized by magnetic particles.

Field trapping and magnetic levitation performances of large single-grain Gd Ba Cu O at different temperatures

NASA Astrophysics Data System (ADS)

Nariki, S.; Fujikura, M.; Sakai, N.; Hirabayashi, I.; Murakami, M.

2005-10-01

We measured the temperature dependence of the trapped field and the magnetic levitation force for c-axis-oriented single-grain Gd-Ba-Cu-O bulk samples 48 mm in diameter. Trapped magnetic field of the samples was 2.1-2.2 T at 77 K and increased with decreasing temperature and reached 4.1 T at 70 K, however the sample fractured during the measurements at lower temperatures due to a large electromagnetic force. The reinforcement by a metal ring was effective in improving the mechanical strength. The sample encapsulated in an Al ring could trap a very high magnetic field of 9.0 T at 50 K. In liquid O 2 the Gd-Ba-Cu-O bulk exhibited a trapped field of 0.42 T and a magnetic levitation force about a half value of that in liquid N 2.

Adhesion and transfer of polytetrafluoroethylene to tungsten studied by field ion microscopy

NASA Technical Reports Server (NTRS)

Brainard, W. A.; Buckley, D. H.

1972-01-01

Mechanical contacts between polytetrafluoroethylene (PTFE) and tungsten field ion tips were made in situ in the field ion microscope. Both load and force of adhesion were measured for varying contact times and for clean and contaminated tungsten tips. Strong adhesion between the PTFE and clean tungsten was observed at contact times greater than 2.5 min (forces of adhesion were greater than three times the load). For times less than 2.5 min, the force of adhesion was immeasurably small. The increase in adhesion with contact time after 2.5 min can be attributed to the increase in true contact area by creep of PTFE. No adhesion was measurable at long contact times with contaminated tungsten tips. Neon field ion micrographs taken after the contacts show many linear and branched arrays which appear to represent PTFE that remains adhered to the surface even at the high electric fields required for imaging.

Traceable measurements of small forces and local mechanical properties

NASA Astrophysics Data System (ADS)

Campbellová, Anna; Valtr, Miroslav; Zůda, Jaroslav; Klapetek, Petr

2011-09-01

Measurement of local mechanical properties is an important topic in the fields of nanoscale device fabrication, thin film deposition and composite material development. Nanoindentation instruments are commonly used to study hardness and related mechanical properties at the nanoscale. However, traceability and uncertainty aspects of the measurement process often remain left aside. In this contribution, the use of a commercial nanoindentation instrument for metrology purposes will be discussed. Full instrument traceability, provided using atomic force microscope cantilevers and a mass comparator (normal force), interferometer (depth) and atomic force microscope (area function) is described. The uncertainty of the loading/unloading curve measurements will be analyzed and the resulting uncertainties for quantities, that are computed from loading curves such as hardness or elastic modulus, are studied. For this calculation a combination of uncertainty propagation law and Monte Carlo uncertainty evaluations are used.

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

PubMed Central

2016-01-01

Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena. PMID:26815602

Machine Learning of Accurate Energy-Conserving Molecular Force Fields

NASA Astrophysics Data System (ADS)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Molecular Mechanics: The Method and Its Underlying Philosophy.

ERIC Educational Resources Information Center

Boyd, Donald B.; Lipkowitz, Kenny B.

1982-01-01

Molecular mechanics is a nonquantum mechanical method for solving problems concerning molecular geometries and energy. Methodology based on: the principle of combining potential energy functions of all structural features of a particular molecule into a total force field; derivation of basic equations; and use of available computer programs is…

Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field.

PubMed

García-Pérez, E; Serra-Crespo, P; Hamad, S; Kapteijn, F; Gascon, J

2014-08-14

Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations of gas adsorption and diffusion of carbon dioxide and methane in NH2-MIL-53(Al) are carried out using a linear combination of two crystallographic structures with rigid force fields. Once the interactions of carbon dioxide molecules and the bridging hydroxyls groups of the framework are optimized, an excellent match is found for simulations and experimental data for the adsorption of methane and carbon dioxide, including the stepwise uptake due to the breathing effect. In addition, diffusivities of pure components are calculated. The pore expansion by the breathing effect influences the self-diffusion mechanism and much higher diffusivities are observed at relatively high adsorbate loadings. This work demonstrates that using a rigid force field combined with a minimum number of experiments, reproduces adsorption and simulates diffusion of carbon dioxide and methane in the flexible metal-organic framework NH2-MIL-53(Al).

Evaluation of DNA Force Fields in Implicit Solvation

PubMed Central

Gaillard, Thomas; Case, David A.

2011-01-01

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.

PubMed

Bell, David R; Qi, Rui; Jing, Zhifeng; Xiang, Jin Yu; Mejias, Christopher; Schnieders, Michael J; Ponder, Jay W; Ren, Pengyu

2016-11-09

Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.

Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.

PubMed

Shao, Qiang; Shi, Jiye; Zhu, Weiliang

2012-09-28

The ability of molecular dynamics simulation to capturing the transient states within the folding pathway of protein is important to the understanding of protein folding mechanism. In the present study, the integrated-tempering-sampling molecular dynamics (ITS-MD) simulation was performed to investigate the transient states including intermediate and unfolded ones in the folding pathway of a miniprotein, Trp-cage. Three force fields (FF03, FF99SB, and FF96) were tested, and both intermediate and unfolded states with their characteristics in good agreement with experiments were observed during the simulations, which supports the hypothesis that observable intermediates might present in the folding pathway of small polypeptides. In addition, it was demonstrated that FF03 force field as combined with ITS-MD is in overall a more proper force field than the others in reproducing experimentally recorded properties in UVRS, ECD, and NMR, Photo-CIDNP NMR, and IR T-jump experiments, and the folding∕unfolding thermodynamics parameters, such as ΔG(U), ΔC(p), and ΔH(U) (T(m)). In summary, the present study showed that using suitable force field and energy sampling method, molecular dynamics simulation could capture the transient states within the folding pathway of protein which are consistent with the experimental measurements, and thus provide information of protein folding mechanism and thermodynamics.

Weber's gravitational force as static weak field approximation

NASA Astrophysics Data System (ADS)

Tiandho, Yuant

2016-02-01

Weber's gravitational force (WGF) is one of gravitational model that can accommodate a non-static system because it depends not only on the distance but also on the velocity and the acceleration. Unlike Newton's law of gravitation, WGF can predict the anomalous of Mercury and gravitational bending of light near massive object very well. Then, some researchers use WGF as an alternative model of gravitation and propose a new mechanics theory namely the relational mechanics theory. However, currently we have known that the theory of general relativity which proposed by Einstein can explain gravity with very accurate. Through the static weak field approximation for the non-relativistic object, we also have known that the theory of general relativity will reduce to Newton's law of gravity. In this work, we expand the static weak field approximation that compatible with relativistic object and we obtain a force equation which correspond to WGF. Therefore, WGF is more precise than Newton's gravitational law. The static-weak gravitational field that we used is a solution of the Einstein's equation in the vacuum that satisfy the linear field approximation. The expression of WGF with ξ = 1 and satisfy the requirement of energy conservation are obtained after resolving the geodesic equation. By this result, we can conclude that WGF can be derived from the general relativity.

Centrifugal Force Based Magnetic Micro-Pump Driven by Rotating Magnetic Fields

NASA Astrophysics Data System (ADS)

Kim, S. H.; Hashi, S.; Ishiyama, K.

2011-01-01

This paper presents a centrifugal force based magnetic micro-pump for the pumping of blood. Most blood pumps are driven by an electrical motor with wired control. To develop a wireless and battery-free blood pump, the proposed pump is controlled by external rotating magnetic fields with a synchronized impeller. Synchronization occurs because the rotor is divided into multi-stage impeller parts and NdFeB permanent magnet. Finally, liquid is discharged by the centrifugal force of multi-stage impeller. The proposed pump length is 30 mm long and19 mm in diameter which much smaller than currently pumps; however, its pumping ability satisfies the requirement for a blood pump. The maximum pressure is 120 mmHg and the maximum flow rate is 5000ml/min at 100 Hz. The advantage of the proposed pump is that the general mechanical problems of a normal blood pump are eliminated by the proposed driving mechanism.

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

PubMed Central

2015-01-01

Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems. PMID:24874104

Nonlinear generation of large-scale magnetic fields in forced spherical shell dynamos

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

Livermore, P. W.; Hughes, D. W.; Tobias, S. M.

2010-03-15

In an earlier paper [P. W. Livermore, D. W. Hughes, and S. M. Tobias, ''The role of helicity and stretching in forced kinematic dynamos in a spherical shell'', Phys. Fluids 19, 057101 (2007)], we considered the kinematic dynamo action resulting from a forced helical flow in a spherical shell. Although mean field electrodynamics suggests that the resulting magnetic field should have a significant mean (axisymmetric) component, we found no evidence for this; the dynamo action was distinctly small scale. Here we extend our investigation into the nonlinear regime in which the magnetic field reacts back on the velocity via themore » Lorentz force. Our main result is somewhat surprising, namely, that nonlinear effects lead to a considerable change in the structure of the magnetic field, its final state having a significant mean component. By investigating the dominant flow-field interactions, we isolate the dynamo mechanism and show schematically how the generation process differs between the kinematic and nonlinear regimes. In addition, we are able to calculate some components of the transport coefficient {alpha} and thus discuss our results within the context of mean field electrodynamics.« less

Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

PubMed

Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

2014-02-01

The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine. Copyright © 2013 Elsevier Inc. All rights reserved.

Force-time profile differences in the delivery of simulated toggle-recoil spinal manipulation by students, instructors, and field doctors of chiropractic.

PubMed

DeVocht, James W; Owens, Edward F; Gudavalli, Maruti Ram; Strazewski, John; Bhogal, Ramneek; Xia, Ting

2013-01-01

The objectives of this study were to examine the force-time profiles of toggle recoil using an instrumented simulator to objectively measure and evaluate students' skill to determine if they become quicker and use less force during the course of their training and to compare them to course instructors and to field doctors of chiropractic (DCs) who use this specific technique in their practices. A load cell was placed within a toggle recoil training device. The preload, speed, and magnitude of the toggle recoil thrusts were measured from 60 students, 2 instructors, and 77 DCs (ie, who use the toggle recoil technique in their regular practice). Student data were collected 3 times during their toggle course (after first exposure, at midterm, and at course end.) Thrusts showed a dual-peak force-time profile not previously described in other forms of spinal manipulation. There was a wide range of values for each quantity measured within and between all 3 subject groups. The median peak load for students decreased over the course of their class, but they became slower. Field doctors were faster than students or instructors and delivered higher peak loads. Toggle recoil thrusts into a dropping mechanism varied based upon subject and amount of time practicing the task. As students progressed through the class, speed reduced as they increased control to lower peak loads. In the group studies, field DCs applied higher forces and were faster than both students and instructors. There appears to be a unique 2-peak feature of the force-time plot that is unique to toggle recoil manipulation with a drop mechanism. Copyright © 2013 National University of Health Sciences. Published by Mosby, Inc. All rights reserved.

Current state of the art in small mass and force metrology within the International System of Units

NASA Astrophysics Data System (ADS)

Shaw, Gordon A.

2018-07-01

This review article summarizes new scientific trends in research for metrology of small mass (1 mg and lower) and small force (10 micronewtons and lower). After a brief introduction to the field, this paper provides an overview of recent developments in methods that demonstrate traceability to the International System of Units (SI) with emphasis on the implications of redefining the kilogram in terms of Planck’s constant. Specific research applications include new metrology facilities, calibration of small mass and force references such as milligram to submilligram masses or atomic force microscope (AFM) cantilevers, and laser power measurement using radiation pressure forces. Also discussed are recent scientific developments that may impact the field moving forward in the study of ultrasmall forces present in trapped and cooled quantum mechanical systems, resonant micro- and nanomechanical mass sensors, and other areas that are potentially well suited for SI metrology. The work reviewed is not intended as a comprehensive review of all research in which small forces are measured, but rather as an overview of a field in which the accurate measurement of small mass and force with quantified uncertainty is the primary goal.

Mechanical forces as information: an integrated approach to plant and animal development

PubMed Central

Hernández-Hernández, Valeria; Rueda, Denisse; Caballero, Lorena; Alvarez-Buylla, Elena R.; Benítez, Mariana

2014-01-01

Mechanical forces such as tension and compression act throughout growth and development of multicellular organisms. These forces not only affect the size and shape of the cells and tissues but are capable of modifying the expression of genes and the localization of molecular components within the cell, in the plasma membrane, and in the plant cell wall. The magnitude and direction of these physical forces change with cellular and tissue properties such as elasticity. Thus, mechanical forces and the mesoscopic fields that emerge from their local action constitute important sources of positional information. Moreover, physical and biochemical processes interact in non-linear ways during tissue and organ growth in plants and animals. In this review we discuss how such mechanical forces are generated, transmitted, and sensed in these two lineages of multicellular organisms to yield long-range positional information. In order to do so we first outline a potentially common basis for studying patterning and mechanosensing that relies on the structural principle of tensegrity, and discuss how tensegral structures might arise in plants and animals. We then provide some examples of morphogenesis in which mechanical forces appear to act as positional information during development, offering a possible explanation for ubiquitous processes, such as the formation of periodic structures. Such examples, we argue, can be interpreted in terms of tensegral phenomena. Finally, we discuss the hypothesis of mechanically isotropic points as a potentially generic mechanism for the localization and maintenance of stem-cell niches in multicellular organisms. This comparative approach aims to help uncovering generic mechanisms of morphogenesis and thus reach a better understanding of the evolution and development of multicellular phenotypes, focusing on the role of physical forces in these processes. PMID:24959170

Mechanical forces as information: an integrated approach to plant and animal development.

PubMed

Hernández-Hernández, Valeria; Rueda, Denisse; Caballero, Lorena; Alvarez-Buylla, Elena R; Benítez, Mariana

2014-01-01

Mechanical forces such as tension and compression act throughout growth and development of multicellular organisms. These forces not only affect the size and shape of the cells and tissues but are capable of modifying the expression of genes and the localization of molecular components within the cell, in the plasma membrane, and in the plant cell wall. The magnitude and direction of these physical forces change with cellular and tissue properties such as elasticity. Thus, mechanical forces and the mesoscopic fields that emerge from their local action constitute important sources of positional information. Moreover, physical and biochemical processes interact in non-linear ways during tissue and organ growth in plants and animals. In this review we discuss how such mechanical forces are generated, transmitted, and sensed in these two lineages of multicellular organisms to yield long-range positional information. In order to do so we first outline a potentially common basis for studying patterning and mechanosensing that relies on the structural principle of tensegrity, and discuss how tensegral structures might arise in plants and animals. We then provide some examples of morphogenesis in which mechanical forces appear to act as positional information during development, offering a possible explanation for ubiquitous processes, such as the formation of periodic structures. Such examples, we argue, can be interpreted in terms of tensegral phenomena. Finally, we discuss the hypothesis of mechanically isotropic points as a potentially generic mechanism for the localization and maintenance of stem-cell niches in multicellular organisms. This comparative approach aims to help uncovering generic mechanisms of morphogenesis and thus reach a better understanding of the evolution and development of multicellular phenotypes, focusing on the role of physical forces in these processes.

Mapping the Drude polarizable force field onto a multipole and induced dipole model

NASA Astrophysics Data System (ADS)

Huang, Jing; Simmonett, Andrew C.; Pickard, Frank C.; MacKerell, Alexander D.; Brooks, Bernard R.

2017-10-01

The induced dipole and the classical Drude oscillator represent two major approaches for the explicit inclusion of electronic polarizability into force field-based molecular modeling and simulations. In this work, we explore the equivalency of these two models by comparing condensed phase properties computed using the Drude force field and a multipole and induced dipole (MPID) model. Presented is an approach to map the electrostatic model optimized in the context of the Drude force field onto the MPID model. Condensed phase simulations on water and 15 small model compounds show that without any reparametrization, the MPID model yields properties similar to the Drude force field with both models yielding satisfactory reproduction of a range of experimental values and quantum mechanical data. Our results illustrate that the Drude oscillator model and the point induced dipole model are different representations of essentially the same physical model. However, results indicate the presence of small differences between the use of atomic multipoles and off-center charge sites. Additionally, results on the use of dispersion particle mesh Ewald further support its utility for treating long-range Lennard Jones dispersion contributions in the context of polarizable force fields. The main motivation in demonstrating the transferability of parameters between the Drude and MPID models is that the more than 15 years of development of the Drude polarizable force field can now be used with MPID formalism without the need for dual-thermostat integrators nor self-consistent iterations. This opens up a wide range of new methodological opportunities for polarizable models.

Machine Learning Force Field Parameters from Ab Initio Data

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

Li, Ying; Li, Hui; Pickard, Frank C.

Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor duringmore » the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.« less

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing

PubMed Central

Vanommeslaeghe, K.; MacKerell, A. D.

2012-01-01

Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF’s complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/. PMID:23146088

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

PubMed

Vanommeslaeghe, K; MacKerell, A D

2012-12-21

Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF's complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/ .

Rapid parameterization of small molecules using the Force Field Toolkit.

PubMed

Mayne, Christopher G; Saam, Jan; Schulten, Klaus; Tajkhorshid, Emad; Gumbart, James C

2013-12-15

The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment). Copyright © 2013 Wiley Periodicals, Inc.

Effect of Position- and Velocity-Dependent Forces on Reaching Movements at Different Speeds

PubMed Central

Summa, Susanna; Casadio, Maura; Sanguineti, Vittorio

2016-01-01

The speed of voluntary movements is determined by the conflicting needs of maximizing accuracy and minimizing mechanical effort. Dynamic perturbations, e.g., force fields, may be used to manipulate movements in order to investigate these mechanisms. Here, we focus on how the presence of position- and velocity-dependent force fields affects the relation between speed and accuracy during hand reaching movements. Participants were instructed to perform reaching movements under visual control in two directions, corresponding to either low or high arm inertia. The subjects were required to maintain four different movement durations (very slow, slow, fast, very fast). The experimental protocol included three phases: (i) familiarization—the robot generated no force; (ii) force field—the robot generated a force; and (iii) after-effect—again, no force. Participants were randomly assigned to four groups, depending on the type of force that was applied during the “force field” phase. The robot was programmed to generate position-dependent forces—with positive (K+) or negative stiffness (K−)—or velocity-dependent forces, with either positive (B+) or negative viscosity (B−). We focused on path curvature, smoothness, and endpoint error; in the latter we distinguished between bias and variability components. Movements in the high-inertia direction are smoother and less curved; smoothness also increases with movement speed. Endpoint bias and variability are greater in, respectively, the high and low inertia directions. A robust dependence on movement speed was only observed in the longitudinal components of both bias and variability. The strongest and more consistent effects of perturbation were observed with negative viscosity (B−), which resulted in increased variability during force field adaptation and in a reduction of the endpoint bias, which was retained in the subsequent after-effect phase. These findings confirm that training with negative viscosity produces lasting effects in movement accuracy at all speeds. PMID:27965559

Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics

PubMed Central

Ben Imeddourene, Akli; Elbahnsi, Ahmad; Guéroult, Marc; Oguey, Christophe; Foloppe, Nicolas; Hartmann, Brigitte

2015-01-01

The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI ↔ BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0εζOLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representation of B-DNA in solution, despite residual shortcomings. This improved representation allows new and deeper interpretation of the experimental observables, including regarding the behavior of facing phosphate groups in complementary dinucleotides, and their modulation by the sequence. It also provides the opportunity to extensively revisit and refine the coupling between backbone states and inter base pair parameters, which emerges as a common theme across all the complementary dinucleotides. In sum, the global agreement between simulations and experiment reveals new aspects of intrinsic DNA mechanics, a key component of DNA-protein recognition. PMID:26657165

Mapping the force field of a hydrogen-bonded assembly

NASA Astrophysics Data System (ADS)

Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

2014-05-01

Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

NASA Astrophysics Data System (ADS)

Chen, Chen; Arntsen, Christopher; Voth, Gregory A.

2017-10-01

Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

Modeling the mechanism of CLN025 beta-hairpin formation

NASA Astrophysics Data System (ADS)

McKiernan, Keri A.; Husic, Brooke E.; Pande, Vijay S.

2017-09-01

Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

PubMed

Arnautova, Yelena A; Abagyan, Ruben A; Totrov, Maxim

2011-02-01

We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the biased probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for four residues loops, 0.84/0.46 Å for eight residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable with those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. © 2010 Wiley-Liss, Inc.

Electron beam detection of a Nanotube Scanning Force Microscope.

PubMed

Siria, Alessandro; Niguès, Antoine

2017-09-14

Atomic Force Microscopy (AFM) allows to probe matter at atomic scale by measuring the perturbation of a nanomechanical oscillator induced by near-field interaction forces. The quest to improve sensitivity and resolution of AFM forced the introduction of a new class of resonators with dimensions at the nanometer scale. In this context, nanotubes are the ultimate mechanical oscillators because of their one dimensional nature, small mass and almost perfect crystallinity. Coupled to the possibility of functionalisation, these properties make them the perfect candidates as ultra sensitive, on-demand force sensors. However their dimensions make the measurement of the mechanical properties a challenging task in particular when working in cavity free geometry at ambient temperature. By using a focused electron beam, we show that the mechanical response of nanotubes can be quantitatively measured while approaching to a surface sample. By coupling electron beam detection of individual nanotubes with a custom AFM we image the surface topography of a sample by continuously measuring the mechanical properties of the nanoresonators. The combination of very small size and mass together with the high resolution of the electron beam detection method offers unprecedented opportunities for the development of a new class of nanotube-based scanning force microscopy.

Magnetically actuated tissue engineered scaffold: insights into mechanism of physical stimulation

NASA Astrophysics Data System (ADS)

Sapir-Lekhovitser, Yulia; Rotenberg, Menahem Y.; Jopp, Juergen; Friedman, Gary; Polyak, Boris; Cohen, Smadar

2016-02-01

Providing the right stimulatory conditions resulting in efficient tissue promoting microenvironment in vitro and in vivo is one of the ultimate goals in tissue development for regenerative medicine. It has been shown that in addition to molecular signals (e.g. growth factors) physical cues are also required for generation of functional cell constructs. These cues are particularly relevant to engineering of biological tissues, within which mechanical stress activates mechano-sensitive receptors, initiating biochemical pathways which lead to the production of functionally mature tissue. Uniform magnetic fields coupled with magnetizable nanoparticles embedded within three dimensional (3D) scaffold structures remotely create transient physical forces that can be transferrable to cells present in close proximity to the nanoparticles. This study investigated the hypothesis that magnetically responsive alginate scaffold can undergo reversible shape deformation due to alignment of scaffold's walls in a uniform magnetic field. Using custom made Helmholtz coil setup adapted to an Atomic Force Microscope we monitored changes in matrix dimensions in situ as a function of applied magnetic field, concentration of magnetic particles within the scaffold wall structure and rigidity of the matrix. Our results show that magnetically responsive scaffolds exposed to an externally applied time-varying uniform magnetic field undergo a reversible shape deformation. This indicates on possibility of generating bending/stretching forces that may exert a mechanical effect on cells due to alternating pattern of scaffold wall alignment and relaxation. We suggest that the matrix structure deformation is produced by immobilized magnetic nanoparticles within the matrix walls resulting in a collective alignment of scaffold walls upon magnetization. The estimated mechanical force that can be imparted on cells grown on the scaffold wall at experimental conditions is in the order of 1 pN, which correlates well with reported threshold to induce mechanotransduction effects on cellular level. This work is our next step in understanding of how to accurately create proper stimulatory microenvironment for promotion of cellular organization to form mature tissue engineered constructs.

Magnetically actuated tissue engineered scaffold: insights into mechanism of physical stimulation

PubMed Central

Sapir-Lekhovitser, Yulia; Rotenberg, Menahem Y.; Jopp, Juergen; Friedman, Gary; Polyak, Boris; Cohen, Smadar

2016-01-01

Providing the right stimulatory conditions resulting in efficient tissue promoting microenvironment in vitro and in vivo is one of the ultimate goals in tissue development for regenerative medicine. It has been shown that in addition to molecular signals (e.g. growth factors) physical cues are also required for generation of functional cell constructs. These cues are particularly relevant to engineering of biological tissues, within which mechanical stress activates mechano-sensitive receptors, initiating biochemical pathways which lead to the production of functionally mature tissue. Uniform magnetic fields coupled with magnetizable nanoparticles embedded within three dimensional (3D) scaffold structures remotely create transient physical forces that can be transferrable to cells present in close proximity to the nanoparticles. This study investigated the hypothesis that magnetically responsive alginate scaffold can undergo reversible shape deformation due to alignment of scaffold’s walls in a uniform magnetic field. Using custom made Helmholtz coil setup adapted to an Atomic Force Microscope we monitored changes in matrix dimensions in situ as a function of applied magnetic field, concentration of magnetic particles within the scaffold wall structure and rigidity of the matrix. Our results show that magnetically responsive scaffolds exposed to an externally applied time-varying uniform magnetic field undergo a reversible shape deformation. This indicates on possibility of generating bending/stretching forces that may exert a mechanical effect on cells due to alternating pattern of scaffold wall alignment and relaxation. We suggest that the matrix structure deformation is produced by immobilized magnetic nanoparticles within the matrix walls resulting in a collective alignment of scaffold walls upon magnetization. The estimated mechanical force that can be imparted on cells grown on the scaffold wall at experimental conditions is in the order of 1 pN, which correlates well with reported threshold to induce mechanotransduction effects on cellular level. This work is our next step in understanding of how to accurately create proper stimulatory microenvironment for promotion of cellular organization to form mature tissue engineered constructs. PMID:26790538

Stochastic generation of MAC waves and implications for convection in Earth's core

NASA Astrophysics Data System (ADS)

Buffett, Bruce; Knezek, Nicholas

2018-03-01

Convection in Earth's core can sustain magnetic-Archemedes-Coriolis (MAC) waves through a variety of mechanisms. Buoyancy and Lorentz forces are viable sources for wave motion, together with the effects of magnetic induction. We develop a quantitative description for zonal MAC waves and assess the source mechanisms using a numerical dynamo model. The largest sources at conditions accessible to the dynamo model are due to buoyancy forces and magnetic induction. However, when these sources are extrapolated to conditions expected in Earth's core, the Lorentz force emerges as the dominant generation mechanism. This source is expected to produce wave velocities of roughly 2 km yr-1 when the internal magnetic field is characterized by a dimensionless Elsasser number of roughly Λ ≈ 10 and the root-mean-square convective velocity defines a magnetic Reynolds number of Rm ≈ 103. Our preferred model has a radially varying stratification and a constant (radial) background magnetic field. It predicts a broad power spectrum for the wave velocity with most power distributed across periods from 30 to 100 yr.

Mechanism analysis of Magnetohydrodynamic heat shield system and optimization of externally applied magnetic field

NASA Astrophysics Data System (ADS)

Li, Kai; Liu, Jun; Liu, Weiqiang

2017-04-01

As a novel thermal protection technique for hypersonic vehicles, Magnetohydrodynamic (MHD) heat shield system has been proved to be of great intrinsic value in the hypersonic field. In order to analyze the thermal protection mechanisms of such a system, a physical model is constructed for analyzing the effect of the Lorentz force components in the counter and normal directions. With a series of numerical simulations, the dominating Lorentz force components are analyzed for the MHD heat flux mitigation in different regions of a typical reentry vehicle. Then, a novel magnetic field with variable included angle between magnetic induction line and streamline is designed, which significantly improves the performance of MHD thermal protection in the stagnation and shoulder areas. After that, the relationships between MHD shock control and MHD thermal protection are investigated, based on which the magnetic field above is secondarily optimized obtaining better performances of both shock control and thermal protection. Results show that the MHD thermal protection is mainly determined by the Lorentz force's effect on the boundary layer. From the stagnation to the shoulder region, the flow deceleration effect of the counter-flow component is weakened while the flow deflection effect of the normal component is enhanced. Moreover, there is no obviously positive correlation between the MHD shock control and thermal protection. But once a good Lorentz force's effect on the boundary layer is guaranteed, the thermal protection performance can be further improved with an enlarged shock stand-off distance by strengthening the counter-flow Lorentz force right after shock.

Measurement of time-varying displacement fields in cell culture for traction force optical coherence microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Mulligan, Jeffrey A.; Adie, Steven G.

2017-02-01

Mechanobiology is an emerging field which seeks to link mechanical forces and properties to the behaviors of cells and tissues in cancer, stem cell growth, and other processes. Traction force microscopy (TFM) is an imaging technique that enables the study of traction forces exerted by cells on their environment to migrate as well as sense and manipulate their surroundings. To date, TFM research has been performed using incoherent imaging modalities and, until recently, has been largely confined to the study of cell-induced tractions within two-dimensions using highly artificial and controlled environments. As the field of mechanobiology advances, and demand grows for research in physiologically relevant 3D culture and in vivo models, TFM will require imaging modalities that support such settings. Optical coherence microscopy (OCM) is an interferometric imaging modality which enables 3D cellular resolution imaging in highly scattering environments. Moreover, optical coherence elastography (OCE) enables the measurement of tissue mechanical properties. OCE relies on the principle of measuring material deformations in response to artificially applied stress. By extension, similar techniques can enable the measurement of cell-induced deformations, imaged with OCM. We propose traction force optical coherence microscopy (TF-OCM) as a natural extension and partner to existing OCM and OCE methods. We report the first use of OCM data and digital image correlation to track temporally varying displacement fields exhibited within a 3D culture setting. These results mark the first steps toward the realization of TF-OCM in 2D and 3D settings, bolstering OCM as a platform for advancing research in mechanobiology.

Structural frequency functions for an impulsive, distributed forcing function

NASA Technical Reports Server (NTRS)

Bateman, Vesta I.

1987-01-01

The response of a penetrator structure to a spatially distributed mechanical impulse with a magnitude approaching field test force levels (1-2 Mlb) were measured. The frequency response function calculated from the response to this unique forcing function is compared to frequency response functions calculated from response to point forces of about 2000 pounds. The results show that the strain gages installed on the penetrator case respond similiarly to a point, axial force and to a spatially distributed, axial force. This result suggests that the distributed axial force generated in a penetration event may be reconstructed as a point axial force when the penetrator behaves in linear manner.

Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods.

PubMed

Torres, Edmanuel; DiLabio, Gino A

2013-08-13

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system.

A Simple Force-Motion Relation for Migrating Cells Revealed by Multipole Analysis of Traction Stress

PubMed Central

Tanimoto, Hirokazu; Sano, Masaki

2014-01-01

For biophysical understanding of cell motility, the relationship between mechanical force and cell migration must be uncovered, but it remains elusive. Since cells migrate at small scale in dissipative circumstances, the inertia force is negligible and all forces should cancel out. This implies that one must quantify the spatial pattern of the force instead of just the summation to elucidate the force-motion relation. Here, we introduced multipole analysis to quantify the traction stress dynamics of migrating cells. We measured the traction stress of Dictyostelium discoideum cells and investigated the lowest two moments, the force dipole and quadrupole moments, which reflect rotational and front-rear asymmetries of the stress field. We derived a simple force-motion relation in which cells migrate along the force dipole axis with a direction determined by the force quadrupole. Furthermore, as a complementary approach, we also investigated fine structures in the stress field that show front-rear asymmetric kinetics consistent with the multipole analysis. The tight force-motion relation enables us to predict cell migration only from the traction stress patterns. PMID:24411233

Shock Magnetic Field and Origin of the Earth

NASA Technical Reports Server (NTRS)

Tunyi, I.; Timko, M.; Roth, L. E.

2001-01-01

To the effects of impulse magnetic field in protoplanetary nebula (fast melting, cooling and magnetization of chondrules), there is added another possible effect - mechanism associated with the forces of attraction between magnetized planetesimals. Additional information is contained in the original extended abstract.

Ratchet baryogenesis and an analogy with the forced pendulum

NASA Astrophysics Data System (ADS)

Bamba, Kazuharu; Barrie, Neil D.; Sugamoto, Akio; Takeuchi, Tatsu; Yamashita, Kimiko

2018-06-01

A new scenario of baryogenesis via the ratchet mechanism is proposed based on an analogy with the forced pendulum. The oscillation of the inflaton field during the reheating epoch after inflation plays the role of the driving force, while the phase 𝜃 of a scalar baryon field (a complex scalar field with baryon number) plays the role of the angle of the pendulum. When the inflaton is coupled to the scalar baryon, the behavior of the phase 𝜃 can be analogous to that of the angle of the forced pendulum. If the oscillation of the driving force is adjusted to the pendulum’s motion, a directed rotation of the pendulum is obtained with a nonvanishing value of 𝜃˙, which models successful baryogenesis since 𝜃˙ is proportional to the baryon number density. Similar ratchet models which lead to directed motion have been used in the study of molecular motors in biology. There, the driving force is supplied by chemical reactions, while in our scenario this role is played by the inflaton during the reheating epoch.

Influence of magnetic pressure on stellar structure: A Mechanism for solar variability

NASA Technical Reports Server (NTRS)

Schatten, K. H.; Endal, A. S.

1980-01-01

A physical mechanism is proposed that couples the Sun's dynamo magnetic field to its gravitational potential energy. The mechanism involves the isotropic field pressure resulting in a lifting force on the convective envelope, thereby raising its potential energy. Decay of the field due to solar activity allows the envelop to subside and releases this energy, which can augment the otherwise steady solar luminosity. Equations are developed and applied to the Sun for several field configurations. The best estimate model suggests that uniform luminosity variations as large as 0.02% for half a sunspot cycle may occur. Brief temporal variations or the rotation of spatial structures could allow larger excursions in the energy released.

Lattice QCD with strong external electric fields.

PubMed

Yamamoto, Arata

2013-03-15

We study particle generation by a strong electric field in lattice QCD. To avoid the sign problem of the Minkowskian electric field, we adopt the "isospin" electric charge. When a strong electric field is applied, the insulating vacuum is broken down and pairs of charged particles are produced by the Schwinger mechanism. The competition against the color confining force is also discussed.

Mechanical design in embryos: mechanical signalling, robustness and developmental defects.

PubMed

Davidson, Lance A

2017-05-19

Embryos are shaped by the precise application of force against the resistant structures of multicellular tissues. Forces may be generated, guided and resisted by cells, extracellular matrix, interstitial fluids, and how they are organized and bound within the tissue's architecture. In this review, we summarize our current thoughts on the multiple roles of mechanics in direct shaping, mechanical signalling and robustness of development. Genetic programmes of development interact with environmental cues to direct the composition of the early embryo and endow cells with active force production. Biophysical advances now provide experimental tools to measure mechanical resistance and collective forces during morphogenesis and are allowing integration of this field with studies of signalling and patterning during development. We focus this review on concepts that highlight this integration, and how the unique contributions of mechanical cues and gradients might be tested side by side with conventional signalling systems. We conclude with speculation on the integration of large-scale programmes of development, and how mechanical responses may ensure robust development and serve as constraints on programmes of tissue self-assembly.This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'. © 2017 The Author(s).

Mechanical Properties of Single Collagen Fibrils Revealed by Force Spectroscopy

NASA Astrophysics Data System (ADS)

Graham, John; Phillips, Charlotte; Grandbois, Michel

2004-03-01

In the field of biomechanics, collagen fibrils are believed to be robust mechanical structures characterized by a low extensibility. Until very recently, information on the mechanical properties of collagen fibrils could only be derived from ensemble measurements performed on complete tissues such as bone, skin and tendon. Here we measure force-elongation/relaxation profiles of single collagen fibrils using atomic force microscopy-based force spectroscopy. The elongation profiles indicate that in vitro assembled heterotrimeric type I collagen fibrils are characterized by a large extensibility. Numerous discontinuities and a plateau in the force profile indicate major reorganization occurs within the fibrils in the 1.5 -- 4.5 nN range. Our study demonstrates that newly assembled collagen fibrils are robust structures with a significant reserve of elasticity that could play a determinant role in cellular motion in the context of tissue growth and morphogenesis. In contrast, homotrimeric collagen fibrils corresponding to osteogenesis imperfecta pathology exhibit a marked difference in their elasticity profile.

Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space.

PubMed

Liu, Zhiwei; Ensing, Bernd; Moore, Preston B

2011-02-08

The free energy surfaces (FESs) of alanine dipeptide are studied to illustrate a new strategy to assess the performance of classical molecular mechanics force field on the full range of the (ϕ-ψ) conformational space. The FES is obtained from metadynamics simulations with five commonly used force fields and from ab initio density functional theory calculations in both gas phase and aqueous solution. The FESs obtained at the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d,p) level of theory are validated by comparison with previously reported MP2 and LMP2 results as well as with experimentally obtained probability distribution between the C5-β (or β-PPII) and αR states. A quantitative assessment is made for each force field in three conformational basins, LeRI (C5-β-C7eq), LeRII (β2-αR), and LeRIII(αL-C7ax-αD) as well as three transition-state regions linking the above conformational basins. The performance of each force field is evaluated in terms of the average free energy of each region in comparison with that of the ab initio results. We quantify how well a force field FES matches the ab initio FES through the calculation of the standard deviation of a free energy difference map between the two FESs. The results indicate that the performance varies largely from region to region or from force field to force field. Although not one force field is able to outperform all others in all conformational areas, the OPLSAA/L force field gives the best performance overall, followed by OPLSAA and AMBER03. For the three top performers, the average free energies differ from the corresponding ab initio values from within the error range (<0.4 kcal/mol) to ∼1.5 kcal/mol for the low-energy regions and up to ∼2.0 kcal/mol for the transition-state regions. The strategy presented and the results obtained here should be useful for improving the parametrization of force fields targeting both accuracy in the energies of conformers and the transition-state barriers.

Young’s modulus calculations for cellulose Iß by MM3 and quantum mechanics

USDA-ARS?s Scientific Manuscript database

Quantum mechanics (QM) and molecular mechanics (MM) calculations were performed to elucidate Young’s moduli for a series of cellulose Iß models. Computations using the second generation empirical force field MM3 with a disaccharide cellulose model, 1,4'-O-dimethyl-ß-cellobioside (DMCB), and an analo...

A simulation of dielectrophoresis force actuated liquid lens

NASA Astrophysics Data System (ADS)

Yao, Xiaoyin; Xia, Jun

2009-11-01

Dielectrophoresis (DEP) and electrowetting on dielectric (EWOD) are based on the electrokinetic mechanisms which have great potential in microfluidic manipulation. DEP dominate the movement of particles induced by polarization effects in nonuniform electric field ,while EWOD has become one of the most widely used tools for manipulating tiny amounts of liquids on solid surfaces. Liquid lens driven by EWOD have been well studied and developed. But liquid lens driven by DEP has not been studied adequately. This paper focuses on modeling liquid lens driven by DEP force. A simulation of DEP driven droplet dynamics was performed by coupling of the electrostatic field and the two-phase flow field. Two incompressible and dielectric liquids with different permittivity were chosen in the two-phase flow field. The DEP force density, in direct proportion to gradient of the square of the electric field intensity, was used as a body force density in Navier-Stokes equation. When voltage applied, the liquid with high permittivity flowed to the place where the gradient of the square of the electric field intensity was higher, and thus change the curvature of interface between two immiscible liquid. The differences between DEP and EWOD liquid lens were also presented.

ELECTROMAGNETICALLY INDUCED DISTORTION OF A FIBRIN MATRIX WITH EMBEDDED MICROPARTICLES

PubMed Central

SCOGIN, TYLER; YESUDASAN, SUMITH; WALKER, MITCHELL L. R.

2018-01-01

Blood clots occur in the human body when they are required to prevent bleeding. In pathological states such as diabetes and sickle cell disease, blood clots can also form undesirably due to hypercoagulable plasma conditions. With the continued effort in developing fibrin therapies for potential life-saving solutions, more mechanical modeling is needed to understand the properties of fibrin structures with inclusions. In this study, a fibrin matrix embedded with magnetic micro particles (MMPs) was subjected to a magnetic field to determine the magnitude of the required force to create plastic deformation within the fibrin clot. Using finite element (FE) analysis, we estimated the magnetic force from an electromagnet at a sample space located approximately 3 cm away from the coil center. This electromagnetic force coupled with gravity was applied on a fibrin mechanical system with MMPs to calculate the stresses and displacements. Using appropriate coil parameters, it was determined that application of a magnetic field of 730 A/m on the fibrin surface was necessary to achieve an electromagnetic force of 36 nN (to engender plastic deformation). PMID:29628543

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

Dang, Liem X.; Vo, Quynh N.; Nilsson, Mikael

We report one of the first simulations using a classical rate theory approach to predict the mechanism of the exchange process between water and aqueous uranyl ions. Using our water and ion-water polarizable force fields and molecular dynamics techniques, we computed the potentials of mean force for the uranyl ion-water pair as the function of pressures at ambient temperature. Subsequently, these simulated potentials of mean force were used to calculate rate constants using the transition rate theory; the time dependent transmission coefficients were also examined using the reactive flux method and Grote-Hynes treatments of the dynamic response of the solvent.more » The computed activation volumes using transition rate theory and the corrected rate constants are positive, thus the mechanism of this particular water-exchange is a dissociative process. We discuss our rate theory results and compare them with previously studies in which non-polarizable force fields were used. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

Comparison of forcing functions in magnetohydrodynamics

NASA Astrophysics Data System (ADS)

McKay, Mairi E.; Linkmann, Moritz; Clark, Daniel; Chalupa, Adam A.; Berera, Arjun

2017-11-01

Results are presented of direct numerical simulations of incompressible, homogeneous magnetohydrodynamic turbulence without a mean magnetic field, subject to different mechanical forcing functions commonly used in the literature. Specifically, the forces are negative damping (which uses the large-scale velocity field as a forcing function), a nonhelical random force, and a nonhelical static sinusoidal force (analogous to helical ABC forcing). The time evolution of the three ideal invariants (energy, magnetic helicity, and cross helicity), the time-averaged energy spectra, the energy ratios, and the dissipation ratios are examined. All three forcing functions produce qualitatively similar steady states with regard to the time evolution of the energy and magnetic helicity. However, differences in the cross-helicity evolution are observed, particularly in the case of the static sinusoidal method of energy injection. Indeed, an ensemble of sinusoidally forced simulations with identical parameters shows significant variations in the cross helicity over long time periods, casting some doubt on the validity of the principle of ergodicity in systems in which the injection of helicity cannot be controlled. Cross helicity can unexpectedly enter the system through the forcing function and must be carefully monitored.

Conductivity affects nanosecond electrical pulse induced pressure transient formation

NASA Astrophysics Data System (ADS)

Roth, Caleb C.; Barnes, Ronald A.; Ibey, Bennett L.; Beier, Hope T.; Glickman, Randolph D.

2016-03-01

Nanoporation occurs in cells exposed to high amplitude short duration (< 1μs) electrical pulses. The biophysical mechanism(s) responsible for nanoporation is unknown although several theories exist. Current theories focus exclusively on the electrical field, citing electrostriction, water dipole alignment and/or electrodeformation as the primary mechanisms for pore formation. Our group has shown that mechanical forces of substantial magnitude are also generated during nsEP exposures. We hypothesize that these mechanical forces may contribute to pore formation. In this paper, we report that alteration of the conductivity of the exposure solution also altered the level of mechanical forces generated during a nsEP exposure. By reducing the conductivity of the exposure solutions, we found that we could completely eliminate any pressure transients normally created by nsEP exposure. The data collected for this proceeding does not definitively show that the pressure transients previously identified contribute to nanoporation; however; it indicates that conductivity influences both survival and pressure transient formation.

Thermal Noise Reduction of Mechanical Oscillators by Actively Controlled External Dissipative Forces

NASA Technical Reports Server (NTRS)

Liang, Shoudan; Medich, David; Czajkowsky, Daniel M.; Sheng, Sitong; Yuan, Jian-Yang; Shao, Zhifeng

1999-01-01

We show that the thermal fluctuations of very soft mechanical oscillators, such as the cantilever in an atomic force microscope (AFM), can be reduced without changing the stiffness of the spring or having to lower the environment temperature. We derive a theoretical relationship between the thermal fluctuations of an oscillator and an actively external-dissipative force. This relationship is verified by experiments with an AFM cantilever where the external active force is coupled through a magnetic field. With simple instrumentation, we have reduced the thermal noise amplitude of the cantilever by a factor of 3.4, achieving an apparent temperature of 25 K with the environment at 295K. This active noise reduction approach can significantly improve the accuracy of static position or static force measurements in a number of practical applications.

Find Your Center

ERIC Educational Resources Information Center

Trauth-Nare, Amy; Pavilonis, Amy; Paganucci, Julia; Ciabattoni, Gemma; Buckley, Jenni

2016-01-01

"Mechanics" is a branch of engineering and physics that deals with forces and motion, and its fundamental principles apply to all objects, whether a bouncing ball, flowing stream, bicycle, or the human body. The field of "biomechanics" applies mechanics concepts specifically to the bodies of humans (and other animals).…

Investigation of mechanical field weakening of axial flux permanent magnet motor

NASA Astrophysics Data System (ADS)

Syaifuddin Mohd, M.; Aziz, A. Rashid A.; Syafiq Mohd, M.

2015-12-01

An investigation of axial flux permanent magnet motor (AFPM) characteristics was conducted with a proposed mechanical field weakening control mechanisms (by means of stator-rotor force manipulation) on the motor through modeling and experimentation. By varying the air gap between at least two bistable positions, the peak torque and top speed of the motor can be extended. The motor high efficiency region can also be extended to cover greater part of the motor operating points. An analytical model of the motor had been developed to study the correlation between the total attraction force (between the rotor and the stator) and the operating parameters of the motor. The test results shows that the motor output complies with the prediction of the research hypothesis and it is likely that a spring locking mechanism can be built to dynamically adjust the air gap of the motor to increase the operating range and could be applied in electric drivetrain applications to improve overall efficiency of electric and hybrid electric vehicles.

Broken Symmetry

ScienceCinema

Englert, Francois

2018-05-24

- Physics, as we know it, attempts to interpret the diverse natural phenomena as particular manifestations of general laws. This vision of a world ruled by general testable laws is relatively recent in the history of mankind. Basically it was initiated by the Galilean inertial principle. The subsequent rapid development of large-scale physics is certainly tributary to the fact that gravitational and electromagnetic forces are long-range and hence can be perceived directly without the mediation of highly sophisticated technical devices. - The discovery of subatomic structures and of the concomitant weak and strong short-range forces raised the question of how to cope with short-range forces in relativistic quantum field theory. The Fermi theory of weak interactions, formulated in terms of point-like current-current interaction, was well-defined in lowest order perturbation theory and accounted for existing experimental data.However, it was inconsistent in higher orders because of uncontrollable divergent quantum fluctuations. In technical terms, in contradistinction to quantum electrodynamics, the Fermi theorywas not “renormalizable”. This difficulty could not be solved by smoothing the point-like interaction by a massive, and therefore short-range, charged “vector” particle exchange: theories with massive charged vector bosons were not renormalizable either. In the early nineteen sixties, there seemed to be insuperable obstacles to formulating a consistent theory with short-range forces mediated by massive vectors. - The breakthrough came from the notion of spontaneous symmetry breaking which arose in the study of phase transitions and was introduced in field theory by Nambu in 1960. - Ferromagnets illustrate the notion in phase transitions. Although no direction is dynamically preferred, the magnetization selects a global orientation. This is a spontaneous broken symmetry(SBS)of rotational invariance. Such continuous SBS imply the existence of “massless” modes (here spin-waves), which are the ancestors of the NG bosons discussed below. Fluctuations of the order parameter (the magnetization) are described by a “massive” SBS mode. - In field theory, Nambu showed that broken chiral symmetry from a spontaneous generation of hadron masses induces massless pseudoscalar modes (identified with a massless limit of pion fields). This illustrates a general phenomenon made explicit by Goldstone: massless Nambu-Goldstone (NG) bosons are a necessary concomitant of spontaneously broken continuous symmetries. Massive SBS scalars bosons describe, as in phase transitions, the fluctuations of the SBS order parameters. - In 1964, with Robert Brout, we discovered a mechanism based on SBS by which short range interactions are generated from long range ones. A similar proposal was then made independently by Higgs in a different approach. Qualitatively, our mechanism works as follows. The long range fundamental electromagnetic and gravitational interactions are governed by extended symmetries,called gauge symmetries, which were supposed to guarantee that the elementary field constituents which transmit the forces, photons or gravitons, be massless. We considered a generalization of the electromagnetic “vector” field, known as Yang-Mills fields, and coupled them to fields which acquire from SBS constant values in the vacuum. These fields pervade space, as did magnetization, but they have no spatial orientation: they are “scalar’’ fields. The vector Yang-Mills fields which interact with the scalar fields become massive and hence the forces they mediate become short ranged. We also showed that the mechanism can survive in absence of elementary scalar fields. - Because of the extended symmetries, the nature of SBS is profoundly altered: the NG fields are absorbed into the massive vector Yang-Mills fields and restore the gauge symmetry. This has a dramatic consequence. To confront precision experiments, the mechanism should be consistent at the quantum mechanical level, or in technical terms, should yield a “renormalizable” theory. From our analysis of the preserved gauge symmetry, we suggested in 1966 that this is indeed the case, in contradistinction to the aforementioned earlier theories of charged massive vector fields. The full proof of “renormalizability” is subtle and was achieved in the impressive work of ‘t Hooft and Veltman. One gains some insight into the subtleties by making explicit the equivalence of Higgs’ approach with ours. - To a large extend, the LHC was build to detect the massive SBS scalar boson, i.e. the fluctuations of the scalar field. More elaborate realizations of the mechanism without elementary scalars are possible, but their experimental confirmation may (or may not) be outside the scope of present available technology. - The mechanism of Brout, Englert and Higgs unified in the same theoretical framework short- and long-range forces. It became the cornerstone of the electroweak theory and opened the way to a modern view on unified laws of nature.

Quantum Field Energy Sensor based on the Casimir Effect

NASA Astrophysics Data System (ADS)

Ludwig, Thorsten

The Casimir effect converts vacuum fluctuations into a measurable force. Some new energy technologies aim to utilize these vacuum fluctuations in commonly used forms of energy like electricity or mechanical motion. In order to study these energy technologies it is helpful to have sensors for the energy density of vacuum fluctuations. In today's scientific instrumentation and scanning microscope technologies there are several common methods to measure sub-nano Newton forces. While the commercial atomic force microscopes (AFM) mostly work with silicon cantilevers, there are a large number of reports on the use of quartz tuning forks to get high-resolution force measurements or to create new force sensors. Both methods have certain advantages and disadvantages over the other. In this report the two methods are described and compared towards their usability for Casimir force measurements. Furthermore a design for a quantum field energy sensor based on the Casimir force measurement will be described. In addition some general considerations on extracting energy from vacuum fluctuations will be given.

Particle physics meets cosmology - The search for decaying neutrinos

NASA Technical Reports Server (NTRS)

Henry, R. C.

1982-01-01

The fundamental physical implications of the possible detection of massive neutrinos are discussed, with an emphasis on the Grand Unified Theories (GUTs) of matter. The Newtonian and general-relativistic pictures of the fundamental forces are compared, and the reduction of electromagnetic and weak forces to one force in the GUTs is explained. The cosmological consequences of the curved-spacetime gravitation concept are considered. Quarks, leptons, and neutrinos are characterized in a general treatment of elementary quantum mechanics. The universe is described in terms of quantized fields, the noninteractive 'particle' fields and the force fields, and cosmology becomes the study of the interaction of gravitation with the other fields, of the 'freezing out' of successive fields with the expansion and cooling of the universe. While the visible universe is the result of the clustering of the quark and electron fields, the distribution of the large number of quanta in neutrino field, like the mass of the neutrino, are unknown. Cosmological models which attribute anomalies in the observed motions of galaxies and stars to clusters or shells of massive neutrinos are shown to be consistent with a small but nonzero neutrino mass and a universe near the open/closed transition point, but direct detection of the presence of massive neutrinos by the UV emission of their decay is required to verify these hypotheses.

Numerical Investigation of Force-Free Magnetophoresis of Nonspherical Microparticles

NASA Astrophysics Data System (ADS)

Zhang, Jie; Wang, Cheng

2017-11-01

Our group recently demonstrated novel force-free magnetophoresis to separate nonspherical particles by shape. In this approach, a uniform magnetic field is used to generate a magnetic torque, which breaks the rotational symmetry of the particles and leads to shape-dependent lateral migration of the particles. We use direct numerical simulations to gain a better understanding of this magnetophoresis mechanism by focusing on ellipsoidal microparticles - a representative type of nonspherical particles encountered in biomedical engineering. We study key effects that influence the rotational and translational behaviors, including particle-wall separation distance, direction and strength of the magnetic field, particle aspect ratio and size. The numerical results show that the lateral migration is negligible in the absence of the magnetic field. When the magnetic field is applied, the particles migrate laterally. The migration direction depends on the direction of external magnetic fields, which controls the symmetry property of the particle rotation. These findings agree well with experiments. Our numerical simulations yield a comprehensive understanding of particle migration mechanism, and provide useful guidelines on design of separating devices for non-spherical micro-particles.

Physical probing of cells

NASA Astrophysics Data System (ADS)

Rehfeldt, Florian; Schmidt, Christoph F.

2017-11-01

In the last two decades, it has become evident that the mechanical properties of the microenvironment of biological cells are as important as traditional biochemical cues for the control of cellular behavior and fate. The field of cell and matrix mechanics is quickly growing and so is the development of the experimental approaches used to study active and passive mechanical properties of cells and their surroundings. Within this topical review we will provide a brief overview, on the one hand, over how cellular mechanics can be probed physically, how different geometries allow access to different cellular properties, and, on the other hand, how forces are generated in cells and transmitted to the extracellular environment. We will describe the following experimental techniques: atomic force microscopy, traction force microscopy, magnetic tweezers, optical stretcher and optical tweezers pointing out both their advantages and limitations. Finally, we give an outlook on the future of the physical probing of cells.

Magnetic field effects on the vestibular system: calculation of the pressure on the cupula due to ionic current-induced Lorentz force.

PubMed

Antunes, A; Glover, P M; Li, Y; Mian, O S; Day, B L

2012-07-21

Large static magnetic fields may be employed in magnetic resonance imaging (MRI). At high magnetic field strengths (usually from about 3 T and above) it is possible for humans to perceive a number of effects. One such effect is mild vertigo. Recently, Roberts et al (2011 Current Biology 21 1635-40) proposed a Lorentz-force mechanism resulting from the ionic currents occurring naturally in the endolymph of the vestibular system. In the present work a more detailed calculation of the forces and resulting pressures in the vestibular system is carried out using a numerical model. Firstly, realistic 3D finite element conductivity and fluid maps of the utricle and a single semi-circular canal containing the current sources (dark cells) and sinks (hair cells) of the utricle and ampulla were constructed. Secondly, the electrical current densities in the fluid are calculated. Thirdly, the developed Lorentz force is used directly in the Navier-Stokes equation and the trans-cupular pressure is computed. Since the driving force field is relatively large in comparison with the advective acceleration, we demonstrate that it is possible to perform an approximation in the Navier-Stokes equations that reduces the problem to solving a simpler Poisson equation. This simplification allows rapid and easy calculation for many different directions of applied magnetic field. At 7 T a maximum cupula pressure difference of 1.6 mPa was calculated for the combined ampullar (0.7 µA) and utricular (3.31 µA) distributed current sources, assuming a hair-cell resting current of 100 pA per unit. These pressure values are up to an order of magnitude lower than those proposed by Roberts et al using a simplistic model and calculation, and are in good agreement with the estimated pressure values for nystagmus velocities in caloric experiments. This modeling work supports the hypothesis that the Lorentz force mechanism is a significant contributor to the perception of magnetic field induced vertigo.

Cell Mechanosensitivity: Mechanical Properties and Interaction with Gravitational Field

PubMed Central

Ogneva, I. V.

2013-01-01

This paper addressed the possible mechanisms of primary reception of a mechanical stimulus by different cells. Data concerning the stiffness of muscle and nonmuscle cells as measured by atomic force microscopy are provided. The changes in the mechanical properties of cells that occur under changed external mechanical tension are presented, and the initial stages of mechanical signal transduction are considered. The possible mechanism of perception of different external mechanical signals by cells is suggested. PMID:23509748

Quantum Correlations of Light from a Room-Temperature Mechanical Oscillator

NASA Astrophysics Data System (ADS)

Sudhir, V.; Schilling, R.; Fedorov, S. A.; Schütz, H.; Wilson, D. J.; Kippenberg, T. J.

2017-07-01

When an optical field is reflected from a compliant mirror, its intensity and phase become quantum-correlated due to radiation pressure. These correlations form a valuable resource: the mirror may be viewed as an effective Kerr medium generating squeezed states of light, or the correlations may be used to erase backaction from an interferometric measurement of the mirror's position. To date, optomechanical quantum correlations have been observed in only a handful of cryogenic experiments, owing to the challenge of distilling them from thermomechanical noise. Accessing them at room temperature, however, would significantly extend their practical impact, with applications ranging from gravitational wave detection to chip-scale accelerometry. Here, we observe broadband quantum correlations developed in an optical field due to its interaction with a room-temperature nanomechanical oscillator, taking advantage of its high-cooperativity near-field coupling to an optical microcavity. The correlations manifest as a reduction in the fluctuations of a rotated quadrature of the field, in a frequency window spanning more than an octave below mechanical resonance. This is due to coherent cancellation of the two sources of quantum noise contaminating the measured quadrature—backaction and imprecision. Supplanting the backaction force with an off-resonant test force, we demonstrate the working principle behind a quantum-enhanced "variational" force measurement.

Magnetotherapy: The quest for tendon regeneration.

PubMed

Pesqueira, Tamagno; Costa-Almeida, Raquel; Gomes, Manuela E

2018-05-09

Tendons are mechanosensitive tissues that connect and transmit the forces generated by muscles to bones by allowing the conversion of mechanical input into biochemical signals. These physical forces perform the fundamental work of preserving tendon homeostasis assuring body movements. However, overloading causes tissue injuries, which leads us to the field of tendon regeneration. Recently published reviews have broadly shown the use of biomaterials and different strategies to attain tendon regeneration. In this review, our focus is the use of magnetic fields as an alternative therapy, which has demonstrated clinical relevance in tendon medicine because of their ability to modulate cell fate. Yet the underlying cellular and molecular mechanisms still need to be elucidated. While providing a brief outlook about specific signalling pathways and intracellular messengers as framework in play by tendon cells, application of magnetic fields as a subcategory of physical forces is explored, opening up a compelling avenue to enhance tendon regeneration. We outline here useful insights on the effects of magnetic fields both at in vitro and in vivo levels, particularly on the expression of tendon genes and inflammatory cytokines, ultimately involved in tendon regeneration. Subsequently, the potential of using magnetically responsive biomaterials in tendon tissue engineering is highlighted and future directions in magnetotherapy are discussed. © 2018 Wiley Periodicals, Inc.

Quantum theory of multiscale coarse-graining.

PubMed

Han, Yining; Jin, Jaehyeok; Wagner, Jacob W; Voth, Gregory A

2018-03-14

Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics. A rigorous derivation of the sufficient thermodynamic consistency condition is first presented via imaginary time Feynman path integrals. It identifies the optimal choice of CG action functional and effective quantum CG (qCG) force field to generate a quantum MS-CG (qMS-CG) description of the equilibrium system that is consistent with the quantum fine-grained model projected onto the CG variables. A variational principle then provides a class of algorithms for optimally approximating the qMS-CG force fields. Specifically, a variational method based on force matching, which was also adopted in the classical MS-CG theory, is generalized to quantum Boltzmann statistics. The qMS-CG numerical algorithms and practical issues in implementing this variational minimization procedure are also discussed. Then, two numerical examples are presented to demonstrate the method. Finally, as an alternative strategy, a quasi-classical approximation for the thermal density matrix expressed in the CG variables is derived. This approach provides an interesting physical picture for coarse-graining in quantum Boltzmann statistical mechanics in which the consistency with the quantum particle delocalization is obviously manifest, and it opens up an avenue for using path integral centroid-based effective classical force fields in a coarse-graining methodology.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy.

PubMed

Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M Baris; Kravchenko, Ivan I; Kalinin, Sergei V; Tselev, Alexander

2017-01-04

Atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm -1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.

Towards an on-chip platform for the controlled application of forces via magnetic particles: A novel device for mechanobiology

NASA Astrophysics Data System (ADS)

Monticelli, M.; Albisetti, E.; Petti, D.; Conca, D. V.; Falcone, M.; Sharma, P. P.; Bertacco, R.

2015-05-01

In-vitro tests and analyses are of fundamental importance for investigating biological mechanisms in cells and bio-molecules. The controlled application of forces to activate specific bio-pathways and investigate their effects, mimicking the role of the cellular environment, is becoming a prominent approach in this field. In this work, we present a non-invasive magnetic on-chip platform which allows for the manipulation of magnetic particles, through micrometric magnetic conduits of Permalloy patterned on-chip. We show, from simulations and experiments, that this technology permits to exert a finely controlled force on magnetic beads along the chip surface. This force can be tuned from few to hundreds pN by applying a variable external magnetic field.

Force Balance and Substorm Effects in the Magnetotail

NASA Technical Reports Server (NTRS)

Kaufmann, Richard L.; Larson, Douglas J.; Kontodinas, Ioannis D.; Ball, Bryan M.

1997-01-01

A model of the quiet time middle magnetotail is developed using a consistent orbit tracing technique. The momentum equation is used to calculate geocentric solar magnetospheric components of the particle and electromagnetic forces throughout the current sheet. Ions generate the dominant x and z force components. Electron and ion forces almost cancel in the y direction because the two species drift earthward at comparable speeds. The force viewpoint is applied to a study of some substorm processes. Generation of the rapid flows seen during substorm injection and bursty bulk flow events implies substantial force imbalances. The formation of a substorm diversion loop is one cause of changes in the magnetic field and therefore in the electromagnetic force. It is found that larger forces are produced when the cross-tail current is diverted to the ionosphere than would be produced if the entire tail current system simply decreased. Plasma is accelerated while the forces are unbalanced resulting in field lines within a diversion loop becoming more dipolar. Field lines become more stretched and the plasma sheet becomes thinner outside a diversion loop. Mechanisms that require thin current sheets to produce current disruption then can create additional diversion loops in the newly thinned regions. This process may be important during multiple expansion substorms and in differentiating pseudoexpansions from full substorms. It is found that the tail field model used here can be generated by a variety of particle distribution functions. However, for a given energy distribution the mixture of particle mirror or reflection points is constrained by the consistency requirement. The study of uniqueness also leads to the development of a technique to select guiding center electrons that will produce charge neutrality all along a flux tube containing nonguiding center ions without the imposition of a parallel electric field.

“Hydraulic Cushion” Type Overload Protection Devices Usable in Mechanical Presses. A Patent Study

NASA Astrophysics Data System (ADS)

Cioară, R.

2016-11-01

The possible consequences of machine-tool overload are well-known. In order to prevent such, machine-tools are equipped with various overload protection devices. Mechanical presses, intensively strained machine-tools, are typically equipped with three protection systems: against accidental access to the working area during machine deployment, against torque overload and force overload. Force overload protection systems include either destructible parts and are used in small to medium nominal force mechanical presses, or non-destructible ones used mostly in medium to large nominal force (H-frame) presses. A particular class of force overload protection systems without destructible parts are “hydraulic cushion” type devices. While such systems do not necessarily cause the machine to stop, the slide's stroke does not reach the initial dead centre and consequently cannot exert the designed technological force on the workpiece. By a patent study referencing 19 relevant patents the paper captures both the diversity of the constrictive solutions of “hydraulic cushion” type protection devices and their positioning modalities within the structure of a mechanical press. An important aim of the study is to highlight the reserve of creativity existing in this field, at least from the viewpoint of the hydraulic cushion positioning, as well as to emphasize the essential requirement of a relative motion between the mobile and the fixed parts of the tool, a motion of opposite sense to that of the slide-crank mechanism.

Large Electric Field-Enhanced-Hardness Effect in a SiO2 Film

NASA Astrophysics Data System (ADS)

Revilla, Reynier I.; Li, Xiao-Jun; Yang, Yan-Lian; Wang, Chen

2014-03-01

Silicon dioxide films are extensively used in nano and micro-electromechanical systems. Here we studied the influence of an external electric field on the mechanical properties of a SiO2 film by using nanoindentation technique of atomic force microscopy (AFM) and friction force microscopy (FFM). A giant augmentation of the relative elastic modulus was observed by increasing the localized electric field. A slight decrease in friction coefficients was also clearly observed by using FFM with the increase of applied tip voltage. The reduction of the friction coefficients is consistent with the great enhancement of sample hardness by considering the indentation-induced deformation during the friction measurements.

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

PubMed

Fonner, John M; Schmidt, Christine E; Ren, Pengyu

2010-10-01

Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials.

Breakpoint-forced and bound long waves in the nearshore: A model comparison

USGS Publications Warehouse

List, Jeffrey H.; ,

1993-01-01

A finite-difference model is used to compare long wave amplitudes arising from two-group forced generation mechanisms in the nearshore: long waves generated at a time-varying breakpoint and the shallow-water extension of the bound long wave. Plane beach results demonstrate that the strong frequency selection in the outgoing wave predicted by the breakpoint-forcing mechanism may not be observable in field data due to this wave's relatively small size and its predicted phase relation with the bound wave. Over a bar/trough nearshore, it is shown that a strong frequency selection in shoreline amplitudes is not a unique result of the time-varying breakpoint model, but a general result of the interaction between topography and any broad-banded forcing of nearshore long waves.

Electron fluctuation induced resonance broadening in nano electromechanical systems: the origin of shear force in vacuum.

PubMed

Siria, A; Barois, T; Vilella, K; Perisanu, S; Ayari, A; Guillot, D; Purcell, S T; Poncharal, P

2012-07-11

This article presents a study of the poorly understood "shear-force" used in an important class of near-field instruments that use mechanical resonance feedback detection. In the case of a metallic probe near a metallic surface in vacuum, we show that in the 10-60 nm range there is no such a thing as a shear-force in the sense of the nonconservative friction force. Fluctuations of the oscillator resonance frequency, likely induced by local charge variations, could account for the reported effects in the literature without introducing a dissipative force.

Vibration analysis and experiment of giant magnetostrictive force sensor

NASA Astrophysics Data System (ADS)

Zhu, Zhiwen; Liu, Fang; Zhu, Xingqiao; Wang, Haibo; Xu, Jia

2017-12-01

In this paper, a kind of giant magnetostrictive force sensor is proposed, ans its magneto-mechanical coupled model is developed. The relationship between output voltage of giant magnetostrictive force sensor and input excitation force is obtained. The phenomena of accuracy aggravation in high frequency and delay of giant magnetostrictive sensor are explained. The experimental results show that the model can describe the actual response of giant magnetostrictive force sensor. The new model of giant magnetostrictive sensor has simple form and is easy to be analyzed in theory, which is helpful to be applied in measuring and control fields.

Titin domains progressively unfolded by force are homogenously distributed along the molecule.

PubMed

Bianco, Pasquale; Mártonfalvi, Zsolt; Naftz, Katalin; Kőszegi, Dorina; Kellermayer, Miklós

2015-07-21

Titin is a giant filamentous protein of the muscle sarcomere in which stretch induces the unfolding of its globular domains. However, the mechanisms of how domains are progressively selected for unfolding and which domains eventually unfold have for long been elusive. Based on force-clamp optical tweezers experiments we report here that, in a paradoxical violation of mechanically driven activation kinetics, neither the global domain unfolding rate, nor the folded-state lifetime distributions of full-length titin are sensitive to force. This paradox is reconciled by a gradient of mechanical stability so that domains are gradually selected for unfolding as the magnitude of the force field increases. Atomic force microscopic screening of extended titin molecules revealed that the unfolded domains are distributed homogenously along the entire length of titin, and this homogeneity is maintained with increasing overstretch. Although the unfolding of domains with progressively increasing mechanical stability makes titin a variable viscosity damper, the spatially randomized variation of domain stability ensures that the induced structural changes are not localized but are distributed along the molecule's length. Titin may thereby provide complex safety mechanims for protecting the sarcomere against structural disintegration under excessive mechanical conditions. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

π -Stacking interactions in YFP, quantum mechanics and force field evaluations in the S0 and S1 states

NASA Astrophysics Data System (ADS)

Merabti, Karim Elhadj; Azizi, Sihem; Ridard, Jacqueline; Lévy, Bernard; Demachy, Isabelle

2017-08-01

We study the π -stacking interaction between the chromophore and Tyr203 in the Yellow Fluorescent Protein (YFP) in order to (i) evaluate the contribution of the internal interaction energy of the isolated Chromophore-Tyrosine complex (Eint) to the 26 nm red shift observed from GFP to YFP, (ii) compare the effects of Eint and of the proteic environment. To that end, we perform quantum mechanical and force field (ff) calculations of the isolated complex in S0 and S1 states on a large sample of geometries, together with molecular dynamics simulations and potential of mean force analysis. The calculated absorption wavelengths are found red shifted with respect to the isolated chromophore by 12-19 nm, that represents a large part of the GFP-YFP shift. We find that the effect of the protein is determinant on the dynamics of the complex while the error that results from using a classicalff is of limited effect.

A simple force-motion relation for migrating cells revealed by multipole analysis of traction stress.

PubMed

Tanimoto, Hirokazu; Sano, Masaki

2014-01-07

For biophysical understanding of cell motility, the relationship between mechanical force and cell migration must be uncovered, but it remains elusive. Since cells migrate at small scale in dissipative circumstances, the inertia force is negligible and all forces should cancel out. This implies that one must quantify the spatial pattern of the force instead of just the summation to elucidate the force-motion relation. Here, we introduced multipole analysis to quantify the traction stress dynamics of migrating cells. We measured the traction stress of Dictyostelium discoideum cells and investigated the lowest two moments, the force dipole and quadrupole moments, which reflect rotational and front-rear asymmetries of the stress field. We derived a simple force-motion relation in which cells migrate along the force dipole axis with a direction determined by the force quadrupole. Furthermore, as a complementary approach, we also investigated fine structures in the stress field that show front-rear asymmetric kinetics consistent with the multipole analysis. The tight force-motion relation enables us to predict cell migration only from the traction stress patterns. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Development of a Scaled Quantum Mechanical Force Field for Peptides in Aqueous Solution

DTIC Science & Technology

1996-03-01

differ. Raman and IR techniques are complimentary which helps in assignment of observed vibrational modes. As described in beginning organic ...1588 I NH, .i.sor(98) 2076 2100 24 CH3 55(95) 2125 2207 82 CH3 as’ (56), CH3 as’ (43) 2235 2253 18 CH3 as’(55), CH3 as’(41) 2888 COff .(100) 3155 NH...Application of self- consistent-field ab initio calculations to organic molecules I. Equilibrium struc- ture and force constants of hydrocarbons

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

Fläschner, G.; Ruschmeier, K.; Schwarz, A., E-mail: aschwarz@physnet.uni-hamburg.de

The sensitivity of atomic force microscopes is fundamentally limited by the cantilever temperature, which can be, in principle, determined by measuring its thermal spectrum and applying the equipartition theorem. However, the mechanical response can be affected by the light field inside the cavity of a Fabry-Perot interferometer due to light absorption, radiation pressure, photothermal forces, and laser noise. By evaluating the optomechanical Hamiltonian, we are able to explain the peculiar distance dependence of the mechanical quality factor as well as the appearance of thermal spectra with symmetrical Lorentzian as well as asymmetrical Fano line shapes. Our results can be appliedmore » to any type of mechanical oscillator in an interferometer-based detection system.« less

Separate representations of dynamics in rhythmic and discrete movements: evidence from motor learning

PubMed Central

Ingram, James N.; Wolpert, Daniel M.

2011-01-01

Rhythmic and discrete arm movements occur ubiquitously in everyday life, and there is a debate as to whether these two classes of movements arise from the same or different underlying neural mechanisms. Here we examine interference in a motor-learning paradigm to test whether rhythmic and discrete movements employ at least partially separate neural representations. Subjects were required to make circular movements of their right hand while they were exposed to a velocity-dependent force field that perturbed the circularity of the movement path. The direction of the force-field perturbation reversed at the end of each block of 20 revolutions. When subjects made only rhythmic or only discrete circular movements, interference was observed when switching between the two opposing force fields. However, when subjects alternated between blocks of rhythmic and discrete movements, such that each was uniquely associated with one of the perturbation directions, interference was significantly reduced. Only in this case did subjects learn to corepresent the two opposing perturbations, suggesting that different neural resources were employed for the two movement types. Our results provide further evidence that rhythmic and discrete movements employ at least partially separate control mechanisms in the motor system. PMID:21273324

On the Evolution of Pulsatile Flow Subject to a Transverse Impulse Body Force

NASA Astrophysics Data System (ADS)

di Labbio, Giuseppe; Keshavarz-Motamed, Zahra; Kadem, Lyes

2014-11-01

In the event of an unexpected abrupt traffic stop or car accident, automotive passengers will experience an abrupt body deceleration. This may lead to tearing or dissection of the aortic wall known as Blunt Traumatic Aortic Rupture (BTAR). BTAR is the second leading cause of death in automotive accidents and, although quite frequent, the mechanisms leading to BTAR are still not clearly identified, particularly the contribution of the flow field. As such, this work is intended to provide a fundamental framework for the investigation of the flow contribution to BTAR. In this fundamental study, pulsatile flow in a three-dimensional, straight pipe of circular cross-section is subjected to a unidirectional, transverse, impulse body force applied on a strictly bounded volume of fluid. These models were simulated using the Computational Fluid Dynamics (CFD) software FLUENT. The evolution of fluid field characteristics was investigated during and after the application of the force. The application of the force significantly modified the flow field. The force induces a transverse pressure gradient causing the development of secondary flow structures that dissipate the energy added by the acceleration. Once the force ceases to act, these structures are carried downstream and gradually dissipate their excess energy.

Transition from a beads-on-string to a spike structure in an electrified viscoelastic jet

NASA Astrophysics Data System (ADS)

Li, Fang; Yin, Xie-Yuan; Yin, Xie-Zhen

2017-02-01

A one-dimensional numerical simulation is performed to study the nonlinear behaviors of a perfectly conducting, slightly viscoelastic liquid jet under a large radial electric field. A singular spike structure different from a beads-on-string structure is detected. The electric field is found to be the key factor for the formation of spikes. The transition from a beads-on-string to a spike structure occurs at sufficiently large electric fields. Moreover, the transition occurs more easily for smaller wave numbers. Viscosity is found to suppress spikes while elasticity promotes them. The mechanism responsible for spike formation is further explored by examining the maximum radius of the jet in the beads-on-string case. The capillary and electrostatic forces prove to be dominant in droplets, and the transition takes place when the electrostatic force exceeds the capillary force. The self-similarity in spikes is discussed. Different from the transition moment, the inertial, electrostatic, and solvent viscous forces are important in a developed spike.

Analytical model for force prediction when machining metal matrix composites

NASA Astrophysics Data System (ADS)

Sikder, Snahungshu

Metal Matrix Composites (MMC) offer several thermo-mechanical advantages over standard materials and alloys which make them better candidates in different applications. Their light weight, high stiffness, and strength have attracted several industries such as automotive, aerospace, and defence for their wide range of products. However, the wide spread application of Meal Matrix Composites is still a challenge for industry. The hard and abrasive nature of the reinforcement particles is responsible for rapid tool wear and high machining costs. Fracture and debonding of the abrasive reinforcement particles are the considerable damage modes that directly influence the tool performance. It is very important to find highly effective way to machine MMCs. So, it is important to predict forces when machining Metal Matrix Composites because this will help to choose perfect tools for machining and ultimately save both money and time. This research presents an analytical force model for predicting the forces generated during machining of Metal Matrix Composites. In estimating the generated forces, several aspects of cutting mechanics were considered including: shearing force, ploughing force, and particle fracture force. Chip formation force was obtained by classical orthogonal metal cutting mechanics and the Johnson-Cook Equation. The ploughing force was formulated while the fracture force was calculated from the slip line field theory and the Griffith theory of failure. The predicted results were compared with previously measured data. The results showed very good agreement between the theoretically predicted and experimentally measured cutting forces.

Dynamical and fractal properties in periodically forced stretch-twist-fold (STF) flow

NASA Astrophysics Data System (ADS)

Aqeel, Muhammad; Ahmad, Salman; Azam, Anam; Ahmed, Faizan

2017-05-01

The periodically forced stretch-twist-fold (STF) flow is introduced in this article. The nonlinear behavior of the STF flow with periodic force along the y -axis is investigated analytically and numerically. The STF flow is a prototype of the dynamo theory that proposes a mechanism of magnetic field generation continuously. The stability analysis is done by Routh Huwritz criteria and Cardano method. Chasing chaos through numerical simulation is determined to demonstrate the chaotic behavior of the forced STF flow. With the help of fractal processes based on the forced STF flow, a multi-wing forced STF flow is obtained that gives a n -wing forced STF flow system.

Magnetically adjustable intraocular lens.

PubMed

Matthews, Michael Wayne; Eggleston, Harry Conrad; Pekarek, Steven D; Hilmas, Greg Eugene

2003-11-01

To provide a noninvasive, magnetic adjustment mechanism to the repeatedly and reversibly adjustable, variable-focus intraocular lens (IOL). University of Missouri-Rolla, Rolla, and Eggleston Adjustable Lens, St. Louis, Missouri, USA. Mechanically adjustable IOLs have been fabricated and tested. Samarium and cobalt rare-earth magnets have been incorporated into the poly(methyl methacrylate) (PMMA) optic of these adjustable lenses. The stability of samarium and cobalt in the PMMA matrix was examined with leaching studies. Operational force testing of the magnetic optics with emphasis on the rotational forces of adjustment was done. Prototype optics incorporating rare-earth magnetic inserts were consistently produced. After 32 days in solution, samarium and cobalt concentration reached a maximum of 5 ppm. Operational force measurements indicate that successful adjustments of this lens can be made using external magnetic fields with rotational torques in excess of 0.6 ounce inch produced. Actual lenses were remotely adjusted using magnetic fields. The magnetically adjustable version of this IOL is a viable and promising means of handling the common issues of postoperative refractive errors without the requirement of additional surgery. The repeatedly adjustable mechanism of this lens also holds promise for the developing eyes of pediatric patients and the changing needs of all patients.

Flow Field Characteristics and Lift Changing Mechanism for Half-Rotating Wing in Hovering Flight

NASA Astrophysics Data System (ADS)

Li, Q.; Wang, X. Y.; Qiu, H.; Li, C. M.; Qiu, Z. Z.

2017-12-01

Half-rotating wing (HRW) is a new similar-flapping wing system based on half-rotating mechanism which could perform rotating-type flapping instead of oscillating-type flapping. The characteristics of flow field and lift changing mechanism for HRW in hovering flight are important theoretical basis to improve the flight capability of HRW aircraft. The driving mechanism and work process of HRW were firstly introduced in this paper. Aerodynamic simulation model of HRW in hovering flight was established and solved using XFlow software, by which lift changing rule of HRW was drawn from the simulation solution. On the other hand, the development and shedding of the distal vortex throughout one stroke would lead to the changes of the lift force. Based on analyzing distribution characteristics of vorticity, velocity and pressure around wing blade, the main features of the flow field for HRW were further given. The distal attached vortex led to the increase of the lift force, which would gradually shed into the wake with a decline of lift in the later downstroke. The wake ring directed by the distal end of the blade would generate the downward accelerating airflow which produced the upward anti-impulse to HRW. The research results mentioned above illustrated that the behavior characteristics of vortex formed in flow field were main cause of lift changing for HRW.

Force feedback delay affects perception of stiffness but not action, and the effect depends on the hand used but not on the handedness.

PubMed

Leib, Raz; Rubin, Inbar; Nisky, Ilana

2018-05-16

Interaction with an object often requires the estimation of its mechanical properties. We examined whether the hand that is used to interact with the object and their handedness affected people's estimation of these properties using stiffness estimation as a test case. We recorded participants' responses on a stiffness discrimination of a virtual elastic force field and the grip force applied on the robotic device during the interaction. In half of the trials, the robotic device delayed the participants' force feedback. Consistent with previous studies, delayed force feedback biased the perceived stiffness of the force field. Interestingly, in both left-handed and right-handed participants, for the delayed force field, there was even less perceived stiffness when participants used their left hand than their right hand. This result supports the idea that haptic processing is affected by laterality in the brain, not by handedness. Consistent with previous studies, participants adjusted their applied grip force according to the correct size and timing of the load force regardless of the hand that was used, the handedness, or the delay. This suggests that in all these conditions, participants were able to form an accurate internal representation of the anticipated trajectory of the load force (size and timing) and that this representation was used for accurate control of grip force independently of the perceptual bias. Thus, these results provide additional evidence for the dissociation between action and perception in the processing of delayed information.

Noise induced aperiodic rotations of particles trapped by a non-conservative force

NASA Astrophysics Data System (ADS)

Ortega-Piwonka, Ignacio; Angstmann, Christopher N.; Henry, Bruce I.; Reece, Peter J.

2018-04-01

We describe a mechanism whereby random noise can play a constructive role in the manifestation of a pattern, aperiodic rotations, that would otherwise be damped by internal dynamics. The mechanism is described physically in a theoretical model of overdamped particle motion in two dimensions with symmetric damping and a non-conservative force field driven by noise. Cyclic motion only occurs as a result of stochastic noise in this system. However, the persistence of the cyclic motion is quantified by parameters associated with the non-conservative forcing. Unlike stochastic resonance or coherence resonance, where noise can play a constructive role in amplifying a signal that is otherwise below the threshold for detection, in the mechanism considered here, the signal that is detected does not exist without the noise. Moreover, the system described here is a linear system.

On the stress calculation within phase-field approaches: a model for finite deformations

NASA Astrophysics Data System (ADS)

Schneider, Daniel; Schwab, Felix; Schoof, Ephraim; Reiter, Andreas; Herrmann, Christoph; Selzer, Michael; Böhlke, Thomas; Nestler, Britta

2017-08-01

Numerical simulations based on phase-field methods are indispensable in order to investigate interesting and important phenomena in the evolution of microstructures. Microscopic phase transitions are highly affected by mechanical driving forces and therefore the accurate calculation of the stresses in the transition region is essential. We present a method for stress calculations within the phase-field framework, which satisfies the mechanical jump conditions corresponding to sharp interfaces, although the sharp interface is represented as a volumetric region using the phase-field approach. This model is formulated for finite deformations, is independent of constitutive laws, and allows using any type of phase inherent inelastic strains.

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions.

PubMed

Trnka, Tomáš; Tvaroška, Igor; Koča, Jaroslav

2018-01-09

Computational studies of the reaction mechanisms of various enzymes are nowadays based almost exclusively on hybrid QM/MM models. Unfortunately, the success of this approach strongly depends on the selection of the QM region, and computational cost is a crucial limiting factor. An interesting alternative is offered by empirical reactive molecular force fields, especially the ReaxFF potential developed by van Duin and co-workers. However, even though an initial parametrization of ReaxFF for biomolecules already exists, it does not provide the desired level of accuracy. We have conducted a thorough refitting of the ReaxFF force field to improve the description of reaction energetics. To minimize the human effort required, we propose a fully automated approach to generate an extensive training set comprised of thousands of different geometries and molecular fragments starting from a few model molecules. Electrostatic parameters were optimized with QM electrostatic potentials as the main target quantity, avoiding excessive dependence on the choice of reference atomic charges and improving robustness and transferability. The remaining force field parameters were optimized using the VD-CMA-ES variant of the CMA-ES optimization algorithm. This method is able to optimize hundreds of parameters simultaneously with unprecedented speed and reliability. The resulting force field was validated on a real enzymatic system, ppGalNAcT2 glycosyltransferase. The new force field offers excellent qualitative agreement with the reference QM/MM reaction energy profile, matches the relative energies of intermediate and product minima almost exactly, and reduces the overestimation of transition state energies by 27-48% compared with the previous parametrization.

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

PubMed

Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

2015-05-12

We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N -acetylglucosamine, N -acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from the extensive analysis of conformational properties of glycoprotein structures reported in the Protein Data Bank. Use of the BPMC search leads to significant improvements in sampling efficiency for glycan simulations. Moreover, good agreement with the X-ray glycoprotein structures is achieved for all glycan chain lengths. Thus, average/median RMSDs are 0.81/0.68 Å for one-residue glycans and 1.32/1.47 Å for three-residue glycans. RMSD from the native structure for the lowest-energy conformation of the 12-residue glycan chain (PDB ID 3og2) is 1.53 Å. Additionally, results obtained for free short oligosaccharides using the new force field are in line with the available experimental data, i.e., the most populated conformations in solution are predicted to be the lowest energy ones. The newly developed parameters allow for the accurate modeling of linear and branched hexopyranose glycosides in heterogeneous systems.

Mean-field dynamos: The old concept and some recent developments. Karl Schwarzschild Award Lecture 2013

NASA Astrophysics Data System (ADS)

Rädler, K.-H.

This article elucidates the basic ideas of electrodynamics and magnetohydrodynamics of mean fields in turbulently moving conducting fluids. It is stressed that the connection of the mean electromotive force with the mean magnetic field and its first spatial derivatives is in general neither local nor instantaneous and that quite a few claims concerning pretended failures of the mean-field concept result from ignoring this aspect. In addition to the mean-field dynamo mechanisms of α2 and α Ω type several others are considered. Much progress in mean-field electrodynamics and magnetohydrodynamics results from the test-field method for calculating the coefficients that determine the connection of the mean electromotive force with the mean magnetic field. As an important example the memory effect in homogeneous isotropic turbulence is explained. In magnetohydrodynamic turbulence there is the possibility of a mean electromotive force that is primarily independent of the mean magnetic field and labeled as Yoshizawa effect. Despite of many efforts there is so far no convincing comprehensive theory of α quenching, that is, the reduction of the α effect with growing mean magnetic field, and of the saturation of mean-field dynamos. Steps toward such a theory are explained. Finally, some remarks on laboratory experiments with dynamos are made.

Polymer-induced forces at interfaces

NASA Astrophysics Data System (ADS)

Rangarajan, Murali

This dissertation concerns studies of forces generated by confined and physisorbed flexible polymers using lattice mean-field theories, and those generated by confined and clamped semiflexible polymers modeled as slender elastic rods. Lattice mean-field theories have been used in understanding and predicting the behavior of polymeric interfacial systems. In order to efficiently tailor such systems for various applications of interest, one has to understand the forces generated in the interface due to the polymer molecules. The present work examines the abilities and limitations of lattice mean-field theories in predicting the structure of physisorbed polymer layers and the resultant forces. Within the lattice mean-field theory, a definition of normal force of compression as the negative derivative of the partition-function-based excess free energy with surface separation gives misleading results because the theory does not explicitly account for the normal stresses involved in the system. Correct expressions for normal and tangential forces are obtained from a continuum-mechanics-based formulation. Preliminary comparisons with lattice Monte Carlo simulations show that mean-field theories fail to predict significant attractive forces when the surfaces are undersaturated, as one would expect. The corrections to the excluded volume (non-reversal chains) and the mean-field (anisotropic field) approximations improve the predictions of layer structure, but not the forces. Bending of semiflexible polymer chains (elastic rods) is considered for two boundary conditions---where the chain is hinged on both ends and where the chain is clamped on one end and hinged on the other. For the former case, the compressive forces and chain shapes obtained are consistent with the inflexional elastica published by Love. For the latter, multiple and higher-order solutions are observed for the hinged-end position for a given force. Preliminary studies are conducted on actin-based motility of Listeria monocytogenes by treating actin filaments as elastic rods, using the actoclampin model. The results show qualitative agreement with calculations where the filaments are modeled as Hookean springs. The feasibility of the actoclampin model to address long length-scale rotation of Listeria during actin-based motility is addressed.

Systematic Parameterization of Lignin for the CHARMM Force Field

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

Vermaas, Joshua; Petridis, Loukas; Beckham, Gregg

Plant cell walls have three primary components, cellulose, hemicellulose, and lignin, the latter of which is a recalcitrant, aromatic heteropolymer that provides structure to plants, water and nutrient transport through plant tissues, and a highly effective defense against pathogens. Overcoming the recalcitrance of lignin is key to effective biomass deconstruction, which would in turn enable the use of biomass as a feedstock for industrial processes. Our understanding of lignin structure in the plant cell wall is hampered by the limitations of the available lignin forcefields, which currently only account for a single linkage between lignins and lack explicit parameterization formore » emerging lignin structures both from natural variants and engineered lignin structures. Since polymerization of lignin occurs via radical intermediates, multiple C-O and C-C linkages have been isolated , and the current force field only represents a small subset of lignin the diverse lignin structures found in plants. In order to take into account the wide range of lignin polymerization chemistries, monomers and dimer combinations of C-, H-, G-, and S-lignins as well as with hydroxycinnamic acid linkages were subjected to extensive quantum mechanical calculations to establish target data from which to build a complete molecular mechanics force field tuned specifically for diverse lignins. This was carried out in a GPU-accelerated global optimization process, whereby all molecules were parameterized simultaneously using the same internal parameter set. By parameterizing lignin specifically, we are able to more accurately represent the interactions and conformations of lignin monomers and dimers relative to a general force field. This new force field will enables computational researchers to study the effects of different linkages on the structure of lignin, as well as construct more accurate plant cell wall models based on observed statistical distributions of lignin that differ between disparate feedstocks, and guide further lignin engineering efforts.« less

A Simplified Model for the Optical Force exerted on a Vertically Oriented Cilium by an Optical Trap and the Resulting Deformation

NASA Astrophysics Data System (ADS)

Lofgren, Ian; Resnick, Andrew

2014-03-01

Eukaryotic cilia are essentially whiplike structures extending from the cell body. Although their existence has been long known, their mechanical and functional properties are poorly understood. Optical traps are a non-contact method of applying a localized force to microscopic objects and an ideal tool for the study of ciliary mechanics. Starting with the discrete dipole approximation, a common means of calculating the optical force on an object that is not spherical, we tackle the problem of the optical force on a cilium. Treating the cilium as a homogeneous nonmagnetic cylinder and the electric field of the laser beam as linearly polarized results in a force applied in the direction of polarization. The force density in the polarization direction is derived from the force on an individual dipole within the cilium, which can be integrated over the volume of the cilium in order to find the total force. Utilizing Euler-Bernoulli beam theory, we integrate the force density over a cross section of the cilium and numerically solve a fourth order differential equation to obtain the final deformation of the cilium. This prediction will later be compared with experimental results to infer the mechanical stiffness of the cilium. Support from the National Institutes of Health, 1R15DK092716 is gratefully acknowledged.

An Engineer's Physics Lab -- using a Large Force Frame

NASA Astrophysics Data System (ADS)

Heid, Christy; Rampolla, Donald

2009-03-01

We have constructed very economical, easy to assemble force frames that are used by students in our general physics laboratory at Chatham University. The force frame is used at the beginning of the semester to study vector properties of forces. The force frame can be used as a horizontal or vertical force table. Angles of forces are measured using a large movable (rotation and translation) Cartesian coordinate board attached to the frame with large binder clips. The force frame is a versatile device which is used for a number of other experiments, including beam bending and torsion, mechanical resonance, projectile trajectories, torque, mechanical equilibrium, an isolated non-magnetic support for magnetic field experiments, easily adjustable support for inclined plane experiments, support for traveling wave experiments with heavy rope, and support for large scale fluid flow experiments. One advantage to a wood frame is that things can be easily stapled, nailed, screwed or glued just about anywhere on the frame, and damaged frame members can be replaced easily. As one of the few remaining women's undergraduate institutions, we have found the use of these frames to provide an additional advantage in helping women overcome their fear of simple power tools and assembly of mechanical parts as they become comfortable with these through working with the force frames throughout the semester. We intend to describe and model these applications during the session.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

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

Balke, Nina Wisinger; Jesse, Stephen; Carmichael, Ben D.

Here, atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. Inmore » combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm –1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.« less

Quantification of In-Contact Probe-Sample Electrostatic Forces with Dynamic Atomic Force Microscopy.

PubMed

Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M; Kravchenko, Ivan; Kalinin, Sergei; Tselev, Alexander

2016-12-13

Atomic Force Microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V/nm at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids. Copyright 2016 IOP Publishing Ltd.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

DOE PAGES

Balke, Nina Wisinger; Jesse, Stephen; Carmichael, Ben D.; ...

2017-01-04

Here, atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. Inmore » combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm –1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.« less

Driving morphological changes in magnetic nanoparticle structures through the application of acoustic waves and magnetic fields

NASA Astrophysics Data System (ADS)

Huang, Ann; Miansari, Morteza; Friend, James

The growing interest in acoustic manipulation of particles in micro to nanofluidics using surface acoustic waves (SAW), together with the many applications of magnetic nanoparticles-whether individual or in arrays-underpins our discovery of how these forces can be used to rapidly, easily, and irreversibly form 1D chains and 2D films. These films and chains are currently difficult to produce yet offer many advantages over individual nanoparticles in suspension. Making use of the scale of the structures formed, 10-9 to 10-5 m, and by taking a balance of the relevant external and interparticle forces, the underlying mechanisms responsible for the phenomena become apparent. For 1D chains, the magnetic field alone is sufficient, though applying an acoustic field drives a topology change from loosely connected chains to loops of 10 -100 particles. Adding the acoustic field drives a transition from these looped structures to dense 2D arrays via interparticle Bjerknes forces. Inter-particle drainage of the surrounding fluid leaves these structures intact after removal of the externally applied forces. Clear morphology transitions are present and depend on the relative amplitude of the incident Brownian, Bjerknes, and magnetic forces. UCSD: Frontiers of Innovation Scholars Program (U-1024).

An excerpt from an eye-tracking comparative study between Poland and Japan with the use of Force Concept Inventory

NASA Astrophysics Data System (ADS)

Rosiek, Roman; Sajka, Mirosława; Ohno, Eizo; Shimojo, Atsushi; Iwata, Michiru; Wcisło, Dariusz

2017-01-01

The paper presents the initial results of a comparative Polish-Japanese study. The research was conducted at the Department of Mathematics, Physics and Technical Science at the Pedagogical University of Cracow and at the University of Hokkaido. The participants of the study were university students of humanistic courses. The research concerns the comparison of the respondents' knowledge and understanding of the concept of force in mechanics and their ways of solving problems in the field of a basic mechanics course. A special theoretical tool was used. It was the standardized, international test diagnosing the understanding of the concept of force - the so-called "Force Concept Inventory" (FCI), in its official Polish and Japanese translations. The eye-tracking method was combined with structured interviews and discussions with all the respondents.

Biased-probe-induced water ion injection into amorphous polymers investigated by electric force microscopy

NASA Astrophysics Data System (ADS)

Knorr, Nikolaus; Rosselli, Silvia; Miteva, Tzenka; Nelles, Gabriele

2009-06-01

Although charging of insulators by atomic force microscopy (AFM) has found widespread interest, often with data storage or nanoxerography in mind, less attention has been paid to the charging mechanism and the nature of the charge. Here we present a systematic study on charging of amorphous polymer films by voltage pulses applied to conducting AFM probes. We find a quadratic space charge limited current law of Kelvin probe force microscopy and electrostatic force microscopy peak volumes in pulse height, offset by a threshold voltage, and a power law in pulse width of positive exponents smaller than one. We interpret the results by a charging mechanism of injection and surface near accumulation of aqueous ions stemming from field induced water adsorption, with threshold voltages linked to the water affinities of the polymers.

Origin of the Earth's Electromagnetic Field Based on the Pulsating Mantle Hypothesis (PMH)

NASA Astrophysics Data System (ADS)

Gholibeigian, Hassan

2017-11-01

In PMH, the Earth's Inner Core's Dislocation (ICD) and Outer Core's Bulge (OCB) phenomena are generated by unbalanced gravitational fields of the Sun and Moon on the Earth. Distance between the Earth's center and inner core's center varies permanently in magnitude and direction inside two hemispheres. Geometrical loci of the inner core's center has the shape of back and force spiral cone in each hemisphere. In other words, the inner core is rotating fast in the outer core inverse of the Earth's rotation a round per day. This mechanism speed up the processes inside the core and generates a Large Scale Forced Convection System (LSFCS) inverse of the Earth's rotation in the core. The LSFCS is the origin of the Earth's electromagnetic field. The LSFCS generates huge mass transfer and momentum of inertia inside the Earth too. The inner core's axis which is the Earth's electromagnetic axis doesn't cross the Earth's geophysical axis and rotates around it per day. The mechanism of this LSFCS has diurnal, monthly and yearly cycles. These cycles are sources of the Earth's electromagnetic field variability. Direction of the variable Earth's magnetic field lines from the South Pole (hemisphere) to the sky and 146 seconds/years apparent solar day length variations can be two observable factors for this mechanism. This dynamic system may occurred inside the other planets like the Sun and the Jupiter.

Equilibrium electrodeformation of a spheroidal vesicle in an ac electric field

NASA Astrophysics Data System (ADS)

Nganguia, H.; Young, Y.-N.

2013-11-01

In this work, we develop a theoretical model to explain the equilibrium spheroidal deformation of a giant unilamellar vesicle (GUV) under an alternating (ac) electric field. Suspended in a leaky dielectric fluid, the vesicle membrane is modeled as a thin capacitive spheroidal shell. The equilibrium vesicle shape results from the balance between mechanical forces from the viscous fluid, the restoring elastic membrane forces, and the externally imposed electric forces. Our spheroidal model predicts a deformation-dependent transmembrane potential, and is able to capture large deformation of a vesicle under an electric field. A detailed comparison against both experiments and small-deformation (quasispherical) theory showed that the spheroidal model gives better agreement with experiments in terms of the dependence on fluid conductivity ratio, permittivity ratio, vesicle size, electric field strength, and frequency. The spheroidal model also allows for an asymptotic analysis on the crossover frequency where the equilibrium vesicle shape crosses over between prolate and oblate shapes. Comparisons show that the spheroidal model gives better agreement with experimental observations.

Electric-field-stimulated protein mechanics

PubMed Central

Hekstra, Doeke R.; White, K. Ian; Socolich, Michael A.; Henning, Robert W.; Šrajer, Vukica; Ranganathan, Rama

2017-01-01

The internal mechanics of proteins—the coordinated motions of amino acids and the pattern of forces constraining these motions—connects protein structure to function. Here we describe a new method combining the application of strong electric field pulses to protein crystals with time-resolved X-ray crystallography to observe conformational changes in spatial and temporal detail. Using a human PDZ domain (LNX2PDZ2) as a model system, we show that protein crystals tolerate electric field pulses strong enough to drive concerted motions on the sub-microsecond timescale. The induced motions are subtle, involve diverse physical mechanisms, and occur throughout the protein structure. The global pattern of electric-field-induced motions is consistent with both local and allosteric conformational changes naturally induced by ligand binding, including at conserved functional sites in the PDZ domain family. This work lays the foundation for comprehensive experimental study of the mechanical basis of protein function. PMID:27926732

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.

PubMed

Caleman, Carl; van Maaren, Paul J; Hong, Minyan; Hub, Jochen S; Costa, Luciano T; van der Spoel, David

2012-01-10

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

PubMed Central

2011-01-01

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields. PMID:22241968

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

PubMed Central

Dodda, Leela S.

2017-01-01

Abstract The accurate calculation of protein/nucleic acid–ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements. PMID:28444340

Benchmark of ReaxFF force field for subcritical and supercritical water.

PubMed

Manzano, Hegoi; Zhang, Weiwei; Raju, Muralikrishna; Dolado, Jorge S; López-Arbeloa, Iñigo; van Duin, Adri C T

2018-06-21

Water in the subcritical and supercritical states has remarkable properties that make it an excellent solvent for oxidation of hazardous chemicals, waste separation, and green synthesis. Molecular simulations are a valuable complement to experiments in order to understand and improve the relevant sub- and super-critical reaction mechanisms. Since water molecules under these conditions can act not only as a solvent but also as a reactant, dissociative force fields are especially interesting to investigate these processes. In this work, we evaluate the capacity of the ReaxFF force field to reproduce the microstructure, hydrogen bonding, dielectric constant, diffusion, and proton transfer of sub- and super-critical water. Our results indicate that ReaxFF is able to simulate water properties in these states in very good quantitative agreement with the existing experimental data, with the exception of the static dielectric constant that is reproduced only qualitatively.

Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF

PubMed Central

2014-01-01

We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157

Vesicle biomechanics in a time-varying magnetic field.

PubMed

Ye, Hui; Curcuru, Austen

2015-01-01

Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. References reporting the magnetic control of cellular mechanics have recently emerged. However, theoretical analysis of the cellular mechanics under a time-varying magnetic field is inadequate. We developed an analytical theory to investigate the biomechanics of a modeled vesicle under a time-varying magnetic field. Following previous publications and to simplify the calculation, this model treated the inner and suspending media as lossy dielectrics, the membrane thickness set at zero, and the electric resistance of the membrane assumed to be negligible. This work provided the first analytical solutions for the surface charges, electric field, radial pressure, overall translational forces, and rotational torques introduced on a vesicle by the time-varying magnetic field. Frequency responses of these measures were analyzed, particularly the frequency used clinically by transcranial magnetic stimulation (TMS). The induced surface charges interacted with the electric field to produce a biomechanical impact upon the vesicle. The distribution of the induced surface charges depended on the orientation of the coil and field frequency. The densities of these charges were trivial at low frequency ranges, but significant at high frequency ranges. The direction of the radial force on the vesicle was dependent on the conductivity ratio between the vesicle and the medium. At relatively low frequencies (<200 KHz), including the frequency used in TMS, the computed radial pressure and translational forces on the vesicle were both negligible. This work provides an analytical framework and insight into factors affecting cellular biomechanics under a time-varying magnetic field. Biological effects of clinical TMS are not likely to occur via alteration of the biomechanics of brain cells.

A triangular prism solid and shell interactive mapping element for electromagnetic sheet metal forming process

NASA Astrophysics Data System (ADS)

Cui, Xiangyang; Li, She; Feng, Hui; Li, Guangyao

2017-05-01

In this paper, a novel triangular prism solid and shell interactive mapping element is proposed to solve the coupled magnetic-mechanical formulation in electromagnetic sheet metal forming process. A linear six-node "Triprism" element is firstly proposed for transient eddy current analysis in electromagnetic field. In present "Triprism" element, shape functions are given explicitly, and a cell-wise gradient smoothing operation is used to obtain the gradient matrices without evaluating derivatives of shape functions. In mechanical field analysis, a shear locking free triangular shell element is employed in internal force computation, and a data mapping method is developed to transfer the Lorentz force on solid into the external forces suffered by shell structure for dynamic elasto-plasticity deformation analysis. Based on the deformed triangular shell structure, a "Triprism" element generation rule is established for updated electromagnetic analysis, which means inter-transformation of meshes between the coupled fields can be performed automatically. In addition, the dynamic moving mesh is adopted for air mesh updating based on the deformation of sheet metal. A benchmark problem is carried out for confirming the accuracy of the proposed "Triprism" element in predicting flux density in electromagnetic field. Solutions of several EMF problems obtained by present work are compared with experiment results and those of traditional method, which are showing excellent performances of present interactive mapping element.

Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

NASA Astrophysics Data System (ADS)

Meyer, Sam; Everaers, Ralf

2015-02-01

The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unknown despite increasing structural knowledge of the complex. In this paper, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We applied the procedure to a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at histone-DNA contact sites, the DNA base-pairs are shifted outwards locally, consistent with locally repulsive forces exerted by the histones. The second step shows that the various force profiles of the structures under analysis derive locally from a unique, sequence-independent, quadratic repulsive force-field, while the sequence preferences are entirely due to internal DNA mechanics. We have thus obtained the first knowledge-derived nanoscale interaction potential for histone-DNA in the nucleosome. The conformations obtained by relaxation of nucleosomal DNA with high-affinity sequences in this potential accurately reproduce the experimental values of binding preferences. Finally we address the more generic binding mechanisms relevant to the 80% genomic sequences incorporated in nucleosomes, by computing the conformation of nucleosomal DNA with sequence-averaged properties. This conformation differs from those found in crystals, and the analysis suggests that repulsive histone forces are related to local stretch tension in nucleosomal DNA, mostly between adjacent contact points. This tension could play a role in the stability of the complex.

Recent advances on glass-forming systems driven far from equilibrium. Special issue marking the completion of the Research Unit FOR 1394 `Nonlinear response to probe vitrification'

NASA Astrophysics Data System (ADS)

Fuchs, Matthias

2017-08-01

The nature of the glass transition is one of the frontier questions in Statistical Physics and Materials Science. Highly cooperative structural processes develop in glass-forming melts exhibiting relaxational dynamics which is spread out over many decades in time. While considerable progress has been made in recent decades towards understanding dynamical slowing-down in quiescent systems, the interplay of glassy dynamics with external fields reveals a wealth of novel phenomena yet to be explored. This special issue focuses on recent results obtained by the Research Unit FOR 1394 `Nonlinear response to probe vitrification' which was funded by the German Science Foundation (DFG). In the projects of the research unit, strong external fields were used in order to gain insights into the complex structural and transport phenomena at the glass transition under far-from-equilibrium conditions. This aimed inter alia to test theories of the glass transition developed for quiescent systems by pushing them beyond their original regime. Combining experimental, simulational, and theoretical efforts, the eight projects within the FOR 1394 measured and determined aspects of the nonlinear response of supercooled metallic, polymeric, and silica melts, of colloidal dispersions, and of ionic liquids. Applied fields included electric and mechanic fields, and forced active probing (`micro-rheology'), where a single probe is forced through the glass-forming host. Nonlinear stress-strain and force-velocity relations as well as nonlinear dielectric susceptibilities and conductivities were observed. While the physical manipulation of melts and glasses is interesting in its own right, especially technologically, the investigations performed by the FOR 1394 suggest to use the response to strong homogeneous and inhomogeneous fields as technique to explore on the microscopic level the cooperative mechanisms in dense melts of strongly interacting constituents. Questions considered concern the (de-)coupling of different dynamical degrees of freedom in an external field, and the ensuing state diagrams. What forces are required to detach a localized probe particle from its initial environment in a supercooled liquid, in a glassy or granular system? Do metallic and colloidal glasses yield homogeneously or by strain localization under differently applied stresses? Which mechanisms determine field-dependent susceptibilities in dielectric and ionically conducting glass formers?

Label-Free Alignment of Nonmagnetic Particles in a Small Uniform Magnetic Field.

PubMed

Wang, Zhaomeng; Wang, Ying; Wu, Rui Ge; Wang, Z P; Ramanujan, R V

2018-01-01

Label-free manipulation of biological entities can minimize damage, increase viability and improve efficiency of subsequent analysis. Understanding the mechanism of interaction between magnetic and nonmagnetic particles in an inverse ferrofluid can provide a mechanism of label-free manipulation of such entities in a uniform magnetic field. The magnetic force, induced by relative magnetic susceptibility difference between nonmagnetic particles and surrounding magnetic particles as well as particle-particle interaction were studied. Label-free alignment of nonmagnetic particles can be achieved by higher magnetic field strength (Ba), smaller particle spacing (R), larger particle size (rp1), and higher relative magnetic permeability difference between particle and the surrounding fluid (Rμr). Rμr can be used to predict the direction of the magnetic force between both magnetic and nonmagnetic particles. A sandwich structure, containing alternate layers of magnetic and nonmagnetic particle chains, was studied. This work can be used for manipulation of nonmagnetic particles in lab-on-a-chip applications.

Atomic Force Microscopy in Characterizing Cell Mechanics for Biomedical Applications: A Review.

PubMed

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-09-01

Cell mechanics is a novel label-free biomarker for indicating cell states and pathological changes. The advent of atomic force microscopy (AFM) provides a powerful tool for quantifying the mechanical properties of single living cells in aqueous conditions. The wide use of AFM in characterizing cell mechanics in the past two decades has yielded remarkable novel insights in understanding the development and progression of certain diseases, such as cancer, showing the huge potential of cell mechanics for practical applications in the field of biomedicine. In this paper, we reviewed the utilization of AFM to characterize cell mechanics. First, the principle and method of AFM single-cell mechanical analysis was presented, along with the mechanical responses of cells to representative external stimuli measured by AFM. Next, the unique changes of cell mechanics in two types of physiological processes (stem cell differentiation, cancer metastasis) revealed by AFM were summarized. After that, the molecular mechanisms guiding cell mechanics were analyzed. Finally the challenges and future directions were discussed.

Strike a Balance: Optimization of Backbone Torsion Parameters of AMBER Polarizable Force Field for Simulations of Proteins and Peptides

PubMed Central

WANG, ZHI-XIANG; ZHANG, WEI; WU, CHUN; LEI, HONGXING; CIEPLAK, PIOTR; DUAN, YONG

2014-01-01

Based on the AMBER polarizable model (ff02), we have reoptimized the parameters related to the main-chain (Φ, Ψ) torsion angles by fitting to the Boltzmann-weighted average quantum mechanical (QM) energies of the important regions (i.e., β, PII, αR, and αL regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace-Ala-Nme, the simulated populations in the β, PII and αR regions were approximately 30, 43, and 26%, respectively. For Ace-(Ala)7-Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization. PMID:16526038

Simplified TiO2 force fields for studies of its interaction with biomolecules

NASA Astrophysics Data System (ADS)

Luan, Binquan; Huynh, Tien; Zhou, Ruhong

2015-06-01

Engineered TiO2 nanoparticles have been routinely applied in nanotechnology, as well as in cosmetics and food industries. Despite active experimental studies intended to clarify TiO2's biological effects, including potential toxicity, the relation between experimentally inferred nanotoxicity and industry standards for safely applying nanoparticles remains somewhat ambiguous with justified concerns. Supplemental to experiments, molecular dynamics simulations have proven to be efficacious in investigating the molecular mechanism of a biological process occurring at nanoscale. In this article, to facilitate the nanotoxicity and nanomedicine research related to this important metal oxide, we provide a simplified force field, based on the original Matsui-Akaogi force field but compatible to the Lennard-Jones potentials normally used in modeling biomolecules, for simulating TiO2 nanoparticles interacting with biomolecules. The force field parameters were tested in simulating the bulk structure of TiO2, TiO2 nanoparticle-water interaction, as well as the adsorption of proteins on the TiO2 nanoparticle. We demonstrate that these simulation results are consistent with experimental data/observations. We expect that simulations will help to better understand the interaction between TiO2 and molecules.

Unorthodox theoretical methods

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

Nedd, Sean

2012-01-01

The use of the ReaxFF force field to correlate with NMR mobilities of amine catalytic substituents on a mesoporous silica nanosphere surface is considered. The interfacing of the ReaxFF force field within the Surface Integrated Molecular Orbital/Molecular Mechanics (SIMOMM) method, in order to replicate earlier SIMOMM published data and to compare with the ReaxFF data, is discussed. The development of a new correlation consistent Composite Approach (ccCA) is presented, which incorporates the completely renormalized coupled cluster method with singles, doubles and non-iterative triples corrections towards the determination of heats of formations and reaction pathways which contain biradical species.

Experimental Investigation of Pool Boiling Heat Transfer Enhancement in Microgravity in the Presence of Electric Fields

NASA Technical Reports Server (NTRS)

Herman, Cila

1996-01-01

Boiling is an effective mode of heat transfer since high heat flux levels are possible driven by relatively small temperature differences. The high heat transfer coefficients associated with boiling have made the use of these processes increasingly attractive to aerospace engineering. Applications of this type include compact evaporators in the thermal control of aircraft avionics and spacecraft environments, heat pipes, and use of boiling to cool electronic equipment. In spite of its efficiency, cooling based on liquid-vapor phase change processes has not yet found wide application in aerospace engineering due to specific problems associated with the low gravity environment. After a heated surface has reached the superheat required for the initiation of nucleate boiling, bubbles will start forming at nucleation sites along the solid interface by evaporation of the liquid. Bubbles in contact with the wall will continue growing by this mechanism until they detach. In terrestrial conditions, bubble detachment is determined by the competition between body forces (e.g. buoyancy) and surface tension forces that act to anchor the bubble along the three phase contact line. For a given body force potential and a balance of tensions along the three phase contact line, bubbles must reach a critical size before the body force can cause them to detach from the wall. In a low gravity environment the critical bubble size for detachment is much larger than under terrestrial conditions, since buoyancy is a less effective means of bubble removal. Active techniques of heat transfer enhancement in single phase and phase change processes by utilizing electric fields have been the subject of intensive research during recent years. The field of electrohydrodynamics (EHD) deals with the interactions between electric fields, flow fields and temperature fields. Previous studies indicate that in terrestrial applications nucleate boiling heat transfer can be increased by a factor of 50 as compared to values obtained for the same system without electric fields. Imposing an external electric field holds the promise to improve pool boiling heat transfer in low gravity, since a phase separation force other than gravity is introduced. The goal of our research is to experimentally investigate the potential of EHD and the mechanisms responsible for EHD heat transfer enhancement in boiling in low gravity conditions.

Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field.

PubMed

Heinz, Hendrik; Lin, Tzu-Jen; Mishra, Ratan Kishore; Emami, Fateme S

2013-02-12

The complexity of the molecular recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic-organic and inorganic-biomolecular interfaces. The parametrization builds on an in-depth understanding of physical-chemical properties on the atomic scale to assign each parameter, especially atomic charges and van der Waals constants, as well as on the validation of macroscale physical-chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, and thermal and mechanical properties. Applications include insight into the assembly of inorganic-organic multiphase materials, the recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and nanomechanics. Limitations and opportunities for further development are also described.

Magnetic fields applied to collagen-coated ferric oxide beads induce stretch-activated Ca2+ flux in fibroblasts.

PubMed

Glogauer, M; Ferrier, J; McCulloch, C A

1995-11-01

The ability to apply controlled forces to the cell membrane may enable elucidation of the mechanisms and pathways involved in signal transduction in response to applied physical stimuli. We have developed a magnetic particle-electromagnet model that allows the application of controlled forces to the plasma membrane of substrate-attached fibroblasts. The system allows applied forces to be controlled by the magnitude of the magnetic field and by the surface area of cell membrane covered with collagen-coated ferric beads. Analysis by single-cell ratio fluorimetry of fura 2-loaded cells demonstrated large calcium transients (50-300 nM) in response to the magnetic force applications. Experiments using either the stretch-activated channel blocker gadolinium chloride or ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid to eliminate external calcium ions, or addition of extracellular manganese ions, indicated that there was a calcium influx through putative stretch-activated channels. The probability of a calcium influx in single cells was increased by higher surface bead loading and the degree of cell spreading. Depolymerization of actin filaments by cytochalasin D increased the amplitude of calcium response twofold. The regulation of calcium flux by filamentous actin content and by cell spreading indicates a possible modulatory role for the cytoskeleton in channel sensitivity. Magnetic force application to beads on single cells provides a controlled model to study mechanisms and heterogeneity in physical force stimulation of cation-permeable channels.

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

Burrage, Clare; Copeland, Edmund J.; Hinds, E.A., E-mail: Clare.Burrage@nottingham.ac.uk, E-mail: Edmund.Copeland@nottingham.ac.uk, E-mail: Ed.Hinds@imperial.ac.uk

Theories of dark energy require a screening mechanism to explain why the associated scalar fields do not mediate observable long range fifth forces. The archetype of this is the chameleon field. Here we show that individual atoms are too small to screen the chameleon field inside a large high-vacuum chamber, and therefore can detect the field with high sensitivity. We derive new limits on the chameleon parameters from existing experiments, and show that most of the remaining chameleon parameter space is readily accessible using atom interferometry.

Accurate interatomic force fields via machine learning with covariant kernels

NASA Astrophysics Data System (ADS)

Glielmo, Aldo; Sollich, Peter; De Vita, Alessandro

2017-06-01

We present a novel scheme to accurately predict atomic forces as vector quantities, rather than sets of scalar components, by Gaussian process (GP) regression. This is based on matrix-valued kernel functions, on which we impose the requirements that the predicted force rotates with the target configuration and is independent of any rotations applied to the configuration database entries. We show that such covariant GP kernels can be obtained by integration over the elements of the rotation group SO (d ) for the relevant dimensionality d . Remarkably, in specific cases the integration can be carried out analytically and yields a conservative force field that can be recast into a pair interaction form. Finally, we show that restricting the integration to a summation over the elements of a finite point group relevant to the target system is sufficient to recover an accurate GP. The accuracy of our kernels in predicting quantum-mechanical forces in real materials is investigated by tests on pure and defective Ni, Fe, and Si crystalline systems.

Modal energy analysis for mechanical systems excited by spatially correlated loads

NASA Astrophysics Data System (ADS)

Zhang, Peng; Fei, Qingguo; Li, Yanbin; Wu, Shaoqing; Chen, Qiang

2018-10-01

MODal ENergy Analysis (MODENA) is an energy-based method, which is proposed to deal with vibroacoustic problems. The performance of MODENA on the energy analysis of a mechanical system under spatially correlated excitation is investigated. A plate/cavity coupling system excited by a pressure field is studied in a numerical example, in which four kinds of pressure fields are involved, which include the purely random pressure field, the perfectly correlated pressure field, the incident diffuse field, and the turbulent boundary layer pressure fluctuation. The total energies of subsystems differ to reference solution only in the case of purely random pressure field and only for the non-excited subsystem (the cavity). A deeper analysis on the scale of modal energy is further conducted via another numerical example, in which two structural modes excited by correlated forces are coupled with one acoustic mode. A dimensionless correlation strength factor is proposed to determine the correlation strength between modal forces. Results show that the error on modal energy increases with the increment of the correlation strength factor. A criterion is proposed to establish a link between the error and the correlation strength factor. According to the criterion, the error is negligible when the correlation strength is weak, in this situation the correlation strength factor is less than a critical value.

A Miniature Magnetic-Force-Based Three-Axis AC Magnetic Sensor with Piezoelectric/Vibrational Energy-Harvesting Functions.

PubMed

Hung, Chiao-Fang; Yeh, Po-Chen; Chung, Tien-Kan

2017-02-08

In this paper, we demonstrate a miniature magnetic-force-based, three-axis, AC magnetic sensor with piezoelectric/vibrational energy-harvesting functions. For magnetic sensing, the sensor employs a magnetic-mechanical-piezoelectric configuration (which uses magnetic force and torque, a compact, single, mechanical mechanism, and the piezoelectric effect) to convert x -axis and y -axis in-plane and z -axis magnetic fields into piezoelectric voltage outputs. Under the x -axis magnetic field (sine-wave, 100 Hz, 0.2-3.2 gauss) and the z -axis magnetic field (sine-wave, 142 Hz, 0.2-3.2 gauss), the voltage output with the sensitivity of the sensor are 1.13-26.15 mV with 8.79 mV/gauss and 1.31-8.92 mV with 2.63 mV/gauss, respectively. In addition, through this configuration, the sensor can harness ambient vibrational energy, i.e., possessing piezoelectric/vibrational energy-harvesting functions. Under x -axis vibration (sine-wave, 100 Hz, 3.5 g) and z -axis vibration (sine-wave, 142 Hz, 3.8 g), the root-mean-square voltage output with power output of the sensor is 439 mV with 0.333 μW and 138 mV with 0.051 μW, respectively. These results show that the sensor, using this configuration, successfully achieves three-axis magnetic field sensing and three-axis vibration energy-harvesting. Due to these features, the three-axis AC magnetic sensor could be an important design reference in order to develop future three-axis AC magnetic sensors, which possess energy-harvesting functions, for practical industrial applications, such as intelligent vehicle/traffic monitoring, processes monitoring, security systems, and so on.

Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations

NASA Astrophysics Data System (ADS)

Cai, Kaicong; Zheng, Xuan; Du, Fenfen

2017-08-01

The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.

Nanosecond pulsed electric field (nsPEF) enhance cytotoxicity of cisplatin to hepatocellular cells by microdomain disruption on plasma membrane.

PubMed

Yin, Shengyong; Chen, Xinhua; Xie, Haiyang; Zhou, Lin; Guo, Danjing; Xu, Yuning; Wu, Liming; Zheng, Shusen

2016-08-15

Previous studies showed nanosecond pulsed electric field (nsPEF) can ablate solid tumors including hepatocellular carcinoma (HCC) but its effect on cell membrane is not fully understood. We hypothesized nsPEF disrupt the microdomains on outer-cellular membrane with direct mechanical force and as a result the plasma membrane permeability increases to facilitate the small molecule intake. Three HCC cells were pulsed one pulse per minute, an interval longer than nanopore resealing time. The cationized ferritin was used to mark up the electronegative microdomains, propidium iodide (PI) for membrane permeabilization, energy dispersive X-ray spectroscopy (EDS) for the negative cell surface charge and cisplatin for inner-cellular cytotoxicity. We demonstrated that the ferritin marked-microdomain and negative cell surface charge were disrupted by nsPEF caused-mechanical force. The cell uptake of propidium and cytotoxicity of DNA-targeted cisplatin increased with a dose effect. Cisplatin gains its maximum inner-cellular cytotoxicity when combining with nsPEF stimulation. We conclude that nsPEF disrupt the microdomains on the outer cellular membrane directly and increase the membrane permeabilization for PI and cisplatin. The microdomain disruption and membrane infiltration changes are caused by the mechanical force from the changes of negative cell surface charge. Copyright © 2016 Elsevier Inc. All rights reserved.

MCPB.py: A Python Based Metal Center Parameter Builder.

PubMed

Li, Pengfei; Merz, Kenneth M

2016-04-25

MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.

Friction laws at the nanoscale.

PubMed

Mo, Yifei; Turner, Kevin T; Szlufarska, Izabela

2009-02-26

Macroscopic laws of friction do not generally apply to nanoscale contacts. Although continuum mechanics models have been predicted to break down at the nanoscale, they continue to be applied for lack of a better theory. An understanding of how friction force depends on applied load and contact area at these scales is essential for the design of miniaturized devices with optimal mechanical performance. Here we use large-scale molecular dynamics simulations with realistic force fields to establish friction laws in dry nanoscale contacts. We show that friction force depends linearly on the number of atoms that chemically interact across the contact. By defining the contact area as being proportional to this number of interacting atoms, we show that the macroscopically observed linear relationship between friction force and contact area can be extended to the nanoscale. Our model predicts that as the adhesion between the contacting surfaces is reduced, a transition takes place from nonlinear to linear dependence of friction force on load. This transition is consistent with the results of several nanoscale friction experiments. We demonstrate that the breakdown of continuum mechanics can be understood as a result of the rough (multi-asperity) nature of the contact, and show that roughness theories of friction can be applied at the nanoscale.

Combining experimental and simulation data of molecular processes via augmented Markov models.

PubMed

Olsson, Simon; Wu, Hao; Paul, Fabian; Clementi, Cecilia; Noé, Frank

2017-08-01

Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few [Formula: see text], which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.

The Effects of the Interplay between Motor and Brownian Forces on the Rheology of Active Gels.

PubMed

Córdoba, Andrés

2018-04-19

Active gels perform key mechanical roles inside the cell, such as cell division, motion, and force sensing. The unique mechanical properties required to perform such functions arise from the interactions between molecular motors and semiflexible polymeric filaments. Molecular motors can convert the energy released in the hydrolysis of ATP into forces of up to piconewton magnitudes. Moreover, the polymeric filaments that form active gels are flexible enough to respond to Brownian forces but also stiff enough to support the large tensions induced by the motor-generated forces. Brownian forces are expected to have a significant effect especially at motor activities at which stable noncontractile in vitro active gels are prepared for rheological measurements. Here, a microscopic mean-field theory of active gels originally formulated in the limit of motor-dominated dynamics is extended to include Brownian forces. In the model presented here, Brownian forces are included accurately, at real room temperature, even in systems with high motor activity. It is shown that a subtle interplay, or competition, between motor-generated forces and Brownian forces has an important impact on the mass transport and rheological properties of active gels. The model predictions show that at low frequencies the dynamic modulus of active gels is determined mostly by motor protein dynamics. However, Brownian forces significantly increase the breadth of the relaxation spectrum and can affect the shape of the dynamic modulus over a wide frequency range even for ratios of motor to Brownian forces of more than a hundred. Since the ratio between motor and Brownian forces is sensitive to ATP concentration, the results presented here shed some light on how the transient mechanical response of active gels changes with varying ATP concentration.

Near- and far-field aerodynamics in insect hovering flight: an integrated computational study.

PubMed

Aono, Hikaru; Liang, Fuyou; Liu, Hao

2008-01-01

We present the first integrative computational fluid dynamics (CFD) study of near- and far-field aerodynamics in insect hovering flight using a biology-inspired, dynamic flight simulator. This simulator, which has been built to encompass multiple mechanisms and principles related to insect flight, is capable of 'flying' an insect on the basis of realistic wing-body morphologies and kinematics. Our CFD study integrates near- and far-field wake dynamics and shows the detailed three-dimensional (3D) near- and far-field vortex flows: a horseshoe-shaped vortex is generated and wraps around the wing in the early down- and upstroke; subsequently, the horseshoe-shaped vortex grows into a doughnut-shaped vortex ring, with an intense jet-stream present in its core, forming the downwash; and eventually, the doughnut-shaped vortex rings of the wing pair break up into two circular vortex rings in the wake. The computed aerodynamic forces show reasonable agreement with experimental results in terms of both the mean force (vertical, horizontal and sideslip forces) and the time course over one stroke cycle (lift and drag forces). A large amount of lift force (approximately 62% of total lift force generated over a full wingbeat cycle) is generated during the upstroke, most likely due to the presence of intensive and stable, leading-edge vortices (LEVs) and wing tip vortices (TVs); and correspondingly, a much stronger downwash is observed compared to the downstroke. We also estimated hovering energetics based on the computed aerodynamic and inertial torques, and powers.

Decay characteristics of electroadhesive forces by periodic electrodes in dielectric layers

NASA Astrophysics Data System (ADS)

Lee, Junseok; Cha, Youngsu

2017-07-01

Electroadhesive force is the force generated by induced dipoles in the gradient of an electric field. Owing to its benefits of mechanical characteristics and versatility, it is widely used to hold and manipulate objects in robotic applications. So far, most studies in this field have been focused on the maximization of the magnitude of electroadhesive force. In this paper, we focus on the decay characteristics of electroadhesive force depending on the spatial distance from electrodes to employ the force to precisely separate a single layer from stacked dielectric layers. It turns out that all configurations with periodically repeating electrodes' arrangement, have the same decay characteristics which significantly depend on the geometrical period of the electrode patterns. Also, we find that the other parameters including the applied voltage and geometry of electrodes have little effect on the decay characteristics. The electric potential of an arbitrary electrode configuration is expanded in terms of the Fourier series, and we use it to analytically prove the high dependence of decay characteristics on the geometrical period. Numerical analysis is performed using the finite element method.

Spin-orbit induced electronic spin separation in semiconductor nanostructures.

PubMed

Kohda, Makoto; Nakamura, Shuji; Nishihara, Yoshitaka; Kobayashi, Kensuke; Ono, Teruo; Ohe, Jun-ichiro; Tokura, Yasuhiro; Mineno, Taiki; Nitta, Junsaku

2012-01-01

The demonstration of quantized spin splitting by Stern and Gerlach is one of the most important experiments in modern physics. Their discovery was the precursor of recent developments in spin-based technologies. Although electrical spin separation of charged particles is fundamental in spintronics, in non-uniform magnetic fields it has been difficult to separate the spin states of charged particles due to the Lorentz force, as well as to the insufficient and uncontrollable field gradients. Here we demonstrate electronic spin separation in a semiconductor nanostructure. To avoid the Lorentz force, which is inevitably induced when an external magnetic field is applied, we utilized the effective non-uniform magnetic field which originates from the Rashba spin-orbit interaction in an InGaAs-based heterostructure. Using a Stern-Gerlach-inspired mechanism, together with a quantum point contact, we obtained field gradients of 10(8) T m(-1) resulting in a highly polarized spin current.

Spin–orbit induced electronic spin separation in semiconductor nanostructures

PubMed Central

Kohda, Makoto; Nakamura, Shuji; Nishihara, Yoshitaka; Kobayashi, Kensuke; Ono, Teruo; Ohe, Jun-ichiro; Tokura, Yasuhiro; Mineno, Taiki; Nitta, Junsaku

2012-01-01

The demonstration of quantized spin splitting by Stern and Gerlach is one of the most important experiments in modern physics. Their discovery was the precursor of recent developments in spin-based technologies. Although electrical spin separation of charged particles is fundamental in spintronics, in non-uniform magnetic fields it has been difficult to separate the spin states of charged particles due to the Lorentz force, as well as to the insufficient and uncontrollable field gradients. Here we demonstrate electronic spin separation in a semiconductor nanostructure. To avoid the Lorentz force, which is inevitably induced when an external magnetic field is applied, we utilized the effective non-uniform magnetic field which originates from the Rashba spin–orbit interaction in an InGaAs-based heterostructure. Using a Stern–Gerlach-inspired mechanism, together with a quantum point contact, we obtained field gradients of 108 T m−1 resulting in a highly polarized spin current. PMID:23011136

Diffusion model of penetration of a chloride-containing environment in the volume of a constructive element

NASA Astrophysics Data System (ADS)

Ovchinnikov, I. I.; Snezhkina, O. V.; Ovchinnikov, I. G.

2018-06-01

A generalized model of diffusional penetration of a chloride-containing medium into the volume of a compressed reinforced concrete element is considered. The equations of deformation values of reinforced concrete structure are presented, taking into account the degradation of concrete and corrosion of reinforcement. At the initial stage, an applied force calculation of section of the structural element with mechanical properties of the material which are determined by the initial field of concentration of aggressive medium, is carried out. Furthermore, at each discrete instant moment of time, the following properties are determined: the distribution law of concentration for chloride field, corresponding to the parameters of the stress-strain state; the calculation of corrosion damage field of reinforcing elements and the applied force calculation of section of the structural element with parameters corresponding to the distribution of the concentration field and the field of corrosion damage are carried out.

Tidal dissipation in rotating fluid bodies: the presence of a magnetic field

NASA Astrophysics Data System (ADS)

Lin, Yufeng; Ogilvie, Gordon I.

2018-02-01

We investigate effects of the presence of a magnetic field on tidal dissipation in rotating fluid bodies. We consider a simplified model consisting of a rigid core and a fluid envelope, permeated by a background magnetic field (either a dipolar field or a uniform axial field). The wave-like tidal responses in the fluid layer are in the form of magnetic Coriolis waves, which are restored by both the Coriolis force and the Lorentz force. Energy dissipation occurs through viscous damping and Ohmic damping of these waves. Our numerical results show that the tidal dissipation can be dominated by Ohmic damping even with a weak magnetic field. The presence of a magnetic field smooths out the complicated frequency dependence of the dissipation rate, and broadens the frequency spectrum of the dissipation rate, depending on the strength of the background magnetic field. However, the frequency-averaged dissipation is independent of the strength and structure of the magnetic field, and of the dissipative parameters in the approximation that the wave-like response is driven only by the Coriolis force acting on the non-wavelike tidal flow. Indeed, the frequency-averaged dissipation quantity is in good agreement with previous analytical results in the absence of magnetic fields. Our results suggest that the frequency-averaged tidal dissipation of the wave-like perturbations is insensitive to detailed damping mechanisms and dissipative properties.

Shaping tissues by balancing active forces and geometric constraints

NASA Astrophysics Data System (ADS)

Foolen, Jasper; Yamashita, Tadahiro; Kollmannsberger, Philip

2016-02-01

The self-organization of cells into complex tissues during growth and regeneration is a combination of physical-mechanical events and biochemical signal processing. Cells actively generate forces at all stages in this process, and according to the laws of mechanics, these forces result in stress fields defined by the geometric boundary conditions of the cell and tissue. The unique ability of cells to translate such force patterns into biochemical information and vice versa sets biological tissues apart from any other material. In this topical review, we summarize the current knowledge and open questions of how forces and geometry act together on scales from the single cell to tissues and organisms, and how their interaction determines biological shape and structure. Starting with a planar surface as the simplest type of geometric constraint, we review literature on how forces during cell spreading and adhesion together with geometric constraints impact cell shape, stress patterns, and the resulting biological response. We then move on to include cell-cell interactions and the role of forces in monolayers and in collective cell migration, and introduce curvature at the transition from flat cell sheets to three-dimensional (3D) tissues. Fibrous 3D environments, as cells experience them in the body, introduce new mechanical boundary conditions and change cell behaviour compared to flat surfaces. Starting from early work on force transmission and collagen remodelling, we discuss recent discoveries on the interaction with geometric constraints and the resulting structure formation and network organization in 3D. Recent literature on two physiological scenarios—embryonic development and bone—is reviewed to demonstrate the role of the force-geometry balance in living organisms. Furthermore, the role of mechanics in pathological scenarios such as cancer is discussed. We conclude by highlighting common physical principles guiding cell mechanics, tissue patterning and matrix organization under geometric constraints across multiple length and time scales.

Propulsive Forces of a Biomimetic Undulating Fin

NASA Astrophysics Data System (ADS)

Kalumuck, Kenneth; Brandt, Alan; Armand, Mehran

2007-11-01

Understanding gained from much recent work on force production mechanisms of aquatic organisms holds great promise for improved undersea vehicle propulsion and maneuvering. One class of fish locomotion is that of the median fin utilized by animals such as squid, cuttlefish, knifefish, and seahorse. It is characterized by undulatory motion that creates traveling waves along the fin. Results of experiments conducted on a submerged mechanical underwater undulating fin test bed are presented. The 0.5 m long fin is mounted to a cylindrical body and consists of a flexible skin attached to ribs driven by an adjustable cam mechanism and variable speed motor that enables changing the characteristics of the undulating wave(s). Forces produced were measured in a captive mode under quiescent conditions as well in the presence of an ambient current. Propulsive forces are characterized as a function of the fin width, oscillation frequency, amplitude, and wavelength. Free swimming experiments were also conducted to determine the point of self propulsion. Flow field structure visualization using dye tracers is presented for selected cases. Estimates of performance and applications for use with larger scale vehicles are discussed.

Cellular and Molecular Mechanisms of High Pressure Inotropy in Cardiac Muscle

DTIC Science & Technology

1989-08-01

on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP Membranes, Cardiac Muscle , Contraction Force, uW - Calcium, Inotropy...elevated hydrostatic pressure over the range of 2 to 150 atmospheres causes an increase in the force of cardiac muscle contraction (1). In the first year...The present findings indicate that elevated hydrostatic pressure enhances cardiac muscle contraction by somehow affecting the disposition of calcium as

Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

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

Wang, Hao; Yang, Weitao, E-mail: weitao.yang@duke.edu; Department of Physics, Duke University, Durham, North Carolina 27708

We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniformmore » external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics’ force fields and nontransferable molecule-specific atomic polarizabilities.« less

Probing dark energy with atom interferometry

NASA Astrophysics Data System (ADS)

Burrage, Clare; Copeland, Edmund J.; Hinds, E. A.

2015-03-01

Theories of dark energy require a screening mechanism to explain why the associated scalar fields do not mediate observable long range fifth forces. The archetype of this is the chameleon field. Here we show that individual atoms are too small to screen the chameleon field inside a large high-vacuum chamber, and therefore can detect the field with high sensitivity. We derive new limits on the chameleon parameters from existing experiments, and show that most of the remaining chameleon parameter space is readily accessible using atom interferometry.

Acoustic manipulation of active spherical carriers: Generation of negative radiation force

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

Rajabi, Majid, E-mail: majid_rajabi@iust.ac.ir; Mojahed, Alireza

2016-09-15

This paper examines theoretically a novel mechanism of generating negative (pulling) radiation force for acoustic manipulation of spherical carriers equipped with piezoelectric actuators in its inner surface. In this mechanism, the spherical particle is handled by common plane progressive monochromatic acoustic waves instead of zero-/higher- order Bessel beams or standing waves field. The handling strategy is based on applying a spatially uniform harmonic electrical voltage at the piezoelectric actuator with the same frequency of handling acoustic waves, in order to change the radiation force effect from repulsive (away from source) to attractive (toward source). This study may be considered asmore » a start point for development of contact-free precise handling and entrapment technology of active carriers which are essential in many engineering and medicine applications.« less

The Classical Theory of Light Colors: a Paradigm for Description of Particle Interactions

NASA Astrophysics Data System (ADS)

Mazilu, Nicolae; Agop, Maricel; Gatu, Irina; Iacob, Dan Dezideriu; Butuc, Irina; Ghizdovat, Vlad

2016-06-01

The color is an interaction property: of the interaction of light with matter. Classically speaking it is therefore akin to the forces. But while forces engendered the mechanical view of the world, the colors generated the optical view. One of the modern concepts of interaction between the fundamental particles of matter - the quantum chromodynamics - aims to fill the gap between mechanics and optics, in a specific description of strong interactions. We show here that this modern description of the particle interactions has ties with both the classical and quantum theories of light, regardless of the connection between forces and colors. In a word, the light is a universal model in the description of matter. The description involves classical Yang-Mills fields related to color.

Reduced yield stress for zirconium exposed to iodine: Reactive force field simulation

DOE PAGES

Rossi, Matthew L.; Taylor, Christopher D.; van Duin, Adri C. T.

2014-11-04

Iodine-induced stress-corrosion cracking (ISCC), a known failure mode for nuclear fuel cladding, occurs when iodine generated during the irradiation of a nuclear fuel pellet escapes the pellet through diffusion or thermal cracking and chemically interacts with the inner surface of the clad material, inducing a subsequent effect on the cladding’s resistance to mechanical stress. To complement experimental investigations of ISCC, a reactive force field (ReaxFF) compatible with the Zr-I chemical and materials systems has been developed and applied to simulate the impact of iodine exposure on the mechanical strength of the material. The study shows that the material’s resistance tomore » stress (as captured by the yield stress of a high-energy grain boundary) is related to the surface coverage of iodine, with the implication that ISCC is the result of adsorption-enhanced decohesion.« less

Origin and structures of solar eruptions II: Magnetic modeling

NASA Astrophysics Data System (ADS)

Guo, Yang; Cheng, Xin; Ding, MingDe

2017-07-01

The topology and dynamics of the three-dimensional magnetic field in the solar atmosphere govern various solar eruptive phenomena and activities, such as flares, coronal mass ejections, and filaments/prominences. We have to observe and model the vector magnetic field to understand the structures and physical mechanisms of these solar activities. Vector magnetic fields on the photosphere are routinely observed via the polarized light, and inferred with the inversion of Stokes profiles. To analyze these vector magnetic fields, we need first to remove the 180° ambiguity of the transverse components and correct the projection effect. Then, the vector magnetic field can be served as the boundary conditions for a force-free field modeling after a proper preprocessing. The photospheric velocity field can also be derived from a time sequence of vector magnetic fields. Three-dimensional magnetic field could be derived and studied with theoretical force-free field models, numerical nonlinear force-free field models, magnetohydrostatic models, and magnetohydrodynamic models. Magnetic energy can be computed with three-dimensional magnetic field models or a time series of vector magnetic field. The magnetic topology is analyzed by pinpointing the positions of magnetic null points, bald patches, and quasi-separatrix layers. As a well conserved physical quantity, magnetic helicity can be computed with various methods, such as the finite volume method, discrete flux tube method, and helicity flux integration method. This quantity serves as a promising parameter characterizing the activity level of solar active regions.

Cytoplasmic motion induced by cytoskeleton stretching and its effect on cell mechanics.

PubMed

Zhang, T

2011-09-01

Cytoplasmic motion assumed as a steady state laminar flow induced by cytoskeleton stretching in a cell is determined and its effect on the mechanical behavior of the cell under externally applied forces is demonstrated. Non-Newtonian fluid is assumed for the multiphase cytoplasmic fluid and the analytical velocity field around the macromolecular chain is obtained by solving the reduced nonlinear momentum equation using homotopy technique. The entropy generation by the fluid internal friction is calculated and incorporated into the entropic elasticity based 8-chain constitutive relations. Numerical examples showed strengthening behavior of cells in response to externally applied mechanical stimuli. The spatial distribution of the stresses within a cell under externally applied fluid flow forces were also studied.

Evaluation of synthetic linear motor-molecule actuation energetics

PubMed Central

Brough, Branden; Northrop, Brian H.; Schmidt, Jacob J.; Tseng, Hsian-Rong; Houk, Kendall N.; Stoddart, J. Fraser; Ho, Chih-Ming

2006-01-01

By applying atomic force microscope (AFM)-based force spectroscopy together with computational modeling in the form of molecular force-field simulations, we have determined quantitatively the actuation energetics of a synthetic motor-molecule. This multidisciplinary approach was performed on specifically designed, bistable, redox-controllable [2]rotaxanes to probe the steric and electrostatic interactions that dictate their mechanical switching at the single-molecule level. The fusion of experimental force spectroscopy and theoretical computational modeling has revealed that the repulsive electrostatic interaction, which is responsible for the molecular actuation, is as high as 65 kcal·mol−1, a result that is supported by ab initio calculations. PMID:16735470

ELECTROMAGNETIC RELEASE MECHANISM

DOEpatents

Michelson, C.

1960-09-13

An electromagnetic release mechanism is offered that may be used, for example, for supporting a safety rod for a nuclear reactor. The release mechanism is designed to have a large excess holding force and a rapid, uniform, and dependable release. The fast release is accomplished by providing the electromagnet with slotttd polts separated by an insulating potting resin, and by constructing the poles with a ferro-nickel alloy. The combination of these two features materially reduces the eddy current power density whenever the magnetic field changes during a release operation. In addition to these features, the design of the armature is such as to provide ready entrance of fluid into any void that might tend to form during release of the armature. This also improves the release time for the mechanism. The large holding force for the mechanism is accomplished by providing a small, selected, uniform air gap between the inner pole piece and the armature.

Laboratory Evidence That Line-Tied Toroidal Magnetic Fields Can Suppress Loss-of-Equilibrium Flux Rope Eruptions in the Solar Corona

NASA Astrophysics Data System (ADS)

Myers, C. E.; Yamada, M.; Belova, E.; Ji, H.; Yoo, J.; Fox, W. R., II; Jara-Almonte, J.

2014-12-01

Loss-of-equilibrium mechanisms such as the ideal torus instability [Kliem & Török, Phys. Rev. Lett. 96, 255002 (2006)] are predicted to drive arched flux ropes in the solar corona to erupt. In recent line-tied flux rope experiments conducted in the Magnetic Reconnection Experiment (MRX), however, we find that quasi-statically driven flux ropes remain confined well beyond the predicted torus instability threshold. In order to understand this behavior, in situ measurements from a 300 channel 2D magnetic probe array are used to comprehensively analyze the force balance between the external (potential) and internal (plasma-generated) magnetic fields. We find that forces due to the line-tied toroidal magnetic field, which are not included in the basic torus instability theory, can play a major role in preventing eruptions. The dependence of these toroidal magnetic forces on various potential field and flux rope parameters will be discussed. This research is supported by DoE Contract Number DE-AC02-09CH11466 and by the NSF/DoE Center for Magnetic Self-Organization (CMSO).

Volcano ecology: flourishing on the flanks of Mount St. Helens

Treesearch

Rhonda Mazza; Charlie Crisafulli

2016-01-01

Mount St. Helens’ explosive eruption on May 18, 1980, was a pivotal moment in the field of disturbance ecology. The subsequent sustained, integrated research effort has shaped the development of volcano ecology, an emerging field of focused research. Excessive heat, burial, and impact force are some of the disturbance mechanisms following an eruption. They are also...

Mechanical reinforcement for RACC cables in high magnetic background fields

NASA Astrophysics Data System (ADS)

Bayer, C. M.; Gade, P. V.; Barth, C.; Preuß, A.; Jung, A.; Weiß, K. P.

2016-02-01

Operable in liquid helium, liquid hydrogen or liquid nitrogen, high temperature superconductor (HTS) cables are investigated as future alternatives to low temperature superconductor (LTS) cables in magnet applications. Different high current HTS cable concepts have been developed and optimized in the last years—each coming with its own benefits and challenges. As the Roebel assembled coated conductor (RACC) is the only fully transposed HTS cable investigated so far, it is attractive for large scale magnet and accelerator magnet applications when field quality and alternating current (AC) losses are of highest importance. However, due to its filamentary character, the RACC is very sensitive to Lorentz forces. In order to increase the mechanical strength of the RACC, each of the HTS strands was covered by an additional copper tape. After investigating the maximum applicable transverse pressure on the strand composition, the cable was clamped into a stainless steel structure to reinforce it against Lorentz forces. A comprehensive test has been carried out in the FBI facility at 4.2 K in a magnetic field of up to 12 T. This publication discusses the maximum applicable pressure as well as the behaviour of the RACC cable as a function of an external magnetic field.

Study on a new self-sensing magnetorheological elastomer bearing

NASA Astrophysics Data System (ADS)

Li, Rui; Zhou, Mengjiao; Wang, Minglian; Yang, Ping-an

2018-06-01

The complexity of a semi-active vibration isolation system results in the difficulty of realizing its role on impact load effectively. Thus, a new self-sensing bearing based on modified anisotropic magnetorheological elastomer (MRE) is proposed in this study. This self-sensing bearing was fabricated by dispersed multi-walled carbon nanotubes and carbonyl iron particles into polydimethylsiloxane matrix under a magnetic field. The working conditions of the bearing were analyzed and decoupled. An optimal structure size of the bearing was selected and used for setting up the experiment test system. The self-sensing characteristic of the MRE bearing under the multi-field coupling of load and magnetic fields was then investigated by this test system. Results showed that the resistance of the modified MRE, in which a preload was applied by the bearing, could change approximately 28%-56% under extrusion force, mechanical force, and external magnetic field. The vibration isolation performance was tested based on the self-sensing characteristic. The bearing had excellent mechanical properties, which could reduce at least 30% of vibration. Thus, the modified MRE of the magnetorheological elastomer bearing could be simultaneously used as an actuator and a sensor.

NIS, IR and Raman spectra with quantum mechanical calculations for analyzing the force field of hypericin model compounds

NASA Astrophysics Data System (ADS)

Ulicny, Jozef; Leulliot, Nicolas; Grajcar, Lydie; Baron, Marie-Hélène; Jobic, Hervé; Ghomi, Mahmoud

1999-06-01

Geometry optimization as well as harmonic force field calculations at HF and DFT levels of theory have been performed in order to elucidate the ground state properties of anthrone and emodin, two polycyclic conjugated molecules considered as hypericin model compounds. NIS, IR and FT-Raman spectra of these compounds have been recorded to validate the calculated results (geometry and vibrational modes). Calculated NIS spectra using the lowest energy conformers are in agreement with experiment. In addition, the intramolecular H-bonds in emodin predicted by the calculations can be evidenced using IR spectra as a function of temperature.

NIS, IR and Raman spectra with quantum mechanical calculations for analyzing the force field of hypericin model compounds

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

Ulicny, Jozef; Department of Biophysics, Safarik University, Jesenna 5, 04154 Kosice; Leulliot, Nicolas

1999-06-15

Geometry optimization as well as harmonic force field calculations at HF and DFT levels of theory have been performed in order to elucidate the ground state properties of anthrone and emodin, two polycyclic conjugated molecules considered as hypericin model compounds. NIS, IR and FT-Raman spectra of these compounds have been recorded to validate the calculated results (geometry and vibrational modes). Calculated NIS spectra using the lowest energy conformers are in agreement with experiment. In addition, the intramolecular H-bonds in emodin predicted by the calculations can be evidenced using IR spectra as a function of temperature.

Combined free and forced convection heat transfer in magneto fluid mechanic pipe flow

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

Gardner, R.A.; Lo, Y.T.

1977-01-01

A study is made of fully developed, laminar, free-and-forced convection heat transfer in an electrically conducting fluid flowing in an electrically insulated, horizontal, circular pipe in a vertical transverse magnetic field. The normalized magnetofluidmechanic and energy equations are reduced to three coupled partial differential equations by the introduction of a stream function of the secondary flow. A perturbation solution is generated in inverse powers of the Lykoudis number, Ly = M/sup 2//..sqrt..Gr, which yields the influence of the magnetic field on the stream function of the secondary flow, axial velocity profiles, temperature profiles, and Nusselt number. 6 figures, 1 table.

Simultaneous Measurement of Multiple Mechanical Properties of Single Cells Using AFM by Indentation and Vibration.

PubMed

Zhang, Chuang; Shi, Jialin; Wang, Wenxue; Xi, Ning; Wang, Yuechao; Liu, Lianqing

2017-12-01

The mechanical properties of cells, which are the main characteristics determining their physical performance and physiological functions, have been actively studied in the fields of cytobiology and biomedical engineering and for the development of medicines. In this study, an indentation-vibration-based method is proposed to simultaneously measure the mechanical properties of cells in situ, including cellular mass (m), elasticity (k), and viscosity (c). The proposed measurement method is implemented based on the principle of forced vibration stimulated by simple harmonic force using an atomic force microscope (AFM) system integrated with a piezoelectric transducer as the substrate vibrator. The corresponding theoretical model containing the three mechanical properties is derived and used to perform simulations and calculations. Living and fixed human embryonic kidney 293 (HEK 293) cells were subjected to indentation and vibration to measure and compare their mechanical parameters and verify the proposed approach. The results that the fixed sample cells are more viscous and elastic than the living sample cells and the measured mechanical properties of cell are consistent within, but not outside of the central region of the cell, are in accordance with the previous studies. This work provides an approach to simultaneous measurement of the multiple mechanical properties of single cells using an integrated AFM system based on the principle force vibration and thickness-corrected Hertz model. This study should contribute to progress in biomedical engineering, cytobiology, medicine, early diagnosis, specific therapy and cell-powered robots.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

PubMed

Antipov, Sergey V; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2017-11-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H 2 , local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

Mathematical Model for Collision-Coalescence Among Inclusions in the Bloom Continuous Caster with M-EMS

NASA Astrophysics Data System (ADS)

Lei, Hong; Jiang, Jimin; Yang, Bin; Zhao, Yan; Zhang, Hongwei; Wang, Weixian; Dong, Guiwen

2018-04-01

Mathematical simulation is an effective tool to analyze the fluid flow and the inclusion behavior in the bloom continuous caster with mold electromagnetic stirring (M-EMS). The mathematical model is applied to the modeling of magnetic field, flow field, and inclusion field. Due to the introduction of Archimedes force, the collision mechanism and inclusion's slipping velocity should be modified in the inclusion mass and population conservation model. Numerically predicted magnetic field, flow field, and the inclusion spatial distribution conform to the experimental results in the existing literature. Lorentz force plays an important role in the fluid flow, and Archimedes force plays an important role in the inclusion distribution in the continuous caster. Due to Brownian collision, Stokes collision, Archimedes collision, and turbulent collision, the coalescence among inclusions occurs in the bloom continuous caster with M-EMS. Among the four types of collisions, turbulent collision occurs most frequently, followed by Archimedes collision and Stokes collision. The frequency of Brownian collision is several orders of magnitudes smaller and is therefore negligible. The inclusion volume concentration, number density, and characteristic radius exhibit a U-shape in the continuous caster without M-EMS. However, with M-EMS, they exhibit an inverted U-shape.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

PubMed Central

Antipov, Sergey V.; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2018-01-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase. PMID:29376107

Tensegrity, cellular biophysics, and the mechanics of living systems

PubMed Central

Ingber, Donald E.; Wang, Ning; Stamenović, Dimitrije

2014-01-01

The recent convergence between physics and biology has led many physicists to enter the fields of cell and developmental biology. One of the most exciting areas of interest has been the emerging field of mechanobiology that centers on how cells control their mechanical properties, and how physical forces regulate cellular biochemical responses, a process that is known as mechanotransduction. In this article, we review the central role that tensegrity (tensional integrity) architecture, which depends on tensile prestress for its mechanical stability, plays in biology. We describe how tensional prestress is a critical governor of cell mechanics and function, and how use of tensegrity by cells contributes to mechanotransduction. Theoretical tensegrity models are also described that predict both quantitative and qualitative behaviors of living cells, and these theoretical descriptions are placed in context of other physical models of the cell. In addition, we describe how tensegrity is used at multiple size scales in the hierarchy of life — from individual molecules to whole living organisms — to both stabilize three-dimensional form and to channel forces from the macroscale to the nanoscale, thereby facilitating mechanochemical conversion at the molecular level. PMID:24695087

An accurate and efficient method for piezoelectric coated functional devices based on the two-dimensional Green’s function for a normal line force and line charge

NASA Astrophysics Data System (ADS)

Hou, Peng-Fei; Zhang, Yang

2017-09-01

Because most piezoelectric functional devices, including sensors, actuators and energy harvesters, are in the form of a piezoelectric coated structure, it is valuable to present an accurate and efficient method for obtaining the electro-mechanical coupling fields of this coated structure under mechanical and electrical loads. With this aim, the two-dimensional Green’s function for a normal line force and line charge on the surface of coated structure, which is a combination of an orthotropic piezoelectric coating and orthotropic elastic substrate, is presented in the form of elementary functions based on the general solution method. The corresponding electro-mechanical coupling fields of this coated structure under arbitrary mechanical and electrical loads can then be obtained by the superposition principle and Gauss integration. Numerical results show that the presented method has high computational precision, efficiency and stability. It can be used to design the best coating thickness in functional devices, improve the sensitivity of sensors, and improve the efficiency of actuators and energy harvesters. This method could be an efficient tool for engineers in engineering applications.

Multiphase-field model of small strain elasto-plasticity according to the mechanical jump conditions

NASA Astrophysics Data System (ADS)

Herrmann, Christoph; Schoof, Ephraim; Schneider, Daniel; Schwab, Felix; Reiter, Andreas; Selzer, Michael; Nestler, Britta

2018-04-01

We introduce a small strain elasto-plastic multiphase-field model according to the mechanical jump conditions. A rate-independent J_2 -plasticity model with linear isotropic hardening and without kinematic hardening is applied exemplary. Generally, any physically nonlinear mechanical model is compatible with the subsequently presented procedure. In contrast to models with interpolated material parameters, the proposed model is able to apply different nonlinear mechanical constitutive equations for each phase separately. The Hadamard compatibility condition and the static force balance are employed as homogenization approaches to calculate the phase-inherent stresses and strains. Several verification cases are discussed. The applicability of the proposed model is demonstrated by simulations of the martensitic transformation and quantitative parameters.

The shape dependence of chameleon screening

NASA Astrophysics Data System (ADS)

Burrage, Clare; Copeland, Edmund J.; Moss, Adam; Stevenson, James A.

2018-01-01

Chameleon scalar fields can screen their associated fifth forces from detection by changing their mass with the local density. These models are an archetypal example of a screening mechanism, and have become an important target for both cosmological surveys and terrestrial experiments. In particular there has been much recent interest in searching for chameleon fifth forces in the laboratory. It is known that the chameleon force is less screened around non-spherical sources, but only the field profiles around a few simple shapes are known analytically. In this work we introduce a numerical code that solves for the chameleon field around arbitrary shapes with azimuthal symmetry placed in a spherical vacuum chamber. We find that deviations from spherical symmetry can increase the chameleon acceleration experienced by a test particle, and that the least screened objects are those which minimize some internal dimension. For the shapes considered in this work, keeping the mass, density and background environment fixed, the accelerations due to the source varied by a factor of ~ 3.

Near-field Light Scattering Techniques for Measuring Nanoparticle-Surface Interaction Energies and Forces.

PubMed

Schein, Perry; Ashcroft, Colby K; O'Dell, Dakota; Adam, Ian S; DiPaolo, Brian; Sabharwal, Manit; Shi, Ce; Hart, Robert; Earhart, Christopher; Erickson, David

2015-08-15

Nanoparticles are quickly becoming commonplace in many commercial and industrial products, ranging from cosmetics to pharmaceuticals to medical diagnostics. Predicting the stability of the engineered nanoparticles within these products a priori remains an important and difficult challenge. Here we describe our techniques for measuring the mechanical interactions between nanoparticles and surfaces using near-field light scattering. Particle-surface interfacial forces are measured by optically "pushing" a particle against a reference surface and observing its motion using scattered near-field light. Unlike atomic force microscopy, this technique is not limited by thermal noise, but instead takes advantage of it. The integrated waveguide and microfluidic architecture allow for high-throughput measurements of about 1000 particles per hour. We characterize the reproducibility of and experimental uncertainty in the measurements made using the NanoTweezer surface instrument. We report surface interaction studies on gold nanoparticles with 50 nm diameters, smaller than previously reported in the literature using similar techniques.

Observation of force-detected nuclear magnetic resonance in a homogeneous field

PubMed Central

Madsen, L. A.; Leskowitz, G. M.; Weitekamp, D. P.

2004-01-01

We report the experimental realization of BOOMERANG (better observation of magnetization, enhanced resolution, and no gradient), a sensitive and general method of magnetic resonance. The prototype millimeter-scale NMR spectrometer shows signal and noise levels in agreement with the design principles. We present 1H and 19F NMR in both solid and liquid samples, including time-domain Fourier transform NMR spectroscopy, multiple-pulse echoes, and heteronuclear J spectroscopy. By measuring a 1H-19F J coupling, this last experiment accomplishes chemically specific spectroscopy with force-detected NMR. In BOOMERANG, an assembly of permanent magnets provides a homogeneous field throughout the sample, while a harmonically suspended part of the assembly, a detector, is mechanically driven by spin-dependent forces. By placing the sample in a homogeneous field, signal dephasing by diffusion in a field gradient is made negligible, enabling application to liquids, in contrast to other force-detection methods. The design appears readily scalable to μm-scale samples where it should have sensitivity advantages over inductive detection with microcoils and where it holds great promise for application of magnetic resonance in biology, chemistry, physics, and surface science. We briefly discuss extensions of the BOOMERANG method to the μm and nm scales. PMID:15326302

Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

NASA Astrophysics Data System (ADS)

Wu, Xiangyang

1999-07-01

The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B-DNA orientations, compromising its ability to act as a faithful template during DNA replication.

Discrimination of Thermal versus Mechanical Effects of Shock on Rock Magnetic Properties of Spherically Shocked up to 10-160 GPa Basalt and Diabase

NASA Astrophysics Data System (ADS)

Bezaeva, N. S.; Swanson-Hysell, N.; Tikoo, S.; Badyukov, D. D.; Kars, M. A. C.; Egli, R.; Chareev, D. A.; Fairchild, L. M.

2016-12-01

Understanding how shock waves generated during hypervelocity impacts affect rock magnetic properties is key for interpreting the paleomagnetic records of lunar rocks, meteorites, and cratered planetary surfaces. Laboratory simulations of impacts show that ultra-high shocks may induce substantial post-shock heating of the target material. At high pressures (>10 GPa), shock heating occurs in tandem with mechanical effects, such as grain fracturing and creation of crystallographic defects and dislocations within magnetic grains. This makes it difficult to conclude whether shock-induced changes in the rock magnetic properties of target materials are primarily associated with mechanical or thermal effects. Here we present novel experimental methods to discriminate between mechanical and thermal effects of shock on magnetic properties and illustrate it with two examples of spherically shocked terrestrial basalt and diabase [1], which were shocked to pressures of 10 to >160 GPa, and investigate possible explanations for the observed shock-induced magnetic hardening (i.e., increase in remanent coercivity Bcr). The methods consist of i) conducting extra heating experiments at temperatures resembling those experienced during high-pressure shock events on untreated equivalents of shocked rocks (with further comparison of Bcr of shocked and heated samples) and ii) quantitative comparison of high-resolution first-order reversal curve (FORC) diagrams (field step: 0.5-0.7 mT) for shocked, heated and untreated specimens. Using this approach, we demonstrated that the shock-induced coercivity hardening in our samples is predominantly due to solid-state, mechanical effects of shock rather than alteration associated with shock heating. Indeed, heating-induced changes in Bcr in the post-shock temperature range were minor. Visual inspection of FORC contours (in addition to detailed analyses) reveals a stretching of the FORC distribution of shocked sample towards higher coercivities, consistent with shock-induced hardening. However, shock does not alter the intrinsic shape of coercivity and the shape of FORC contours (apart from field scaling) while heating does, which is seen as a significant alteration of FORC contours. Reference: [1] Swanson-Hysell N. L. et al. 2014. G3 15:2039-2047.

The Role of Nongyrotropy in Balancing the Reconnection Diffusion Region

NASA Astrophysics Data System (ADS)

Hesse, M.; Liu, Y. H.; Chen, L. J.; Bessho, N.; Wang, S.; Burch, J. L.; Moretto, T.; Genestreti, K.; Phan, T.; Tenfjord, P.

2017-12-01

The structure of the reconnection diffusion region is, to a large degree, determined by the requirement to balance both the current flow and its dissipation processes, and the forces exerted onto the current layer by the inflow magnetic pressure. These balances are critical: without resupply processes, the transport of accelerated and current-carrying particles away from the diffusion region would generate a current density depletion, which, in principle, could lead to a mismatch with the curl of the magnetic field. Similarly, without heating processes, the convection of hot plasma away from the diffusion region would generate a force imbalance with the ambient magnetic field. The fact that neither of these imbalances occur is a consequence of the reconnection electric field, which is therefore not only required to facilitate magnetic flux transport, but also to provide the energization required to maintain balance in the diffusion region. In this presentation, we will use particle-in-cell simulations to analyze these balance conditions. We will furthermore show that nongyrotropic particle dynamics plays a key role both as current dissipation mechanism, and as overall heating mechanism in the diffusion region current layer.

Nanopatterning on calixarene thin films via low-energy field-emission scanning probe lithography.

PubMed

He, Xiaoyue; Li, Peng; Liu, Pengchong; Zhang, Xiaoxian; Zhou, Xiangqian; Liu, Wei; Qiu, Xiaohui

2018-08-10

Field-emitted, low-energy electrons from the conducting tip of an atomic force microscope were adopted for nanolithography on calixarene ultrathin films coated on silicon wafers. A structural evolution from protrusion to depression down to a 30 nm spatial resolution was reproducibly obtained by tuning the sample voltage and exposure current in the lithography process. Close analyses of the profiles showed that the nanostructures formed by a single exposure with a high current are almost identical to those created by cumulative exposure with a lower current but an equal number of injected electrons. Surface potential imaging by Kelvin probe force microscopy found a negatively charged region surrounding the groove structures once the structures were formed. We conclude that the mechanism related to the formation of a temporary negative state and molecule decomposition, rather than thermal ablation, is responsible for the low-energy field-emission electron lithography on a calixarene molecular resist. We hope that our elucidation of the underlying mechanism is helpful for molecular resist design and further improving the reproducibility and throughput of nanolithography.

Novel approaches to optomechanical transduction

NASA Astrophysics Data System (ADS)

Cernotik, Ondrej; Hammerer, Klemens

In recent years, mechanical oscillators received attention as a promising tool for frequency conversion between microwaves and light. A general, bi-directional transducer with high efficiency is still far from reach of current technology; finding new strategies for optomechanical transduction allows us to relax the requirements and bring these systems closer to an experimental realization. An interesting example is generation of entanglement between two superconducting qubits using measurement and postselection. Here, the mechanical oscillators interacts directly with the superconducting transmon qubit in such a way that it feels a qubit-state dependent force. This force can then be read out using a cavity field; reading out two such systems sequentially realizes an effective total spin measurement. Starting from a suitable initial state and employing postselection, entanglement can be generated. Another interesting approach is to use an array of optomechanical transducers in which the output fields of one transducer are fed into the input of the next. The periodicity of the array results in a joint dispersion relation for the propagating microwave and optical fields. The resulting structure can be used to control the conversion bandwidth and forward and backward scattering.

Non-kinematic Flux-transport Dynamos Including the Effects of Diffusivity Quenching

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

Ichimura, Chiaki; Yokoyama, Takaaki

2017-04-10

Turbulent magnetic diffusivity is quenched when strong magnetic fields suppress turbulent motion in a phenomenon known as diffusivity quenching. Diffusivity quenching can provide a mechanism for amplifying magnetic field and influencing global velocity fields through Lorentz force feedback. To investigate this effect, we conducted mean field flux-transport dynamo simulations that included the effects of diffusivity quenching in a non-kinematic regime. We found that toroidal magnetic field strength is amplified by up to approximately 1.5 times in the convection zone as a result of diffusivity quenching. This amplification is much weaker than that in kinematic cases as a result of Lorentzmore » force feedback on the system’s differential rotation. While amplified toroidal fields lead to the suppression of equatorward meridional flow locally near the base of the convection zone, large-scale equatorward transport of magnetic flux via meridional flow, which is the essential process of the flux-transport dynamo, is sustainable in our calculations.« less

Extending the Range for Force Calibration in Magnetic Tweezers

PubMed Central

Daldrop, Peter; Brutzer, Hergen; Huhle, Alexander; Kauert, Dominik J.; Seidel, Ralf

2015-01-01

Magnetic tweezers are a wide-spread tool used to study the mechanics and the function of a large variety of biomolecules and biomolecular machines. This tool uses a magnetic particle and a strong magnetic field gradient to apply defined forces to the molecule of interest. Forces are typically quantified by analyzing the lateral fluctuations of the biomolecule-tethered particle in the direction perpendicular to the applied force. Since the magnetic field pins the anisotropy axis of the particle, the lateral fluctuations follow the geometry of a pendulum with a short pendulum length along and a long pendulum length perpendicular to the field lines. Typically, the short pendulum geometry is used for force calibration by power-spectral-density (PSD) analysis, because the movement of the bead in this direction can be approximated by a simple translational motion. Here, we provide a detailed analysis of the fluctuations according to the long pendulum geometry and show that for this direction, both the translational and the rotational motions of the particle have to be considered. We provide analytical formulas for the PSD of this coupled system that agree well with PSDs obtained in experiments and simulations and that finally allow a faithful quantification of the magnetic force for the long pendulum geometry. We furthermore demonstrate that this methodology allows the calibration of much larger forces than the short pendulum geometry in a tether-length-dependent manner. In addition, the accuracy of determination of the absolute force is improved. Our force calibration based on the long pendulum geometry will facilitate high-resolution magnetic-tweezers experiments that rely on short molecules and large forces, as well as highly parallelized measurements that use low frame rates. PMID:25992733

Operations Odyssey Dawn and Unified Protector: Another Win for Warden s Theory

DTIC Science & Technology

2014-12-04

Gortney’s response was clear, “they were mechanized positions and they were advancing on Benghazi. And so to protect the Libyan people we took them under ...them under attack.” Targeting the fielded forces played a primary role in protecting the Libyan people. Coalition fighter aircraft targeted... protection of civilians, with the major limitation of prohibiting foreign ground forces from the operations. Because of this limitation, airpower was the

Coastal Benthic Boundary Layer (CBBL) Research Program

DTIC Science & Technology

1998-09-01

of gas volume and bubble size distribution on the basis of field seismo-acoustic signature remains . Indirect seismic evidence (large scale) of gas...regime was dominated by reversing tidal currents with typical speeds of 10-cm s -1 or less. Maximum bed shear stresses remained too low to resuspend or...Waals attractive force are assumed to remain unchanged for separations less than the cut-off distance, and (2) the mechanical interparticle normal force

Gas Bubble Dynamics under Mechanical Vibrations

NASA Astrophysics Data System (ADS)

Mohagheghian, Shahrouz; Elbing, Brian

2017-11-01

The scientific community has a limited understanding of the bubble dynamics under mechanical oscillations due to over simplification of Navier-Stockes equation by neglecting the shear stress tensor and not accounting for body forces when calculating the acoustic radiation force. The current work experimental investigates bubble dynamics under mechanical vibration and resulting acoustic field by measuring the bubble size and velocity using high-speed imaging. The experimental setup consists of a custom-designed shaker table, cast acrylic bubble column, compressed air injection manifold and an optical imaging system. The mechanical vibrations resulted in accelerations between 0.25 to 10 times gravitational acceleration corresponding to frequency and amplitude range of 8 - 22Hz and 1 - 10mm respectively. Throughout testing the void fraction was limited to <5%. The bubble size is larger than resonance size and smaller than acoustic wavelength. The amplitude of acoustic pressure wave was estimated using the definition of Bjerknes force in combination with Rayleigh-Plesset equation. Physical behavior of the system was capture and classified. Bubble size, velocity as well as size and spatial distribution will be presented.

The Vainshtein mechanism in the cosmic web

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

Falck, Bridget; Koyama, Kazuya; Zhao, Gong-bo

We investigate the dependence of the Vainshtein screening mechanism on the cosmic web morphology of both dark matter particles and halos as determined by ORIGAMI. Unlike chameleon and symmetron screening, which come into effect in regions of high density, Vainshtein screening instead depends on the dimensionality of the system, and screened bodies can still feel external fields. ORIGAMI is well-suited to this problem because it defines morphologies according to the dimensionality of the collapsing structure and does not depend on a smoothing scale or density threshold parameter. We find that halo particles are screened while filament, wall, and void particlesmore » are unscreened, and this is independent of the particle density. However, after separating halos according to their large scale cosmic web environment, we find no difference in the screening properties of halos in filaments versus halos in clusters. We find that the fifth force enhancement of dark matter particles in halos is greatest well outside the virial radius. We confirm the theoretical expectation that even if the internal field is suppressed by the Vainshtein mechanism, the object still feels the fifth force generated by the external fields, by measuring peculiar velocities and velocity dispersions of halos. Finally, we investigate the morphology and gravity model dependence of halo spins, concentrations, and shapes.« less

The effect of rotating magnetic field on the microstructure of in situ TiB2/Cu composites

NASA Astrophysics Data System (ADS)

Zou, C.; Kang, H.; Li, R.; Li, M.; Wang, W.; Chen, Z.; Wang, T.

2016-03-01

Nano ceramic particulate reinforced metal matrix composites are confronted with the problem of particle aggregation emerging in the process of solidification. It sharply deteriorates the mechanical properties of the composites. In order to improve the microstructure and particle distribution, in situ TiB2/Cu composites were prepared using Ti and Cu-B master alloys in a vacuum medium frequency induction furnace equipped with a rotating magnetic field (RMF). The effect of RMF magnetic field intensity employed on the microstructure and particles distribution of the TiB2/Cu composites were investigated. The results show that with the applied RMF, TiB2 particles are homogeneously distributed in the copper matrix, which significantly improves the mechanical properties of TiB2/Cu composites. The mechanism of RMF may be ascribed to the following two aspects. On the one hand, the electromagnetic body force generated by appropriate RMF drives forced convection in the equatorial plane of composite melt during solidification. On the other hand, a secondary flow in the meridional plane is engendered by a radial pressure gradient, thus making a strong agitation in the melt. These two effects result in a homogenous dispersion of TiB2 particles in the copper matrix, and hence excellent properties of TiB2/Cu composites were obtained.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

DOE PAGES

Huang, Jing; Mei, Ye; König, Gerhard; ...

2017-01-24

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

PubMed

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

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

Huang, Jing; Mei, Ye; König, Gerhard

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

Theoretical analysis for the design of the French watt balance experiment force comparator

NASA Astrophysics Data System (ADS)

Pinot, Patrick; Genevès, Gerard; Haddad, Darine; David, Jean; Juncar, Patrick; Lecollinet, Michel; Macé, Stéphane; Villar, François

2007-09-01

This paper presents a preliminary analysis for designing a force comparator to be used in the French watt balance experiment. The first stage of this experiment consists in a static equilibrium, by means of a mechanical beam balance, between a gravitational force (a weight of an artefact having a known mass submitted to the acceleration due to the gravity) and a vertical electromagnetic force acting on a coil driven by a current subject to the magnetic induction field provided by a permanent magnet. The principle of the force comparison in the French experiment is explained. The general design configuration of the force balance using flexure strips as pivots is discussed and theoretical calculation results based on realistic assumptions of the static and dynamic behaviors of the balance are presented.

Theoretical analysis for the design of the French watt balance experiment force comparator.

PubMed

Pinot, Patrick; Genevès, Gerard; Haddad, Darine; David, Jean; Juncar, Patrick; Lecollinet, Michel; Macé, Stéphane; Villar, François

2007-09-01

This paper presents a preliminary analysis for designing a force comparator to be used in the French watt balance experiment. The first stage of this experiment consists in a static equilibrium, by means of a mechanical beam balance, between a gravitational force (a weight of an artefact having a known mass submitted to the acceleration due to the gravity) and a vertical electromagnetic force acting on a coil driven by a current subject to the magnetic induction field provided by a permanent magnet. The principle of the force comparison in the French experiment is explained. The general design configuration of the force balance using flexure strips as pivots is discussed and theoretical calculation results based on realistic assumptions of the static and dynamic behaviors of the balance are presented.

The New Field Quantities and the Poynting Theorem in Material Medium with Magnetic Monopoles

NASA Astrophysics Data System (ADS)

Zor, Ömer

2016-12-01

The duality transformation was used to define the polarization mechanisms that arise from magnetic monopoles. Then, a dimensional analysis was conducted to describe the displacement and magnetic intensity vectors (constitutive equations) in SI units. Finally, symmetric Maxwell equations in a material medium with new field quantities were introduced. Hence, the Lorentz force and the Poynting theorem were defined with these new field quantities, and many possible definitions of them were constructed.

Thermal runaway of metal nano-tips during intense electron emission

NASA Astrophysics Data System (ADS)

Kyritsakis, A.; Veske, M.; Eimre, K.; Zadin, V.; Djurabekova, F.

2018-06-01

When an electron emitting tip is subjected to very high electric fields, plasma forms even under ultra high vacuum conditions. This phenomenon, known as vacuum arc, causes catastrophic surface modifications and constitutes a major limiting factor not only for modern electron sources, but also for many large-scale applications such as particle accelerators, fusion reactors etc. Although vacuum arcs have been studied thoroughly, the physical mechanisms that lead from intense electron emission to plasma ignition are still unclear. In this article, we give insights to the atomic scale processes taking place in metal nanotips under intense field emission conditions. We use multi-scale atomistic simulations that concurrently include field-induced forces, electron emission with finite-size and space-charge effects, Nottingham and Joule heating. We find that when a sufficiently high electric field is applied to the tip, the emission-generated heat partially melts it and the field-induced force elongates and sharpens it. This initiates a positive feedback thermal runaway process, which eventually causes evaporation of large fractions of the tip. The reported mechanism can explain the origin of neutral atoms necessary to initiate plasma, a missing key process required to explain the ignition of a vacuum arc. Our simulations provide a quantitative description of in the conditions leading to runaway, which shall be valuable for both field emission applications and vacuum arc studies.

It's Rather like Learning a Language: Development of talk and conceptual understanding in mechanics lessons

NASA Astrophysics Data System (ADS)

Rincke, Karsten

2011-01-01

Although a broad literature exists concerning the development of conceptual understanding of force and other topics within mechanics, little is known about the role and development of students' talk about the subject. The paper presents an in-depth investigation of students' talk whilst being introduced to the concept of force. The main research goal was to investigate and understand how students develop an understanding of the concept of force and how they use and understand the term 'force'. Therefore, we make relation to the research field of students' preconceptions and the field of second language learning. Two classes of students (N = 47) were videotaped during a time period of nine lessons, each transcribed and analysed using a category system. Additional data were obtained via written tasks, logs kept by the students, and tests. The detailed analysis of the talk and the results of the tests indicate that students face difficulties in using the term 'force' scientifically similar to those in a foreign language instruction. Vygotsky already recognised a relationship between learning in science and learning a language. In this paper, important aspects of this relationship are discussed based upon empirical data. We conclude that in some respects it might be useful to make reference to the research related to language learning when thinking about improving science education. In particular, according to Selinker's concept of interlanguage describing language-learning processes within language instruction, the language used by the students during physics lessons can be viewed as a 'scientific interlanguage'.

Acoustic radiation force due to arbitrary incident fields on spherical particles in soft tissue

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

Treweek, Benjamin C., E-mail: btreweek@utexas.edu; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.

Acoustic radiation force is of interest in a wide variety of biomedical applications ranging from tissue characterization (e.g. elastography) to tissue treatment (e.g. high intensity focused ultrasound, kidney stone fragment removal). As tissue mechanical properties are reliable indicators of tissue health, the former is the focus of the present contribution. This is accomplished through an investigation of the acoustic radiation force on a spherical scatterer embedded in tissue. Properties of both the scatterer and the surrounding tissue are important in determining the magnitude and the direction of the force. As these properties vary, the force computation shows changes in magnitudemore » and direction, which may enable more accurate noninvasive determination of tissue properties.« less

Acoustic radiation force due to arbitrary incident fields on spherical particles in soft tissue

NASA Astrophysics Data System (ADS)

Treweek, Benjamin C.; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.; Hamilton, Mark F.

2015-10-01

Acoustic radiation force is of interest in a wide variety of biomedical applications ranging from tissue characterization (e.g. elastography) to tissue treatment (e.g. high intensity focused ultrasound, kidney stone fragment removal). As tissue mechanical properties are reliable indicators of tissue health, the former is the focus of the present contribution. This is accomplished through an investigation of the acoustic radiation force on a spherical scatterer embedded in tissue. Properties of both the scatterer and the surrounding tissue are important in determining the magnitude and the direction of the force. As these properties vary, the force computation shows changes in magnitude and direction, which may enable more accurate noninvasive determination of tissue properties.

A nonadditive methanol force field: Bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model

NASA Astrophysics Data System (ADS)

Patel, Sandeep; Brooks, Charles L.

2005-01-01

We study the bulk and interfacial properties of methanol via molecular dynamics simulations using a CHARMM (Chemistry at HARvard Molecular Mechanics) fluctuating charge force field. We discuss the parametrization of the electrostatic model as part of the ongoing CHARMM development for polarizable protein force fields. The bulk liquid properties are in agreement with available experimental data and competitive with existing fixed-charge and polarizable force fields. The liquid density and vaporization enthalpy are determined to be 0.809 g/cm3 and 8.9 kcal/mol compared to the experimental values of 0.787 g/cm3 and 8.94 kcal/mol, respectively. The liquid structure as indicated by radial distribution functions is in keeping with the most recent neutron diffraction results; the force field shows a slightly more ordered liquid, necessarily arising from the enhanced condensed phase electrostatics (as evidenced by an induced liquid phase dipole moment of 0.7 D), although the average coordination with two neighboring molecules is consistent with the experimental diffraction study as well as with recent density functional molecular dynamics calculations. The predicted surface tension of 19.66±1.03 dyn/cm is slightly lower than the experimental value of 22.6 dyn/cm, but still competitive with classical force fields. The interface demonstrates the preferential molecular orientation of molecules as observed via nonlinear optical spectroscopic methods. Finally, via canonical molecular dynamics simulations, we assess the model's ability to reproduce the vapor-liquid equilibrium from 298 to 423 K, the simulation data then used to obtain estimates of the model's critical temperature and density. The model predicts a critical temperature of 470.1 K and critical density of 0.312 g/cm3 compared to the experimental values of 512.65 K and 0.279 g/cm3, respectively. The model underestimates the critical temperature by 8% and overestimates the critical density by 10%, and in this sense is roughly equivalent to the underlying fixed-charge CHARMM22 force field.

Strong quantum squeezing of mechanical resonator via parametric amplification and coherent feedback

NASA Astrophysics Data System (ADS)

You, Xiang; Li, Zongyang; Li, Yongmin

2017-12-01

A scheme to achieve strong quantum squeezing of a mechanical resonator in a membrane-in-the-middle optomechanical system is developed. To this end, simultaneous linear and nonlinear coupling between the mechanical resonator and the cavity modes is applied. A two-tone driving light field, comprising unequal red-detuned and blue-detuned sidebands, helps in generating a coherent feedback force through the linear coupling with the membrane resonator. Another driving light field with its amplitude modulated at twice the mechanical frequency drives the mechanical parametric amplification through a second-order coupling with the resonator. The combined effect produces strong quantum squeezing of the mechanical state. The proposed scheme is quite robust to excess second-order coupling observed in coherent feedback operations and can suppress the fluctuations in the mechanical quadrature to far below the zero point and achieve strong squeezing (greater than 10 dB) for realistic parameters.

The force analysis for superparamagnetic nanoparticles-based gene delivery in an oscillating magnetic field

NASA Astrophysics Data System (ADS)

Sun, Jiajia; Shi, Zongqian; Jia, Shenli; Zhang, Pengbo

2017-04-01

Due to the peculiar magnetic properties and the ability to function in cell-level biological interaction, superparamagnetic nanoparticles (SMNP) have been being the attractive carrier for gene delivery. The superparamagnetic nanoparticles with surface-bound gene vector can be attracted to the surface of cells by the Kelvin force provided by external magnetic field. In this article, the influence of the oscillating magnetic field on the characteristics of magnetofection is studied in terms of the magnetophoretic velocity. The magnetic field of a cylindrical permanent magnet is calculated by equivalent current source (ECS) method, and the Kelvin force is derived by using the effective moment method. The results show that the static magnetic field accelerates the sedimentation of the particles, and drives the particles inward towards the axis of the magnet. Based on the investigation of the magnetophoretic velocity of the particle under horizontally oscillating magnetic field, an oscillating velocity within the amplitude of the magnet oscillation is observed. Furthermore, simulation results indicate that the oscillating amplitude plays an important role in regulating the active region, where the particles may present oscillating motion. The analysis of the magnetophoretic velocity gives us an insight into the physical mechanism of the magnetofection. It's also helpful to the optimal design of the magnetofection system.

Experimental and Numerical Studies of Mechanically- and Convectively-Driven Turbulence in Planetary Interiors

NASA Astrophysics Data System (ADS)

Grannan, Alexander Michael

2017-08-01

The energy for driving turbulent flows in planetary fluid layers comes from a combination of thermocompositional sources and the motion of the boundary in contact with the fluid through mechanisms like precessional, tidal, and librational forcing. Characterizing the resulting turbulent fluid motions are necessary for understanding many aspects of the planet's dynamics and evolution including the generation of magnetic fields in the electrically conducting fluid layers and dissipation in the oceans. Although such flows are strongly inertial they are also strongly influenced by the Coriolis force whose source is in the rotation of the body and tends to constrain the inertial effects and provide support for fluid instabilities that might in-turn generate turbulence. Furthermore, the magnetic fields generated by the electrically conducting fluids act back on the fluid through the Lorentz force that also tends to constrain the flow. The goal of this dissertation is to investigate the characteristics of turbulent flows under the influence of mechanical, convective, rotational and magnetic forcing. In order to investigate the response of the fluid to mechanical forcing, I have modified a unique set of laboratory experiments that allows me to quantify the generation of turbulence driven by the periodic oscillations of the fluid containing boundary through tides and libration. These laboratory experiments replicate the fundamental ingredients found in planetary environments and are necessary for the excitation of instabilities that drive the turbulent fluid motions. For librational forcing, a rigid ellipsoidal container and ellipsoidal shell of isothermal unstratified fluid is made to rotate with a superimposed oscillation while, for tidal forcing, an elastic ellipsoidal container of isothermal unstratified fluid is made to rotate while an independently rotating perturbance also flexes the elastic container. By varying the strength and frequencies of these oscillations the characteristics of the resulting turbulence are investigated using meridional views to identify the dominate modes and spatial location of the turbulence. For the first time, measurements of the velocity in the equatorial plane are coupled with high resolution numerical simulations of the full flow field in identical geometry to characterize the instability mechanism, energy deposited into the fluid layer, and long-term evolution of the flow. The velocities determined through laboratory and numerical simulations when extrapolated to planets allow me to argue that the dynamics of mechanical forcing in low viscosity fluids may an important role as new and potentially large source of dissipation in planetary interiors. To study convective forcing, I have modified and performed a set of rotating and non-rotating hydrodynamic convection experiments using water as well as rotating and non-rotating magnetohydrodynamic convection in gallium. These studies are performed in a cylindrical geometry representing a model of high latitude planetary core style convection wherein the axis of rotation and gravity are aligned. For the studies using water, the steady columns that are characteristic of rotating convection and present in the dynamo models are likely to destabilize at the more extreme planetary parameters giving way to transitions to more complex styles of rotating turbulent flow. In the studies of liquid metal where the viscosity is lower, the onset of rotating convection occurs through oscillatory columnar convection well below the onset of steady columns. Such oscillatory modes are not represented at the parameters used by current dynamo models. Furthermore a suite of laboratory experiments shows that the imposition of rotational forces and magnetic forces both separately and together generate zeroeth order flow transitions that change the fundamental convective modes and heat transfer. Such regimes are more easily accessible to laboratory experiments then to numerical simulations but demonstrate the need for a new generation of dynamo simulations capable of including the fundamental properties of liquid metals as are relevant for understanding the dynamics of planetary interiors.

Contact-free calibration of an asymmetric multi-layer interferometer for the surface force balance

NASA Astrophysics Data System (ADS)

Balabajew, Marco; van Engers, Christian D.; Perkin, Susan

2017-12-01

The Surface Force Balance (SFB, also known as Surface Force Apparatus, SFA) has provided important insights into many phenomena within the field of colloid and interface science. The technique relies on using white light interferometry to measure the distance between surfaces with sub-nanometer resolution. Up until now, the determination of the distance between the surfaces required a so-called "contact calibration," an invasive procedure during which the surfaces are brought into mechanical contact. This requirement for a contact calibration limits the range of experimental systems that can be investigated with SFB, for example, it precludes experiments with substrates that would be irreversibly modified or damaged by mechanical contact. Here we present a non-invasive method to measure absolute distances without performing a contact calibration. The method can be used for both "symmetric" and "asymmetric" systems. We foresee many applications for this general approach including, most immediately, experiments using single layer graphene electrodes in the SFB which may be damaged when brought into mechanical contact.

TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field

NASA Astrophysics Data System (ADS)

Dziedzic, Jacek; Mao, Yuezhi; Shao, Yihan; Ponder, Jay; Head-Gordon, Teresa; Head-Gordon, Martin; Skylaris, Chris-Kriton

2016-09-01

We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression for the Hamiltonian of the coupled QM/MM system, which we minimize using gradient methods. The QM subsystem is described by the onetep linear-scaling DFT approach, which makes use of strictly localized orbitals expressed in a set of periodic sinc basis functions equivalent to plane waves. The MM subsystem is described by the multipolar, polarizable force field AMOEBA, as implemented in tinker. Distributed multipole analysis is used to obtain, on the fly, a classical representation of the QM subsystem in terms of atom-centered multipoles. This auxiliary representation is used for all polarization interactions between QM and MM, allowing us to treat them on the same footing as in AMOEBA. We validate our method in tests of solute-solvent interaction energies, for neutral and charged molecules, demonstrating the simultaneous optimization of the quantum and classical degrees of freedom. Encouragingly, we find that the inclusion of explicit polarization in the MM part of QM/MM improves the agreement with fully QM calculations.

Effect of molecular environment on the vibrational dynamics of pyrimidine bases as analysed by NIS, optical spectroscopy and quantum mechanical force fields

NASA Astrophysics Data System (ADS)

Ghomi, M.; Aamouche, A.; Cadioli, B.; Berthier, G.; Grajcar, L.; Baron, M. H.

1997-06-01

A complete set of vibrational spectra, obtained from several spectroscopic techniques, i.e. neutron inelastic scattering (NIS), Raman scattering and infrared absorption (IR), has been used in order to assign the vibrational modes of pyrimidine bases (uracil, thymine, cytosine) and their N-deuterated species. The spectra of solid and aqueous samples allowed us to analyse the effects of hydrogen bonding in crystal and in solution. In a first step, to assign the observed vibrational modes, we have resorted to harmonic quantum mechanical force field, calculated at SCF + MP2 level using double-zeta 6-31G and D95V basis sets with non-standard exponents for d-orbital polarisation functions. In order to improve the agreement between the experimental results obtained in condensed phases and the calculated ones based on isolated molecules, the molecular force field has been scaled. In a second step, to estimate the effect of intermolecular interactions on the vibrational dynamics of pyrimidine bases, we have undertaken additional calculations with the density functional theory (DFT) method using B3LYP functionals and polarised 6-31G basis sets. Two theoretical models have been considered: 1. a uracil embedded in a dielectric continuum ( ɛ = 78), and 2. a uracil H-bonded to two water molecules (through N1 and N3 atoms).

Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations.

PubMed

Cai, Kaicong; Zheng, Xuan; Du, Fenfen

2017-08-05

The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

Engineering cortical neuron polarity with nanomagnets on a chip.

PubMed

Kunze, Anja; Tseng, Peter; Godzich, Chanya; Murray, Coleman; Caputo, Anna; Schweizer, Felix E; Di Carlo, Dino

2015-01-01

Intra- and extracellular signaling play critical roles in cell polarity, ultimately leading to the development of functional cell-cell connections, tissues, and organs. In the brain, pathologically oriented neurons are often the cause for disordered circuits, severely impacting motor function, perception, and memory. Aside from control through gene expression and signaling pathways, it is known that nervous system development can be manipulated by mechanical stimuli (e.g., outgrowth of axons through externally applied forces). The inverse is true as well: intracellular molecular signals can be converted into forces to yield axonal outgrowth. The complete role played by mechanical signals in mediating single-cell polarity, however, remains currently unclear. Here we employ highly parallelized nanomagnets on a chip to exert local mechanical stimuli on cortical neurons, independently of the amount of superparamagnetic nanoparticles taken up by the cells. The chip-based approach was utilized to quantify the effect of nanoparticle-mediated forces on the intracellular cytoskeleton as visualized by the distribution of the microtubule-associated protein tau. While single cortical neurons prefer to assemble tau proteins following poly-L-lysine surface cues, an optimal force range of 4.5-70 pN by the nanomagnets initiated a tau distribution opposed to the pattern cue. In larger cell clusters (groups comprising six or more cells), nanoparticle-mediated forces induced tau repositioning in an observed range of 190-270 pN, and initiation of magnetic field-directed cell displacement was observed at forces above 300 pN. Our findings lay the groundwork for high-resolution mechanical encoding of neural networks in vitro, mechanically driven cell polarization in brain tissues, and neurotherapeutic approaches using functionalized superparamagnetic nanoparticles to potentially restore disordered neural circuits.

Nanomechanics of Cells and Biomaterials Studied by Atomic Force Microscopy.

PubMed

Kilpatrick, Jason I; Revenko, Irène; Rodriguez, Brian J

2015-11-18

The behavior and mechanical properties of cells are strongly dependent on the biochemical and biomechanical properties of their microenvironment. Thus, understanding the mechanical properties of cells, extracellular matrices, and biomaterials is key to understanding cell function and to develop new materials with tailored mechanical properties for tissue engineering and regenerative medicine applications. Atomic force microscopy (AFM) has emerged as an indispensable technique for measuring the mechanical properties of biomaterials and cells with high spatial resolution and force sensitivity within physiologically relevant environments and timescales in the kPa to GPa elastic modulus range. The growing interest in this field of bionanomechanics has been accompanied by an expanding array of models to describe the complexity of indentation of hierarchical biological samples. Furthermore, the integration of AFM with optical microscopy techniques has further opened the door to a wide range of mechanotransduction studies. In recent years, new multidimensional and multiharmonic AFM approaches for mapping mechanical properties have been developed, which allow the rapid determination of, for example, cell elasticity. This Progress Report provides an introduction and practical guide to making AFM-based nanomechanical measurements of cells and surfaces for tissue engineering applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Force-Mediating Magnetic Nanoparticles to Engineer Neuronal Cell Function

PubMed Central

Gahl, Trevor J.; Kunze, Anja

2018-01-01

Cellular processes like membrane deformation, cell migration, and transport of organelles are sensitive to mechanical forces. Technically, these cellular processes can be manipulated through operating forces at a spatial precision in the range of nanometers up to a few micrometers through chaperoning force-mediating nanoparticles in electrical, magnetic, or optical field gradients. But which force-mediating tool is more suitable to manipulate cell migration, and which, to manipulate cell signaling? We review here the differences in forces sensation to control and engineer cellular processes inside and outside the cell, with a special focus on neuronal cells. In addition, we discuss technical details and limitations of different force-mediating approaches and highlight recent advancements of nanomagnetics in cell organization, communication, signaling, and intracellular trafficking. Finally, we give suggestions about how force-mediating nanoparticles can be used to our advantage in next-generation neurotherapeutic devices. PMID:29867315

Force-Mediating Magnetic Nanoparticles to Engineer Neuronal Cell Function.

PubMed

Gahl, Trevor J; Kunze, Anja

2018-01-01

Cellular processes like membrane deformation, cell migration, and transport of organelles are sensitive to mechanical forces. Technically, these cellular processes can be manipulated through operating forces at a spatial precision in the range of nanometers up to a few micrometers through chaperoning force-mediating nanoparticles in electrical, magnetic, or optical field gradients. But which force-mediating tool is more suitable to manipulate cell migration, and which, to manipulate cell signaling? We review here the differences in forces sensation to control and engineer cellular processes inside and outside the cell, with a special focus on neuronal cells. In addition, we discuss technical details and limitations of different force-mediating approaches and highlight recent advancements of nanomagnetics in cell organization, communication, signaling, and intracellular trafficking. Finally, we give suggestions about how force-mediating nanoparticles can be used to our advantage in next-generation neurotherapeutic devices.

An Atomic Force Microscope with Dual Actuation Capability for Biomolecular Experiments

NASA Astrophysics Data System (ADS)

Sevim, Semih; Shamsudhin, Naveen; Ozer, Sevil; Feng, Luying; Fakhraee, Arielle; Ergeneman, Olgaç; Pané, Salvador; Nelson, Bradley J.; Torun, Hamdi

2016-06-01

We report a modular atomic force microscope (AFM) design for biomolecular experiments. The AFM head uses readily available components and incorporates deflection-based optics and a piezotube-based cantilever actuator. Jetted-polymers have been used in the mechanical assembly, which allows rapid manufacturing. In addition, a FeCo-tipped electromagnet provides high-force cantilever actuation with vertical magnetic fields up to 0.55 T. Magnetic field calibration has been performed with a micro-hall sensor, which corresponds well with results from finite element magnetostatics simulations. An integrated force resolution of 1.82 and 2.98 pN, in air and in DI water, respectively was achieved in 1 kHz bandwidth with commercially available cantilevers made of Silicon Nitride. The controller and user interface are implemented on modular hardware to ensure scalability. The AFM can be operated in different modes, such as molecular pulling or force-clamp, by actuating the cantilever with the available actuators. The electromagnetic and piezoelectric actuation capabilities have been demonstrated in unbinding experiments of the biotin-streptavidin complex.

Laboratory evidence that line-tied tension forces can suppress loss-of-equilibrium flux rope eruptions in the solar corona

NASA Astrophysics Data System (ADS)

Myers, C. E.; Yamada, M.; Belova, E.; Ji, H.; Yoo, J.; Fox, W.; Jara-Almonte, J.; Gao, L.

2014-10-01

Loss-of-equilibrium mechanisms such as the ideal torus instability [Kliem & Török, Phys. Rev. Lett. 96, 255002 (2006)] are predicted to drive arched flux ropes in the solar corona to erupt. In recent line-tied flux rope experiments conducted in the Magnetic Reconnection Experiment (MRX), however, we find that quasi-statically driven flux ropes remain confined well beyond the predicted torus instability threshold. In order to understand this behavior, in situ measurements from a 300 channel 2D magnetic probe array are used to comprehensively analyze the force balance between the external (vacuum) and internal (plasma-generated) magnetic fields. We find that the line-tied tension force--a force that is not included in the basic torus instability theory--plays a major role in preventing eruptions. The dependence of this tension force on various vacuum field and flux rope parameters will be discussed. This research is supported by DoE Contract Number DE-AC02-09CH11466 and by the NSF/DoE Center for Magnetic Self-Organization (CMSO).

An Atomic Force Microscope with Dual Actuation Capability for Biomolecular Experiments

PubMed Central

Sevim, Semih; Shamsudhin, Naveen; Ozer, Sevil; Feng, Luying; Fakhraee, Arielle; Ergeneman, Olgaç; Pané, Salvador; Nelson, Bradley J.; Torun, Hamdi

2016-01-01

We report a modular atomic force microscope (AFM) design for biomolecular experiments. The AFM head uses readily available components and incorporates deflection-based optics and a piezotube-based cantilever actuator. Jetted-polymers have been used in the mechanical assembly, which allows rapid manufacturing. In addition, a FeCo-tipped electromagnet provides high-force cantilever actuation with vertical magnetic fields up to 0.55 T. Magnetic field calibration has been performed with a micro-hall sensor, which corresponds well with results from finite element magnetostatics simulations. An integrated force resolution of 1.82 and 2.98 pN, in air and in DI water, respectively was achieved in 1 kHz bandwidth with commercially available cantilevers made of Silicon Nitride. The controller and user interface are implemented on modular hardware to ensure scalability. The AFM can be operated in different modes, such as molecular pulling or force-clamp, by actuating the cantilever with the available actuators. The electromagnetic and piezoelectric actuation capabilities have been demonstrated in unbinding experiments of the biotin-streptavidin complex. PMID:27273214

Orbital revolution of a pair of bubbles in an acoustic field

NASA Astrophysics Data System (ADS)

Shirota, Minori; Yamashita, Kou; Inamura, Takao

2011-11-01

This experimental study aims to clarify the mechanism of orbital motion of two oscillating bubbles in an acoustic field. Trajectory of the orbital motion was observed using a high-speed video camera. Because of a good repeatability in volume oscillation of bubbles, we were also able to observe the radial motion driven at 24 kHz by stroboscopic like imaging; the cyclic bubble oscillation was appeared to slow down by capturing images at the framing rate close to the forcing frequency. The orbital motions of bubbles raging from 0.13 to 0.18 mm were examined with different forcing amplitude and in different viscous oils. As a result, we found that pairs of bubbles revolve along a circular orbit around the center of mass of the orbiting two bubbles. We also found that the two bubbles perform anti-phase radial oscillation. Although this radial oscillation should result in a repulsive secondary Bjerknes force, the bubbles kept a constant separate distance of about 1 mm, which indicates the existence of centripetal primary Bjerknes force. The angular velocity of orbital revolution increases linearly with the increase in Bjerknes force.

The design and development of a high-throughput magneto-mechanostimulation device for cartilage tissue engineering.

PubMed

Brady, Mariea A; Vaze, Reva; Amin, Harsh D; Overby, Darryl R; Ethier, C Ross

2014-02-01

To recapitulate the in vivo environment and create neo-organoids that replace lost or damaged tissue requires the engineering of devices, which provide appropriate biophysical cues. To date, bioreactors for cartilage tissue engineering have focused primarily on biomechanical stimulation. There is a significant need for improved devices for articular cartilage tissue engineering capable of simultaneously applying multiple biophysical (electrokinetic and mechanical) stimuli. We have developed a novel high-throughput magneto-mechanostimulation bioreactor, capable of applying static and time-varying magnetic fields, as well as multiple and independently adjustable mechanical loading regimens. The device consists of an array of 18 individual stations, each of which uses contactless magnetic actuation and has an integrated Hall Effect sensing system, enabling the real-time measurements of applied field, force, and construct thickness, and hence, the indirect measurement of construct mechanical properties. Validation tests showed precise measurements of thickness, within 14 μm of gold standard calliper measurements; further, applied force was measured to be within 0.04 N of desired force over a half hour dynamic loading, which was repeatable over a 3-week test period. Finally, construct material properties measured using the bioreactor were not significantly different (p=0.97) from those measured using a standard materials testing machine. We present a new method for articular cartilage-specific bioreactor design, integrating combinatorial magneto-mechanostimulation, which is very attractive from functional and cost viewpoints.

Flux pinning mechanism in codoped-MgB2 with Al2O3 and SiC

NASA Astrophysics Data System (ADS)

Kiafiroozkoohi, Narjess Sadat; Ghorbani, Shaban Reza; Arabi, Hadi

2018-05-01

MgB2 superconductor samples, co-doped with 0.02 wt of Al2O3 and 0.02 wt SiC, have been examined by M-H loop measurements and calculation of the critical current density based on the Bean model. Normalized volume pinning force, f = F/Fmax, as a function of the reduced magnetic field, h = H/Hmax has been obtained at each temperature. Hughochi flux pinning model, which was included the normal point pinning, the normal surface pinning, and the pinning based on spatial variation in the Ginzburg-Landau parameter, was used to study the flux pinning mechanisms. It was found that the Δκ effect and the normal point pinning mechanisms play the main role in the flux pinning at the magnetic field lower than Hmax and the contribution of the Δκ mechanism increases with the increasing temperature, while the contribution of normal point pinning mechanism decreases. At magnetic field larger than Hmax, the only mechanism that acts as the flux pinning was the normal surface pinning mechanism.

Strong coupling in electromechanical computation

NASA Astrophysics Data System (ADS)

Füzi, János

2000-06-01

A method is presented to carry out simultaneously electromagnetic field and force computation, electrical circuit analysis and mechanical computation to simulate the dynamic operation of electromagnetic actuators. The equation system is solved by a predictor-corrector scheme containing a Powell error minimization algorithm which ensures that every differential equation (coil current, field strength rate, flux rate, speed of the keeper) is fulfilled within the same time step.

An analysis of the effects of temperatures and circulations on the strength of the low-level jet in the Turkana Channel in East Africa

NASA Astrophysics Data System (ADS)

Hartman, Adam T.

2018-05-01

The Turkana Low-Level Jet (LLJ) was discovered in the early 1980s, yet there are still questions about the primary forcing mechanisms that drive and sustain the jet throughout the year. A few studies have addressed these questions, but most focus on numerical simulations of mechanical forcing mechanisms, such as orography, channeling flow, and monsoon background flow. No studies have shown the effects of thermal forcing from differential heating in the regions in and around the Turkana Channel. This paper uses National Centers for Environmental Prediction (NCEP) Climate Forecast System Reanalysis (CFSR) data and the National Aeronautics and Space Administration (NASA) Modern-Era Retrospective Analysis for Research and Applications (MERRA) data in order to analyze and find relationships between temperature gradients and the strength of the Turkana LLJ. In addition to temperature, potential temperature, divergence, wind magnitude, wind fields, and vertical motion are also examined. This analysis attempts to show that thermal forcing is one of the most important factors, if not the primary factor, in the initiation and maintenance of the jet and propose that more research and model simulations should be implemented to determine the contributions from thermal forcing.

High-pressure microhydraulic actuator

DOEpatents

Mosier, Bruce P [San Francisco, CA; Crocker, Robert W [Fremont, CA; Patel, Kamlesh D [Dublin, CA

2008-06-10

Electrokinetic ("EK") pumps convert electric to mechanical work when an electric field exerts a body force on ions in the Debye layer of a fluid in a packed bed, which then viscously drags the fluid. Porous silica and polymer monoliths (2.5-mm O.D., and 6-mm to 10-mm length) having a narrow pore size distribution have been developed that are capable of large pressure gradients (250-500 psi/mm) when large electric fields (1000-1500 V/cm) are applied. Flowrates up to 200 .mu.L/min and delivery pressures up to 1200 psi have been demonstrated. Forces up to 5 lb-force at 0.5 mm/s (12 mW) have been demonstrated with a battery-powered DC-DC converter. Hydraulic power of 17 mW (900 psi@ 180 uL/min) has been demonstrated with wall-powered high voltage supplies. The force and stroke delivered by an actuator utilizing an EK pump are shown to exceed the output of solenoids, stepper motors, and DC motors of similar size, despite the low thermodynamic efficiency.

Magnetic Alignment of γ-Fe2O3 Nanoparticles in Polymer Nanocomposites

NASA Astrophysics Data System (ADS)

Jimenez, Andrew; Kumar, Sanat K.; Jestin, Jacques

Recent work in nanocomposites has been heavily focused on controlling the dispersion state of filler particles. The use of internal self-assembly based on matrix properties provides a limited solution to the desire for specified organizations. By introducing a magnetic field during the casting of a polymer solution it has been shown that particles can be oriented to form anisotropic structures - commonly sought after for improved mechanical properties. Here, magnetic nanoparticles were cast in two different polymer matrices to study the effect of various forces that lead to this highly desired alignment. The addition of the magnetic field as an external trigger was shown to not necessarily force the clustering, but rather orient the agglomerates already available in solution. This demonstrates the importance of other dominant forces introduced into the system by characteristics of the polymers themselves. While this magnetic field provides a direction for the sample, the key forces lie in the interactions between the polymers and nanoparticles (as well as their solvent). The study shows a dependence of anisotropy on the particle loading, matrix, and casting time, from which continued work hopes to quantify the clustering necessary to optimize alignment in the composite.

Measurement of Unsteady Aerodynamics Load on the Blade of Field Horizontal Axis Wind Turbine

NASA Astrophysics Data System (ADS)

Kamada, Yasunari; Maeda, Takao; Naito, Keita; Ouchi, Yuu; Kozawa, Masayoshi

This paper describes an experimental field study of the rotor aerodynamics of wind turbines. The test wind turbine is a horizontal axis wind turbine, or: HAWT with a diameter of 10m. The pressure distributions on the rotating blade are measured with multi point pressure transducers. Sectional aerodynamic forces are analyzed from pressure distribution. Blade root moments are measured simultaneously by a pair of strain gauges. The inflow wind is measured by a three component sonic anemometer, the local inflow of the blade section are measured by a pair of 7 hole Pitot tubes. The relation between the aerodynamic moments on the blade root from pressure distribution and the mechanical moment from strain gauges is discussed. The aerodynamic moments are estimated from the sectional aerodynamic forces and show oscillation caused by local wind speed and direction change. The mechanical moment shows similar oscillation to the aerodynamic excepting the short period oscillation of the blade first mode frequency. The fluctuation of the sectional aerodynamic force triggers resonant blade oscillations. Where stall is present along the blade section, the blade's first mode frequency is dominant. Without stall, the rotating frequency is dominant in the blade root moment.

CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca(2+)-ATPase.

PubMed

Komuro, Yasuaki; Re, Suyong; Kobayashi, Chigusa; Muneyuki, Eiro; Sugita, Yuji

2014-09-09

Adenosine triphosphate (ATP) is an indispensable energy source in cells. In a wide variety of biological phenomena like glycolysis, muscle contraction/relaxation, and active ion transport, chemical energy released from ATP hydrolysis is converted to mechanical forces to bring about large-scale conformational changes in proteins. Investigation of structure-function relationships in these proteins by molecular dynamics (MD) simulations requires modeling of ATP in solution and ATP bound to proteins with accurate force-field parameters. In this study, we derived new force-field parameters for the triphosphate moiety of ATP based on the high-precision quantum calculations of methyl triphosphate. We tested our new parameters on membrane-embedded sarcoplasmic reticulum Ca(2+)-ATPase and four soluble proteins. The ATP-bound structure of Ca(2+)-ATPase remains stable during MD simulations, contrary to the outcome in shorter simulations using original parameters. Similar results were obtained with the four ATP-bound soluble proteins. The new force-field parameters were also tested by investigating the range of conformations sampled during replica-exchange MD simulations of ATP in explicit water. Modified parameters allowed a much wider range of conformational sampling compared with the bias toward extended forms with original parameters. A diverse range of structures agrees with the broad distribution of ATP conformations in proteins deposited in the Protein Data Bank. These simulations suggest that the modified parameters will be useful in studies of ATP in solution and of the many ATP-utilizing proteins.

Alfvenic Generation of Field-Aligned Currents and Displacement Currents in the M-I Coupling System and the Formation of Discrete Auroral Arcs

NASA Astrophysics Data System (ADS)

Song, Y.; Lysak, R. L.

2016-12-01

In previous theories (e.g., Hasegawa and Sato, 1979; Sato and Iijima, 1979; Vasyliunas, 1984), field-aligned current (FAC) generation is derived from current continuity assumption plus the force balance between the Lorentz force and other forces in the MHD momentum equation. These theories suggest that the FAC is generated by other forces, such as the inertia and/or pressure gradients. In fact, the FAC cannot be generated by these forces. From Maxwell's equations, FAC generation is associated with enhanced sheared magnetic fields and free magnetic energy where a dynamo action and Alfven waves are needed to generate and transport free magnetic energy. It is obvious that the mechanism of FAC generation cannot be given by analyzing a local force balance. We propose that FACs are generated by Alfvenic interactions in the M-I coupling driven system. From a full set of the dynamical equations, we have found that the generation of the total FAC (J||total ) is associated with spatial gradients of the parallel vorticity, where J||total=J||+J||D, and J||D=(1/4∏)(∂E||/∂t) is the displacement current, which describes E|| generation (Song and Lysak, 2006). The J||total generation is a dynamo process associated with the increase of the azimuthal magnetic flux caused by the axial torque acting on FAC flux tubes. Although the magnitude of the J||D is often very small relative to J||, neglecting this term, we cannot find the mechanism of the E|| generation. When the plasma density is low J||D becomes important relative to the current. We will demonstrate how the generation of E|| and the formation of auroral arcs can redistribute perpendicular mechanical and magnetic stresses which can cause a sudden and violent tail energy release and enhance the total FAC leading to the substorm auroral poleward expansion. We will also show how the nonlinear interaction of incident and reflected Alfven wave packets in the auroral acceleration region can produce quasi-stationary non-propagating electromagnetic plasma structures, such as Alfvenic double layers. These structures will sustain the J||D and can constitute powerful high energy particle accelerators, where electromagnetic energy can be efficiently converted to the particle energy.

Multifield Control of Domains in a Room-Temperature Multiferroic 0.85BiTi0.1Fe0.8Mg0.1O3-0.15CaTiO3 Thin Film.

PubMed

Jia, Tingting; Fan, Ziran; Yao, Junxiang; Liu, Cong; Li, Yuhao; Yu, Junxi; Fu, Bi; Zhao, Hongyang; Osada, Minoru; Esfahani, Ehsan Nasr; Yang, Yaodong; Wang, Yuanxu; Li, Jiang-Yu; Kimura, Hideo; Cheng, Zhenxiang

2018-06-20

Single-phase materials that combine electric polarization and magnetization are promising for applications in multifunctional sensors, information storage, spintronic devices, etc. Following the idea of a percolating network of magnetic ions (e.g., Fe) with strong superexchange interactions within a structural scaffold with a polar lattice, a solid solution thin film with perovskite structure at a morphotropic phase boundary with a high level of Fe atoms on the B site of perovskite structure is deposited to combine both ferroelectric and ferromagnetic ordering at room temperature with magnetoelectric coupling. In this work, a 0.85BiTi 0.1 Fe 0.8 Mg 0.1 O 3 -0.15CaTiO 3 thin film has been deposited by pulsed laser deposition (PLD). Both the ferroelectricity and the magnetism were characterized at room temperature. Large polarization and a large piezoelectric effective coefficient d 33 were obtained. Multifield coupling of the thin film has been characterized by scanning force microscopy. Ferroelectric domains and magnetic domains could be switched by magnetic field ( H), electric field ( E), mechanical force ( F), and, indicating that complex cross-coupling exists among the electric polarization, magnetic ordering and elastic deformation in 0.85BiTi 0.1 F e0.8 Mg 0.1 O 3 -0.15CaTiO 3 thin film at room temperature. This work also shows the possibility of writing information with electric field, magnetic field, and mechanical force and then reading data by magnetic field. We expect that this work will benefit information applications.

Hybrid immersed interface-immersed boundary methods for AC dielectrophoresis

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

Hossan, Mohammad Robiul; Department of Engineering and Physics, University of Central Oklahoma, Edmond, OK 73034-5209; Dillon, Robert

2014-08-01

Dielectrophoresis, a nonlinear electrokinetic transport mechanism, has become popular in many engineering applications including manipulation, characterization and actuation of biomaterials, particles and biological cells. In this paper, we present a hybrid immersed interface–immersed boundary method to study AC dielectrophoresis where an algorithm is developed to solve the complex Poisson equation using a real variable formulation. An immersed interface method is employed to obtain the AC electric field in a fluid media with suspended particles and an immersed boundary method is used for the fluid equations and particle transport. The convergence of the proposed algorithm as well as validation of themore » hybrid scheme with experimental results is presented. In this paper, the Maxwell stress tensor is used to calculate the dielectrophoretic force acting on particles by considering the physical effect of particles in the computational domain. Thus, this study eliminates the approximations used in point dipole methods for calculating dielectrophoretic force. A comparative study between Maxwell stress tensor and point dipole methods for computing dielectrophoretic forces are presented. The hybrid method is used to investigate the physics of dielectrophoresis in microfluidic devices using an AC electric field. The numerical results show that with proper design and appropriate selection of applied potential and frequency, global electric field minima can be obtained to facilitate multiple particle trapping by exploiting the mechanism of negative dielectrophoresis. Our numerical results also show that electrically neutral particles form a chain parallel to the applied electric field irrespective of their initial orientation when an AC electric field is applied. This proposed hybrid numerical scheme will help to better understand dielectrophoresis and to design and optimize microfluidic devices.« less

Long-Range Self-Assembly via the Mutual Lorentz Force of Plasmon Radiation.

PubMed

Ji, Haojie; Trevino, Jacob; Tu, Raymond; Knapp, Ellen; McQuade, James; Yurkiv, Vitaliy; Mashayek, Farzad; Vuong, Luat T

2018-04-11

Long-range interactions often proceed as a sequence of hopping through intermediate, statistically favored events. Here, we demonstrate predictable mechanical dynamics of particles that arise from the Lorentz force between plasmons. Even if the radiation is weak, the nonconservative Lorentz force produces stable locations perpendicular to the plasmon oscillation; over time, distinct patterns emerge. Experimentally, linearly polarized light illumination leads to the formation of 80 nm diameter Au nanoparticle chains, perpendicularly aligned, with lengths that are orders of magnitude greater than their plasmon near-field interaction. There is a critical intensity threshold and optimal concentration for observing self-assembly.

Deformation of red blood cells using acoustic radiation forces

PubMed Central

Mishra, Puja; Hill, Martyn; Glynne-Jones, Peter

2014-01-01

Acoustic radiation forces have been used to manipulate cells and bacteria in a number of recent microfluidic applications. The net force on a cell has been subject to careful investigation over a number of decades. We demonstrate that the radiation forces also act to deform cells. An ultrasonic standing wave field is created in a 0.1 mm glass capillary at a frequency of 7.9 MHz. Using osmotically swollen red-blood cells, we show observable deformations up to an aspect ratio of 1.35, comparable to deformations created by optical tweezing. In contrast to optical technologies, ultrasonic devices are potentially capable of deforming thousands of cells simultaneously. We create a finite element model that includes both the acoustic environment of the cell, and a model of the cell membrane subject to forces resulting from the non-linear aspects of the acoustic field. The model is found to give reasonable agreement with the experimental results, and shows that the deformation is the result of variation in an acoustic force that is directed outwards at all points on the cell membrane. We foresee applications in diagnostic devices, and in the possibility of mechanically stimulating cells to promote differentiation and physiological effects. PMID:25379070

Influences on Distribution of Solute Atoms in Cu-8Fe Alloy Solidification Process Under Rotating Magnetic Field

NASA Astrophysics Data System (ADS)

Zou, Jin; Zhai, Qi-Jie; Liu, Fang-Yu; Liu, Ke-Ming; Lu, De-Ping

2018-05-01

A rotating magnetic field (RMF) was applied in the solidification process of Cu-8Fe alloy. Focus on the mechanism of RMF on the solid solution Fe(Cu) atoms in Cu-8Fe alloy, the influences of RMF on solidification structure, solute distribution, and material properties were discussed. Results show that the solidification behavior of Cu-Fe alloy have influenced through the change of temperature and solute fields in the presence of an applied RMF. The Fe dendrites were refined and transformed to rosettes or spherical grains under forced convection. The solute distribution in Cu-rich phase and Fe-rich phase were changed because of the variation of the supercooling degree and the solidification rate. Further, the variation in solute distribution was impacted the strengthening mechanism and conductive mechanism of the material.

Characteristic of Secondary Flow Caused by Local Density Change in Standing Acoustic Fields

NASA Astrophysics Data System (ADS)

Tonsho, Kazuyuki; Hirosawa, Takuya; Kusakawa, Hiroshi; Kuwahara, Takuo; Tanabe, Mitsuaki

Secondary flow is a flow which is caused by the interference between standing acoustic fields and local density change. The behavior of the secondary flow depends on the location of the given local density change in the standing acoustic fields. When the density change is given at the middle of a velocity node and the neighboring velocity anti-node (middle point) or when it is given at the velocity anti-node in standing acoustic fields, the secondary flow shows particular behavior. Characteristic of the secondary flow at the two positions was predicted by numerical simulations. It was examined from these simulations whether the driving mechanism of the flow can be explained by the kind of acoustic radiation force that has been proposed so far. The predicted secondary flow was verified by experiments. For both the simulations and experiments, the standing acoustic fields generated in a cylinder are employed. In the experiments, the acoustic fields are generated by two loud speakers that are vibrated in same phase in a chamber. The employed resonance frequency is about 1000 Hz. The chamber is filled with air of room temperature and atmospheric pressure. In the numerical simulations and experiments, the local density change is given by heating or cooling. Because the secondary flow is influenced by buoyancy, the numerical simulations were done without taking gravity force into account and a part of the experiments were done by the microgravity condition using a drop tower. As a result of the simulations, at the middle point, the heated air was blown toward the node and the cooled air was blown toward the anti-node. It is clarified that the secondary flow is driven by the expected kind of acoustic radiation force. At the anti-node, both the heated and cooled air expands perpendicular to the traveling direction of the sound wave. The driving mechanism of the secondary flow can not be explained by the acoustic radiation force, and a detailed analysis is done. Through the comparison between experimental and numerical results, it was verified that the secondary flow is qualitatively predictable by the numerical simulations.

Multi-scale mechanics of granular solids from grain-resolved X-ray measurements

NASA Astrophysics Data System (ADS)

Hurley, R. C.; Hall, S. A.; Wright, J. P.

2017-11-01

This work discusses an experimental technique for studying the mechanics of three-dimensional (3D) granular solids. The approach combines 3D X-ray diffraction and X-ray computed tomography to measure grain-resolved strains, kinematics and contact fabric in the bulk of a granular solid, from which continuum strains, grain stresses, interparticle forces and coarse-grained elasto-plastic moduli can be determined. We demonstrate the experimental approach and analysis of selected results on a sample of 1099 stiff, frictional grains undergoing multiple uniaxial compression cycles. We investigate the inter-particle force network, elasto-plastic moduli and associated length scales, reversibility of mechanical responses during cyclic loading, the statistics of microscopic responses and microstructure-property relationships. This work serves to highlight both the fundamental insight into granular mechanics that is furnished by combined X-ray measurements and describes future directions in the field of granular materials that can be pursued with such approaches.

Effect of magnetic field on the flux pinning mechanisms in Al and SiC co-doped MgB2 superconductor

NASA Astrophysics Data System (ADS)

Kia, N. S.; Ghorbani, S. R.; Arabi, H.; Hossain, M. S. A.

2018-07-01

MgB2 superconductor samples co-doped with 0.02 wt. Al2O3 and 0-0.05 wt. SiC were studied by magnetization - magnetic field (M-H) loop measurements at different temperatures. The critical current density has been calculated by the Bean model, and the irreversibility field, Hirr, has been obtained by the Kramer method. The pinning mechanism of the co-doped sample with 2% Al and 5% SiC was investigated in particular due to its having the highest Hirr. The normalized volume pinning force f = F/Fmax as a function of reduced magnetic field h = H/Hirr has been obtained, and the pinning mechanism was studied by the Dew-Houghes model. It was found that the normal point pinning (NPP), the normal surface pinning (NSP), and the normal volume pinning (NVP) mechanisms play the main roles. The magnetic field and temperature dependence of contributions of the NPP, NSP, and NVP pinning mechanisms were obtained. The results show that the contributions of the pinning mechanisms depend on the temperature and magnetic field. From the temperature dependence of the critical current density within the collective pinning theory, it was found that both the δl pinning due to spatial fluctuations of the charge-carrier mean free path and the δTc pinning due to randomly distributed spatial variations in the transition temperature coexist at zero magnetic field in co-doped samples. Yet, the charge-carrier mean-free-path fluctuation pinning (δl) is the only important pinning mechanism at non-zero magnetic fields.

Numerical simulations of current generation and dynamo excitation in a mechanically forced turbulent flow.

PubMed

Bayliss, R A; Forest, C B; Nornberg, M D; Spence, E J; Terry, P W

2007-02-01

The role of turbulence in current generation and self-excitation of magnetic fields has been studied in the geometry of a mechanically driven, spherical dynamo experiment, using a three-dimensional numerical computation. A simple impeller model drives a flow that can generate a growing magnetic field, depending on the magnetic Reynolds number Rm=micro0sigmaVa and the fluid Reynolds number Re=Vanu of the flow. For Re<420, the flow is laminar and the dynamo transition is governed by a threshold of Rmcrit=100, above which a growing magnetic eigenmode is observed that is primarily a dipole field transverse to the axis of symmetry of the flow. In saturation, the Lorentz force slows the flow such that the magnetic eigenmode becomes marginally stable. For Re>420 and Rm approximately 100 the flow becomes turbulent and the dynamo eigenmode is suppressed. The mechanism of suppression is a combination of a time varying large-scale field and the presence of fluctuation driven currents (such as those predicted by the mean-field theory), which effectively enhance the magnetic diffusivity. For higher Rm, a dynamo reappears; however, the structure of the magnetic field is often different from the laminar dynamo. It is dominated by a dipolar magnetic field aligned with the axis of symmetry of the mean-flow, which is apparently generated by fluctuation-driven currents. The magnitude and structure of the fluctuation-driven currents have been studied by applying a weak, axisymmetric seed magnetic field to laminar and turbulent flows. An Ohm's law analysis of the axisymmetric currents allows the fluctuation-driven currents to be identified. The magnetic fields generated by the fluctuations are significant: a dipole moment aligned with the symmetry axis of the mean-flow is generated similar to those observed in the experiment, and both toroidal and poloidal flux expulsion are observed.

Large Electric Field–Enhanced–Hardness Effect in a SiO2 Film

PubMed Central

Revilla, Reynier I.; Li, Xiao-Jun; Yang, Yan-Lian; Wang, Chen

2014-01-01

Silicon dioxide films are extensively used in nano and micro–electromechanical systems. Here we studied the influence of an external electric field on the mechanical properties of a SiO2 film by using nanoindentation technique of atomic force microscopy (AFM) and friction force microscopy (FFM). A giant augmentation of the relative elastic modulus was observed by increasing the localized electric field. A slight decrease in friction coefficients was also clearly observed by using FFM with the increase of applied tip voltage. The reduction of the friction coefficients is consistent with the great enhancement of sample hardness by considering the indentation–induced deformation during the friction measurements. PMID:24681517

The electrobrachistochrone

NASA Astrophysics Data System (ADS)

Lipscombe, Trevor C.; Mungan, Carl E.

2018-05-01

The brachistochrone problem consists of finding the track of shortest travel time between given initial and final points for a particle sliding frictionlessly along it under the influence of a given external force field. Solvable variations of the standard example of a uniform gravitational field would be suitable for homework and computer projects by undergraduate physics students studying intermediate mechanics and electromagnetism. An electrobrachistochrone problem is here proposed, in which a charged particle moves along a frictionless track under the influence of its electrostatic force of attraction to an image charge in a grounded conducting plane below the track. The path of least time is found to be a foreshortened cycloid and its properties are investigated analytically and graphically.

Flux pinning forces in irradiated a-axis oriented EuBa{sub 2}Cu{sub 3}O{sub 7} films

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

Martin, J. I.; Gonzalez, E. M.; Kwok, W.-K

1999-10-12

{alpha}-axis oriented EuBa{sub 2}Cu{sub 3}O{sub 7} films have been irradiated with high energy heavy ions in different configurations to study the possible pinning role of the artificial defects in this kind of samples. The original pinning limiting mechanism of the samples is not essentially altered what the irradiation is parallel to the CuO{sub 2} planes. However, when it is deviated from this direction, an increase in critical current density and a change in pinning force are observed when the magnetic field is parallel to the columnar defects at values around the matching field.

Recent Advances of MEMS Resonators for Lorentz Force Based Magnetic Field Sensors: Design, Applications and Challenges.

PubMed

Herrera-May, Agustín Leobardo; Soler-Balcazar, Juan Carlos; Vázquez-Leal, Héctor; Martínez-Castillo, Jaime; Vigueras-Zuñiga, Marco Osvaldo; Aguilera-Cortés, Luz Antonio

2016-08-24

Microelectromechanical systems (MEMS) resonators have allowed the development of magnetic field sensors with potential applications such as biomedicine, automotive industry, navigation systems, space satellites, telecommunications and non-destructive testing. We present a review of recent magnetic field sensors based on MEMS resonators, which operate with Lorentz force. These sensors have a compact structure, wide measurement range, low energy consumption, high sensitivity and suitable performance. The design methodology, simulation tools, damping sources, sensing techniques and future applications of magnetic field sensors are discussed. The design process is fundamental in achieving correct selection of the operation principle, sensing technique, materials, fabrication process and readout systems of the sensors. In addition, the description of the main sensing systems and challenges of the MEMS sensors are discussed. To develop the best devices, researches of their mechanical reliability, vacuum packaging, design optimization and temperature compensation circuits are needed. Future applications will require multifunctional sensors for monitoring several physical parameters (e.g., magnetic field, acceleration, angular ratio, humidity, temperature and gases).

Recent Advances of MEMS Resonators for Lorentz Force Based Magnetic Field Sensors: Design, Applications and Challenges

PubMed Central

Herrera-May, Agustín Leobardo; Soler-Balcazar, Juan Carlos; Vázquez-Leal, Héctor; Martínez-Castillo, Jaime; Vigueras-Zuñiga, Marco Osvaldo; Aguilera-Cortés, Luz Antonio

2016-01-01

Microelectromechanical systems (MEMS) resonators have allowed the development of magnetic field sensors with potential applications such as biomedicine, automotive industry, navigation systems, space satellites, telecommunications and non-destructive testing. We present a review of recent magnetic field sensors based on MEMS resonators, which operate with Lorentz force. These sensors have a compact structure, wide measurement range, low energy consumption, high sensitivity and suitable performance. The design methodology, simulation tools, damping sources, sensing techniques and future applications of magnetic field sensors are discussed. The design process is fundamental in achieving correct selection of the operation principle, sensing technique, materials, fabrication process and readout systems of the sensors. In addition, the description of the main sensing systems and challenges of the MEMS sensors are discussed. To develop the best devices, researches of their mechanical reliability, vacuum packaging, design optimization and temperature compensation circuits are needed. Future applications will require multifunctional sensors for monitoring several physical parameters (e.g., magnetic field, acceleration, angular ratio, humidity, temperature and gases). PMID:27563912

Large pinning forces and matching effects in YBa2Cu3O7-δ thin films with Ba2Y(Nb/Ta)O6 nano-precipitates

NASA Astrophysics Data System (ADS)

Opherden, Lars; Sieger, Max; Pahlke, Patrick; Hühne, Ruben; Schultz, Ludwig; Meledin, Alexander; van Tendeloo, Gustaaf; Nast, Rainer; Holzapfel, Bernhard; Bianchetti, Marco; MacManus-Driscoll, Judith L.; Hänisch, Jens

2016-02-01

The addition of mixed double perovskite Ba2Y(Nb/Ta)O6 (BYNTO) to YBa2Cu3O7-δ (YBCO) thin films leads to a large improvement of the in-field current carrying capability. For low deposition rates, BYNTO grows as well-oriented, densely distributed nanocolumns. We achieved a pinning force density of 25 GN/m3 at 77 K at a matching field of 2.3 T, which is among the highest values reported for YBCO. The anisotropy of the critical current density shows a complex behavior whereby additional maxima are developed at field dependent angles. This is caused by a matching effect of the magnetic fields c-axis component. The exponent N of the current-voltage characteristics (inversely proportional to the creep rate S) allows the depinning mechanism to be determined. It changes from a double-kink excitation below the matching field to pinning-potential-determined creep above it.

Hydrodynamic interactions in dense active suspensions: From polar order to dynamical clusters

NASA Astrophysics Data System (ADS)

Yoshinaga, Natsuhiko; Liverpool, Tanniemola B.

2017-08-01

We study the role of hydrodynamic interactions in the collective behavior of collections of microscopic active particles suspended in a fluid. We introduce a calculational framework that allows us to separate the different contributions to their collective dynamics from hydrodynamic interactions on different length scales. Hence we are able to systematically show that lubrication forces when the particles are very close to each other play as important a role as long-range hydrodynamic interactions in determining their many-body behavior. We find that motility-induced phase separation is suppressed by near-field interactions, leading to open gel-like clusters rather than dense clusters. Interestingly, we find a globally polar ordered phase appears for neutral swimmers with no force dipole that is enhanced by near-field lubrication forces in which the collision process rather than long-range interaction dominates the alignment mechanism.

Shaping metallic glasses by electromagnetic pulsing

PubMed Central

Kaltenboeck, Georg; Demetriou, Marios D.; Roberts, Scott; Johnson, William L.

2016-01-01

With damage tolerance rivalling advanced engineering alloys and thermoplastic forming capabilities analogous to conventional plastics, metallic glasses are emerging as a modern engineering material. Here, we take advantage of their unique electrical and rheological properties along with the classic Lorentz force concept to demonstrate that electromagnetic coupling of electric current and a magnetic field can thermoplastically shape a metallic glass without conventional heating sources or applied mechanical forces. Specifically, we identify a process window where application of an electric current pulse in the presence of a normally directed magnetic field can ohmically heat a metallic glass to a softened state, while simultaneously inducing a large enough magnetic body force to plastically shape it. The heating and shaping is performed on millisecond timescales, effectively bypassing crystallization producing fully amorphous-shaped parts. This electromagnetic forming approach lays the groundwork for a versatile, time- and energy-efficient manufacturing platform for ultrastrong metals. PMID:26853460

Rigorous force field optimization principles based on statistical distance minimization

DOE PAGES

Vlcek, Lukas; Chialvo, Ariel A.

2015-10-12

We use the concept of statistical distance to define a measure of distinguishability between a pair of statistical mechanical systems, i.e., a model and its target, and show that its minimization leads to general convergence of the model’s static measurable properties to those of the target. Here we exploit this feature to define a rigorous basis for the development of accurate and robust effective molecular force fields that are inherently compatible with coarse-grained experimental data. The new model optimization principles and their efficient implementation are illustrated through selected examples, whose outcome demonstrates the higher robustness and predictive accuracy of themore » approach compared to other currently used methods, such as force matching and relative entropy minimization. We also discuss relations between the newly developed principles and established thermodynamic concepts, which include the Gibbs-Bogoliubov inequality and the thermodynamic length.« less

Orbital motions of bubbles in an acoustic field

NASA Astrophysics Data System (ADS)

Shirota, Minori; Yamashita, Ko; Inamura, Takao

2012-09-01

This experimental study aims to clarify the mechanism of orbital motion of two oscillating bubbles in an acoustic field. Trajectory of the orbital motion on the wall of a spherical levitator was observed using a high-speed video camera. Because of a good repeatability in volume oscillation of bubbles, we were also able to observe the radial motion driven at 24 kHz by stroboscopic like imaging technique. The orbital motions of bubbles raging from 0.13 to 0.18 mm were examined with different forcing amplitude and in different viscous oils. As a result, we found that pairs of bubbles revolve along an elliptic orbit around the center of mass of the bubbles. We also found that the two bubbles perform anti-phase radial oscillation. Although this radial oscillation should result in a repulsive secondary Bjerknes force, the bubbles kept a constant separate distance of about 1 mm, which indicates the existence of centripetal primary Bjerknes force.

Quantitative characterization of 3D deformations of cell interactions with soft biomaterials

NASA Astrophysics Data System (ADS)

Franck, Christian

In recent years, the importance of mechanical forces in directing cellular function has been recognized as a significant factor in biological and physiological processes. In fact, these physical forces are now viewed equally as important as biochemical stimuli in controlling cellular response. Not only do these cellular forces, or cell tractions, play an important role in cell migration, they are also significant to many other physiological and pathological processes, both at the tissue and organ level, including wound healing, inflammation, angiogenesis, and embryogenesis. A complete quantification of cell tractions during cell-material interactions can lead to a deeper understanding of the fundamental role these forces play in cell biology. Thus, understanding the function and role of a cell from a mechanical framework can have important implications towards the development of new implant materials and drug treatments. Previous research has contributed significant descriptions of cell-tissue interactions by quantifying cell tractions in two-dimensional environments; however, most physiological processes are three-dimensional in nature. Recent studies have shown morphological differences in cells cultured on two-dimensional substrates versus three-dimensional matrices, and that the intrinsic extracellular matrix interactions and migration behavior are different in three dimensions versus two dimensions. Hence, measurement techniques are needed to investigate cellular behavior in all three dimensions. This thesis presents a full-field imaging technique capable of quantitatively measuring cell traction forces in all three spatial dimensions, and hence addresses the need of a three-dimensional quantitative imaging technique to gain insight into the fundamental role of physical forces in biological processes. The technique combines laser scanning confocal microscopy (LSCM) with digital volume correlation (DVC) to track the motion of fluorescent particles during cell-induced or externally applied deformations. This method is validated by comparing experimentally measured non-uniform deformation fields near hard and soft spherical inclusions under uniaxial compression with the corresponding analytical solution. Utilization of a newly developed computationally efficient stretch-correlation and deconvolution algorithm is shown to improve the overall measurement accuracy, in particular under large deformations. Using this technique, the full three-dimensional substrate displacement fields are experimentally determined during the migration of individual fibroblast cells on polyacrylamide gels. This is the first study to show the highly three-dimensional structure of cell-induced displacement and traction fields. These new findings suggest a three-dimensional push-pull cell motility, which differs from the traditional theories based on two-dimensional data. These results provide new insight into the dynamic cell-matrix force exchange or mechanotransduction of migrating cells, and will aid in the development of new three-dimensional cell motility and adhesion models. As this study reveals, the mechanical interactions of cells and their extracellular matrix appear to be highly three-dimensional. It also shows that the LSCM-DVC technique is well suited for investigating the mechanics of cell-matrix interactions while providing a platform to access detailed information of the intricate biomechanical coupling for many cellular responses. Thus, this method has the capability to provide direct quantitative experimental data showing how cells interact with their surroundings in three dimensions and might stimulate new avenues of scientific thought in understanding the fundamental role physical forces play in regulating cell behavior.

A dynamic model of the eye nystagmus response to high magnetic fields.

PubMed

Glover, Paul M; Li, Yan; Antunes, Andre; Mian, Omar S; Day, Brian L

2014-02-07

It was recently shown that high magnetic fields evoke nystagmus in human subjects with functioning vestibular systems. The proposed mechanism involves interaction between ionic currents in the endolymph of the vestibular labyrinth and the static magnetic field. This results in a Lorentz force that causes endolymph flow to deflect the cupulae of the semi-circular canals to evoke a vestibular-ocular reflex (VOR). This should be analogous to stimulation by angular acceleration or caloric irrigation. We made measurements of nystagmus slow-phase velocities in healthy adults experiencing variable magnetic field profiles of up to 7 T while supine on a bed that could be moved smoothly into the bore of an MRI machine. The horizontal slow-phase velocity data were reliably modelled by a linear transfer function incorporating a low-pass term and a high-pass adaptation term. The adaptation time constant was estimated at 39.3 s from long exposure trials. When constrained to this value, the low-pass time constant was estimated at 13.6 ± 3.6 s (to 95% confidence) from both short and long exposure trials. This confidence interval overlaps with values obtained previously using angular acceleration and caloric stimulation. Hence it is compatible with endolymph flow causing a cupular deflection and therefore supports the hypothesis that the Lorentz force is a likely transduction mechanism of the magnetic field-evoked VOR.

Polarizable Force Fields for CO2 and CH4 Adsorption in M-MOF-74

PubMed Central

2017-01-01

The family of M-MOF-74, with M = Co, Cr, Cu, Fe, Mg, Mn, Ni, Ti, V, and Zn, provides opportunities for numerous energy related gas separation applications. The pore structure of M-MOF-74 exhibits a high internal surface area and an exceptionally large adsorption capacity. The chemical environment of the adsorbate molecule in M-MOF-74 can be tuned by exchanging the metal ion incorporated in the structure. To optimize materials for a given separation process, insights into how the choice of the metal ion affects the interaction strength with adsorbate molecules and how to model these interactions are essential. Here, we quantitatively highlight the importance of polarization by comparing the proposed polarizable force field to orbital interaction energies from DFT calculations. Adsorption isotherms and heats of adsorption are computed for CO2, CH4, and their mixtures in M-MOF-74 with all 10 metal ions. The results are compared to experimental data, and to previous simulation results using nonpolarizable force fields derived from quantum mechanics. To the best of our knowledge, the developed polarizable force field is the only one so far trying to cover such a large set of possible metal ions. For the majority of metal ions, our simulations are in good agreement with experiments, demonstrating the effectiveness of our polarizable potential and the transferability of the adopted approach. PMID:28286598

Force-field parameters from the SAFT-γ equation of state for use in coarse-grained molecular simulations.

PubMed

Müller, Erich A; Jackson, George

2014-01-01

A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.

Deformable membranes actuated by high mechanical power density composite electroactive polymers using tailored electric field

NASA Technical Reports Server (NTRS)

Bar-Cohen, Y.; Bhattacharya, K.

2003-01-01

The objective of the project was to develop a versatile electroactuator based on a specific class of EAP, conductive polymer, that is capable of developing high forces and displacements in both bending and linear contraction/expansion movements.

A low-frequency chip-scale optomechanical oscillator with 58 kHz mechanical stiffening and more than 100th-order stable harmonics.

PubMed

Huang, Yongjun; Flores, Jaime Gonzalo Flor; Cai, Ziqiang; Yu, Mingbin; Kwong, Dim-Lee; Wen, Guangjun; Churchill, Layne; Wong, Chee Wei

2017-06-29

For the sensitive high-resolution force- and field-sensing applications, the large-mass microelectromechanical system (MEMS) and optomechanical cavity have been proposed to realize the sub-aN/Hz 1/2 resolution levels. In view of the optomechanical cavity-based force- and field-sensors, the optomechanical coupling is the key parameter for achieving high sensitivity and resolution. Here we demonstrate a chip-scale optomechanical cavity with large mass which operates at ≈77.7 kHz fundamental mode and intrinsically exhibiting large optomechanical coupling of 44 GHz/nm or more, for both optical resonance modes. The mechanical stiffening range of ≈58 kHz and a more than 100 th -order harmonics are obtained, with which the free-running frequency instability is lower than 10 -6 at 100 ms integration time. Such results can be applied to further improve the sensing performance of the optomechanical inspired chip-scale sensors.

Aerodynamics of high frequency flapping wings

NASA Astrophysics Data System (ADS)

Hu, Zheng; Roll, Jesse; Cheng, Bo; Deng, Xinyan

2010-11-01

We investigated the aerodynamic performance of high frequency flapping wings using a 2.5 gram robotic insect mechanism developed in our lab. The mechanism flaps up to 65Hz with a pair of man-made wing mounted with 10cm wingtip-to-wingtip span. The mean aerodynamic lift force was measured by a lever platform, and the flow velocity and vorticity were measured using a stereo DPIV system in the frontal, parasagittal, and horizontal planes. Both near field (leading edge vortex) and far field flow (induced flow) were measured with instantaneous and phase-averaged results. Systematic experiments were performed on the man-made wings, cicada and hawk moth wings due to their similar size, frequency and Reynolds number. For insect wings, we used both dry and freshly-cut wings. The aerodynamic force increase with flapping frequency and the man-made wing generates more than 4 grams of lift at 35Hz with 3 volt input. Here we present the experimental results and the major differences in their aerodynamic performances.

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

On Predicting the Crystal Structure of Energetic Materials From Quantum Mechanics

DTIC Science & Technology

2008-12-01

DE ABSTRACT A quantum-mechanically-based potential energy function that describes interactions of dimers of the explosive ...method is capable of producing force fields for interactions of the molecular crystalline explosive RDX, and appears to be suitable to enable reliable...Ridge, TN. Byrd, E.F.C., Scuseria, G.E., Chabalowski, C.F., 2004: “An ab initio study of solid nitromethane , HMX, RDX and CL20: Successes and

Battle Staff Operations: Synchronization of Planning at Battalion and Brigade Level

DTIC Science & Technology

1989-06-02

tactical employment of the tank and mechanized infantry battalion task force. In consonance with Airland Battle doctrine, the document emphasizes ...letter entitled *Emphasis on Rapid Estimates and Decisions on the Atomic Battlefield.’ Emphasizing the increased tempo of the post war mechanized army...If so, a copy of the message is automatically canted to the user(s) identified in the distribution field. Queries are messages retrived records from

Magnetic dynamo activity in mechanically driven compressible magnetohydrodynamic turbulence

NASA Technical Reports Server (NTRS)

Shebalin, John V.; Montgomery, David

1989-01-01

Magnetic dynamo activity in a homogeneous, dissipative, polytropic, two-dimensional, turbulent magneto-fluid is simulated numerically. The magneto-fluid is simulated numerically. The magneto-fluid is, in a number of cases, mechanically forced so that energy input balances dissipation, thereby maintaining constant energy. In the presence of a mean magnetic field, a magneto-fluid whose initial turbulent magnetic energy is zero quickly arrives at a state of non-zero turbulent magnetic energy. If the mean magnetic field energy density is small, the turbulent magnetic field can achieve a local energy density more than four hundred times larger; if the mean magnetic field energy density is large, then equipartition between the turbulent magnetic and kinetic energy is achieved. Compared to the presence of a mean magnetic field, compressibility appears to have only a marginal effect in mediating the transfer of turbulent kinetic energy into magnetic energy.

Identification of nanoparticles and nanosystems in biological matrices with scanning probe microscopy.

PubMed

Angeloni, Livia; Reggente, Melania; Passeri, Daniele; Natali, Marco; Rossi, Marco

2018-04-17

Identification of nanoparticles and nanosystems into cells and biological matrices is a hot research topic in nanobiotechnologies. Because of their capability to map physical properties (mechanical, electric, magnetic, chemical, or optical), several scanning probe microscopy based techniques have been proposed for the subsurface detection of nanomaterials in biological systems. In particular, atomic force microscopy (AFM) can be used to reveal stiff nanoparticles in cells and other soft biomaterials by probing the sample mechanical properties through the acquisition of local indentation curves or through the combination of ultrasound-based methods, like contact resonance AFM (CR-AFM) or scanning near field ultrasound holography. Magnetic force microscopy can detect magnetic nanoparticles and other magnetic (bio)materials in nonmagnetic biological samples, while electric force microscopy, conductive AFM, and Kelvin probe force microscopy can reveal buried nanomaterials on the basis of the differences between their electric properties and those of the surrounding matrices. Finally, scanning near field optical microscopy and tip-enhanced Raman spectroscopy can visualize buried nanostructures on the basis of their optical and chemical properties. Despite at a still early stage, these methods are promising for detection of nanomaterials in biological systems as they could be truly noninvasive, would not require destructive and time-consuming specific sample preparation, could be performed in vitro, on alive samples and in water or physiological environment, and by continuously imaging the same sample could be used to dynamically monitor the diffusion paths and interaction mechanisms of nanomaterials into cells and biological systems. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology. © 2018 Wiley Periodicals, Inc.

Shear stress cleaning for surface departiculation

NASA Technical Reports Server (NTRS)

Musselman, R. P.; Yarbrough, T. W.

1986-01-01

A cleaning technique widely used by the nuclear utility industry for removal of radioactive surface contamination has proven effective at removing non-hazardous contaminant particles as small as 0.1 micrometer. The process employs a controlled high velocity liquid spray inside a vapor containment enclosure to remove particles from a surface. The viscous drag force generated by the cleaning fluid applies a shear stress greater than the adhesion force that holds small particles to a substrate. Fluid mechanics and field tests indicate general cleaning parameters.

Experiments and models of MHD jets and their relevance to astrophysics and solar physics

NASA Astrophysics Data System (ADS)

Bellan, Paul M.

2018-05-01

Magnetohydrodynamic (MHD)-driven jets involve poloidal and toroidal magnetic fields, finite pressure gradients, and unbalanced forces. The mechanism driving these jets is first discussed qualitatively by decomposing the magnetic force into a curvature and a gradient component. The mechanism is then considered quantitatively by consideration of all terms in the three components of the MHD equation of motion and in addition, the implications of Ampere's law, Faraday's law, the ideal Ohm's law, and the equation of continuity. The analysis shows that jets are self-collimating with the tip of the jet moving more slowly than the main column of the jet so there is a continuous stagnation near the tip in the jet frame. Experiments supporting these conclusions are discussed and it is shown how this mechanism relates to jets in astrophysical and solar corona contexts.

Biological Experiments in Microgravity Conditions Using Magnetic Micro- and Nano-Particles

NASA Astrophysics Data System (ADS)

Nechitailo, Galina S.; Kuznetsov, Anatoli; Kuznetsov, Oleg

2016-07-01

Gravity affects all living organisms on Earth, and plays a role in multiple processes in them. In microgravity conditions (e.g., on board of a spacecraft) many of these processes are disturbed, e.g., spatial orientation is lost, mass and heat exchange is distorted, many adaptive mechanisms no longer function, etc. Negation of these adverse effects by creation of pseudo-gravity to by centrifugation is complicated, expensive and unpractical. We propose to use naturally occurring magnetic heterogeneity of all living cells and high gradient magnetic fields as an alternative approach to negating the adverse effects of microgravity on living systems. In non-uniform magnetic field, magnetically heterogeneous objects experience a system of ponderomotive forces. For a weak magnetic particle, the net ponderomotive magnetic force: Fm = Δχ•V•grad(H2/2), where Δχ is the difference of susceptibilities of the particle and the surrounding media, V is the volume of the particle, grad(H2/2) is the dynamic factor of the magnetic field. We studied magnetic heterogeneity of plant gravity receptor cells, prepared and conducted experiments on board of the space station "Mir" on providing a gravity-like stimulus for flax seedlings using high gradient magnetic field ("Magnetogravistat" experiment). Later, a more sophisticated version of this experiment was flown on STS-107. These experiments provided new data on the mechanisms of plant gravity reception and created a method for substituting gravity for a living organism by a force of a different physical nature, to negate the adverse effects of microgravity. Since the ponderomotive force is proportional to the dynamic factor of the field grad(H2/2), the stronger the field, and the faster it changes over distance, the higher is the dynamic factor and the stronger the ponderomotive force. Therefore, in the small vicinity of a small ferromagnetic particle (preferably metallic micro or nano-particles), the forces are very significant even for weak magnetic objects, and can have significant effects on multiple processes in living cells/organisms. It was reported, that such high gradient magnetic fields can affect cell differentiation and cell proliferation processes in ground-based experiments. To prevent oxidation of ultradisperse ferromagnetic particles in aqueous media, it is beneficial to coat their surface with carbon. Suitable protected metallic micro- and nano-particles can be produced by a variety of techniques (CVD, plasmachemistry, joint grinding, etc.). Ferro-carbon particles produced by plasmachemical technique have high sorption capacities for various organic and inorganic compounds (as well as for various cell metabolites), can be formed in rather stable aqueous suspensions, and be controlled (e.g., sedimented) by a magnetic field. This makes these particles a very interesting research tool. In our opinion, biological experiments with ferro-carbon nano-structured particles in microgravity will generate important scientific data and will allow creating new methods of negating the adverse effects of microgravity on living systems.

Controlled nanopatterning of a polymerized ionic liquid in a strong electric field

DOE PAGES

Bocharova, Vera; Agapov, Alexander L.; Tselev, Alexander; ...

2014-12-17

Nanolithography has become a driving force in advancements of the modern day's electronics, allowing for miniaturization of devices and a steady increase of the calculation, power, and storage densities. Among various nanofabrication approaches, scanning probe techniques, including atomic force microscopy (AFM), are versatile tools for creating nanoscale patterns utilizing a range of physical stimuli such as force, heat, or electric field confined to the nanoscale. In this study, the potential of using the electric field localized at the apex of an AFM tip to induce and control changes in the mechanical properties of an ion containing polymer—a polymerized ionic liquidmore » (PolyIL)—on a very localized scale is explored. In particular, it is demonstrated that by means of AFM, one can form topographical features on the surface of PolyIL-based thin films with a significantly lower electric potential and power consumption as compared to nonconductive polymer materials. Lastly,, by tuning the applied voltage and ambient air humidity, control over dimensions of the formed structures is reproducibly achieved.« less

In silico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level

PubMed Central

Yang, Changwon; Kulkarni, Mandar; Lim, Manho

2017-01-01

Abstract The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged time scale (10–12 μs) parallel tempering metadynamics (PTMetaD) simulation method in conjunction with a modified version of the AMBER bsc1 force field. For unbiased descriptions of the folding free energy landscape of TBA-15, this force field was minimally modified. From this direct folding simulation using the modified bsc1 force field, reasonably converged free energy landscapes were obtained in K+-rich aqueous solution (150 mM), providing detailed atomistic pictures of GQ folding mechanisms for TBA-15. This study found that the TBA folding occurred via multiple folding pathways with two major free energy barriers of 13 and 15 kcal/mol in the presence of several intermediate states of G-triplex variants. The early formation of these intermediates was associated with a single K+ ion capturing. Interestingly, these intermediate states appear to undergo facile transitions among themselves through relatively small energy barriers. PMID:29112755

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

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.

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

NASA Astrophysics Data System (ADS)

Velazquez, Hector A.; Hamelberg, Donald

2015-02-01

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.

Spectroscopically determined force field for water dimer: physically enhanced treatment of hydrogen bonding in molecular mechanics energy functions.

PubMed

Mannfors, Berit; Palmo, Kim; Krimm, Samuel

2008-12-11

Our ab initio transformed spectroscopically determined force field (SDFF) methodology emphasizes, in addition to accurate structure and energy performance, comparable prediction of vibrational properties in order to improve reproduction of interaction forces. It is now applied to the determination of a molecular mechanics (MM) force field for the water monomer and dimer as an initial step in developing a more physically based treatment of the hydrogen bonding that not only underlies condensed-phase water but also must be important in molecular-level protein-water interactions. Essential electrical components of the SDFF for monomer water are found to be the following: an off-plane charge distribution, this distribution consisting of four off-atom charge sites in traditional lone pair (LP) but also in inverted lone pair (ILP) positions; allowance for a diffuse size to these off-atom sites; and the incorporation of charge fluxes (i.e., the change in charge with change in internal coordinate). Parametrization of such an LP/ILP model together with the SDFF analytically transformed valence force field results in essentially exact agreement with ab initio (in this case MP2/6-31++G(d,p)) structure, electrical, and vibrational properties. Although we demonstrate that the properties of this monomer electrical model together with its van der Waals and polarization interactions are transferable to the dimer, this is not sufficient in reproducing comparable dimer properties, most notably the huge increase in infrared intensity of a donor OH stretch mode. This deficiency, which can be eliminated by a large dipole-derivative-determined change in the effective charge flux of the donor hydrogen-bonded OH bond, is not accounted for by the charge flux change in this bond due to the induction effects of the acceptor electric field alone, and can only be fully removed by an added bond flux associated with the extent of overlap of the wave functions of the two molecules. We show that this overlap charge flux (OCF) emulates an actual O-H...LP-O intermolecular dipole flux, reflecting the unitary nature of the hydrogen-bonded system in the context of MM-separable molecules. The effectiveness of incorporating the OCF noncanonical character demonstrates that a distinctively QM-unique property can be substantively represented in MM energy functions.

Multiply charged ion generation according to magnetic field configurations in Hall thruster plasmas

NASA Astrophysics Data System (ADS)

Kim, Holak; Lee, Seunghun; Kim, Junbum; Lim, Youbong; Choe, Wonho; KIMS Collaboration

2016-09-01

Plasma propulsion is the most promising techniques to operate satellites for low earth orbit as well as deep space exploration. A typical plasma propulsion system is Hall thruster (HT) that uses crossed electromagnetic fields to ionize a propellant gas and to accelerate the ionized gas. In HT the tailoring of magnetic fields is significant due to that the electron confinement in the electromagnetic fields affects thruster performances such as thrust force, specific impulse, power efficiency, and life time. We designed an anode layer HT (TAL) with the magnetic field tailoring. The TAL is possible to keep discharge in 1 2 kilovolts, which voltage is useful to obtain high specific impulse The magnetic field tailoring is adapted to minimize undesirable heat dissipations and secondary electron emissions at a wall surrounding plasma In presentation, we will report TAL performances including thrust force, specific impulse, and anode efficiency measured by a pendulum thrust stand. This mechanical measurement will be compared to the plasma diagnostics conducted by angular Faraday probe, retarding potential analyzer, and ExB probe Grant No. 2014M1A3A3A02034510.

Controllable deformation of salt water-filled carbon nanotubes using an electric field with application to molecular sieving

NASA Astrophysics Data System (ADS)

Ye, Hongfei; Zheng, Yonggang; Zhang, Zhongqiang; Zhang, Hongwu; Chen, Zhen

2016-08-01

Precisely controlling the deformation of carbon nanotubes (CNTs) has practical application in the development of nanoscale functional devices, although it is a challenging task. Here, we propose a novel method to guide the deformation of CNTs through filling them with salt water and applying an electric field. With the electric field along the axial direction, the height of CNTs is enlarged by the axial electric force due to the internal ions and polar water molecules. Under an electric field with two mutually orthogonal components, the transverse electric force could further induce the bending deformation of CNTs. Based on the classical rod and beam theories, two mechanical models are constructed to verify and quantitatively describe the relationships between the tension and bending deformations of CNTs and the electric field intensity. Moreover, by means of the electric field-driven tension behavior of CNTs, we design a stretchable molecular sieve to control the flow rate of mixed gas and collect a single high-purity gas. The present work opens up new avenues in the design and fabrication of nanoscale controlling units.

Opto-Mechanical Design of FIR Diagnostic System for C-2W

NASA Astrophysics Data System (ADS)

Beall, Michael; Deng, B. H.; Settles, G.; Rouillard, M.; Schroeder, J.; Gota, H.; Thompson, M.; Snitchler, G.; Ziaei, S.; the TAE Team

2016-10-01

The goal of the C-2W far-infrared (FIR) diagnostic system is to provide highly accurate, simultaneous polarimetry and interferometry information about the generation, equilibrium and time evolution of the advanced beam-driven field-reversed configuration (FRC). Thorough spatial coverage of the confinement vessel will be provided by a set of 14 chords at the central plane, with half of the chords tilted at a 15°angle to provide additional polarimetry information. Due to the very low (<.5°) Faraday rotation expected in the field-reversed plasma, the system has a design goal of .25 μm maximum allowable vibration over the lifetime of the shot. Due to large eddy-current forces from simulation of magnetic-field ramp-up, a non-metallic canvas phenolic material has been selected for the primary breadboards, which are mounted on a rigid, sand-filled support structure. Given the size of the structure and the magnetic impact, the support structure does not use pneumatic or mechanical isolation. Dynamic vibration analysis with Ansys, based on measurements of local ground vibration and simulations of magnetic forces, predicts that the system will meet the design goal.

Beam trapping in high-current cyclic accelerators with strong-focusing fields. Memorandum report, January-December 1984

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

Sprangle, P.; Kapetanakos, C.A.

1985-03-06

In cyclic induction accelerators, the energy of the particles increases slowly in synchronism with the vertical (betatron) magnetic field. As a consequence of the slow acceleration, the charged particles must be confined by the weak-focusing magnetic field over long periods of time, and thus field errors, instabilities, and radiation losses can impose limitations on the acceleration process. These limitations can be substantially relaxed if the acceleration were to occur rapidly, say over a few microseconds. An appropriate name for such an accelerator is REBA-TRON (Rapid Electron Beam Accelerator). This paper considers a possible mechanism which could trap a high currentmore » electron beam in the strong focusing magnetic fields of the rebatron. We investigate a possible mechanism for trapping an intense relativistic electron beam confined by strong focusing fields. In our model the electron beam is assumed to be injected into torsatron fields off axis, near the chamber walls. The finite resistivity of the walls results in a drag force on the beam centroid which may cause the beam to spiral inward towards the axis of the chamber. We have analyzed this mechanism and obtained decay rates for the inward spiraling beam motion.« less

Development of Finite Elements for Two-Dimensional Structural Analysis Using the Integrated Force Method

NASA Technical Reports Server (NTRS)

Kaljevic, Igor; Patnaik, Surya N.; Hopkins, Dale A.

1996-01-01

The Integrated Force Method has been developed in recent years for the analysis of structural mechanics problems. This method treats all independent internal forces as unknown variables that can be calculated by simultaneously imposing equations of equilibrium and compatibility conditions. In this paper a finite element library for analyzing two-dimensional problems by the Integrated Force Method is presented. Triangular- and quadrilateral-shaped elements capable of modeling arbitrary domain configurations are presented. The element equilibrium and flexibility matrices are derived by discretizing the expressions for potential and complementary energies, respectively. The displacement and stress fields within the finite elements are independently approximated. The displacement field is interpolated as it is in the standard displacement method, and the stress field is approximated by using complete polynomials of the correct order. A procedure that uses the definitions of stress components in terms of an Airy stress function is developed to derive the stress interpolation polynomials. Such derived stress fields identically satisfy the equations of equilibrium. Moreover, the resulting element matrices are insensitive to the orientation of local coordinate systems. A method is devised to calculate the number of rigid body modes, and the present elements are shown to be free of spurious zero-energy modes. A number of example problems are solved by using the present library, and the results are compared with corresponding analytical solutions and with results from the standard displacement finite element method. The Integrated Force Method not only gives results that agree well with analytical and displacement method results but also outperforms the displacement method in stress calculations.

Frictional forces in material removal for glasses and ceramics using magnetorheological finishing

NASA Astrophysics Data System (ADS)

Miao, Chunlin

Magnetorheological finishing (MRF) spotting experiments on stationary parts are conducted in this work to understand the material removal mechanism in MRF. Drag force and normal force are measured in situ, simultaneously for the first time for a variety of optical materials in MRF. We study material removal process in MRF as a function of material mechanical properties. We experimentally demonstrate that material removal in MRF is strongly related to shear stress. Shear stress is predominantly determined by material mechanical properties. A modified Preston's equation is proposed to estimate the material removal in MRF by combining shear stress and material mechanical properties. We investigate extensively the effect of various MRF process parameters, including abrasive concentration, magnetic field strength, penetration depth and wheel speed, on material removal efficiency. Material removal rate model is expanded to include these parameters. We develop a nonaqueous magnetorheological (MR) fluid for examining the mechanical contribution in MRF material removal. This fluid is based on a combination of two CI particles and a combination of two organic liquids. Material removal with this nonaqueous MR fluid is discussed. We formulate a new corrosion resistant MR fluid which is based on metal oxide coated carbonyl iron (CI) particles. The rheological behavior, stability and corrosion resistance are examined.

Amplitude-Stabilized Oscillator for a Capacitance-Probe Electrometer

NASA Technical Reports Server (NTRS)

Blaes, Brent R.; Schaefer, Rembrandt T.

2012-01-01

A multichannel electrometer voltmeter that employs a mechanical resonator maintained in sustained amplitude-stabilized oscillation has been developed for the space-based measurement of an Internal Electrostatic Discharge Monitor (IESDM) sensor. The IESDM is new sensor technology targeted for integration into a Space Environmental Monitor (SEM) subsystem used for the characterization and monitoring of deep dielectric charging on spacecraft. Creating a stable oscillator from the mechanical resonator was achieved by employing magnetic induction for sensing the resonator s velocity, and forcing a current through a coil embedded in the resonator to produce a Lorentz actuation force that overcomes the resonator s dissipative losses. Control electronics employing an AGC loop provide conditions for stabilized, constant amplitude harmonic oscillation. The prototype resonator was composed of insulating FR4 printed-wireboard (PWB) material containing a flat, embedded, rectangular coil connected through flexure springs to a base PWB, and immersed in a magnetic field having two regions of opposite field direction generated by four neodymium block magnets. In addition to maintaining the mechanical movement needed for the electrometer s capacitor-probe transducer, this oscillator provides a reference signal for synchronous detection of the capacitor probe s output signal current so drift of oscillation frequency due to environmental effects is inconsequential.

Effects of pulsed electromagnetic field vibration on tooth movement induced by magnetic and mechanical forces: a preliminary study.

PubMed

Darendeliler, M Ali; Zea, A; Shen, G; Zoellner, H

2007-12-01

This study was designed to determine whether or not high-frequency and low-magnitude vibration affects orthodontic tooth movement caused by magnetic or/and mechanical forces. Forty-four 7-week-old Wistar rats were randomly divided into four groups, with each group further divided into experimental and control subgroups. Neodymium-Iron-Boron (Nd-Fe-B) magnets and Sentalloy closed coil springs were placed between maxillary or mandibular first molars and incisors to activate tooth movement. The animals of experimental subgroups were exposed to the vibration induced by pulsed electromagnetic fields (PEMF) whilst the control subgroups were under normal atmosphere. The experiment lasted for 14 days and all of the animals were sacrificed for examination. The changes in the space between the molar and incisor were measured to indicate the amount of tooth movement. The coil springs, either with sham or active magnets, move molar much more than magnets alone, regardless of absence or presence of PEMF (p < 0.001). Under PEMF, the coil spring moved significantly more amount of tooth movement than that of coil-magnet combination (p < 0.01), as did the magnets compared to sham magnets (p < 0.019). Under a non-PEMF scenario, there was no significant difference in tooth movement between coil spring and coil-magnets combination, nor was there difference between magnets and sham magnets. It is suggested that the PEMF-induced vibration may enhance the effect of mechanical and magnetic forces on tooth movement.

A comparative analysis of physiological responses at submaximal workloads during different laboratory simulations of field cycling.

PubMed

Kenny, G P; Reardon, F D; Marion, A; Thoden, J S

1995-01-01

The purpose of this study was to evaluate the relationships between heart rate (fc), oxygen consumption (VO2), peak force and average force developed at the crank in response to submaximal exercise employing a racing bicycle which was attached to an ergometer (RE), ridden on a treadmill (TC) and ridden on a 400-m track (FC). Eight male trained competitive cyclists rode at three pre-determined work intensities set at a proportion of their maximal oxygen consumption (VO2max): (1) below lactate threshold [work load that produces a VO2 which is 10% less than the lactate threshold VO2 (sub-LT)], (2) lactate threshold VO2 (LT), and (3) above lactate threshold [workload that produces a VO2 which is 10% greater than lactate threshold VO2 (supra-LT)], and equated across exercise modes on the basis of fc. Voltage signals from the crank arm were recorded as FM signals for subsequent representation of peak and average force. Open circuit VO2 measurements were done in the field by Douglas bag gas collection and in the laboratory by automated gas collection and analysis. fc was recorded with a telemeter (Polar Electro Sport Tester, PE3000). Significant differences (P < 0.05) were observed: (1) in VO2 between FC and both laboratory conditions at sub-LT intensity and LT intensities, (2) in peak force between FC and TC at sub-LT intensity, (3) in average force between FC and RE at sub-LT. No significant differences were demonstrated at supra-LT intensity for VO2. Similarly no significant differences were observed in peak and average force for either LT or supra-LT intensities. These data indicate that equating work intensities on the basis of fc measured in laboratory conditions would overestimate the VO2 which would be generated in the field and conversely, that using fc measured in the laboratory to establish field work intensity would underestimate mechanical workload experienced in the field.

Proper body mechanics from an engineering perspective.

PubMed

Mohr, Edward G

2010-04-01

The economic viability of the manual therapy practitioner depends on the number of massages/treatments that can be given in a day or week. Fatigue or injuries can have a major impact on the income potential and could ultimately reach the point which causes the practitioner to quit the profession, and seek other, less physically demanding, employment. Manual therapy practitioners in general, and massage therapists in particular, can utilize a large variety of body postures while giving treatment to a client. The hypothesis of this paper is that there is an optimal method for applying force to the client, which maximizes the benefit to the client, and at the same time minimizes the strain and effort required by the practitioner. Two methods were used to quantifiably determine the effect of using "poor" body mechanics (Improper method) and "best" body mechanics (Proper/correct method). The first approach uses computer modeling to compare the two methods. Both postures were modeled, such that the biomechanical effects on the practitioner's elbow, shoulder, hip, knee and ankle joints could be calculated. The force applied to the client, along with the height and angle of application of the force, was held constant for the comparison. The second approach was a field study of massage practitioners (n=18) to determine their maximal force capability, again comparing methods using "Improper and Proper body mechanics". Five application methods were tested at three different application heights, using a digital palm force gauge. Results showed that there was a definite difference between the two methods, and that the use of correct body mechanics can have a large impact on the health and well being of the massage practitioner over both the short and long term. Copyright 2009 Elsevier Ltd. All rights reserved.

A novel model of interaction between high frequency electromagnetic non-ionizing fields and microtubules viewed as coupled two-degrees of freedom harmonic oscillators.

PubMed

Caligiuri, Luigi Maxmilian

2015-01-01

The question regarding the potential biological and adverse health effects of non-ionizing electromagnetic fields on living organisms is of primary importance in biophysics and medicine. Despite the several experimental evidences showing such occurrence in a wide frequency range from extremely low frequency to microwaves, a definitive theoretical model able to explain a possible mechanism of interaction between electromagnetic fields and living matter, especially in the case of weak and very weak intensities, is still missing. In this paper it has been suggested a possible mechanism of interaction involving the resonant absorption of electromagnetic radiation by microtubules. To this aim these have been modeled as non-dissipative forced harmonic oscillators characterized by two coupled "macroscopic" degrees of freedom, respectively describing longitudinal and transversal vibrations induced by the electromagnetic field. We have shown that the proposed model, although at a preliminary stage, is able to explain the ability of even weak electromagnetic radiating electromagnetic fields to transfer high quantities of energy to living systems by means of a resonant mechanism, so capable to easily damage microtubules structure.

Holographic Interferometry and Laminar Jet Diffusion Flames in the Presence of Non-Uniform Magnetic Fields

NASA Technical Reports Server (NTRS)

Baker, J.; Calvert, M. E.; Saito, K.; VanderWal, R.

2001-01-01

Magnetic fields impact combustion processes in a manner analogous to that of buoyancy, i.e., as a body force. It is well known that in a terrestrial environment buoyancy is one of the principal transport mechanisms associated with diffusion flame behavior. Unfortunately, in a terrestrial environment it is difficult if not impossible to isolate flame behavior due magnetic fields from the behavior associated with buoyancy. A micro-, or reduced, gravity environment is ideally suited for studying the impact of magnetic fields on diffusion flames due to the decreased impact of buoyancy on flame behavior.

An oppositely charged insect exclusion screen with gap-free multiple electric fields

NASA Astrophysics Data System (ADS)

Matsuda, Yoshinori; Kakutani, Koji; Nonomura, Teruo; Kimbara, Junji; Kusakari, Shin-ichi; Osamura, Kazumi; Toyoda, Hideyoshi

2012-12-01

An electric field screen was constructed to examine insect attraction mechanisms in multiple electric fields generated inside the screen. The screen consisted of two parallel insulated conductor wires (ICWs) charged with equal but opposite voltages and two separate grounded nets connected to each other and placed on each side of the ICW layer. Insects released inside the fields were charged either positively or negatively as a result of electricity flow from or to the insect, respectively. The force generated between the charged insects and opposite ICW charges was sufficient to capture all insects.

Theoretical analysis of flux amplification by soft magnetic material in a putative biological magnetic-field receptor.

PubMed

Shcherbakov, Valera P; Winklhofer, Michael

2010-03-01

Birds are endowed with a magnetic sense that allows them to detect Earth's magnetic field and to use it for orientation. Physiological and behavioral experiments have shown the upper beak to host a magnetoreceptor. Putative magnetoreceptive structures in the beak are nerve terminals that each contain a dozen or so of micrometer-sized clusters of superparamagnetic nanocrystals made of magnetite/maghemite and numerous electron-opaque platelets filled with a so far unidentified, amorphous ferric iron compound. The platelets typically form chainlike structures, which have been proposed to function as magnetic flux focusers for detecting the intensity of the geomagnetic field. Here, we test that proposition from first principles and develop an unconstrained model to determine the equilibrium distribution of magnetization along a linear chain of platelets which we assume to behave magnetically soft and to have no magnetic remanence. Our analysis, which is valid for arbitrary values of the intrinsic magnetic susceptibility chi , shows that chi needs to be much greater than unity to amplify the external field by two orders of magnitude in a chain of platelets. However, the high amplification is confined to the central region of the chain and subsides quadratically toward the ends of the chain. For large values of chi , the possibility opens up of realizing magnetoreceptor mechanisms on the basis of attraction forces between adjacent platelets in a linear chain. The force in the central region of the chain may amount to several pN, which would be sufficient to convert magnetic input energy into mechanical output energy. The striking feature of an ensemble of platelets is its ability to organize into tightly spaced chains under the action of an external field of given strength. We discuss how this property can be exploited for a magnetoreception mechanism.

Topology Counts: Force Distributions in Circular Spring Networks.

PubMed

Heidemann, Knut M; Sageman-Furnas, Andrew O; Sharma, Abhinav; Rehfeldt, Florian; Schmidt, Christoph F; Wardetzky, Max

2018-02-09

Filamentous polymer networks govern the mechanical properties of many biological materials. Force distributions within these networks are typically highly inhomogeneous, and, although the importance of force distributions for structural properties is well recognized, they are far from being understood quantitatively. Using a combination of probabilistic and graph-theoretical techniques, we derive force distributions in a model system consisting of ensembles of random linear spring networks on a circle. We show that characteristic quantities, such as the mean and variance of the force supported by individual springs, can be derived explicitly in terms of only two parameters: (i) average connectivity and (ii) number of nodes. Our analysis shows that a classical mean-field approach fails to capture these characteristic quantities correctly. In contrast, we demonstrate that network topology is a crucial determinant of force distributions in an elastic spring network. Our results for 1D linear spring networks readily generalize to arbitrary dimensions.

Implementation of robotic force control with position accommodation

NASA Technical Reports Server (NTRS)

Ryan, Michael J.

1992-01-01

As the need for robotic manipulation in fields such as manufacturing and telerobotics increases, so does the need for effective methods of controlling the interaction forces between the manipulators and their environment. Position Accommodation (PA) is a form of robotic force control where the nominal path of the manipulator is modified in response to forces and torques sensed at the tool-tip of the manipulator. The response is tailored such that the manipulator emulates a mechanical impedance to its environment. PA falls under the category of position-based robotic force control, and may be viewed as a form of Impedance Control. The practical implementations are explored of PA into an 18 degree-of-freedom robotic testbed consisting of two PUMA 560 arms mounted on two 3 DOF positioning platforms. Single and dual-arm architectures for PA are presented along with some experimental results. Characteristics of position-based force control are discussed, along with some of the limitations of PA.

Measurement of interaction between water droplets and curved super-hydrophobic substrates in the air

NASA Astrophysics Data System (ADS)

Wang, Zhiyi; Zhao, Meirong; Jiang, Jile; Zhang, Lele; Zhuang, Shuya; Zhao, Yuchen; Huang, Yinguo; Zheng, Yelong

2018-04-01

The interaction force is very important in the study of the contact process of droplets and super-hydrophobic substrates. Accurate interaction force measurement in the air has far-reaching impact on industrial production and biomimetic field. However, limited by the evaporation of small droplets, interaction force can only be measured in the liquid by AFM and other devices. A millimetric cantilever was used to make it possible to measure the interaction between droplets and super-hydrophobic substrates in the air. The optical lever was calibrated with the electrostatic force. The super- hydrophobic substrates were fabricated using nano particles and copper grids. We finally acquired the interaction force and wetting time between the droplet and super- hydrophobic substrates with different grid fractions and similar contact angle. The results showed that the interaction force decreased with the increase of the grid fraction. These would open a new way of understanding the mechanism of hydrophobic.

Design of a magnetorheological automotive shock absorber

NASA Astrophysics Data System (ADS)

Lindler, Jason E.; Dimock, Glen A.; Wereley, Norman M.

2000-06-01

Double adjustable shock absorbers allow for independent adjustment of the yield force and post-yield damping in the force versus velocity response. To emulate the performance of a conventional double adjustable shock absorber, a magnetorheological (MR) automotive shock absorber was designed and fabricated at the University of Maryland. Located in the piston head, an applied magnetic field between the core and flux return increases the force required for a given piston rod velocity. Between the core and flux return, two different shaped gaps meet the controllable performance requirements of a double adjustable shock. A uniform gap between the core and the flux return primarily adjusts the yield force of the shock absorber, while a non-uniform gap allows for control of the post-yield damping. Force measurements from sinusoidal displacement cycles, recorded on a mechanical damper dynamometer, validate the performance of uniform and non- uniform gaps for adjustment of the yield force and post-yield damping, respectively.

Predictions of wing and pylon forces caused by propeller installation

NASA Technical Reports Server (NTRS)

Martinez, Rudolph

1987-01-01

Replacement of current turbojets by high-efficiency unducted propfans could have the unfortunate side effect of increasing cabin noise, essentially because unsteady-aerodynamic mechanisms are likely to be introduced whereby some of the energy saved may be lost again, to the production of propeller noise and to wing/pylon vibrations coupling to the cabin as a sounding board. The present study estimates theoretically associated harmonic aerodynamic forces for two candidate configurations: a pusher propeller which chops through the mean wake of the pylon supporting it, and in the process generates a blade-rate force driving the structure, and a tractor wing-mounted propeller, whose trailing rotating wake induces an unsteady downwash field generating unsteady wing airloads. Reported predictions of such propfan aerodynamic sources of structure-borne sound, or vibration, could be the basis for devising means for their mechanical isolation, and thus for the effective interruption of the structural noise path into the cabin. Both mechanisms are analyzed taking advantage of the high subsonic Mach number and high reduced frequency of the interaction between the impinging flow and the affected aerodynamic element.

A new mechanically braked bicycle ergometer with electronic read out.

PubMed

Bonde-Petersen, F

1983-01-01

The ergometer is mechanically braked by a band in series with a spring. Each end of the band passes over one of two spherical ball bearings, and is attached to the free end of a spring steel bar mounted on the same plate as the two ball bearings. By means of a spindle and cogwheel the plate can be tilted in such a way as to vary the tension in the braking band. The spring steel bar is furnished with four strain-gauges coupled as a Wheatstone's bridge. The system forms a differential force transducer measuring the differences in tension between the two ends of the band. A force is, therefore, only recorded if the flywheel is moving, because at rest forces influencing the bar from the band will be opposite and equal. The ergometer offers certain advantages over the conventional mechanically braked ergometers because it has an electronic read out, and it can be used in field studies. It is independent of the attitude in relation to the vertical, and can thus be used on tilting platforms or in weightless conditions.

Upgrades to the NSTX HHFW antenna

NASA Astrophysics Data System (ADS)

Ellis, R.; Brunkhorst, C.; Hosea, J.

2014-02-01

The High Harmonic Fast Wave (HHFW) antenna for the National Spherical Torus Experiment (NSTX) at PPPL will be upgraded as part of the NSTX upgrade project. Higher magnetic fields and plasma current result in disruption forces on the current straps that can be up to four times the original design values. The current straps on the HHFW antenna are presently fed by coaxial feedthroughs with rigid center conductors. The additional forces on the current straps require a compliant section in the center conductor in order to minimize the forces on the feedthrough. The design of this compliant section has been an integrated effort involving electrostatic calculations in parallel with mechanical and thermal analyses, in order to arrive at a design that is optimized for mechanical, thermal and electrical considerations. The voltage standoff obtained from this design will be verified when a prototype antenna is evaluated on our RF test stand. This paper describes the design of the compliant section of the center conductor, mechanical, thermal and electrostatic calculations, and plans for full implementation of the upgrade on NSTX.

Numerical modelling of electromagnetic loads on fusion device structures

NASA Astrophysics Data System (ADS)

Bettini, Paolo; Furno Palumbo, Maurizio; Specogna, Ruben

2014-03-01

In magnetic confinement fusion devices, during abnormal operations (disruptions) the plasma begins to move rapidly towards the vessel wall in a vertical displacement event (VDE), producing plasma current asymmetries, vessel eddy currents and open field line halo currents, each of which can exert potentially damaging forces upon the vessel and in-vessel components. This paper presents a methodology to estimate electromagnetic loads, on three-dimensional conductive structures surrounding the plasma, which arise from the interaction of halo-currents associated to VDEs with a magnetic field of the order of some Tesla needed for plasma confinement. Lorentz forces, calculated by complementary formulations, are used as constraining loads in a linear static structural analysis carried out on a detailed model of the mechanical structures of a representative machine.

Electrostatics of proteins in dielectric solvent continua. I. Newton's third law marries qE forces

NASA Astrophysics Data System (ADS)

Stork, Martina; Tavan, Paul

2007-04-01

The authors reformulate and revise an electrostatic theory treating proteins surrounded by dielectric solvent continua [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)] to make the resulting reaction field (RF) forces compatible with Newton's third law. Such a compatibility is required for their use in molecular dynamics (MD) simulations, in which the proteins are modeled by all-atom molecular mechanics force fields. According to the original theory the RF forces, which are due to the electric field generated by the solvent polarization and act on the partial charges of a protein, i.e., the so-called qE forces, can be quite accurately computed from Gaussian RF dipoles localized at the protein atoms. Using a slightly different approximation scheme also the RF energies of given protein configurations are obtained. However, because the qE forces do not account for the dielectric boundary pressure exerted by the solvent continuum on the protein, they do not obey the principle that actio equals reactio as required by Newton's third law. Therefore, their use in MD simulations is severely hampered. An analysis of the original theory has led the authors now to a reformulation removing the main difficulties. By considering the RF energy, which represents the dominant electrostatic contribution to the free energy of solvation for a given protein configuration, they show that its negative configurational gradient yields mean RF forces obeying the reactio principle. Because the evaluation of these mean forces is computationally much more demanding than that of the qE forces, they derive a suggestion how the qE forces can be modified to obey Newton's third law. Various properties of the thus established theory, particularly issues of accuracy and of computational efficiency, are discussed. A sample application to a MD simulation of a peptide in solution is described in the following paper [M. Stork and P. Tavan, J. Chem. Phys., 126, 165106 (2007).

Modeling tensional homeostasis in multicellular clusters.

PubMed

Tam, Sze Nok; Smith, Michael L; Stamenović, Dimitrije

2017-03-01

Homeostasis of mechanical stress in cells, or tensional homeostasis, is essential for normal physiological function of tissues and organs and is protective against disease progression, including atherosclerosis and cancer. Recent experimental studies have shown that isolated cells are not capable of maintaining tensional homeostasis, whereas multicellular clusters are, with stability increasing with the size of the clusters. Here, we proposed simple mathematical models to interpret experimental results and to obtain insight into factors that determine homeostasis. Multicellular clusters were modeled as one-dimensional arrays of linearly elastic blocks that were either jointed or disjointed. Fluctuating forces that mimicked experimentally measured cell-substrate tractions were obtained from Monte Carlo simulations. These forces were applied to the cluster models, and the corresponding stress field in the cluster was calculated by solving the equilibrium equation. It was found that temporal fluctuations of the cluster stress field became attenuated with increasing cluster size, indicating that the cluster approached tensional homeostasis. These results were consistent with previously reported experimental data. Furthermore, the models revealed that key determinants of tensional homeostasis in multicellular clusters included the cluster size, the distribution of traction forces, and mechanical coupling between adjacent cells. Based on these findings, we concluded that tensional homeostasis was a multicellular phenomenon. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Is mudflow in Sidoarjo, East Java due to the pumping mechanism of hot air bubbles? : Laboratory simulations and field observations

NASA Astrophysics Data System (ADS)

Nurhandoko, Bagus Endar B.

2015-09-01

Extraordinary mudflow has happened in Sidoarjo, East Java, Indonesia since 2006. This mud comes from the giant crater that is located close to the BJP - 01. Thousands of homes have been submerged due to mudflow. Till today this giant mud crater is still has great strength despite the mud flowing over 8 years. This is a very rare phenomenon in the world. This mud flow mechanism raises big questions, because it has been going on for years, naturally the mudflow will stop by itself because the pressure should be reduced. This research evaluates all aspects of integrated observations, laboratory tests and field observations since the beginning of this ongoing mudflow. Laboratory tests were done by providing hot air bubbles into the fluid inside the inverted funnel showed that the fluid can flow with a high altitude. It is due to the mechanism of buoyant force from air bubbles to the water where the contrast density of the water and the air is quite large. Quantity of air bubbles provides direct effect to the debit of fluid flow. Direct observation in the field, in 2006 and 2007, with TIMNAS and LPPM ITB showed the large number of air bubbles on the surface of the mud craters. Temperature observation on the surface of mud crater is around 98 degree C whereas at greater depth shows the temperature is increasingly rising. This strengthens the hypothesis or proves that the mud pumping mechanism comes from buoyant force of hot air bubbles. Inversion gravity images show that the deep subsurface of main crater is close to volcanic layers or root of Arjuna mountain. Based on the simulation laboratory and field observation data, it can be concluded that the geothermal factor plays a key role in the mudflow mechanism.

A Miniature Magnetic-Force-Based Three-Axis AC Magnetic Sensor with Piezoelectric/Vibrational Energy-Harvesting Functions

PubMed Central

Hung, Chiao-Fang; Yeh, Po-Chen; Chung, Tien-Kan

2017-01-01

In this paper, we demonstrate a miniature magnetic-force-based, three-axis, AC magnetic sensor with piezoelectric/vibrational energy-harvesting functions. For magnetic sensing, the sensor employs a magnetic–mechanical–piezoelectric configuration (which uses magnetic force and torque, a compact, single, mechanical mechanism, and the piezoelectric effect) to convert x-axis and y-axis in-plane and z-axis magnetic fields into piezoelectric voltage outputs. Under the x-axis magnetic field (sine-wave, 100 Hz, 0.2–3.2 gauss) and the z-axis magnetic field (sine-wave, 142 Hz, 0.2–3.2 gauss), the voltage output with the sensitivity of the sensor are 1.13–26.15 mV with 8.79 mV/gauss and 1.31–8.92 mV with 2.63 mV/gauss, respectively. In addition, through this configuration, the sensor can harness ambient vibrational energy, i.e., possessing piezoelectric/vibrational energy-harvesting functions. Under x-axis vibration (sine-wave, 100 Hz, 3.5 g) and z-axis vibration (sine-wave, 142 Hz, 3.8 g), the root-mean-square voltage output with power output of the sensor is 439 mV with 0.333 μW and 138 mV with 0.051 μW, respectively. These results show that the sensor, using this configuration, successfully achieves three-axis magnetic field sensing and three-axis vibration energy-harvesting. Due to these features, the three-axis AC magnetic sensor could be an important design reference in order to develop future three-axis AC magnetic sensors, which possess energy-harvesting functions, for practical industrial applications, such as intelligent vehicle/traffic monitoring, processes monitoring, security systems, and so on. PMID:28208693

Predicting the melting temperature of ice-Ih with only electronic structure information as input.

PubMed

Pinnick, Eric R; Erramilli, Shyamsunder; Wang, Feng

2012-07-07

The melting temperature of ice-Ih was calculated with only electronic structure information as input by creating a problem-specific force field. The force field, Water model by AFM for Ice and Liquid (WAIL), was developed with the adaptive force matching (AFM) method by fitting to post-Hartree-Fock quality forces obtained in quantum mechanics∕molecular mechanics calculations. WAIL predicts the ice-Ih melting temperature to be 270 K. The model also predicts the densities of ice and water, the temperature of maximum density of water, the heat of vaporizations, and the radial distribution functions for both ice and water in good agreement with experimental measurements. The non-dissociative WAIL model is very similar to a flexible version of the popular TIP4P potential and has comparable computational cost. By customizing to problem-specific configurations with the AFM approach, the resulting model is remarkably more accurate than any variants of TIP4P for simulating ice-Ih and water in the temperature range from 253 K and 293 K under ambient pressure.

Characterization of a small Terfenol-D transducer in mechanically blocked configuration

NASA Astrophysics Data System (ADS)

Faidley, LeAnn E.; Dapino, Marcelo J.; Flatau, Alison B.

2001-08-01

In numerous applications, smart material transducers are employed to actuate upon virtually immovable structures, that is, structures whose stiffness approaches infinity in comparison with that of the transducer itself. Such mechanically blocked transducer configurations can be found in applications ranging from seismic testing and isolation of civil structures, to clamping mechanisms in linear or rotational inchworm motors. In addition to providing high blocking forces, smart materials for this type of applications must often be small in size and lightweight in order for design constraints to be met. This paper provides a characterization of the force produced by a 0.9 cm (0.35 in) diameter, 2.0 cm (0.79i in) long Terfenol-D operated under mechanically blocked conditions. Experimental results are shown for several mechanical preloads as well as various magnetic field intensities, waveforms, and frequencies. Optimal levels are deduced and discussed and the results are compared to published data for a PZT transducer of similar size operated in mechanically blocked configuration. The comparison reveals that the Terfenol-D rod provides higher blocking forces than its PZT counterpart. It is thus feasible to employ small magnetostrictive drivers in applications involving zero or near-zero displacement, particularly those based on hybrid magnetostrictive/piezoelectric designs in which high efficiencies are achieved by driving the two electrically complementary transducer materials at electrical resonance.

A Finite-Element Method Model of Soft Tissue Response to Impulsive Acoustic Radiation Force

PubMed Central

Palmeri, Mark L.; Sharma, Amy C.; Bouchard, Richard R.; Nightingale, Roger W.; Nightingale, Kathryn R

2010-01-01

Several groups are studying acoustic radiation force and its ability to image the mechanical properties of tissue. Acoustic radiation force impulse (ARFI) imaging is one modality using standard diagnostic ultrasound scanners to generate localized, impulsive, acoustic radiation forces in tissue. The dynamic response of tissue is measured via conventional ultrasonic speckle-tracking methods and provides information about the mechanical properties of tissue. A finite-element method (FEM) model has been developed that simulates the dynamic response of tissues, with and without spherical inclusions, to an impulsive acoustic radiation force excitation from a linear array transducer. These FEM models were validated with calibrated phantoms. Shear wave speed, and therefore elasticity, dictates tissue relaxation following ARFI excitation, but Poisson’s ratio and density do not significantly alter tissue relaxation rates. Increased acoustic attenuation in tissue increases the relative amount of tissue displacement in the near field compared with the focal depth, but relaxation rates are not altered. Applications of this model include improving image quality, and distilling material and structural information from tissue’s dynamic response to ARFI excitation. Future work on these models includes incorporation of viscous material properties and modeling the ultrasonic tracking of displaced scatterers. PMID:16382621

Measurement of rolling friction by a damped oscillator

NASA Technical Reports Server (NTRS)

Dayan, M.; Buckley, D. H.

1983-01-01

An experimental method for measuring rolling friction is proposed. The method is mechanically simple. It is based on an oscillator in a uniform magnetic field and does not involve any mechanical forces except for the measured friction. The measured pickup voltage is Fourier analyzed and yields the friction spectral response. The proposed experiment is not tailored for a particular case. Instead, various modes of operation, suitable to different experimental conditions, are discussed.

Anti-Mechanized Defense: A Computerized Simulation for Squad Leader Training.

DTIC Science & Technology

1983-09-01

applicability of cybernetic principles is easily transformed to meet the needs of this research. Specifi- cally, the basic principle governing management...and as in other areas this is better meas- ured in actual field conditions. COMMAND AND CONTROL (S2A.2) Control of Organic Fi repower In general...AD-AI34 962 UNCLASSIFIED ANTI-MECHANIZED DEFENSE: A COMPUTERIZED SQUAD LEADER TRAINING(U) AIR FORCE INST WRIGHT-PATTERSON AFB OH SCHOOL OF SYST

Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems.

PubMed

Velez-Vega, Camilo; Gilson, Michael K

2012-03-13

The field of host-guest chemistry provides computationally tractable yet informative model systems for biomolecular recognition. We applied molecular dynamics simulations to study the forces and mechanical stresses associated with forced dissociation of aqueous cucurbituril-guest complexes with high binding affinities. First, the unbinding transitions were modeled with constant velocity pulling (steered dynamics) and a soft spring constant, to model atomic force microscopy (AFM) experiments. The computed length-force profiles yield rupture forces in good agreement with available measurements. We also used steered dynamics with high spring constants to generate paths characterized by a tight control over the specified pulling distance; these paths were then equilibrated via umbrella sampling simulations and used to compute time-averaged mechanical stresses along the dissociation pathways. The stress calculations proved to be informative regarding the key interactions determining the length-force profiles and rupture forces. In particular, the unbinding transition of one complex is found to be a stepwise process, which is initially dominated by electrostatic interactions between the guest's ammoniums and the host's carbonyl groups, and subsequently limited by the extraction of the guest's bulky bicyclooctane moiety; the latter step requires some bond stretching at the cucurbituril's extraction portal. Conversely, the dissociation of a second complex with a more slender guest is mainly driven by successive electrostatic interactions between the different guest's ammoniums and the host's carbonyl groups. The calculations also provide information on the origins of thermodynamic irreversibilities in these forced dissociation processes.

Direct numerical simulation of the effect of an electric field on flame stability

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

Belhi, Memdouh; Domingo, Pascale; Vervisch, Pierre

2010-12-15

The role of electric fields in stabilising combustion is a well-known phenomenon. Among the possible mechanisms favouring the anchorage of the flame base, the ion-driven wind acting directly on flow momentum ahead of the flame base could be the leading one. Direct numerical simulation has been used to verify this hypothesis and lead to a better understanding of diffusion flame base anchoring in the presence of an externally applied voltage. In this context, a simplified modelling approach is proposed to describe combustion in the presence of electric body forces. The model reproduces the tendencies of experimental observations found in themore » literature. The sensitivity of the flame lift-off height to the applied voltage is studied and the modification of the velocity field ahead of the flame base induced by the electric volume forces is highlighted. (author)« less

Pair interactions of heavy vortices in quantum fluids

NASA Astrophysics Data System (ADS)

Pshenichnyuk, Ivan A.

2018-02-01

The dynamics of quantum vortex pairs carrying heavy doping matter trapped inside their cores is studied. The nonlinear classical matter field formalism is used to build a universal mathematical model of a heavy vortex applicable to different types of quantum mixtures. It is shown how the usual vortex dynamics typical for undoped pairs qualitatively changes when heavy dopants are used: heavy vortices with opposite topological charges (chiralities) attract each other, while vortices with the same charge are repelled. The force responsible for such behavior appears as a result of superposition of vortices velocity fields in the presence of doping substance and can be considered as a special realization of the Magnus effect. The force is evaluated quantitatively and its inverse proportionality to the distance is demonstrated. The mechanism described in this paper gives an example of how a light nonlinear classical field may realize repulsive and attractive interactions between embedded heavy impurities.

Close encounters with DNA

PubMed Central

Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A.

2014-01-01

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena and we review the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field. PMID:25238560

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

S. Chouhan, J. DeKamp, A. Zeller, P. Brindza, S. Lassiter, M. Fowler, E. Sun

A collaboration between NSCL and Jlab has developed the reference design and coil winding for Jlab's Super High Momentum Spectrometer (SHMS) horizontal bend magnet. A warm iron ??C?? type superferric dipole magnet will bend the 12 GeV/c particles horizontally by 3?? to allow the SHMS to reach angles as low as 5.5??. This requires an integral field strength of up to 2.1 T.m. The major challenges are the tight geometry, high and unbalanced forces and a required low fringe field in primary beam path. A coil design based on flattened SSC Rutherford cable that provides a large current margin andmore » commercially available fiberglass prepreg epoxy tape has been developed. A complete test coil has been wound and will be cold tested. This paper present the modified magnet design includes coil forces, coil restraint system and fringe field. In addition, coil properties, quench calculations and the full mechanical details are also presented.« less

Close encounters with DNA.

PubMed

Maffeo, C; Yoo, J; Comer, J; Wells, D B; Luan, B; Aksimentiev, A

2014-10-15

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

Action-at-a-distance metamaterials: Distributed local actuation through far-field global forces

NASA Astrophysics Data System (ADS)

Hedayati, R.; Mirzaali, M. J.; Vergani, L.; Zadpoor, A. A.

2018-03-01

Mechanical metamaterials are a sub-category of designer materials where the geometry of the material at the small-scale is rationally designed to give rise to unusual properties and functionalities. Here, we propose the concept of "action-at-a-distance" metamaterials where a specific pattern of local deformation is programmed into the fabric of (cellular) materials. The desired pattern of local actuation could then be achieved simply through the application of one single global and far-field force. We proposed graded designs of auxetic and conventional unit cells with changing Poisson's ratios as a way of making "action-at-a-distance" metamaterials. We explored five types of graded designs including linear, two types of radial gradients, checkered, and striped. Specimens were fabricated with indirect additive manufacturing and tested under compression, tension, and shear. Full-field strain maps measured with digital image correlation confirmed different patterns of local actuation under similar far-field strains. These materials have potential applications in soft (wearable) robotics and exosuits.

Mechanical properties investigation on single-wall ZrO2 nanotubes: A finite element method with equivalent Poisson's ratio for chemical bonds

NASA Astrophysics Data System (ADS)

Yang, Xiao; Li, Huijian; Hu, Minzheng; Liu, Zeliang; Wärnå, John; Cao, Yuying; Ahuja, Rajeev; Luo, Wei

2018-04-01

A method to obtain the equivalent Poisson's ratio in chemical bonds as classical beams with finite element method was proposed from experimental data. The UFF (Universal Force Field) method was employed to calculate the elastic force constants of Zrsbnd O bonds. By applying the equivalent Poisson's ratio, the mechanical properties of single-wall ZrNTs (ZrO2 nanotubes) were investigated by finite element analysis. The nanotubes' Young's modulus (Y), Poisson's ratio (ν) of ZrNTs as function of diameters, length and chirality have been discussed, respectively. We found that the Young's modulus of single-wall ZrNTs is calculated to be between 350 and 420 GPa.

On a full Bayesian inference for force reconstruction problems

NASA Astrophysics Data System (ADS)

Aucejo, M.; De Smet, O.

2018-05-01

In a previous paper, the authors introduced a flexible methodology for reconstructing mechanical sources in the frequency domain from prior local information on both their nature and location over a linear and time invariant structure. The proposed approach was derived from Bayesian statistics, because of its ability in mathematically accounting for experimenter's prior knowledge. However, since only the Maximum a Posteriori estimate was computed, the posterior uncertainty about the regularized solution given the measured vibration field, the mechanical model and the regularization parameter was not assessed. To answer this legitimate question, this paper fully exploits the Bayesian framework to provide, from a Markov Chain Monte Carlo algorithm, credible intervals and other statistical measures (mean, median, mode) for all the parameters of the force reconstruction problem.

Mechanism of the quasi-zero axial acoustic radiation force experienced by elastic and viscoelastic spheres in the field of a quasi-Gaussian beam and particle tweezing.

PubMed

Mitri, F G; Fellah, Z E A

2014-01-01

The present analysis investigates the (axial) acoustic radiation force induced by a quasi-Gaussian beam centered on an elastic and a viscoelastic (polymer-type) sphere in a nonviscous fluid. The quasi-Gaussian beam is an exact solution of the source free Helmholtz wave equation and is characterized by an arbitrary waist w₀ and a diffraction convergence length known as the Rayleigh range z(R). Examples are found where the radiation force unexpectedly approaches closely to zero at some of the elastic sphere's resonance frequencies for kw₀≤1 (where this range is of particular interest in describing strongly focused or divergent beams), which may produce particle immobilization along the axial direction. Moreover, the (quasi)vanishing behavior of the radiation force is found to be correlated with conditions giving extinction of the backscattering by the quasi-Gaussian beam. Furthermore, the mechanism for the quasi-zero force is studied theoretically by analyzing the contributions of the kinetic, potential and momentum flux energy densities and their density functions. It is found that all the components vanish simultaneously at the selected ka values for the nulls. However, for a viscoelastic sphere, acoustic absorption degrades the quasi-zero radiation force. Copyright © 2013 Elsevier B.V. All rights reserved.

Kinematics and dynamics of Nubia-Somalia divergence along the East African rift

NASA Astrophysics Data System (ADS)

Stamps, Dorothy Sarah

Continental rifting is fundamental to the theory of plate tectonics, yet the force balance driving Earth's largest continental rift system, the East African Rift (EAR), remains debated. The EAR actively diverges the Nubian and Somalian plates spanning ˜5000 km N-S from the Red Sea to the Southwest Indian Ridge and ˜3000 km NW-SE from eastern Congo to eastern Madagascar. Previous studies suggest either lithospheric buoyancy forces or horizontal tractions dominate the force balance acting to rupture East Africa. In this work, we investigate the large-scale dynamics of Nubia-Somalia divergence along the EAR driving present-day kinematics. Because Africa is largely surrounded by spreading ridges, we assume plate-plate interactions are minimal and that the major driving forces are gradients in gravitational potential energy (GPE), which includes the effect of vertical mantle tractions, and horizontal basal tractions arising from viscous coupling to horizontal mantle flow. We quantify a continuous strain rate and velocity field based on kinematic models, an updated GPS velocity solution, and the style of earthquake focal mechanisms, which we use as an observational constraint on surface deformation. We solve the 3D force balance equations and calculate vertically averaged deviatoric stress for a 100 km thick lithosphere constrained by the CRUST2.0 crustal density and thickness model. By comparing vertically integrated deviatoric stress with integrated lithospheric strength we demonstrate forces arising from gradients in gravitational potential energy are insufficient to rupture strong lithosphere, hence weakening mechanisms are required to initiate continental rupture. The next step involves inverting for a stress field boundary condition that is the long-wavelength minimum energy deviatoric stress field required to best-fit the style of our continuous strain rate field in addition to deviatoric stress from gradients in GPE. We infer the stress field boundary condition is an estimate of basal shear stress from viscous coupling to horizontal mantle flow. The stress field boundary condition is small (˜1.6 MPa) compared to deviatoric stress from GPE gradients (8-20 MPa) and does not improve the fit to surface deformation indicators more than 8% when combined with deviatoric stress from GPE gradients. Hence we suggest the style of deformation across the EAR can be explained by forces derived from gradients in GPE. We then calculate dynamic velocities using two types of forward models to solve the instantaneous momentum equations. One method is regional and requires vertically averaged effective viscosity to define lithospheric structure with velocity boundary conditions and a free-slip basal boundary condition. The second is a global model that accounts for a brittle upper crust and viscous mantle lithosphere with velocity boundary conditions imposed at the base of the lithosphere from 5 mantle flow models. With both methods we find deformation driven by internal lithospheric buoyancy forces provides the best-fit to GPS observations of surface velocities on the Somalian plate. We find that any additional contribution from horizontal tractions results in overpredicting surface velocities. This work indicates horizontal mantle flow plays a minimal role in Nubia-Somalia divergence and the EAR is driven largely by gradients in GPE.

Microdevice arrays of high aspect ratio poly(dimethylsiloxane) pillars for the investigation of multicellular tumour spheroid mechanical properties.

PubMed

Aoun, Laurène; Weiss, Pierre; Laborde, Adrian; Ducommun, Bernard; Lobjois, Valérie; Vieu, Christophe

2014-07-07

We report the design, fabrication and evaluation of an array of microdevices composed of high aspect ratio PDMS pillars, dedicated to the study of tumour spheroid mechanical properties. The principle of the microdevice is to confine a spheroid within a circle of micropillars acting as peripheral flexible force sensors. We present a technological process for fabricating high aspect ratio micropillars (300 μm high) with tunable feature dimensions (diameter and spacing) enabling production of flexible PDMS pillars with a height comparable to spheroid sizes. This represents an upscale of 10 along the vertical direction in comparison to more conventional PDMS pillar force sensors devoted to single cell studies, while maintaining their force sensitivity in the same order of magnitude. We present a method for keeping these very high aspect ratio PDMS pillars stable and straight in liquid solution. We demonstrate that microfabricated devices are biocompatible and adapted to long-term spheroid growth. Finally, we show that the spheroid interaction with the micropillars' surface is dependent on PDMS cellular adhesiveness. Time-lapse recordings of growth-induced micropillars' bending coupled with a software program to automatically detect and analyse micropillar displacements are presented. The use of these microdevices as force microsensors opens new prospects in the fields of tissue mechanics and pharmacological drug screening.

Levitation forces of a bulk YBCO superconductor in gradient varying magnetic fields

NASA Astrophysics Data System (ADS)

Jiang, J.; Gong, Y. M.; Wang, G.; Zhou, D. J.; Zhao, L. F.; Zhang, Y.; Zhao, Y.

2015-09-01

The levitation forces of a bulk YBCO superconductor in gradient varying high and low magnetic fields generated from a superconducting magnet were investigated. The magnetic field intensity of the superconducting magnet was measured when the exciting current was 90 A. The magnetic field gradient and magnetic force field were both calculated. The YBCO bulk was cooled by liquid nitrogen in field-cooling (FC) and zero-field-cooling (ZFC) condition. The results showed that the levitation forces increased with increasing the magnetic field intensity. Moreover, the levitation forces were more dependent on magnetic field gradient and magnetic force field than magnetic field intensity.

Effects of high-gradient magnetic fields on living cell machinery

NASA Astrophysics Data System (ADS)

Zablotskii, V.; Lunov, O.; Kubinova, S.; Polyakova, T.; Sykova, E.; Dejneka, A.

2016-12-01

A general interest in biomagnetic effects is related to fundamental studies of the influence of magnetic fields on living objects on the cellular and whole organism levels. Emerging technologies offer new directions for the use of high-gradient magnetic fields to control cell machinery and to understand the intracellular biological processes of the emerging field of nanomedicine. In this review we aim at highlighting recent advances made in identifying fundamental mechanisms by which magnetic gradient forces act on cell fate specification and cell differentiation. The review also provides an analysis of the currently available magnetic systems capable of generating magnetic fields with spatial gradients of up to 10 MT m-1, with the focus on their suitability for use in cell therapy. Relationships between experimental factors and underlying biophysical mechanisms and assumptions that would ultimately lead to a deeper understanding of cell machinery and the development of more predictive models for the evaluation of the effects of magnetic fields on cells, tissue and organisms are comprehensively discussed.

Novel compliant actuator for wearable robotics applications.

PubMed

Claros, M; Soto, R; Rodríguez, J J; Cantú, C; Contreras-Vidal, José L

2013-01-01

In the growing fields of wearable robotics, rehabilitation robotics, prosthetics, and walking robots, variable impedance and force actuators are being designed and implemented because of their ability to dynamically modulate the intrinsic viscoelastic properties such as stiffness and damping. This modulation is crucial to achieve an efficient and safe human-robot interaction that could lead to electronically generate useful emergent dynamical behaviors. In this work we propose a novel actuation system in which is implemented a control scheme based on equilibrium forces for an active joint capable to provide assistance/resistance as needed and also achieve minimal mechanical impedance when tracking the movement of the user limbs. The actuation system comprises a DC motor with a built in speed reducer, two force-sensing resistors (FSR), a mechanism which transmits to the FSRs the torque developed in the joint and a controller which regulate the amount of energy that is delivered to the DC motor. The proposed system showed more impedance reduction, by the effect of the controlled contact forces, compared with the ones in the reviewed literature.

Computational mechanics of viral capsids.

PubMed

Gibbons, Melissa M; Perotti, Luigi E; Klug, William S

2015-01-01

Viral capsids undergo significant mechanical deformations during their assembly, maturation, and infective life-span. In order to characterize the mechanics of viral capsids, their response to applied external forces is analyzed in several experimental studies using, for instance, Atomic Force Microscope (AFM) indentation experiments. In recent years, a broader approach to study the mechanics of viral capsids has leveraged the theoretical tools proper of continuum mechanics. Even though the theory of continuum elasticity is most commonly used to study deformable bodies at larger macroscopic length scales, it has been shown that this very rich theoretical field can still offer useful insights into the mechanics of viral structures at the nanometer scale. Here we show the construction of viral capsid continuum mechanics models starting from different forms of experimental data. We will discuss the kinematics assumptions, the issue of the reference configuration, the material constitutive laws, and the numerical discretization necessary to construct a complete Finite Element capsid mechanical model. Some examples in the second part of the chapter will show the predictive capabilities of the constructed models and underline useful practical aspects related to efficiency and accuracy. We conclude each example by collecting several key findings discovered by simulating AFM indentation experiments using the constructed numerical models.

MHD Simulation for Investigating the Dynamic State Transition Responsible for a Solar Eruption in Active Region 12158

NASA Astrophysics Data System (ADS)

Lee, Hwanhee; Magara, Tetsuya

2018-06-01

We present a magnetohydrodynamic model of solar eruption based on the dynamic state transition from the quasi-static state to the eruptive state of an active region (AR) magnetic field. For the quasi-static state before an eruption, we consider the existence of a slow solar wind originating from an AR, which may continuously make the AR magnetic field deviate from mechanical equilibrium. In this model, we perform a three-dimensional magnetohydrodynamic simulation of AR 12158 producing a coronal mass ejection, where the initial magnetic structure of the simulation is given by a nonlinear force-free field derived from an observed photospheric vector magnetic field. We then apply a pressure-driven outflow to the upper part of the magnetic structure to achieve a quasi-static pre-eruptive state. The simulation shows that the eruptive process observed in this AR may be caused by the dynamic state transition of an AR magnetic field, which is essentially different from the destabilization of a static magnetic field. The dynamic state transition is determined from the shape evolution of the magnetic field line according to the κH-mechanism. This work demonstrates how the mechanism works to produce a solar eruption in the dynamic solar corona governed by the gravitational field and the continuous outflows of solar wind.

Computational Materials Research

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A. (Editor); Gates, Thomas S. (Editor)

1996-01-01

Computational Materials aims to model and predict thermodynamic, mechanical, and transport properties of polymer matrix composites. This workshop, the second coordinated by NASA Langley, reports progress in measurements and modeling at a number of length scales: atomic, molecular, nano, and continuum. Assembled here are presentations on quantum calculations for force field development, molecular mechanics of interfaces, molecular weight effects on mechanical properties, molecular dynamics applied to poling of polymers for electrets, Monte Carlo simulation of aromatic thermoplastics, thermal pressure coefficients of liquids, ultrasonic elastic constants, group additivity predictions, bulk constitutive models, and viscoplasticity characterization.

A deployable .015 inch diameter wire antenna

NASA Technical Reports Server (NTRS)

Dibiasi, L.

1979-01-01

This mechanism was developed to dispense a small diameter wire which serves as a receiving antenna for electric field measurements on an Earth orbiting satellite. The antenna is deployed radially from a spinning satellite. A brushless dc motor drives a storage spool to dispense the wire at a controlled rate. Centrifugal force, acting on a mass attached to the end of the wire, keeps the wire in the radial position. The mechanism design, testing, and performance characteristics are discussed. Finally, operational data of the mechanism while in orbit are presented.

Upconverting Nanoparticles as Optical Sensors of Nano- to Micro-Newton Forces.

PubMed

Lay, Alice; Wang, Derek S; Wisser, Michael D; Mehlenbacher, Randy D; Lin, Yu; Goodman, Miriam B; Mao, Wendy L; Dionne, Jennifer A

2017-07-12

Mechanical forces affect a myriad of processes, from bone growth to material fracture to touch-responsive robotics. While nano- to micro-Newton forces are prevalent at the microscopic scale, few methods have the nanoscopic size and signal stability to measure them in vivo or in situ. Here, we develop an optical force-sensing platform based on sub-25 nm NaYF 4 nanoparticles (NPs) doped with Yb 3+ , Er 3+ , and Mn 2+ . The lanthanides Yb 3+ and Er 3+ enable both photoluminescence and upconversion, while the energetically coupled d-metal Mn 2+ adds force tunability through its crystal field sensitivity. Using a diamond anvil cell to exert up to 3.5 GPa pressure or ∼10 μN force per particle, we track stress-induced spectral responses. The red (660 nm) to green (520, 540 nm) emission ratio varies linearly with pressure, yielding an observed color change from orange to red for α-NaYF 4 and from yellow-green to green for d-metal optimized β-NaYF 4 when illuminated in the near infrared. Consistent readouts are recorded over multiple pressure cycles and hours of illumination. With the nanoscopic size, a dynamic range of 100 nN to 10 μN, and photostability, these nanoparticles lay the foundation for visualizing dynamic mechanical processes, such as stress propagation in materials and force signaling in organisms.

Upconverting Nanoparticles as Optical Sensors of Nano- to Micro-Newton Forces

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

Lay, Alice; Wang, Derek S.; Wisser, Michael D.

Mechanical forces affect a myriad of processes, from bone growth to material fracture to touch-responsive robotics. While nano- to micro-Newton forces are prevalent at the microscopic scale, few methods have the nanoscopic size and signal stability to measure them in vivo or in situ. Here, we develop an optical force-sensing platform based on sub-25 nm NaYF4 nanoparticles (NPs) doped with Yb3+, Er3+, and Mn2+. The lanthanides Yb3+ and Er3+ enable both photoluminescence and upconversion, while the energetically coupled d-metal Mn2+ adds force tunability through its crystal field sensitivity. Using a diamond anvil cell to exert up to 3.5 GPa pressuremore » or ~10 μN force per particle, we track stress-induced spectral responses. The red (660 nm) to green (520, 540 nm) emission ratio varies linearly with pressure, yielding an observed color change from orange to red for α-NaYF4 and from yellow–green to green for d-metal optimized β-NaYF4 when illuminated in the near infrared. Consistent readouts are recorded over multiple pressure cycles and hours of illumination. With the nanoscopic size, a dynamic range of 100 nN to 10 μN, and photostability, these nanoparticles lay the foundation for visualizing dynamic mechanical processes, such as stress propagation in materials and force signaling in organisms.« less

Upconverting Nanoparticles as Optical Sensors of Nano- to Micro-Newton Forces

DOE PAGES

Lay, Alice; Wang, Derek S.; Wisser, Michael D.; ...

2017-06-13

Mechanical forces affect a myriad of processes, from bone growth to material fracture to touch-responsive robotics. While nano- to micro-Newton forces are prevalent at the microscopic scale, few methods have the nanoscopic size and signal stability to measure them in vivo or in situ. Here, we develop an optical force-sensing platform based on sub-25 nm NaYF 4 nanoparticles (NPs) doped with Yb 3+, Er 3+, and Mn 2+. The lanthanides Yb 3+ and Er 3+ enable both photoluminescence and upconversion, while the energetically coupled d-metal Mn 2+ adds force tunability through its crystal field sensitivity. IN using a diamond anvilmore » cell to exert up to 3.5 GPa pressure or ~10 μN force per particle, we track stress-induced spectral responses. The red (660 nm) to green (520, 540 nm) emission ratio varies linearly with pressure, yielding an observed color change from orange to red for α-NaYF 4 and from yellow–green to green for d-metal optimized β-NaYF 4 when illuminated in the near infrared. We record consistent readouts over multiple pressure cycles and hours of illumination. With the nanoscopic size, a dynamic range of 100 nN to 10 μN, and photostability, these nanoparticles lay the foundation for visualizing dynamic mechanical processes, such as stress propagation in materials and force signaling in organisms.« less

Upconverting Nanoparticles as Optical Sensors of Nano- to Micro-Newton Forces

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

Lay, Alice; Wang, Derek S.; Wisser, Michael D.

Mechanical forces affect a myriad of processes, from bone growth to material fracture to touch-responsive robotics. While nano- to micro-Newton forces are prevalent at the microscopic scale, few methods have the nanoscopic size and signal stability to measure them in vivo or in situ. Here, we develop an optical force-sensing platform based on sub-25 nm NaYF 4 nanoparticles (NPs) doped with Yb 3+, Er 3+, and Mn 2+. The lanthanides Yb 3+ and Er 3+ enable both photoluminescence and upconversion, while the energetically coupled d-metal Mn 2+ adds force tunability through its crystal field sensitivity. IN using a diamond anvilmore » cell to exert up to 3.5 GPa pressure or ~10 μN force per particle, we track stress-induced spectral responses. The red (660 nm) to green (520, 540 nm) emission ratio varies linearly with pressure, yielding an observed color change from orange to red for α-NaYF 4 and from yellow–green to green for d-metal optimized β-NaYF 4 when illuminated in the near infrared. We record consistent readouts over multiple pressure cycles and hours of illumination. With the nanoscopic size, a dynamic range of 100 nN to 10 μN, and photostability, these nanoparticles lay the foundation for visualizing dynamic mechanical processes, such as stress propagation in materials and force signaling in organisms.« less

Nanomechanical force transducers for biomolecular and intracellular measurements: is there room to shrink and why do it?

PubMed

Sirbuly, Donald J; Friddle, Raymond W; Villanueva, Joshua; Huang, Qian

2015-02-01

Over the past couple of decades there has been a tremendous amount of progress on the development of ultrasensitive nanomechanical instruments, which has enabled scientists to peer for the first time into the mechanical world of biomolecular systems. Currently, work-horse instruments such as the atomic force microscope and optical/magnetic tweezers have provided the resolution necessary to extract quantitative force data from various molecular systems down to the femtonewton range, but it remains difficult to access the intracellular environment with these analytical tools as they have fairly large sizes and complicated feedback systems. This review is focused on highlighting some of the major milestones and discoveries in the field of biomolecular mechanics that have been made possible by the development of advanced atomic force microscope and tweezer techniques as well as on introducing emerging state-of-the-art nanomechanical force transducers that are addressing the size limitations presented by these standard tools. We will first briefly cover the basic setup and operation of these instruments, and then focus heavily on summarizing advances in in vitro force studies at both the molecular and cellular level. The last part of this review will include strategies for shrinking down the size of force transducers and provide insight into why this may be important for gaining a more complete understanding of cellular activity and function.

Knudsen torque: A rotational mechanism driven by thermal force

NASA Astrophysics Data System (ADS)

Li, Qi; Liang, Tengfei; Ye, Wenjing

2014-09-01

Thermally induced mechanical loading has been shown to have significant effects on micro- and nano-objects immersed in a gas with a nonuniform temperature field. While the majority of existing studies and related applications focus on forces, we investigate the torque, and thus the rotational motion, produced by such a mechanism. Our study has found that a torque can be induced if the configuration of the system is asymmetric. In addition, both the magnitude and the direction of the torque depend highly on the system configuration, indicating the possibility of manipulating the rotational motion via geometrical design. Based on this feature, two types of rotational micromotor that are of practical importance, namely pendulum motor and unidirectional motor, are designed. The magnitude of the torque at Kn =0.5 can reach to around 2nN×μm for a rectangular microbeam with a length of 100μm.

Bidimensional nano-optomechanics and topological backaction in a non-conservative radiation force field.

PubMed

Gloppe, A; Verlot, P; Dupont-Ferrier, E; Siria, A; Poncharal, P; Bachelier, G; Vincent, P; Arcizet, O

2014-11-01

Optomechanics, which explores the fundamental coupling between light and mechanical motion, has made important advances in manipulating macroscopic mechanical oscillators down to the quantum level. However, dynamical effects related to the vectorial nature of the optomechanical interaction remain to be investigated. Here we study a nanowire with subwavelength dimensions coupled strongly to a tightly focused beam of light, enabling an ultrasensitive readout of the nanoresonator dynamics. We determine experimentally the vectorial structure of the optomechanical interaction and demonstrate that a bidimensional dynamical backaction governs the nanowire dynamics. Moreover, the spatial topology of the optomechanical interaction is responsible for novel canonical signatures of strong coupling between mechanical modes, which leads to a topological instability that underlies the non-conservative nature of the optomechanical interaction. These results have a universal character and illustrate the increased sensitivity of nanomechanical devices towards spatially varying interactions, opening fundamental perspectives in nanomechanics, optomechanics, ultrasensitive scanning force microscopy and nano-optics.

Determination of Coronal Magnetic Fields from Vector Magnetograms

NASA Technical Reports Server (NTRS)

Mikic, Zoran

1997-01-01

During the course of the present contract we developed an 'evolutionary technique' for the determination of force-free coronal magnetic fields from vector magnetograph observations. The method can successfully generate nonlinear force- free fields (with non-constant-a) that match vector magnetograms. We demonstrated that it is possible to determine coronal magnetic fields from photospheric measurements, and we applied it to vector magnetograms of active regions. We have also studied theoretical models of coronal fields that lead to disruptions. Specifically, we have demonstrated that the determination of force-free fields from exact boundary data is a well-posed mathematical problem, by verifying that the computed coronal field agrees with an analytic force-free field when boundary data for the analytic field are used; demonstrated that it is possible to determine active-region coronal magnetic fields from photospheric measurements, by computing the coronal field above active region 5747 on 20 October 1989, AR6919 on 15 November 1991, and AR7260 on 18 August 1992, from data taken with the Stokes Polarimeter at Mees Solar Observatory, University of Hawaii; started to analyze active region 7201 on 19 June 1992 using measurements made with the Advanced Stokes Polarimeter at NSO/Sac Peak; investigated the effects of imperfections in the photospheric data on the computed coronal magnetic field; documented the coronal field structure of AR5747 and compared it to the morphology of footpoint emission in a flare, showing that the 'high- pressure' H-alpha footpoints are connected by coronal field lines; shown that the variation of magnetic field strength along current-carrying field lines is significantly different from the variation in a potential field, and that the resulting near-constant area of elementary flux tubes is consistent with observations; begun to develop realistic models of coronal fields which can be used to study flare trigger mechanisms; demonstrated that magnetic nonequilibrium can disrupt sheared coronal arcades, and that helmet streamers can disrupt, leading to coronal mass ejections. Our model has significantly extended the realism with which the coronal magnetic field can be inferred from actual observations. In a subsequent contract awarded by NASA, we have continued to apply and improve the evolutionary technique, to study the physical properties of active regions, and to develop theoretical models of magnetic fields.

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

Large pinning forces and matching effects in YBa2Cu3O7-δ thin films with Ba2Y(Nb/Ta)O6 nano-precipitates

PubMed Central

Opherden, Lars; Sieger, Max; Pahlke, Patrick; Hühne, Ruben; Schultz, Ludwig; Meledin, Alexander; Van Tendeloo, Gustaaf; Nast, Rainer; Holzapfel, Bernhard; Bianchetti, Marco; MacManus-Driscoll, Judith L.; Hänisch, Jens

2016-01-01

The addition of mixed double perovskite Ba2Y(Nb/Ta)O6 (BYNTO) to YBa2Cu3O7−δ (YBCO) thin films leads to a large improvement of the in-field current carrying capability. For low deposition rates, BYNTO grows as well-oriented, densely distributed nanocolumns. We achieved a pinning force density of 25 GN/m3 at 77 K at a matching field of 2.3 T, which is among the highest values reported for YBCO. The anisotropy of the critical current density shows a complex behavior whereby additional maxima are developed at field dependent angles. This is caused by a matching effect of the magnetic fields c-axis component. The exponent N of the current-voltage characteristics (inversely proportional to the creep rate S) allows the depinning mechanism to be determined. It changes from a double-kink excitation below the matching field to pinning-potential-determined creep above it. PMID:26887291

Nanoparticle-Cell Interaction: A Cell Mechanics Perspective.

PubMed

Septiadi, Dedy; Crippa, Federica; Moore, Thomas Lee; Rothen-Rutishauser, Barbara; Petri-Fink, Alke

2018-05-01

Progress in the field of nanoparticles has enabled the rapid development of multiple products and technologies; however, some nanoparticles can pose both a threat to the environment and human health. To enable their safe implementation, a comprehensive knowledge of nanoparticles and their biological interactions is needed. In vitro and in vivo toxicity tests have been considered the gold standard to evaluate nanoparticle safety, but it is becoming necessary to understand the impact of nanosystems on cell mechanics. Here, the interaction between particles and cells, from the point of view of cell mechanics (i.e., bionanomechanics), is highlighted and put in perspective. Specifically, the ability of intracellular and extracellular nanoparticles to impair cell adhesion, cytoskeletal organization, stiffness, and migration are discussed. Furthermore, the development of cutting-edge, nanotechnology-driven tools based on the use of particles allowing the determination of cell mechanics is emphasized. These include traction force microscopy, colloidal probe atomic force microscopy, optical tweezers, magnetic manipulation, and particle tracking microrheology. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A locomotion mechanism with external magnetic guidance for active capsule endoscope.

PubMed

Wang, Xiaona; Meng, Max Q H; Chen, Xijun

2010-01-01

Gastrointestinal (GI) disorder is one of the most common diseases in human body. The swallowable wireless capsule endoscopy has been proved to be a convenient, painless and effective way to examine the whole GI tract. However, lack of motion control makes the movement of the capsule substantially random, resulting in missing diagnosis. In this paper, a locomotion mechanism is developed for the next-generation active capsule endoscope. An internal actuator integrated on-board the capsule is designed to provide driving force and improve the dexterity. A small permanent magnet enclosed inside the capsule interacts with an external magnetic field to control the capsule's orientation and offer extra driving force. This mechanism avoids sophisticated and bulky control system and reduces power consumption inside the capsule. Ex-vivo experimental results showed that it can make a controllable movement inside the porcine large intestine. The mechanism also has the potential to be a platform for further development, such as devices of operations, spraying medicine, biopsy etc.

The dynamics of copper intercalated molybdenum ditelluride

NASA Astrophysics Data System (ADS)

Onofrio, Nicolas; Guzman, David; Strachan, Alejandro

2016-11-01

Layered transition metal dichalcogenides are emerging as key materials in nanoelectronics and energy applications. Predictive models to understand their growth, thermomechanical properties, and interaction with metals are needed in order to accelerate their incorporation into commercial products. Interatomic potentials enable large-scale atomistic simulations connecting first principle methods and devices. We present a ReaxFF reactive force field to describe molybdenum ditelluride and its interactions with copper. We optimized the force field parameters to describe the energetics, atomic charges, and mechanical properties of (i) layered MoTe2, Mo, and Cu in various phases, (ii) the intercalation of Cu atoms and small clusters within the van der Waals gap of MoTe2, and (iii) bond dissociation curves. The training set consists of an extensive set of first principles calculations computed using density functional theory (DFT). We validate the force field via the prediction of the adhesion of a single layer MoTe2 on a Cu(111) surface and find good agreement with DFT results not used in the training set. We characterized the mobility of the Cu ions intercalated into MoTe2 under the presence of an external electric field via finite temperature molecular dynamics simulations. The results show a significant increase in drift velocity for electric fields of approximately 0.4 V/Å and that mobility increases with Cu ion concentration.

Acoustic radiation force control: Pulsating spherical carriers.

PubMed

Rajabi, Majid; Mojahed, Alireza

2018-02-01

The interaction between harmonic plane progressive acoustic beams and a pulsating spherical radiator is studied. The acoustic radiation force function exerted on the spherical body is derived as a function of the incident wave pressure and the monopole vibration characteristics (i.e., amplitude and phase) of the body. Two distinct strategies are presented in order to alter the radiation force effects (i.e., pushing and pulling states) by changing its magnitude and direction. In the first strategy, an incident wave field with known amplitude and phase is considered. It is analytically shown that the zero- radiation force state (i.e., radiation force function cancellation) is achievable for specific pulsation characteristics belong to a frequency-dependent straight line equation in the plane of real-imaginary components (i.e., Nyquist Plane) of prescribed surface displacement. It is illustrated that these characteristic lines divide the mentioned displacement plane into two regions of positive (i.e., pushing) and negative (i.e., pulling) radiation forces. In the second strategy, the zero, negative and positive states of radiation force are obtained through adjusting the incident wave field characteristics (i.e., amplitude and phase) which insonifies the radiator with prescribed pulsation characteristics. It is proved that zero radiation force state occurs for incident wave pressure characteristics belong to specific frequency-dependent circles in Nyquist plane of incident wave pressure. These characteristic circles divide the Nyquist plane into two distinct regions corresponding to positive (out of circles) and negative (in the circles) values of radiation force function. It is analytically shown that the maximum amplitude of negative radiation force is exactly equal to the amplitude of the (positive) radiation force exerted upon the sphere in the passive state, by the same incident field. The developed concepts are much more deepened by considering the required power supply for distinct cases of zero, negative and positive radiation force states along with the frequency dependent asymmetry index. In addition, considering the effect of phase difference between the incident wave field and the pulsating object, and its possible variation with respect to spatial position of object, some practical points about the spatial average of generated radiation force, the optimal state of operation, the stability of zero radiation force states and the possibly of precise motion control are discussed. This work would extend the novel concept of smart carriers to and may be helpful for robust single-beam acoustic handling techniques. Furthermore, the shown capability of precise motion control may be considered as a new way toward smart acoustic driven micro-mechanisms and micro-machines. Copyright © 2017 Elsevier B.V. All rights reserved.

S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

PubMed

Chaudret, Robin; Gresh, Nohad; Narth, Christophe; Lagardère, Louis; Darden, Thomas A; Cisneros, G Andrés; Piquemal, Jean-Philip

2014-09-04

We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar response level. This opens up the possibility of embodying explicit scalar relativistic effects in molecular mechanics thanks to the direct transferability of ab initio pseudopotentials. Therefore, incorporating GEM-like electron density for a metal cation enable the introduction of nonambiguous short-range quantum effects within any point-dipole based polarizable force field without the need of an extensive parametrization.

Pre-breakdown cavitation nanopores in the dielectric fluid in the inhomogeneous, pulsed electric fields

NASA Astrophysics Data System (ADS)

Pekker, Mikhail; Shneider, Mikhail N.

2015-10-01

This paper discusses the nanopores emerging and developing in a liquid dielectric under the action of the ponderomotive electrostrictive forces in a nonuniform electric field. It is shown that the gradient of the electric field in the vicinity of the rupture (cavitation nanopore) substantially increases and determines whether the rupture grows or collapses. The cavitation rupture in the liquid (nanopore) tends to stretch along the lines of the original field. The mechanism of the breakdown associated with the generation of secondary ruptures in the vicinity of the poles of the nanopore is proposed. The estimations of the extension time for nanopore in water and oil (polar and nonpolar liquids, respectively) are presented. A new mechanism of nano- and subnanosecond breakdown in the insulating (transformer) oil that can be realized in the vicinity of water microdroplets in nanosecond high-voltage devices is considered.

Kestrel: force protection and Intelligence, Surveillance, and Reconnaissance (ISR) persistent surveillance on aerostats

NASA Astrophysics Data System (ADS)

Luber, David R.; Marion, John E.; Fields, David

2012-05-01

Logos Technologies has developed and fielded the Kestrel system, an aerostat-based, wide area persistent surveillance system dedicated to force protection and ISR mission execution operating over forward operating bases. Its development included novel imaging and stabilization capability for day/night operations on military aerostat systems. The Kestrel system's contribution is a substantial enhancement to aerostat-based, force protection systems which to date have relied on narrow field of view ball gimbal sensors to identify targets of interest. This inefficient mechanism to conduct wide area field of view surveillance is greatly enhanced by Kestrel's ability to maintain a constant motion imagery stare of the entire forward operating base (FOB) area. The Kestrel airborne sensor enables 360° coverage out to extended ranges which covers a city sized area at moderate resolution, while cueing a narrow field of view sensor to provide high resolution imagery of targets of interest. The ground station exploitation system enables operators to autonomously monitor multiple regions of interest in real time, and allows for backtracking through the recorded imagery, while continuing to monitor ongoing activity. Backtracking capability allows operators to detect threat networks, their CONOPS, and locations of interest. Kestrel's unique advancement has already been utilized successfully in OEF operations.

Optical tweezers based force measurement system for quantitating binding interactions: system design and application for the study of bacterial adhesion.

PubMed

Fällman, Erik; Schedin, Staffan; Jass, Jana; Andersson, Magnus; Uhlin, Bernt Eric; Axner, Ove

2004-06-15

An optical force measurement system for quantitating forces in the pN range between micrometer-sized objects has been developed. The system was based upon optical tweezers in combination with a sensitive position detection system and constructed around an inverted microscope. A trapped particle in the focus of the high numerical aperture microscope-objective behaves like an omnidirectional mechanical spring in response to an external force. The particle's displacement from the equilibrium position is therefore a direct measure of the exerted force. A weak probe laser beam, focused directly below the trapping focus, was used for position detection of the trapped particle (a polystyrene bead). The bead and the condenser focus the light to a distinct spot in the far field, monitored by a position sensitive detector. Various calibration procedures were implemented in order to provide absolute force measurements. The system has been used to measure the binding forces between Escherichia coli bacterial adhesins and galabiose-functionalized beads.

Optical tweezers for the measurement of binding forces: system description and application for the study of E. coli adhesion

NASA Astrophysics Data System (ADS)

Fallman, Erik G.; Schedin, Staffan; Andersson, Magnus J.; Jass, Jana; Axner, Ove

2003-06-01

Optical tweezers together with a position sensitive detection system allows measurements of forces in the pN range between micro-sized biological objects. A prototype force measurement system has been constructed around in inverted microscope with an argon-ion pumped Ti:sapphire laser as light source for optical trapping. A trapped particle in the focus of the high numerical aperture microscope-objective behaves like an omni-directional mechanical spring if an external force displaces it. The displacement from the equilibrium position is a measure of the exerted force. For position detection of the trapped particle (polystyrene beads), a He-Ne laser beam is focused a small distance below the trapping focus. An image of the bead appears as a distinct spot in the far field, monitored by a photosensitive detector. The position data is converted to a force measurement by a calibration procedure. The system has been used for measuring the binding forces between E-coli bacterial adhesin and their receptor sugars.

Influence of the Convection Electric Field Models on Predicted Plasmapause Positions During Magnetic Storms

NASA Technical Reports Server (NTRS)

Pierrard, V.; Khazanov, G.; Cabrera, J.; Lemaire, J.

2007-01-01

In the present work, we determine how three well documented models of the magnetospheric electric field, and two different mechanisms proposed for the formation of the plasmapause influence the radial distance, the shape and the evolution of the plasmapause during the geomagnetic storms of 28 October 2001 and of 17 April 2002. The convection electric field models considered are: Mcllwain's E51) electric field model, Volland-Stern's model and Weimer's statistical model compiled from low-Earth orbit satellite data. The mechanisms for the formation of the plasmapause to be tested are: (i) the MHD theory where the plasmapause should correspond to the last-closed- equipotential (LCE) or last-closed-streamline (LCS), if the E-field distribution is stationary or time-dependent respectively; (ii) the interchange mechanism where the plasmapause corresponds to streamlines tangent to a Zero-Parallel-Force surface where the field-aligned plasma distribution becomes convectively unstable during enhancements of the E-field intensity in the nightside local time sector. The results of the different time dependent simulations are compared with concomitant EUV observations when available. The plasmatails or plumes observed after both selected geomagnetic storms are predicted in all simulations and for all E-field models. However, their shapes are quite different depending on the E-field models and the mechanisms that are used. Despite the partial success of the simulations to reproduce plumes during magnetic storms and substorms, there remains a long way to go before the detailed structures observed in the EUV observations during periods of geomagnetic activity can be accounted for very precisely by the existing E-field models. Furthermore, it cannot be excluded that the mechanisms currently identified to explain the formation of "Carpenter's knee" during substorm events, will', have to be revised or complemented in the cases of geomagnetic storms.

Reactor vibration reduction based on giant magnetostrictive materials

NASA Astrophysics Data System (ADS)

Rongge, Yan; Weiying, Liu; Yuechao, Wu; Menghua, Duan; Xiaohong, Zhang; Lihua, Zhu; Ling, Weng; Ying, Sun

2017-05-01

The vibration of reactors not only produces noise pollution, but also affects the safe operation of reactors. Giant magnetostrictive materials can generate huge expansion and shrinkage deformation in a magnetic field. With the principle of mutual offset between the giant magnetostrictive force produced by the giant magnetostrictive material and the original vibration force of the reactor, the vibration of the reactor can be reduced. In this paper, magnetization and magnetostriction characteristics in silicon steel and the giant magnetostrictive material are measured, respectively. According to the presented magneto-mechanical coupling model including the electromagnetic force and the magnetostrictive force, reactor vibration is calculated. By comparing the vibration of the reactor with different inserted materials in the air gaps between the reactor cores, the vibration reduction effectiveness of the giant magnetostrictive material is validated.

ON ESTIMATING FORCE-FREENESS BASED ON OBSERVED MAGNETOGRAMS

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

Zhang, X. M.; Zhang, M.; Su, J. T., E-mail: xmzhang@nao.cas.cn

It is a common practice in the solar physics community to test whether or not measured photospheric or chromospheric vector magnetograms are force-free, using the Maxwell stress as a measure. Some previous studies have suggested that magnetic fields of active regions in the solar chromosphere are close to being force-free whereas there is no consistency among previous studies on whether magnetic fields of active regions in the solar photosphere are force-free or not. Here we use three kinds of representative magnetic fields (analytical force-free solutions, modeled solar-like force-free fields, and observed non-force-free fields) to discuss how measurement issues such asmore » limited field of view (FOV), instrument sensitivity, and measurement error could affect the estimation of force-freeness based on observed magnetograms. Unlike previous studies that focus on discussing the effect of limited FOV or instrument sensitivity, our calculation shows that just measurement error alone can significantly influence the results of estimates of force-freeness, due to the fact that measurement errors in horizontal magnetic fields are usually ten times larger than those in vertical fields. This property of measurement errors, interacting with the particular form of a formula for estimating force-freeness, would result in wrong judgments of the force-freeness: a truly force-free field may be mistakenly estimated as being non-force-free and a truly non-force-free field may be estimated as being force-free. Our analysis calls for caution when interpreting estimates of force-freeness based on measured magnetograms, and also suggests that the true photospheric magnetic field may be further away from being force-free than it currently appears to be.« less

A novel experimental mechanics method for measuring the light pressure acting on a solar sail membrane

NASA Astrophysics Data System (ADS)

Shi, Aiming; Jiang, Li; Dowell, Earl H.; Qin, Zhixuan

2017-02-01

Solar sail is a high potential `sailing craft' for interstellar exploration. The area of the first flight solar sail demonstrator named "IKAROS" is 200 square meters. Future interplanetary missions will require solar sails at least on the order of 10000 square meters (or larger). Due to the limitation of ground facilities, the size of experimental sample should not be large. Furthermore the ground experiments have to be conducted in gravitational field, so the gravity effect must be considered in a ground test. To obtain insight into the solar sail membrane dynamics, a key membrane flutter (or limit cycle oscillations) experiment with light forces acting on it must be done. But one big challenge is calibrating such a tiny light force by as a function of the input power. In this paper, a gravity-based measuring method for light pressure acting on membrane is presented. To explain the experimental principle, an ideal example of a laser beam with expanders and a metal film is studied. Based on calculations, this experimental mechanics method for calibrating light pressure with an accuracy of 0.01 micro-Newton may be realized by making the light force balance the gravity force on the metal films. This gravity-based measuring method could not only be applied to study the dynamics characteristics of solar sail membrane structure with different light forces, but could also be used to determine more accurate light forces/loads acting on solar sail films and hence to enhance the determination of the mechanical properties of the solar sail membrane structure.

Note: Design of FPGA based system identification module with application to atomic force microscopy

NASA Astrophysics Data System (ADS)

Ghosal, Sayan; Pradhan, Sourav; Salapaka, Murti

2018-05-01

The science of system identification is widely utilized in modeling input-output relationships of diverse systems. In this article, we report field programmable gate array (FPGA) based implementation of a real-time system identification algorithm which employs forgetting factors and bias compensation techniques. The FPGA module is employed to estimate the mechanical properties of surfaces of materials at the nano-scale with an atomic force microscope (AFM). The FPGA module is user friendly which can be interfaced with commercially available AFMs. Extensive simulation and experimental results validate the design.

Ultrathin nanoporous membranes for insulator-based dielectrophoresis

NASA Astrophysics Data System (ADS)

Mukaibo, Hitomi; Wang, Tonghui; Perez-Gonzalez, Victor H.; Getpreecharsawas, Jirachai; Wurzer, Jack; Lapizco-Encinas, Blanca H.; McGrath, James L.

2018-06-01

Insulator-based dielectrophoresis (iDEP) is a simple, scalable mechanism that can be used for directly manipulating particle trajectories in pore-based filtration and separation processes. However, iDEP manipulation of nanoparticles presents unique challenges as the dielectrophoretic force ({F}{{D}{{E}}{{P}}}) exerted on the nanoparticles can easily be overshadowed by opposing kinetic forces. In this study, a molecularly thin, SiN-based nanoporous membrane (NPN) is explored as a breakthrough technology that enhances {F}{{D}{{E}}{{P}}}. By numerically assessing the gradient of the electric field square ({{\

Convectively driven decadal zonal accelerations in Earth's fluid core

NASA Astrophysics Data System (ADS)

More, Colin; Dumberry, Mathieu

2018-04-01

Azimuthal accelerations of cylindrical surfaces co-axial with the rotation axis have been inferred to exist in Earth's fluid core on the basis of magnetic field observations and changes in the length-of-day. These accelerations have a typical timescale of decades. However, the physical mechanism causing the accelerations is not well understood. Scaling arguments suggest that the leading order torque averaged over cylindrical surfaces should arise from the Lorentz force. Decadal fluctuations in the magnetic field inside the core, driven by convective flows, could then force decadal changes in the Lorentz torque and generate zonal accelerations. We test this hypothesis by constructing a quasi-geostrophic model of magnetoconvection, with thermally driven flows perturbing a steady, imposed background magnetic field. We show that when the Alfvén number in our model is similar to that in Earth's fluid core, temporal fluctuations in the torque balance are dominated by the Lorentz torque, with the latter generating mean zonal accelerations. Our model reproduces both fast, free Alfvén waves and slow, forced accelerations, with ratios of relative strength and relative timescale similar to those inferred for the Earth's core. The temporal changes in the magnetic field which drive the time-varying Lorentz torque are produced by the underlying convective flows, shearing and advecting the magnetic field on a timescale associated with convective eddies. Our results support the hypothesis that temporal changes in the magnetic field deep inside Earth's fluid core drive the observed decadal zonal accelerations of cylindrical surfaces through the Lorentz torque.

Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

PubMed

Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

2013-08-15

Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

Ultrahigh resolution optical coherence elastography combined with a rigid micro-endoscope (Conference Presentation)

NASA Astrophysics Data System (ADS)

Fang, Qi; Curatolo, Andrea; Wijesinghe, Philip; Hamzah, Juliana; Ganss, Ruth; Noble, Peter B.; Karnowski, Karol; Sampson, David D.; Kim, Jun Ki; Lee, Wei M.; Kennedy, Brendan F.

2017-02-01

The mechanical forces that living cells experience represent an important framework in the determination of a range of intricate cellular functions and processes. Current insight into cell mechanics is typically provided by in vitro measurement systems; for example, atomic force microscopy (AFM) measurements are performed on cells in culture or, at best, on freshly excised tissue. Optical techniques, such as Brillouin microscopy and optical elastography, have been used for ex vivo and in situ imaging, recently achieving cellular-scale resolution. The utility of these techniques in cell mechanics lies in quick, three-dimensional and label-free mechanical imaging. Translation of these techniques toward minimally invasive in vivo imaging would provide unprecedented capabilities in tissue characterization. Here, we take the first steps along this path by incorporating a gradient-index micro-endoscope into an ultrahigh resolution optical elastography system. Using this endoscope, a lateral resolution of 2 µm is preserved over an extended depth-of-field of 80 µm, achieved by Bessel beam illumination. We demonstrate this combined system by imaging stiffness of a silicone phantom containing stiff inclusions and a freshly excised murine liver tissue. Additionally, we test this system on murine ribs in situ. We show that our approach can provide high quality extended depth-of-field images through an endoscope and has the potential to measure cell mechanics deep in tissue. Eventually, we believe this tool will be capable of studying biological processes and disease progression in vivo.

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.

PubMed

Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper; Kongsted, Jacob

2015-04-14

Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.

Probing cytoskeleton organisation of neuroblastoma cells with single-cell force spectroscopy.

PubMed

Mescola, Andrea; Vella, Serena; Scotto, Marco; Gavazzo, Paola; Canale, Claudio; Diaspro, Alberto; Pagano, Aldo; Vassalli, Massimo

2012-05-01

Single-cell force spectroscopy is an emerging technique in the field of biomedicine because it has proved to be a unique tool to obtain mechanical and functional information on living cells, with force resolution up to single molecular bonds. This technique was applied to the study of the cytoskeleton organisation of neuroblastoma cells, a life-threatening cancer typically developing during childhood, and the results were interpreted on the basis of reference experiments on human embryonic kidney cell line. An intimate connection emerges among cellular state, cytoskeleton organisation and experimental outcome that can be potentially exploited towards a new method for cancer stadiation of neuroblastoma cells. Copyright © 2012 John Wiley & Sons, Ltd.

Enabling Computational Nanotechnology through JavaGenes in a Cycle Scavenging Environment

NASA Technical Reports Server (NTRS)

Globus, Al; Menon, Madhu; Srivastava, Deepak; Biegel, Bryan A. (Technical Monitor)

2002-01-01

A genetic algorithm procedure is developed and implemented for fitting parameters for many-body inter-atomic force field functions for simulating nanotechnology atomistic applications using portable Java on cycle-scavenged heterogeneous workstations. Given a physics based analytic functional form for the force field, correlated parameters in a multi-dimensional environment are typically chosen to fit properties given either by experiments and/or by higher accuracy quantum mechanical simulations. The implementation automates this tedious procedure using an evolutionary computing algorithm operating on hundreds of cycle-scavenged computers. As a proof of concept, we demonstrate the procedure for evaluating the Stillinger-Weber (S-W) potential by (a) reproducing the published parameters for Si using S-W energies in the fitness function, and (b) evolving a "new" set of parameters using semi-empirical tightbinding energies in the fitness function. The "new" parameters are significantly better suited for Si cluster energies and forces as compared to even the published S-W potential.

Alfven seismic vibrations of crustal solid-state plasma in quaking paramagnetic neutron star

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

Bastrukov, S.; Xu, R.-X.; Molodtsova, I.

2010-11-15

Magneto-solid-mechanical model of two-component, core-crust, paramagnetic neutron star responding to quake-induced perturbation by differentially rotational, torsional, oscillations of crustal electron-nuclear solid-state plasma about axis of magnetic field frozen in the immobile paramagnetic core is developed. Particular attention is given to the node-free torsional crust-against-core vibrations under combined action of Lorentz magnetic and Hooke's elastic forces; the damping is attributed to Newtonian force of shear viscose stresses in crustal solid-state plasma. The spectral formulas for the frequency and lifetime of this toroidal mode are derived in analytic form and discussed in the context of quasiperiodic oscillations of the x-ray outburst fluxmore » from quaking magnetars. The application of obtained theoretical spectra to modal analysis of available data on frequencies of oscillating outburst emission suggests that detected variability is the manifestation of crustal Alfven's seismic vibrations restored by Lorentz force of magnetic field stresses.« less

Analysis of Plasma Detachment through Magnetic Nozzle via Canonical Field Theory

NASA Astrophysics Data System (ADS)

Takagaki, Yu

In this paper, I have investigated the mechanism of plasma detachment through magnetic nozzle via canonical field theory, especially by considering canonical vorticity flux Psisigma contour and dissipative force vector Rsigma. As one of the most recent experimental proofs of plasma detachment, Olsen et al., observed and investigated three key indications of plasma detachment. However, after solving for numerical fits with their experimental data, I found that constant ion flux lines did not actually separate from constant magnetic flux lines. Thus, their first key indication becomes incorrect now. Whereas, my analytical results are consistent with the other two key indications. At the beginning, plasma detached from canonical vorticity flux contours due to non-zero dissipative force and attached on magnetic flux lines instead. However, vector Rsigma [is asymptotically equal to] 0 force makes plasma re-attach on canonical vorticity flux contours around the plume edge region. As the most significant and notable result through my analysis, I confirmed the existence of returning plasma flow around the plume edge region.

Understanding Mechanobiology: Physical Therapists as a Force in Mechanotherapy and Musculoskeletal Regenerative Rehabilitation

PubMed Central

Thompson, William R.; Scott, Alexander; Loghmani, M. Terry; Ward, Samuel R.

2016-01-01

Achieving functional restoration of diseased or injured tissues is the ultimate goal of both regenerative medicine approaches and physical therapy interventions. Proper integration and healing of the surrogate cells, tissues, or organs introduced using regenerative medicine techniques are often dependent on the co-introduction of therapeutic physical stimuli. Thus, regenerative rehabilitation represents a collaborative approach whereby rehabilitation specialists, basic scientists, physicians, and surgeons work closely to enhance tissue restoration by creating tailored rehabilitation treatments. One of the primary treatment regimens that physical therapists use to promote tissue healing is the introduction of mechanical forces, or mechanotherapies. These mechanotherapies in regenerative rehabilitation activate specific biological responses in musculoskeletal tissues to enhance the integration, healing, and restorative capacity of implanted cells, tissues, or synthetic scaffolds. To become future leaders in the field of regenerative rehabilitation, physical therapists must understand the principles of mechanobiology and how mechanotherapies augment tissue responses. This perspective article provides an overview of mechanotherapy and discusses how mechanical signals are transmitted at the tissue, cellular, and molecular levels. The synergistic effects of physical interventions and pharmacological agents also are discussed. The goals are to highlight the critical importance of mechanical signals on biological tissue healing and to emphasize the need for collaboration within the field of regenerative rehabilitation. As this field continues to emerge, physical therapists are poised to provide a critical contribution by integrating mechanotherapies with regenerative medicine to restore musculoskeletal function. PMID:26637643

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

PubMed Central

Zhou, Rui; Maisuradze, Gia G.; Suñol, David; Todorovski, Toni; Macias, Maria J.; Xiao, Yi; Scheraga, Harold A.; Czaplewski, Cezary; Liwo, Adam

2014-01-01

To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding. PMID:25489078

Experimental study of dielectrophoresis and liquid dielectrophoresis mechanisms for particle capture in a droplet.

PubMed

Tsai, Sung-Lin; Hong, Jhih-Lin; Chen, Ming-Kun; Jang, Ling-Sheng

2011-06-01

This work presents a microfluidic system that can transport, concentrate, and capture particles in a controllable droplet. Dielectrophoresis (DEP), a phenomenon in which a force is exerted on a dielectric particle when it is subjected to a non-uniform electric field, is used to manipulate particles. Liquid dielectrophoresis (LDEP), a phenomenon in which a liquid moves toward regions of high electric field strength under a non-uniform electric field, is used to manipulate the fluid. In this study, a mechanism of droplet creation presented in a previous work that uses DEP and LDEP is improved. A driving electrode with a DEP gap is used to prevent beads from getting stuck at the interface between air and liquid, which is actuated with an AC signal of 200 V(pp) at a frequency of 100 kHz. DEP theory is used to calculate the DEP force in the liquid, and LDEP theory is used to analyze the influence of the DEP gap. The increment of the actuation voltage due to the electrode with a DEP gap is calculated. A set of microwell electrodes is used to capture a bead using DEP force, which is actuated with an AC signal of 20 V(pp) at a frequency of 5 MHz. A simulation is carried out to investigate the dimensions of the DEP gap and microwell electrodes. Experiments are performed to demonstrate the creation of a 100-nL droplet and the capture of individual 10-μm polystyrene latex beads in the droplet. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multipolar Ewald Methods, 2: Applications Using a Quantum Mechanical Force Field

PubMed Central

2015-01-01

A fully quantum mechanical force field (QMFF) based on a modified “divide-and-conquer” (mDC) framework is applied to a series of molecular simulation applications, using a generalized Particle Mesh Ewald method extended to multipolar charge densities. Simulation results are presented for three example applications: liquid water, p-nitrophenylphosphate reactivity in solution, and crystalline N,N-dimethylglycine. Simulations of liquid water using a parametrized mDC model are compared to TIP3P and TIP4P/Ew water models and experiment. The mDC model is shown to be superior for cluster binding energies and generally comparable for bulk properties. Examination of the dissociative pathway for dephosphorylation of p-nitrophenylphosphate shows that the mDC method evaluated with the DFTB3/3OB and DFTB3/OPhyd semiempirical models bracket the experimental barrier, whereas DFTB2 and AM1/d-PhoT QM/MM simulations exhibit deficiencies in the barriers, the latter for which is related, in part, to the anomalous underestimation of the p-nitrophenylate leaving group pKa. Simulations of crystalline N,N-dimethylglycine are performed and the overall structure and atomic fluctuations are compared with the experiment and the general AMBER force field (GAFF). The QMFF, which was not parametrized for this application, was shown to be in better agreement with crystallographic data than GAFF. Our simulations highlight some of the application areas that may benefit from using new QMFFs, and they demonstrate progress toward the development of accurate QMFFs using the recently developed mDC framework. PMID:25691830

Probing cooperative force generation in collective cancer invasion

NASA Astrophysics Data System (ADS)

Alobaidi, Amani A.; Xu, Yaopengxiao; Chen, Shaohua; Jiao, Yang; Sun, Bo

2017-08-01

Collective cellular dynamics in the three-dimensional extracellular matrix (ECM) plays a crucial role in many physiological processes such as cancer invasion. Both chemical and mechanical signaling support cell-cell communications on a variety of length scales, leading to collective migratory behaviors. Here we conduct experiments using 3D in vitro tumor models and develop a phenomenological model in order to probe the cooperativity of force generation in the collective invasion of breast cancer cells. In our model, cell-cell communication is characterized by a single parameter that quantifies the correlation length of cellular migration cycles. We devise a stochastic reconstruction method to generate realizations of cell colonies with specific contraction phase correlation functions and correlation length a. We find that as a increases, the characteristic size of regions containing cells with similar contraction phases grows. For small a values, the large fluctuations in individual cell contraction phases smooth out the temporal fluctuations in the time-dependent deformation field in the ECM. For large a values, the periodicity of an individual cell contraction cycle is clearly manifested in the temporal variation of the overall deformation field in the ECM. Through quantitative comparisons of the simulated and experimentally measured deformation fields, we find that the correlation length for collective force generation in the breast cancer diskoid in geometrically micropatterned ECM (DIGME) system is a≈ 25~μ \\text{m} , which is roughly twice the linear size of a single cell. One possible mechanism for this intermediate cell correlation length is the fiber-mediated stress propagation in the 3D ECM network in the DIGME system.

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

PubMed

Zhou, Rui; Maisuradze, Gia G; Suñol, David; Todorovski, Toni; Macias, Maria J; Xiao, Yi; Scheraga, Harold A; Czaplewski, Cezary; Liwo, Adam

2014-12-23

To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.

On the glitches in the force transmitted by an electrodynamic exciter to a structure

NASA Technical Reports Server (NTRS)

Rao, Dantam K.

1987-01-01

Around resonance, the force transmitted by an exciter into a structure will be smaller or greater than a reference force generated by its coils due to electromechanical interaction. A simple analysis is presented which reveals how this phenomenon of force drop-off is controlled by three factors. The first factor, called Armature Mass Factor, describes a purely mechanical interaction between the structure and the exciter. The electromechanical energy conversion and its interaction with the structure yields two additional factors, called Electrical Resistance and Electrical Inductance Factors. They describe the effects of coil resistance, inductance and magnetic field strength relative to structural damping and stiffness. Present analysis indicates that, under proper circumstances, more than 90 percent of the force drop-off can be eliminated if armature-to-structure mass ratio is smaller or equal to half of modal loss factor.

Nanomechanics of biocompatible hollow thin-shell polymer microspheres.

PubMed

Glynos, Emmanouil; Koutsos, Vasileios; McDicken, W Norman; Moran, Carmel M; Pye, Stephen D; Ross, James A; Sboros, Vassilis

2009-07-07

The nanomechanical properties of biocompatible thin-shell hollow polymer microspheres with approximately constant ratio of shell thickness to microsphere diameter were measured by nanocompression tests in aqueous conditions. These microspheres encapsulate an inert gas and are used as ultrasound contrast agents by releasing free microbubbles in the presence of an ultrasound field as a result of free gas leakage from the shell. The tests were performed using an atomic force microscope (AFM) employing the force-distance curve technique. An optical microscope, on which the AFM was mounted, was used to guide the positioning of tipless cantilevers on top of individual microspheres. We performed a systematic study using several cantilevers with spring constants varying from 0.08 to 2.3 N/m on a population of microspheres with diameters from about 2 to 6 microm. The use of several cantilevers with various spring constants allowed a systematic study of the mechanical properties of the microsphere thin shell at different regimes of force and deformation. Using thin-shell mechanics theory for small deformations, the Young's modulus of the thin wall material was estimated and was shown to exhibit a strong size effect: it increased as the shell became thinner. The Young's modulus of thicker microsphere shells converged to the expected value for the macroscopic bulk material. For high applied forces, the force-deformation profiles showed a reversible and/or irreversible nonlinear behavior including "steps" and "jumps" which were attributed to mechanical instabilities such as buckling events.

A model for wave control on coral breakage and species distribution in the Hawaiian Islands

USGS Publications Warehouse

Storlazzi, C.D.; Brown, E.K.; Field, M.E.; Rodgers, K.; Jokiel, P.L.

2005-01-01

The fringing reef off southern Molokai, Hawaii, is currently being studied as part of a multi-disciplinary project led by the US Geological Survey. As part of this study, modeling and field observations were utilized to help understand the physical controls on reef morphology and the distribution of different coral species. A model was developed that calculates wave-induced hydrodynamic forces on corals of a specific form and mechanical strength. From these calculations, the wave conditions under which specific species of corals would either be stable or would break due to the imposed wave-induced forces were determined. By combining this hydrodynamic force-balance model with various wave model output for different oceanographic conditions experienced in the study area, we were able to map the locations where specific coral species should be stable (not subject to frequent breakage) in the study area. The combined model output was then compared with data on coral species distribution and coral cover at 12 sites along Molokai's south shore. Observations and modeling suggest that the transition from one coral species to another may occur when the ratio of the coral colony's mechanical strengths to the applied (wave-induced) forces may be as great as 5:1, and not less than 1:1 when corals would break. This implies that coral colony's mechanical strength and wave-induced forces may be important in defining gross coral community structure over large (orders of 10's of meters) spatial scales. ?? Springer-Verlag 2004.

Remote sensing of the correlation between breakpoint oscillations and infragravity waves in the surf and swash zone

NASA Astrophysics Data System (ADS)

Moura, T.; Baldock, T. E.

2017-04-01

A novel remote sensing methodology to determine the dominant infragravity mechanism in the inner surf and swash zone in the field is presented. Video observations of the breakpoint motion are correlated with the shoreline motion and inner surf zone water levels to determine the relationship between the time-varying breakpoint oscillations and the shoreline motion. The results of 13 field data sets collected from three different beaches indicate that, inside the surf zone, the dominance of bound wave or breakpoint forcing is strongly dependent on the surf zone width and the type of short wave breaking. Infragravity generation by bound wave release was stronger for conditions with relatively narrow surf zones and plunging waves; breakpoint forcing was dominant for wider surf zones and spilling breaker conditions.