Uncertainties in forces extracted from non-contact atomic force microscopy measurements by fitting of long-range background forces.

PubMed

Sweetman, Adam; Stannard, Andrew

2014-01-01

In principle, non-contact atomic force microscopy (NC-AFM) now readily allows for the measurement of forces with sub-nanonewton precision on the atomic scale. In practice, however, the extraction of the often desired 'short-range' force from the experimental observable (frequency shift) is often far from trivial. In most cases there is a significant contribution to the total tip-sample force due to non-site-specific van der Waals and electrostatic forces. Typically, the contribution from these forces must be removed before the results of the experiment can be successfully interpreted, often by comparison to density functional theory calculations. In this paper we compare the 'on-minus-off' method for extracting site-specific forces to a commonly used extrapolation method modelling the long-range forces using a simple power law. By examining the behaviour of the fitting method in the case of two radically different interaction potentials we show that significant uncertainties in the final extracted forces may result from use of the extrapolation method.

Very-Low-Cost, Rugged Vacuum System

NASA Technical Reports Server (NTRS)

Kline-Schoder, Robert; Sorensen, Paul; Passow, Christian; Bilski, Steve

2013-01-01

NASA, DoD, DHS, and commercial industry have a need for miniaturized, rugged, low-cost vacuum systems. Recent advances in sensor technology have led to the development of very small mass spectrometer detectors as well as other miniature analytical instruments. However, the vacuum systems to support these sensors remain large, heavy, and power-hungry. To meet this need, a miniaturized vacuum system was created based on a very small, rugged, and inexpensive- to-manufacture molecular drag pump (MDP). The MDP is enabled by the development of a miniature, veryhigh- speed, rugged, low-power, brushless DC motor optimized for wide temperature operation and long life. Such a pump represents an order-of-magnitude reduction in mass, volume, and cost over current, commercially available, state-ofthe- art vacuum pumps. The vacuum system consists of the MDP coupled to a ruggedized rough pump (for terrestrial applications or for planets with substantial atmospheres). The rotor in the MDP consists of a simple smooth cylinder of aluminum spinning at approximately 200,000 RPM inside an outer stator housing. The pump stator comprises a cylindrical aluminum housing with one or more specially designed grooves that serve as flow channels. To minimize the length of the pump, the gas is forced down the flow channels of the outer stator to the base of the pump. The gas is then turned and pulled toward the top through a second set of channels cut into an inner stator housing that surrounds the motor. The compressed gas then flows down channels in the motor housing to the exhaust port of the pump. The exhaust port of the pump is connected to a diaphragm or scroll pump. This pump delivers very high performance in a very small envelope. The design was simplified so that a smaller compression ratio, easier manufacturing process, and enhanced ruggedness can be achieved at the lowest possible cost. The machining of the rotor and stators is very simple compared to that necessary to fabricate TMP (turbo molecular pump) rotor and stator blades. Also, the symmetry of the rotor is such that dynamic balancing of the rotor is greatly simplified. Finally, because of the simplified design, the number of parts in the unit is cut by nearly a factor of three. In fact, there are only five parts, not counting the motor and off-the-shelf screws and O-rings. This reduces the amount of machining and also makes fit-up much simpler while allowing the maintenance of close tolerances.

Soil Analysis Micro-Mission Concepts Derived from the MSP 2001 Mars Environmental Compatibility Assessment (MECA)

NASA Technical Reports Server (NTRS)

Hecht, M. H.; Meloy, T. P.; Anderson, M. S.; Buehler, M. G.; Frant, M. A.; Grannan, S. M.; Fuerstenau, S. D.; Keller, H. U.; Markiewicz, W. J.; Marshall, J.

1999-01-01

The Mars Environmental Compatibility Assessment (MECA) will evaluate the Martian environment for soil and dust-related hazards to human exploration as part of the Mars Surveyor Program 2001 Lander. The integrated MECA payload contains a wet-chemistry laboratory, a microscopy station, an electrometer to characterize the electrostatic environment, and arrays of material patches to study abrasion and adhesion. Heritage will be all-important for low cost micro-missions, and adaptations of instruments developed for the Pathfinder, '98 and '01 Landers should be strong contenders for '03 flights. This talk has three objectives: (1) Familiarize the audience with MECA instrument capabilities; (2) present concepts for stand-alone and/or mobile versions of MECA instruments; and (3) broaden the context of the MECA instruments from human exploration to a comprehensive scientific survey of Mars. Due to time limitations, emphasis will be on the chemistry and microscopy experiments. Ion-selective electrodes and related sensors in MECA's wet-chemistry laboratory will evaluate total dissolved solids, redox potential, pH, and the concentration of many soluble ions and gases in wet Martian soil. These electrodes can detect potentially dangerous heavy-metal ions, emitted pathogenic gases, and the soil's corrosive potential, and experiments will include cyclic voltammetry and anodic stripping. For experiments beyond 2001, enhancements could allow multiple use of the cells (for mobile experiments) and reagent addition (for quantitative mineralogical and exobiological analysis). MECA's microscopy station combines optical and atomic-force microscopy (AFM) in an actively focused, controlled illumination environment to image particles from millimeters to nanometers in size. Careful selection of substrates allows controlled experiments in adhesion, abrasion, hardness, aggregation, magnetic and other properties. Special tools allow primitive manipulation (brushing and scraping) of samples. Soil particle properties including size, shape, color, hardness, adhesive potential (electrostatic and magnetic), will be determined using an array of sample receptacles and collection substrates. The simple, rugged atomic-force microscope will image in the submicron size range and has the capability of performing a particle-by-particle analysis of the dust and soil. Future implementations might enhance the optical microscopy with spectroscopy, or incorporate advanced AFM techniques for thermogravimetric and chemical analysis.

Universal aspects of brittle fracture, adhesion, and atomic force microscopy

NASA Technical Reports Server (NTRS)

Banerjea, Amitava; Ferrante, John; Smith, John R.

1989-01-01

This universal relation between binding energy and interatomic separation was originally discovered for adhesion at bimetallic interfaces involving the simple metals Al, Zn, Mg, and Na. It is shown here that the same universal relation extends to adhesion at transition-metal interfaces. Adhesive energies have been computed for the low-index interfaces of Al, Ni, Cu, Ag, Fe, and W, using the equivalent-crystal theory (ECT) and keeping the atoms in each semiinfinite slab fixed rigidly in their equilibrium positions. These adhesive energy curves can be scaled onto each other and onto the universal adhesion curve. The effect of tip shape on the adhesive forces in the atomic-force microscope (AFM) is studied by computing energies and forces using the ECT. While the details of the energy-distance and force-distance curves are sensitive to tip shape, all of these curves can be scaled onto the universal adhesion curve.

Infrared absorption nano-spectroscopy using sample photoexpansion induced by tunable quantum cascade lasers.

PubMed

Lu, Feng; Belkin, Mikhail A

2011-10-10

We report a simple technique that allows obtaining mid-infrared absorption spectra with nanoscale spatial resolution under low-power illumination from tunable quantum cascade lasers. Light absorption is detected by measuring associated sample thermal expansion with an atomic force microscope. To detect minute thermal expansion we tune the repetition frequency of laser pulses in resonance with the mechanical frequency of the atomic force microscope cantilever. Spatial resolution of better than 50 nm is experimentally demonstrated.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

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

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Photon calorimeter

DOEpatents

Chow, Tze-Show

1988-04-22

A photon calorimeter is provided that comprises a laminar substrate that is uniform in density and homogeneous in atomic composition. A plasma-sprayed coating, that is generally uniform in density and homogeneous in atomic composition within the proximity of planes that are parallel to the surfaces of the substrate, is applied to either one or both sides of the laminar substrate. The plasma-sprayed coatings may be very efficiently spectrally tailored in atomic number. Thermocouple measuring junctions, are positioned within the plasma-sprayed coatings. The calorimeter is rugged, inexpensive, and equilibrates in temperature very rapidly. 4 figs.

Method for lateral force calibration in atomic force microscope using MEMS microforce sensor.

PubMed

Dziekoński, Cezary; Dera, Wojciech; Jarząbek, Dariusz M

2017-11-01

In this paper we present a simple and direct method for the lateral force calibration constant determination. Our procedure does not require any knowledge about material or geometrical parameters of an investigated cantilever. We apply a commercially available microforce sensor with advanced electronics for direct measurement of the friction force applied by the cantilever's tip to a flat surface of the microforce sensor measuring beam. Due to the third law of dynamics, the friction force of the equal value tilts the AFM cantilever. Therefore, torsional (lateral force) signal is compared with the signal from the microforce sensor and the lateral force calibration constant is determined. The method is easy to perform and could be widely used for the lateral force calibration constant determination in many types of atomic force microscopes. Copyright © 2017 Elsevier B.V. All rights reserved.

Simple Piezoelectric Probe for Detection and Measurement of SO2

ERIC Educational Resources Information Center

Frechette, Michael W.; Fasching, James L.

1973-01-01

Describes a new system for the detection and measurement of sulfur dioxide using a coated piezoelectric crystal. The device is rugged, portable, inexpensive, and should lend itself easily to automation. (JR)

Few-layer graphene growth from polystyrene as solid carbon source utilizing simple APCVD method

NASA Astrophysics Data System (ADS)

Ahmadi, Shahrokh; Afzalzadeh, Reza

2016-07-01

This research article presents development of an economical, simple, immune and environment friendly process to grow few-layer graphene by controlling evaporation rate of polystyrene on copper foil as catalyst and substrate utilizing atmospheric pressure chemical vapor deposition (APCVD) method. Evaporation rate of polystyrene depends on molecular structure, amount of used material and temperature. We have found controlling rate of evaporation of polystyrene by controlling the source temperature is easier than controlling the material weight. Atomic force microscopy (AFM) as well as Raman Spectroscopy has been used for characterization of the layers. The frequency of G‧ to G band ratio intensity in some samples varied between 0.8 and 1.6 corresponding to few-layer graphene. Topography characterization by atomic force microscopy confirmed Raman results.

Reversible monolayer-to-crystalline phase transition in amphiphilic silsesquioxane at the air-water interface

DOE PAGES

Banerjee, R.; Sanyal, M. K.; Bera, M. K.; ...

2015-02-17

We report on the counter intuitive reversible crystallisation of two-dimensional monolayer of Trisilanolisobutyl Polyhedral Oligomeric SilSesquioxane (TBPOSS) on water surface using synchrotron x-ray scattering measurements. Amphiphilic TBPOSS form rugged monolayers and Grazing Incidence X-ray Scattering (GIXS) measurements reveal that the in-plane inter-particle correlation peaks, characteristic of two-dimensional system, observed before transition is replaced by intense localized spots after transition. The measured x-ray scattering data of the non-equilibrium crystalline phase on the air-water interface could be explained with a model that assumes periodic stacking of the TBPOSS dimers. These crystalline stacking relaxes upon decompression and the TBPOSS layer retains its initialmore » monolayer state. The existence of these crystals in compressed phase is confirmed by atomic force microscopy measurements by lifting the materials on a solid substrate.« less

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

Dalvit, Diego; Messina, Riccardo; Maia Neto, Paulo

We develop the scattering approach for the dispersive force on a ground state atom on top of a corrugated surface. We present explicit results to first order in the corrugation amplitude. A variety of analytical results are derived in different limiting cases, including the van der Waals and Casimir-Polder regimes. We compute numerically the exact first-order dispersive potential for arbitrary separation distances and corrugation wavelengths, for a Rubidium atom on top of a silicon or gold corrugated surface. We consider in detail the correction to the proximity force approximation, and present a very simple approximation algorithm for computing the potential.

Traveltime computation and imaging from rugged topography in 3D TTI media

NASA Astrophysics Data System (ADS)

Liu, Shaoyong; Wang, Huazhong; Yang, Qinyong; Fang, Wubao

2014-02-01

Foothill areas with rugged topography are of great potential for oil and gas seismic exploration, but subsurface imaging in these areas is very challenging. Seismic acquisition with larger offset and wider azimuth is necessary for seismic imaging in complex areas. However, the scale anisotropy in this case must be taken into account. To generalize the pre-stack depth migration (PSDM) to 3D transversely isotropic media with vertical symmetry axes (VTI) and tilted symmetry axes (TTI) from rugged topography, a new dynamic programming approach for the first-arrival traveltime computation method is proposed. The first-arrival time on every uniform mesh point is calculated based on Fermat's principle with simple calculus techniques and a systematic mapping scheme. In order to calculate the minimum traveltime, a set of nonlinear equations is solved on each mesh point, where the group velocity is determined by the group angle. Based on the new first-arrival time calculation method, the corresponding PSDM and migration velocity analysis workflow for 3D anisotropic media from rugged surface is developed. Numerical tests demonstrate that the proposed traveltime calculation method is effective in both VTI and TTI media. The migration results for 3D field data show that it is necessary to choose a smooth datum to remove the high wavenumber move-out components for PSDM with rugged topography and take anisotropy into account to achieve better images.

Photon Calorimeter

DOEpatents

Chow, Tze-Show

1989-01-01

A photon calorimeter (20, 40) is provided that comprises a laminar substrate (10, 22, 42) that is uniform in density and homogeneous in atomic composition. A plasma-sprayed coating (28, 48, 52), that is generally uniform in density and homogeneous in atomic composition within the proximity of planes that are parallel to the surfaces of the substrate, is applied to either one or both sides of the laminar substrate. The plasma-sprayed coatings may be very efficiently spectrally tailored in atomic number. Thermocouple measuring junctions (30, 50, 54) are positioned within the plasma-sprayed coatings. The calorimeter is rugged, inexpensive, and equilibrates in temperature very rapidly.

Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; ...

2016-06-23

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

Simple Model for the Benzene Hexafluorobenzene Interaction

DOE PAGES

Tillack, Andreas F.; Robinson, Bruce H.

2017-06-05

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. Here, the simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions,more » and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.« less

Simple Model for the Benzene Hexafluorobenzene Interaction

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

Tillack, Andreas F.; Robinson, Bruce H.

While the experimental intermolecular distance distribution functions of pure benzene and pure hexafluorobenzene are well described by transferable all-atom force fields, the interaction between the two molecules (in a 1:1 mixture) is not well simulated. We demonstrate that the parameters of the transferable force fields are adequate to describe the intermolecular distance distribution if the charges are replaced by a set of charges that are not located at the atoms. Here, the simplest model that well describes the experimental distance distribution, between benzene and hexafluorobenzene, is that of a single ellipsoid for each molecule, representing the van der Waals interactions,more » and a set of three point charges (on the axis perpendicular to the arene plane) which give the same quadrupole moment as do the all atom charges from the transferable force fields.« less

Microwave resonance lamp absorption technique for measuring temperature and OH number density in combustion environments

NASA Technical Reports Server (NTRS)

Lempert, Walter R.

1988-01-01

A simple technique for simultaneous determination of temperature and OH number density is described, along with characteristic results obtained from measurements using a premixed, hydrogen air flat flame burner. The instrumentation is based upon absorption of resonant radiation from a flowing microwave discharge lamp, and is rugged, relatively inexpensive, and very simple to operate.

Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

PubMed

Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

2015-12-28

Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

Nuclear Stability and Nucleon-Nucleon Interactions in Introductory and General Chemistry Textbooks

ERIC Educational Resources Information Center

Millevolte, Anthony

2010-01-01

The nucleus is a highly dense and highly charged substructure of atoms. In the nuclei of all atoms beyond hydrogen, multiple protons are in close proximity to each other in spite of strong electrostatic repulsions between them. The attractive internucleon strong force is described and its origin explained by using a simple quark model for the…

On the origin of amplitude reduction mechanism in tapping mode atomic force microscopy

NASA Astrophysics Data System (ADS)

Keyvani, Aliasghar; Sadeghian, Hamed; Goosen, Hans; van Keulen, Fred

2018-04-01

The origin of amplitude reduction in Tapping Mode Atomic Force Microscopy (TM-AFM) is typically attributed to the shift in resonance frequency of the cantilever due to the nonlinear tip-sample interactions. In this paper, we present a different insight into the same problem which, besides explaining the amplitude reduction mechanism, provides a simple reasoning for the relationship between tip-sample interactions and operation parameters (amplitude and frequency). The proposed formulation, which attributes the amplitude reduction to an interference between the tip-sample and dither force, only deals with the linear part of the system; however, it fully agrees with experimental results and numerical solutions of the full nonlinear model of TM-AFM.

Radiometric temperature reference

NASA Technical Reports Server (NTRS)

Monford, L. G., Jr.

1969-01-01

Radiometric Temperature Reference uses a thermistor as both a heating and sensing element to maintain its resistance at a preselected level to continuously control the power supplying it. The fixed infrared radiation level must be simple, rugged, and capable of high temperature operation.

Characterisation of the membrane affinity of an isoniazide peptide conjugate by tensiometry, atomic force microscopy and sum-frequency vibrational spectroscopy, using a phospholipid Langmuir monolayer model.

PubMed

Hill, Katalin; Pénzes, Csanád Botond; Schnöller, Donát; Horváti, Kata; Bosze, Szilvia; Hudecz, Ferenc; Keszthelyi, Tamás; Kiss, Eva

2010-10-07

Tensiometry, sum-frequency vibrational spectroscopy, and atomic force microscopy were employed to assess the cell penetration ability of a peptide conjugate of the antituberculotic agent isoniazide. Isoniazide was conjugated to peptide (91)SEFAYGSFVRTVSLPV(106), a functional T-cell epitope of the immunodominant 16 kDa protein of Mycobacterium tuberculosis. As a simple but versatile model of the cell membrane a phospholipid Langmuir monolayer at the liquid/air interface was used. Changes induced in the structure of the phospholipid monolayer by injection of the peptide conjugate into the subphase were followed by tensiometry and sum-frequency vibrational spectroscopy. The drug penetrated lipid films were transferred to a solid support by the Langmuir-Blodgett technique, and their structures were characterized by atomic force microscopy. Peptide conjugation was found to strongly enhance the cell penetration ability of isoniazide.

Electric Vehicle Modeling and Simulation.

DTIC Science & Technology

1983-08-01

RD-RI39 709 ELECTRIC VEHICLE MODELING RHD SIMULRTION(U) AIR FORCE lit INST OF TECH NRIGHT-PRTTERSON RFD OH SCHOOL OF ENGINEERING A R DEMISPELARE RUG...for Public Release Distribution Unlimited Fl School of Engineering Air Force Institute of Technology Wright-Patterson Air Force Base, Ohio Table of... Engineering , 49: 49-51 (27 August 1979). 36. Renner -Smith, S. "Battery-Saving Flywheel Gives Electric Car Freeway Zip," Popular Science, 215(10): 82-84

Microphone Detects Boiler-Tube Leaks

NASA Technical Reports Server (NTRS)

Parthasarathy, S. P.

1985-01-01

Unit simple, sensitive, rugged, and reliable. Diaphragmless microphone detects leaks from small boiler tubes. Porous plug retains carbon granules in tube while allowing pressure changes to penetrate to granules. Has greater life expectancy than previous controllers and used in variety of hot corrosive atmospheres.

Theory of hydrophobicity: transient cavities in molecular liquids

NASA Technical Reports Server (NTRS)

Pratt, L. R.; Pohorille, A.

1992-01-01

Observation of the size distribution of transient cavities in computer simulations of water, n-hexane, and n-dodecane under benchtop conditions shows that the sizes of cavities are more sharply defined in liquid water but the most-probable-size cavities are about the same size in each of these liquids. The calculated solvent atomic density in contact with these cavities shows that water applies more force per unit area of cavity surface than do the hydrocarbon liquids. This contact density, or "squeezing" force, reaches a maximum near cavity diameters of 2.4 angstroms. The results for liquid water are compared to the predictions of simple theories and, in addition, to results for a reference simple liquid. The numerical data for water at a range of temperatures are analyzed to extract a surface free energy contribution to the work of formation of atomic-size cavities. Comparison with the liquid-vapor interfacial tensions of the model liquids studied here indicates that the surface free energies extracted for atomic-size cavities cannot be accurately identified with the macroscopic surface tensions of the systems.

Theory of hydrophobicity: Transient cavities in molecular liquids

PubMed Central

Pratt, Lawrence R.; Pohorille, Andrew

1992-01-01

Observation of the size distribution of transient cavities in computer simulations of water, n-hexane, and n-dodecane under benchtop conditions shows that the sizes of cavities are more sharply defined in liquid water but the most-probable-size cavities are about the same size in each of these liquids. The calculated solvent atomic density in contact with these cavities shows that water applies more force per unit area of cavity surface than do the hydrocarbon liquids. This contact density, or “squeezing” force, reaches a maximum near cavity diameters of 2.4 Å. The results for liquid water are compared to the predictions of simple theories and, in addition, to results for a reference simple liquid. The numerical data for water at a range of temperatures are analyzed to extract a surface free energy contribution to the work of formation of atomic-size cavities. Comparison with the liquid-vapor interfacial tensions of the model liquids studies here indicates that the surface free energies extracted for atomic-size cavities cannot be accurately identified with the macroscopic surface tensions of the systems. PMID:11537863

Developing model asphalt systems using molecular simulation : final model.

DOT National Transportation Integrated Search

2009-09-01

Computer based molecular simulations have been used towards developing simple mixture compositions whose : physical properties resemble those of real asphalts. First, Monte Carlo simulations with the OPLS all-atom force : field were used to predict t...

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

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

Friction force microscopy: a simple technique for identifying graphene on rough substrates and mapping the orientation of graphene grains on copper

NASA Astrophysics Data System (ADS)

Marsden, A. J.; Phillips, M.; Wilson, N. R.

2013-06-01

At a single atom thick, it is challenging to distinguish graphene from its substrate using conventional techniques. In this paper we show that friction force microscopy (FFM) is a simple and quick technique for identifying graphene on a range of samples, from growth substrates to rough insulators. We show that FFM is particularly effective for characterizing graphene grown on copper where it can correlate the graphene growth to the three-dimensional surface topography. Atomic lattice stick-slip friction is readily resolved and enables the crystallographic orientation of the graphene to be mapped nondestructively, reproducibly and at high resolution. We expect FFM to be similarly effective for studying graphene growth on other metal/locally crystalline substrates, including SiC, and for studying growth of other two-dimensional materials such as molybdenum disulfide and hexagonal boron nitride.

Nonperturbative theory of atom-surface interaction: corrections at short separations

NASA Astrophysics Data System (ADS)

Bordag, M.; Klimchitskaya, G. L.; Mostepanenko, V. M.

2018-02-01

The nonperturbative expressions for the free energy and force of interaction between a ground-state atom and a real-material surface at any temperature are presented. The transition to the Matsubara representation is performed, whereupon the comparison is made with the commonly used perturbative results based on the standard Lifshitz theory. It is shown that the Lifshitz formulas for the free energy and force of an atom-surface interaction follow from the nonperturbative ones in the lowest order of the small parameter. Numerical computations of the free energy and force for the atoms of He{\\hspace{0pt}}\\ast and Na interacting with a surface of an Au plate have been performed using the frequency-dependent dielectric permittivity of Au and highly accurate dynamic atomic polarizabilities in the framework of both the nonperturbative and perturbative theories. According to our results, the maximum deviations between the two theories are reached at the shortest atom-surface separations of about 1 nm. Simple analytic expressions for the atom-surface free energy are derived in the classical limit and for an ideal-metal plane. In the lowest order of the small parameter, they are found in agreement with the perturbative ones following from the standard Lifshitz theory. Possible applications of the obtained results in the theory of van der Waals adsorption are discussed.

The atomic simulation environment-a Python library for working with atoms.

PubMed

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

2017-07-12

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

The atomic simulation environment—a Python library for working with atoms

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

2017-07-01

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Portable automatic blood analyzer

NASA Technical Reports Server (NTRS)

Coleman, R. L.

1975-01-01

Analyzer employs chemical-sensing electrodes for determination of blood, gas, and ion concentrations. It is rugged, easily serviced, and comparatively simple to operate. System can analyze up to eight parameters and can be modified to measure other blood constituents including nonionic species, such as urea, glucose, and oxygen.

The Smoluchowski limit for a simple mechanical model

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

Calderoni, P.; Duerr, D.

1989-05-01

The authors consider a vertical stick constantly accelerated along the x-axis by a force F and which elastically collides with point particles of the same mass (atoms). The atoms are initially Poisson distributed and are allowed to have four velocities only. It is shown that under suitable scaling of the system the displacement Q(t) of the stick satisfies a nontrivial CLT: Q(t) = vFt + D{sup 1/2}W(t) (Smoluchowski equation), where the values of v and D depend on the fact that one atom may collide several times.

Evolutionary Strategies for Protein Folding

NASA Astrophysics Data System (ADS)

Murthy Gopal, Srinivasa; Wenzel, Wolfgang

2006-03-01

The free energy approach for predicting the protein tertiary structure describes the native state of a protein as the global minimum of an appropriate free-energy forcefield. The low-energy region of the free-energy landscape of a protein is extremely rugged. Efficient optimization methods must therefore speed up the search for the global optimum by avoiding high energy transition states, adapt large scale moves or accept unphysical intermediates. Here we investigate an evolutionary strategies(ES) for optimizing a protein conformation in our all-atom free-energy force field([1],[2]). A set of random conformations is evolved using an ES to get a diverse population containing low energy structure. The ES is shown to balance energy improvement and yet maintain diversity in structures. The ES is implemented as a master-client model for distributed computing. Starting from random structures and by using this optimization technique, we were able to fold a 20 amino-acid helical protein and 16 amino-acid beta hairpin[3]. We compare ES to basin hopping method. [1]T. Herges and W. Wenzel,Biophys.J. 87,3100(2004) [2] A. Verma and W. Wenzel Stabilization and folding of beta-sheet and alpha-helical proteins in an all-atom free energy model(submitted)(2005) [3] S. M. Gopal and W. Wenzel Evolutionary Strategies for Protein Folding (in preparation)

Multifunctional hydrogel nano-probes for atomic force microscopy

PubMed Central

Lee, Jae Seol; Song, Jungki; Kim, Seong Oh; Kim, Seokbeom; Lee, Wooju; Jackman, Joshua A.; Kim, Dongchoul; Cho, Nam-Joon; Lee, Jungchul

2016-01-01

Since the invention of the atomic force microscope (AFM) three decades ago, there have been numerous advances in its measurement capabilities. Curiously, throughout these developments, the fundamental nature of the force-sensing probe—the key actuating element—has remained largely unchanged. It is produced by long-established microfabrication etching strategies and typically composed of silicon-based materials. Here, we report a new class of photopolymerizable hydrogel nano-probes that are produced by bottom-up fabrication with compressible replica moulding. The hydrogel probes demonstrate excellent capabilities for AFM imaging and force measurement applications while enabling programmable, multifunctional capabilities based on compositionally adjustable mechanical properties and facile encapsulation of various nanomaterials. Taken together, the simple, fast and affordable manufacturing route and multifunctional capabilities of hydrogel AFM nano-probes highlight the potential of soft matter mechanical transducers in nanotechnology applications. The fabrication scheme can also be readily utilized to prepare hydrogel cantilevers, including in parallel arrays, for nanomechanical sensor devices. PMID:27199165

Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

DOE PAGES

Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; ...

2015-06-04

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

PubMed Central

2015-01-01

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

Graphene thickness dependent adhesion force and its correlation to surface roughness

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

Pourzand, Hoorad; Tabib-Azar, Massood, E-mail: azar.m@utah.edu; Biomedical Engineering, University of Utah, Salt Lake City, Utah 84112

2014-04-28

In this paper, adhesion force of graphene layers on 300 nm silicon oxide is studied. A simple model for measuring adhesion force for a flat surface with sub-nanometer roughness was developed and is shown that small surface roughness decreases adhesion force while large roughness results in an effectively larger adhesion forces. We also show that surface roughness over scales comparable to the tip radius increase by nearly a factor of two, the effective adhesion force measured by the atomic force microscopy. Thus, we demonstrate that surface roughness is an important parameter that should be taken into account in analyzing the adhesionmore » force measurement results.« less

Digital force-feedback for protein unfolding experiments using atomic force microscopy

NASA Astrophysics Data System (ADS)

Bippes, Christian A.; Janovjak, Harald; Kedrov, Alexej; Muller, Daniel J.

2007-01-01

Since its invention in the 1990s single-molecule force spectroscopy has been increasingly applied to study protein (un-)folding, cell adhesion, and ligand-receptor interactions. In most force spectroscopy studies, the cantilever of an atomic force microscope (AFM) is separated from a surface at a constant velocity, thus applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently, Fernandez and co-workers introduced the so-called force-clamp technique. Single proteins were subjected to a defined constant force allowing their life times and life time distributions to be directly measured. Up to now, the force-clamping was performed by analogue PID controllers, which require complex additional hardware and might make it difficult to combine the force-feedback with other modes such as constant velocity. These points may be limiting the applicability and versatility of this technique. Here we present a simple, fast, and all-digital (software-based) PID controller that yields response times of a few milliseconds in combination with a commercial AFM. We demonstrate the performance of our feedback loop by force-clamp unfolding of single Ig27 domains of titin and the membrane proteins bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA.

Radiant energy dosimeter for field use

Treesearch

A. Broido; A.W. McMasters

1967-01-01

Thermal radiation measurements in Project Flambeau fires involved a limited number of conventional radiometers located outside the fire periphery. A simple, cheap, easily-fabricated, light-weight, self-contained, rugged dosimeter was desired to withstand a hot fire environment, including a specific energy input of 5,000 cal cm -2, and to record...

Reliable low-cost battery voltage indicator for light aircraft and automobiles

NASA Technical Reports Server (NTRS)

Miller, R. L.

1973-01-01

Voltage indicator fits into cigarette lighter socket and utilizes light emitting and Zener diodes to display three levels of battery voltage. Indicator is superior to typical conventional electrical system indicators in that it gives a positive discrete indication of battery voltage. It is simple, inexpensive, and rugged.

One-Piece Force-Transducer Body

NASA Technical Reports Server (NTRS)

Meyer, R. A.

1986-01-01

Rugged unit designed to operate in severe environment. Forcetransducer body designed for measurement of loads on specimens tested in hydrogen gas at temperatures up to 2,000 degree F (1,090 degree C). Body has symmetrical radial-shear-beam configuration and machined in one piece from bar stock.

A simple and efficient quasi 3-dimensional viscoelastic model and software for simulation of tapping-mode atomic force microscopy

DOE PAGES

Solares, Santiago D.

2015-11-26

This study introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretationmore » of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tappingmode imaging, for both of which the force curves exhibit the expected features. Lastly, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.« less

A simple and efficient quasi 3-dimensional viscoelastic model and software for simulation of tapping-mode atomic force microscopy.

PubMed

Solares, Santiago D

2015-01-01

This paper introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretation of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tapping-mode imaging, for both of which the force curves exhibit the expected features. Finally, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.

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.

Seismic migration in generalized coordinates

NASA Astrophysics Data System (ADS)

Arias, C.; Duque, L. F.

2017-06-01

Reverse time migration (RTM) is a technique widely used nowadays to obtain images of the earth’s sub-surface, using artificially produced seismic waves. This technique has been developed for zones with flat surface and when applied to zones with rugged topography some corrections must be introduced in order to adapt it. This can produce defects in the final image called artifacts. We introduce a simple mathematical map that transforms a scenario with rugged topography into a flat one. The three steps of the RTM can be applied in a way similar to the conventional ones just by changing the Laplacian in the acoustic wave equation for a generalized one. We present a test of this technique using the Canadian foothills SEG velocity model.

Atomic force microscopy reveals the mechanical design of a modular protein

PubMed Central

Li, Hongbin; Oberhauser, Andres F.; Fowler, Susan B.; Clarke, Jane; Fernandez, Julio M.

2000-01-01

Tandem modular proteins underlie the elasticity of natural adhesives, cell adhesion proteins, and muscle proteins. The fundamental unit of elastic proteins is their individually folded modules. Here, we use protein engineering to construct multimodular proteins composed of Ig modules of different mechanical strength. We examine the mechanical properties of the resulting tandem modular proteins by using single protein atomic force microscopy. We show that by combining modules of known mechanical strength, we can generate proteins with novel elastic properties. Our experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering. PMID:10823913

Atomic force microscopy reveals the mechanical design of a modular protein.

PubMed

Li, H; Oberhauser, A F; Fowler, S B; Clarke, J; Fernandez, J M

2000-06-06

Tandem modular proteins underlie the elasticity of natural adhesives, cell adhesion proteins, and muscle proteins. The fundamental unit of elastic proteins is their individually folded modules. Here, we use protein engineering to construct multimodular proteins composed of Ig modules of different mechanical strength. We examine the mechanical properties of the resulting tandem modular proteins by using single protein atomic force microscopy. We show that by combining modules of known mechanical strength, we can generate proteins with novel elastic properties. Our experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering.

Nonconservative dynamics in long atomic wires

NASA Astrophysics Data System (ADS)

Cunningham, Brian; Todorov, Tchavdar N.; Dundas, Daniel

2014-09-01

The effect of nonconservative current-induced forces on the ions in a defect-free metallic nanowire is investigated using both steady-state calculations and dynamical simulations. Nonconservative forces were found to have a major influence on the ion dynamics in these systems, but their role in increasing the kinetic energy of the ions decreases with increasing system length. The results illustrate the importance of nonconservative effects in short nanowires and the scaling of these effects with system size. The dependence on bias and ion mass can be understood with the help of a simple pen and paper model. This material highlights the benefit of simple preliminary steady-state calculations in anticipating aspects of brute-force dynamical simulations, and provides rule of thumb criteria for the design of stable quantum wires.

Contact stiffness and damping of liquid films in dynamic atomic force microscope

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

Xu, Rong-Guang; Leng, Yongsheng, E-mail: leng@gwu.edu

2016-04-21

The mechanical properties and dissipation behaviors of nanometers confined liquid films have been long-standing interests in surface force measurements. The correlation between the contact stiffness and damping of the nanoconfined film is still not well understood. We establish a novel computational framework through molecular dynamics (MD) simulation for the first time to study small-amplitude dynamic atomic force microscopy (dynamic AFM) in a simple nonpolar liquid. Through introducing a tip driven dynamics to mimic the mechanical oscillations of the dynamic AFM tip-cantilever assembly, we find that the contact stiffness and damping of the confined film exhibit distinct oscillations within 6-7 monolayermore » distances, and they are generally out-of-phase. For the solid-like film with integer monolayer thickness, further compression of the film before layering transition leads to higher stiffness and lower damping, while much lower stiffness and higher damping occur at non-integer monolayer distances. These two alternating mechanisms dominate the mechanical properties and dissipation behaviors of simple liquid films under cyclic elastic compression and inelastic squeeze-out. Our MD simulations provide a direct picture of correlations between the structural property, mechanical stiffness, and dissipation behavior of the nanoconfined film.« less

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Contact resonance atomic force microscopy imaging in air and water using photothermal excitation.

PubMed

Kocun, Marta; Labuda, Aleksander; Gannepalli, Anil; Proksch, Roger

2015-08-01

Contact Resonance Force Microscopy (CR-FM) is a leading atomic force microscopy technique for measuring viscoelastic nano-mechanical properties. Conventional piezo-excited CR-FM measurements have been limited to imaging in air, since the "forest of peaks" frequency response associated with acoustic excitation methods effectively masks the true cantilever resonance. Using photothermal excitation results in clean contact, resonance spectra that closely match the ideal frequency response of the cantilever, allowing unambiguous and simple resonance frequency and quality factor measurements in air and liquids alike. This extends the capabilities of CR-FM to biologically relevant and other soft samples in liquid environments. We demonstrate CR-FM in air and water on both stiff silicon/titanium samples and softer polystyrene-polyethylene-polypropylene polymer samples with the quantitative moduli having very good agreement between expected and measured values.

Practical Physics Labs: A Resource Manual.

ERIC Educational Resources Information Center

Goodwin, Peter

This resource manual focuses on physics labs that relate to the world around us and utilize simple equipment and situations. Forty-five laboratories are included that relate to thermodynamics, electricity, magnetism, dynamics, optics, wave transmission, centripetal force, and atomic physics. Each lab has three sections. The first section…

Nanotechnology in Space Exploration: Report of the National Nanotechnology Initiative Workshop Held in Palo Alto, California on 24-26 August 2004

DTIC Science & Technology

2006-01-01

Nanosensors and Instrumentation Nanotechnology in Space Exploration 19 simple, rugged design. Multiwalled carbon nanotube ( MWCNT ) cathodes were grown...probe tips. Existing approaches use both SWCNTs and MWCNTs . A unique fabrication process development at NASA Ames (see ref. [4] in Chapter 6...produces very robust MWCNT tips with a high aspect ratio (> 1 µm in length and 10 nm to 20 nm in diameter). In addition, a novel and simple tip sharpening

Predicting hydration Gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data.

PubMed

Garrido, Nuno M; Jorge, Miguel; Queimada, António J; Gomes, José R B; Economou, Ioannis G; Macedo, Eugénia A

2011-10-14

The Gibbs energy of hydration is an important quantity to understand the molecular behavior in aqueous systems at constant temperature and pressure. In this work we review the performance of some popular force fields, namely TraPPE, OPLS-AA and Gromos, in reproducing the experimental Gibbs energies of hydration of several alkyl-aromatic compounds--benzene, mono-, di- and tri-substituted alkylbenzenes--using molecular simulation techniques. In the second part of the paper, we report a new model that is able to improve such hydration energy predictions, based on Lennard Jones parameters from the recent TraPPE-EH force field and atomic partial charges obtained from natural population analysis of density functional theory calculations. We apply a scaling factor determined by fitting the experimental hydration energy of only two solutes, and then present a simple rule to generate atomic partial charges for different substituted alkyl-aromatics. This rule has the added advantages of eliminating the unnecessary assumption of fixed charge on every substituted carbon atom and providing a simple guideline for extrapolating the charge assignment to any multi-substituted alkyl-aromatic molecule. The point charges derived here yield excellent predictions of experimental Gibbs energies of hydration, with an overall absolute average deviation of less than 0.6 kJ mol(-1). This new parameter set can also give good predictive performance for other thermodynamic properties and liquid structural information.

A New Paradigm for Robotic Rovers

NASA Astrophysics Data System (ADS)

Clark, P. E.; Curtis, S. A.; Rilee, M. L.

We are in the process of developing rovers with extreme mobility needed to explore remote, rugged terrain. We call these systems Tetrahedral Explorer Technologies (TETs). Architecture is based on conformable tetrahedra, the simplest space-filling form, as building blocks, single or networked, where apices act as nodes from which struts reversibly deploy. The tetrahedral framework acts as a simple skeletal muscular structure. We have already prototyped a simple robotic walker from a single reconfigurable tetrahedron capable of tumbling and a more evolved 12Tetrahedral Walker, the Autonomous Landed Investigator (ALI), which has interior nodes for payload, more continuous motion, and is commandable through a user friendly interface. ALI is an EMS level mission concept which would allow autonomous in situ exploration of the lunar poles within the next decade. ALI would consist of one or more 12tetrahedral walkers capable of rapid locomotion with the many degrees of freedom and equipped for navigation in the unilluminated, inaccessible and thus largely unexplored rugged terrains where lunar resources are likely to be found: the Polar Regions. ALI walkers would act as roving reconnaissance teams for unexplored regions, analyzing samples along the way.

Integrated system for single leg walking

NASA Astrophysics Data System (ADS)

Simmons, Reid; Krotkov, Eric; Roston, Gerry

1990-07-01

The Carnegie Mellon University Planetary Rover project is developing a six-legged walking robot capable of autonomously navigating, exploring, and acquiring samples in rugged, unknown environments. This report describes an integrated software system capable of navigating a single leg of the robot over rugged terrain. The leg, based on an early design of the Ambler Planetary Rover, is suspended below a carriage that slides along rails. To walk, the system creates an elevation map of the terrain from laser scanner images, plans an appropriate foothold based on terrain and geometric constraints, weaves the leg through the terrain to position it above the foothold, contacts the terrain with the foot, and applies force enough to advance the carriage along the rails. Walking both forward and backward, the system has traversed hundreds of meters of rugged terrain including obstacles too tall to step over, trenches too deep to step in, closely spaced obstacles, and sand hills. The implemented system consists of a number of task-specific processes (two for planning, two for perception, one for real-time control) and a central control process that directs the flow of communication between processes.

Application of a simple column-switching ion chromatography technique for removal of matrix interferences and sensitive fluorescence determination of acidic compounds (pharmaceutical drugs) in complex samples.

PubMed

Muhammad, Nadeem; Subhani, Qamar; Wang, Fenglian; Guo, Dandan; Zhao, Qiming; Wu, Shuchao; Zhu, Yan

2017-09-15

This work illustrates the introduction of a simple, rugged and flexible column-switching ion chromatography (IC) technique for an automated on-line QuEChERS extracted samples extracts washing followed by sensitive fluorescence (FLD) determination of five acidic pharmaceutical drugs namely; clofibric acid (CLO), ibuprofen (IBU), aspirin (ASP), naproxen (NAP) and flurobrofen (FLU) in three complex samples (spinach, apple and hospital sewage sludge). An old anion exchange column IonPac ® AS11-HC was utilized as a pre-treatment column for on-line washing of inorganic and organic interferences followed by isocratic separation of five acidic drugs with another anion exchange IonPac ® AS12A analytical column by exploiting the column-switching technique. This novel method exhibited good linearity with correlation coefficients (r 2 ) for all drugs were in the range 0.976-0.996. The limit of detection and quantification of all five acidic drugs were in the range 0.024μg/kg to 8.70μg/kg and 0.082μg/kg to 0.029mg/kg, respectively, and better recoveries in the range 81.17-112.5% with percentage relative standard deviations (RSDs) less than 17.8% were obtained. This on-line sample pre-treatment method showed minimum matrix effect in the range of 0.87-1.25 except for aspirin. This simple rugged and flexible column-switching system required only 28min for maximum elimination of matrices and interferences in three complex samples extracts, isocratic separation of five acidic drugs and for the continuous regeneration of pre-treatment column prior to every subsequent analysis. Finally, this simple automated IC system was appeared so rugged and flexible, which can eliminate and wash out most of interference, impurities and matrices in complex samples, simply by adjusting the NaOH and acetonitrile concentration in washing mobile phase with maximum recoveries of acidic analytes of interest. Copyright © 2017. Published by Elsevier B.V.

Atomic Force Microscope Studies of the Fusion of Floating Lipid Bilayers

PubMed Central

Abdulreda, Midhat H.; Moy, Vincent T.

2007-01-01

This study investigated the fusion of apposing floating bilayers of egg L-α-phosphatidylcholine (egg PC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine. Atomic force microscope measurements of fusion forces under different compression rates were acquired to reveal the energy landscape of the fusion process under varied lipid composition and temperature. Between compression rates of ∼1000 and ∼100,000 pN/s, applied forces in the range from ∼100 to ∼500 pN resulted in fusion of floating bilayers. Our atomic force microscope measurements indicated that one main energy barrier dominated the fusion process. The acquired dynamic force spectra were fit with a simple model based on the transition state theory with the assumption that the fusion activation potential is linear. A significant shift in the energy landscape was observed when bilayer fluidity and composition were modified, respectively, by temperature and different cholesterol concentrations (15% ≤ chol ≤ 25%). Such modifications resulted in a more than twofold increase in the width of the fusion energy barrier for egg PC and 1,2-dimyristoyl-sn-glycero-3-phosphocholine floating bilayers. The addition of 25% cholesterol to egg PC bilayers increased the activation energy by ∼1.0 kBT compared with that of bilayers with egg PC alone. These results reveal that widening of the energy barrier and consequently reduction in its slope facilitated membrane fusion. PMID:17400691

Atomic force microscope studies of the fusion of floating lipid bilayers.

PubMed

Abdulreda, Midhat H; Moy, Vincent T

2007-06-15

This study investigated the fusion of apposing floating bilayers of egg L-alpha-phosphatidylcholine (egg PC) or 1,2-dimyristoyl-sn-glycero-3-phosphocholine. Atomic force microscope measurements of fusion forces under different compression rates were acquired to reveal the energy landscape of the fusion process under varied lipid composition and temperature. Between compression rates of approximately 1000 and approximately 100,000 pN/s, applied forces in the range from approximately 100 to approximately 500 pN resulted in fusion of floating bilayers. Our atomic force microscope measurements indicated that one main energy barrier dominated the fusion process. The acquired dynamic force spectra were fit with a simple model based on the transition state theory with the assumption that the fusion activation potential is linear. A significant shift in the energy landscape was observed when bilayer fluidity and composition were modified, respectively, by temperature and different cholesterol concentrations (15% < or = chol < or = 25%). Such modifications resulted in a more than twofold increase in the width of the fusion energy barrier for egg PC and 1,2-dimyristoyl-sn-glycero-3-phosphocholine floating bilayers. The addition of 25% cholesterol to egg PC bilayers increased the activation energy by approximately 1.0 k(B)T compared with that of bilayers with egg PC alone. These results reveal that widening of the energy barrier and consequently reduction in its slope facilitated membrane fusion.

Atomic force microscopy based nanoindentation study of onion abaxial epidermis walls in aqueous environment

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

Xi, Xiaoning; Tittmann, Bernhard; Kim, Seong H.

An atomic force microscopy based nanoindentation method was employed to study how the structure of cellulose microfibril packing and matrix polymers affect elastic modulus of fully hydrated primary plant cell walls. The isolated, single-layered abaxial epidermis cell wall of an onion bulb was used as a test system since the cellulose microfibril packing in this cell wall is known to vary systematically from inside to outside scales and the most abundant matrix polymer, pectin, can easily be altered through simple chemical treatments such as ethylenediaminetetraacetic acid and calcium ions. Experimental results showed that the pectin network variation has significant impactsmore » on the cell wall modulus, and not the cellulose microfibril packing.« less

Imaging of viscoelastic soft matter with small indentation using higher eigenmodes in single-eigenmode amplitude-modulation atomic force microscopy.

PubMed

Nikfarjam, Miead; López-Guerra, Enrique A; Solares, Santiago D; Eslami, Babak

2018-01-01

In this short paper we explore the use of higher eigenmodes in single-eigenmode amplitude-modulation atomic force microscopy (AFM) for the small-indentation imaging of soft viscoelastic materials. In viscoelastic materials, whose response depends on the deformation rate, the tip-sample forces generated as a result of sample deformation increase as the tip velocity increases. Since the eigenfrequencies in a cantilever increase with eigenmode order, and since higher oscillation frequencies lead to higher tip velocities for a given amplitude (in viscoelastic materials), the sample indentation can in some cases be reduced by using higher eigenmodes of the cantilever. This effect competes with the lower sensitivity of higher eigenmodes, due to their larger force constant, which for elastic materials leads to greater indentation for similar amplitudes, compared with lower eigenmodes. We offer a short theoretical discussion of the key underlying concepts, along with numerical simulations and experiments to illustrate a simple recipe for imaging soft viscoelastic matter with reduced indentation.

Nanoindentation hardness and atomic force microscope imaging studies of pressure-quenched zirconium metal

NASA Astrophysics Data System (ADS)

Catledge, Shane A.; Spencer, Philemon T.; Vohra, Yogesh K.

2000-11-01

We have carried out mechanical property measurements on zirconium metal compressed in a diamond anvil cell to 19 GPa at room temperature with subsequent quenching to room pressure. The irreversible transformation from the ambient hexagonal-close-packed phase to the simple hexagonal ω phase (AlB2 structure) is confirmed by synchrotron energy dispersive x-ray diffraction followed by nanoindentation of the pressure-quenched sample. We document an 80% increase in hardness as a consequence of the pressure-induced transformation to the ω phase at room temperature. This is a large increase for a metallic phase transformation and can be attributed to the presence of sp2-hybrid bonds forming graphite-like nets in the (0001) plane of the AlB2 structure. Atomic force microscopy of the indents shows that a plastic deformation of 2 μm in depth was achieved with a force of 200 mN.

Contact resonance atomic force microscopy imaging in air and water using photothermal excitation

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

Kocun, Marta; Labuda, Aleksander; Gannepalli, Anil

2015-08-15

Contact Resonance Force Microscopy (CR-FM) is a leading atomic force microscopy technique for measuring viscoelastic nano-mechanical properties. Conventional piezo-excited CR-FM measurements have been limited to imaging in air, since the “forest of peaks” frequency response associated with acoustic excitation methods effectively masks the true cantilever resonance. Using photothermal excitation results in clean contact, resonance spectra that closely match the ideal frequency response of the cantilever, allowing unambiguous and simple resonance frequency and quality factor measurements in air and liquids alike. This extends the capabilities of CR-FM to biologically relevant and other soft samples in liquid environments. We demonstrate CR-FM inmore » air and water on both stiff silicon/titanium samples and softer polystyrene-polyethylene-polypropylene polymer samples with the quantitative moduli having very good agreement between expected and measured values.« less

Evaluation of the electrical contact area in contact-mode scanning probe microscopy

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

Celano, Umberto, E-mail: celano@imec.be, E-mail: u.celano@gmail.com; Chintala, Ravi Chandra; Vandervorst, Wilfried

The tunneling current through an atomic force microscopy (AFM) tip is used to evaluate the effective electrical contact area, which exists between tip and sample in contact-AFM electrical measurements. A simple procedure for the evaluation of the effective electrical contact area is described using conductive atomic force microscopy (C-AFM) in combination with a thin dielectric. We characterize the electrical contact area for coated metal and doped-diamond tips operated at low force (<200 nN) in contact mode. In both cases, we observe that only a small fraction (<10 nm{sup 2}) of the physical contact (∼100 nm{sup 2}) is effectively contributing to the transportmore » phenomena. Assuming this reduced area is confined to the central area of the physical contact, these results explain the sub-10 nm electrical resolution observed in C-AFM measurements.« less

Measuring the mechanical properties of molecular conformers

NASA Astrophysics Data System (ADS)

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

2015-09-01

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

Precise and direct method for the measurement of the torsion spring constant of the atomic force microscopy cantilevers

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

Jarząbek, D. M., E-mail: djarz@ippt.pan.pl

2015-01-15

A direct method for the evaluation of the torsional spring constants of the atomic force microscope cantilevers is presented in this paper. The method uses a nanoindenter to apply forces at the long axis of the cantilever and in the certain distance from it. The torque vs torsion relation is then evaluated by the comparison of the results of the indentations experiments at different positions on the cantilever. Next, this relation is used for the precise determination of the torsional spring constant of the cantilever. The statistical analysis shows that the standard deviation of the calibration measurements is equal tomore » approximately 1%. Furthermore, a simple method for calibration of the photodetector’s lateral response is proposed. The overall procedure of the lateral calibration constant determination has the accuracy approximately equal to 10%.« less

Native flexibility of structurally homologous proteins: insights from anisotropic network model.

PubMed

Sarkar, Ranja

2017-01-01

Single-molecule microscopic experiments can measure the mechanical response of proteins to pulling forces applied externally along different directions (inducing different residue pairs in the proteins by uniaxial tension). This response to external forces away from equilibrium should in principle, correlate with the flexibility or stiffness of proteins in their folded states. Here, a simple topology-based atomistic anisotropic network model (ANM) is shown which captures the protein flexibility as a fundamental property that determines the collective dynamics and hence, the protein conformations in native state. An all-atom ANM is used to define two measures of protein flexibility in the native state. One measure quantifies overall stiffness of the protein and the other one quantifies protein stiffness along a particular direction which is effectively the mechanical resistance of the protein towards external pulling force exerted along that direction. These measures are sensitive to the protein sequence and yields reliable values through computations of normal modes of the protein. ANM at an atomistic level (heavy atoms) explains the experimental (atomic force microscopy) observations viz., different mechanical stability of structurally similar but sequentially distinct proteins which, otherwise were implied to possess similar mechanical properties from analytical/theoretical coarse-grained (backbone only) models. The results are exclusively demonstrated for human fibronectin (FN) protein domains. The topology of interatomic contacts in the folded states of proteins essentially determines the native flexibility. The mechanical differences of topologically similar proteins are captured from a high-resolution (atomic level) ANM at a low computational cost. The relative trend in flexibility of such proteins is reflected in their stability differences that they exhibit while unfolding in atomic force microscopic (AFM) experiments.

Mechanical Characterization of Microengineered Epithelial Cysts by Using Atomic Force Microscopy.

PubMed

Shen, Yusheng; Guan, Dongshi; Serien, Daniela; Takeuchi, Shoji; Tong, Penger; Yobas, Levent; Huang, Pingbo

2017-01-24

Most organs contain interconnected tubular tissues that are one-cell-thick, polarized epithelial monolayers enclosing a fluid-filled lumen. Such tissue organization plays crucial roles in developmental and normal physiology, and the proper functioning of these tissues depends on their regulation by complex biochemical perturbations and equally important, but poorly understood, mechanical perturbations. In this study, by combining micropatterning techniques and atomic force microscopy, we developed a simple in vitro experimental platform for characterizing the mechanical properties of the MDCK II cyst, the simplest model of lumen-enclosing epithelial monolayers. By using this platform, we estimated the elasticity of the cyst monolayer and showed that the presence of a luminal space influences cyst mechanics substantially, which could be attributed to polarization and tissue-level coordination. More interestingly, the results from force-relaxation experiments showed that the cysts also displayed tissue-level poroelastic characteristics that differed slightly from those of single cells. Our study provides the first quantitative findings, to our knowledge, on the tissue-level mechanics of well-polarized epithelial cysts and offers new insights into the interplay between cyst mechanics and cyst physiology. Moreover, our simple platform is a potentially useful tool for enhancing the current understanding of cyst mechanics in health and disease. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

Morante, S., E-mail: morante@roma2.infn.it; Rossi, G.C., E-mail: rossig@roma2.infn.it; Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Compendio del Viminale, Piazza del Viminale 1, I-00184 Rome

We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg–Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann–Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.

Bifurcation, chaos, and scan instability in dynamic atomic force microscopy

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

Cantrell, John H., E-mail: john.h.cantrell@nasa.gov; Cantrell, Sean A., E-mail: scantrell@nlsanalytics.com

The dynamical motion at any point on the cantilever of an atomic force microscope can be expressed quite generally as a superposition of simple harmonic oscillators corresponding to the vibrational modes allowed by the cantilever shape. Central to the dynamical equations is the representation of the cantilever-sample interaction force as a polynomial expansion with coefficients that account for the interaction force “stiffness,” the cantilever-to-sample energy transfer, and the displacement amplitude of cantilever oscillation. Renormalization of the cantilever beam model shows that for a given cantilever drive frequency cantilever dynamics can be accurately represented by a single nonlinear mass-spring model withmore » frequency-dependent stiffness and damping coefficients [S. A. Cantrell and J. H. Cantrell, J. Appl. Phys. 110, 094314 (2011)]. Application of the Melnikov method to the renormalized dynamical equation is shown to predict a cascade of period doubling bifurcations with increasing cantilever drive force that terminates in chaos. The threshold value of the drive force necessary to initiate bifurcation is shown to depend strongly on the cantilever setpoint and drive frequency, effective damping coefficient, nonlinearity of the cantilever-sample interaction force, and the displacement amplitude of cantilever oscillation. The model predicts the experimentally observed interruptions of the bifurcation cascade for cantilevers of sufficiently large stiffness. Operational factors leading to the loss of image quality in dynamic atomic force microscopy are addressed, and guidelines for optimizing scan stability are proposed using a quantitative analysis based on system dynamical parameters and choice of feedback loop parameter.« less

Laser controlled atom source for optical clocks.

PubMed

Kock, Ole; He, Wei; Świerad, Dariusz; Smith, Lyndsie; Hughes, Joshua; Bongs, Kai; Singh, Yeshpal

2016-11-18

Precision timekeeping has been a driving force in innovation, from defining agricultural seasons to atomic clocks enabling satellite navigation, broadband communication and high-speed trading. We are on the verge of a revolution in atomic timekeeping, where optical clocks promise an over thousand-fold improvement in stability and accuracy. However, complex setups and sensitivity to thermal radiation pose limitations to progress. Here we report on an atom source for a strontium optical lattice clock which circumvents these limitations. We demonstrate fast (sub 100 ms), cold and controlled emission of strontium atomic vapours from bulk strontium oxide irradiated by a simple low power diode laser. Our results demonstrate that millions of strontium atoms from the vapour can be captured in a magneto-optical trap (MOT). Our method enables over an order of magnitude reduction in scale of the apparatus. Future applications range from satellite clocks testing general relativity to portable clocks for inertial navigation systems and relativistic geodesy.

Laser controlled atom source for optical clocks

PubMed Central

Kock, Ole; He, Wei; Świerad, Dariusz; Smith, Lyndsie; Hughes, Joshua; Bongs, Kai; Singh, Yeshpal

2016-01-01

Precision timekeeping has been a driving force in innovation, from defining agricultural seasons to atomic clocks enabling satellite navigation, broadband communication and high-speed trading. We are on the verge of a revolution in atomic timekeeping, where optical clocks promise an over thousand-fold improvement in stability and accuracy. However, complex setups and sensitivity to thermal radiation pose limitations to progress. Here we report on an atom source for a strontium optical lattice clock which circumvents these limitations. We demonstrate fast (sub 100 ms), cold and controlled emission of strontium atomic vapours from bulk strontium oxide irradiated by a simple low power diode laser. Our results demonstrate that millions of strontium atoms from the vapour can be captured in a magneto-optical trap (MOT). Our method enables over an order of magnitude reduction in scale of the apparatus. Future applications range from satellite clocks testing general relativity to portable clocks for inertial navigation systems and relativistic geodesy. PMID:27857214

The possibility of multi-layer nanofabrication via atomic force microscope-based pulse electrochemical nanopatterning

NASA Astrophysics Data System (ADS)

Kim, Uk Su; Morita, Noboru; Lee, Deug Woo; Jun, Martin; Park, Jeong Woo

2017-05-01

Pulse electrochemical nanopatterning, a non-contact scanning probe lithography process using ultrashort voltage pulses, is based primarily on an electrochemical machining process using localized electrochemical oxidation between a sharp tool tip and the sample surface. In this study, nanoscale oxide patterns were formed on silicon Si (100) wafer surfaces via electrochemical surface nanopatterning, by supplying external pulsed currents through non-contact atomic force microscopy. Nanoscale oxide width and height were controlled by modulating the applied pulse duration. Additionally, protruding nanoscale oxides were removed completely by simple chemical etching, showing a depressed pattern on the sample substrate surface. Nanoscale two-dimensional oxides, prepared by a localized electrochemical reaction, can be defined easily by controlling physical and electrical variables, before proceeding further to a layer-by-layer nanofabrication process.

Unexpected Huge Dimerization Ratio in One-Dimensional Carbon Atomic Chains.

PubMed

Lin, Yung-Chang; Morishita, Shigeyuki; Koshino, Masanori; Yeh, Chao-Hui; Teng, Po-Yuan; Chiu, Po-Wen; Sawada, Hidetaka; Suenaga, Kazutomo

2017-01-11

Peierls theory predicted atomic distortion in one-dimensional (1D) crystal due to its intrinsic instability in 1930. Free-standing carbon atomic chains created in situ in transmission electron microscope (TEM)1-3 are an ideal example to experimentally observe the dimerization behavior of carbon atomic chain within a finite length. We report here a surprisingly huge distortion found in the free-standing carbon atomic chains at 773 K, which is 10 times larger than the value expected in the system. Such an abnormally distorted phase only dominates at the elevated temperatures, while two distinct phases, distorted and undistorted, coexist at lower or ambient temperatures. Atom-by-atom spectroscopy indeed shows considerable variations in the carbon 1s spectra at each atomic site but commonly observes a slightly downshifted π* peak, which proves its sp 1 bonding feature. These results suggest that the simple model, relaxed and straight, is not fully adequate to describe the realistic 1D structure, which is extremely sensitive to perturbations such as external force or boundary conditions.

Bubble colloidal AFM probes formed from ultrasonically generated bubbles.

PubMed

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

2008-02-05

Here we introduce a simple and effective experimental approach to measuring the interaction forces between two small bubbles (approximately 80-140 microm) in aqueous solution during controlled collisions on the scale of micrometers to nanometers. The colloidal probe technique using atomic force microscopy (AFM) was extended to measure interaction forces between a cantilever-attached bubble and surface-attached bubbles of various sizes. By using an ultrasonic source, we generated numerous small bubbles on a mildly hydrophobic surface of a glass slide. A single bubble picked up with a strongly hydrophobized V-shaped cantilever was used as the colloidal probe. Sample force measurements were used to evaluate the pure water bubble cleanliness and the general consistency of the measurements.

Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature.

PubMed

Nguyen, Phuong H; Derreumaux, Philippe

2012-01-14

One challenge in computational biophysics and biology is to develop methodologies able to estimate accurately the configurational entropy of macromolecules. Among many methods, the quasiharmonic approximation (QH) is most widely used as it is simple in both theory and implementation. However, it has been shown that this method becomes inaccurate by overestimating entropy for systems with rugged free energy landscapes. Here, we propose a simple method to improve the QH approximation, i.e., to reduce QH entropy. We approximate the potential energy landscape of the system by an effective harmonic potential, and request that this potential must produce exactly the configurational temperature of the system. Due to this constraint, the force constants associated with the effective harmonic potential are increased, or equivalently, entropy of motion governed by this effective harmonic potential is reduced. We also introduce the effective configurational temperature concept which can be used as an indicator to check the anharmonicity of the free energy landscape. To validate the new method we compare it with the recently developed expansion approximate method by calculating entropy of one simple model system and two peptides with 3 and 16 amino acids either in gas phase or in explicit solvent. We show that the new method appears to be a good choice in practice as it is a compromise between accuracy and computational speed. A modification of the expansion approximate method is also introduced and advantages are discussed in some detail.

Internal Energy Transfer and Dissociation Model Development using Accelerated First-Principles Simulations of Hypersonic Flow Features

DTIC Science & Technology

2013-07-09

through a potential energy surface (PES), such as the simple Lennard - Jones (LJ) PES [23] shown in the inset of Fig. 3, which is given by the following...a  normal  shock  wave.  Inset  shows  a   simple   Lennard -­‐ Jones  (LJ)   potential  energy  surface  (PES)  dictating...model input into such simulations is the potential energy surface (PES) that governs individual atomic interaction forces, developed by chemists and

Multi-Spoked Wheel Assembly

NASA Technical Reports Server (NTRS)

Greer, Lawrence (Inventor); Krasowski, Michael (Inventor)

2017-01-01

A robust ground traction (drive) assembly for remotely controlled vehicles, which not only operates smoothly on surfaces that are flat, but also upon surfaces that include rugged terrain, snow, mud, and sand, is provided. The assembly includes a sun gear and a braking gear. The sun gear is configured to cause rotational force to be applied to second planetary gears through a coupling of first planetary gears. The braking gear is configured to cause the assembly (or the second planetary gears) to rotate around the braking gear when an obstacle or braking force is applied.

Field Demonstration of a Novel Biotreatment Process for Perchlorate Reduction in Groundwater

DTIC Science & Technology

2010-06-01

biological reduction and/or reaction with ZVI, and arsenic hexavalent chromium and/or uranium by adsorption on corrosion products. • Simple rugged...problems and troubleshooting measures ................................... 22 5.2 Laboratory Evaluation of Porosity Decrease and Corrosion Products...reactor when it was dismantled showing the heavy deposits of iron corrosion products and quasi total loss of porosity. Figure 5.14 Picture of the column

Growth of near-infrared spectroscopy in pharmaceutical and medical sciences

NASA Astrophysics Data System (ADS)

Ciurczak, Emil W.

2002-06-01

Near-IR Spectroscopy (NIRS) is used extensively in the health services industries: medical research, pharmaceutical production, and bioprocessing. NIRS Is rugged, simple to operate, flexible, and relatively inexpensive. It may be used to monitor the progress biochemical reactions. It is used to control mixing, blending, drying, and coating in pharmaceutical production and is used for imaging and chemical determinations in living patients.

Characterization of the surface charge distribution on kaolinite particles using high resolution atomic force microscopy

NASA Astrophysics Data System (ADS)

Kumar, Naveen; Zhao, Cunlu; Klaassen, Aram; van den Ende, Dirk; Mugele, Frieder; Siretanu, Igor

2016-02-01

Most solid surfaces, in particular clay minerals and rock surfaces, acquire a surface charge upon exposure to an aqueous environment due to adsorption and/or desorption of ionic species. Macroscopic techniques such as titration and electrokinetic measurements are commonly used to determine the surface charge and ζ -potential of these surfaces. However, because of the macroscopic averaging character these techniques cannot do justice to the role of local heterogeneities on the surfaces. In this work, we use dynamic atomic force microscopy (AFM) to determine the distribution of surface charge on the two (gibbsite-like and silica-like) basal planes of kaolinite nanoparticles immersed in aqueous electrolyte with a lateral resolution of approximately 30 nm. The surface charge density is extracted from force-distance curves using DLVO theory in combination with surface complexation modeling. While the gibbsite-like and the silica-like facet display on average positive and negative surface charge values as expected, our measurements reveal lateral variations of more than a factor of two on seemingly atomically smooth terraces, even if high resolution AFM images clearly reveal the atomic lattice on the surface. These results suggest that simple surface complexation models of clays that attribute a unique surface chemistry and hence homogeneous surface charge densities to basal planes may miss important aspects of real clay surfaces.

Contact area of rough spheres: Large scale simulations and simple scaling laws

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

Pastewka, Lars, E-mail: lars.pastewka@kit.edu; Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218; Robbins, Mark O., E-mail: mr@pha.jhu.edu

2016-05-30

We use molecular simulations to study the nonadhesive and adhesive atomic-scale contact of rough spheres with radii ranging from nanometers to micrometers over more than ten orders of magnitude in applied normal load. At the lowest loads, the interfacial mechanics is governed by the contact mechanics of the first asperity that touches. The dependence of contact area on normal force becomes linear at intermediate loads and crosses over to Hertzian at the largest loads. By combining theories for the limiting cases of nominally flat rough surfaces and smooth spheres, we provide parameter-free analytical expressions for contact area over the wholemore » range of loads. Our results establish a range of validity for common approximations that neglect curvature or roughness in modeling objects on scales from atomic force microscope tips to ball bearings.« less

Naalyehe Ba Hooghan--"House of Merchandise": The Navajo Trading Post as an Institution of Cultural Change, 1900 to 1930.

ERIC Educational Resources Information Center

McPherson, Robert S.

1992-01-01

Navajo Reservation trading posts held an influential position between two cultures and operated on Navajo terms but also were an assimilative force emphasizing white values through the marketing of Navajo wool and rugs, traffic in prehistoric artifacts, and employment of Navajos in a mixed barter and wage economy. (SV)

Construction and performance of rugged ceramic cup soil water samplers

Treesearch

Douglas M. Stone; James L. Robl

1996-01-01

To assess solute concentration changes associated with soil compaction and organic matter removal resulting from forest harvesting, we constructed and field tested ceramic cup soil water samplers designed to withstand the forces of compaction by heavy equipment. They were installed with the cup at either the 30-or 60-cm depth; the vacuum and collection tubes rested on...

Electronic Transport Through Carbon Nanotubes: Effects of Structural Deformation and the Tube Chirality

NASA Technical Reports Server (NTRS)

Maiti, Amitesh; Svizhenko, Alexei; Anantram, M. P.; Biegel, Bryan (Technical Monitor)

2001-01-01

Atomistic simulations using a combination of classical force field and Density-Functional-Theory (DFT) show that carbon atoms remain essentially sp2 coordinated in either bent tubes or tubes pushed by an atomically sharp AFM tip. Subsequent Green's-function-based transport calculations reveal that for armchair tubes there is no significant drop in conductance, while for zigzag tubes the conductance can drop by several orders of magnitude in AFM-pushed tubes. The effect can be attributed to simple stretching of the tube under tip deformation, which opens up an energy gap at the Fermi surface.

Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis.

PubMed

Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

2009-12-31

To systematically construct a low-dimensional free-energy landscape of RNA systems from a classical molecular dynamics simulation, various versions of the principal component analysis (PCA) are compared: the cPCA using the Cartesian coordinates of all atoms, the dPCA using the sine/cosine-transformed six backbone dihedral angles as well as the glycosidic torsional angle chi and the pseudorotational angle P, the aPCA which ignores the circularity of the 6 + 2 dihedral angles of the RNA, and the dPCA(etatheta), which approximates the 6 backbone dihedral angles by 2 pseudotorsional angles eta and theta. As representative examples, a 10-nucleotide UUCG hairpin and the 36-nucleotide segment SL1 of the Psi site of HIV-1 are studied by classical molecular dynamics simulation, using the Amber all-atom force field and explicit solvent. It is shown that the conformational heterogeneity of the RNA hairpins can only be resolved by an angular PCA such as the dPCA but not by the cPCA using Cartesian coordinates. Apart from possible artifacts due to the coupling of overall and internal motion, this is because the details of hydrogen bonding and stacking interactions but also of global structural rearrangements of the RNA are better discriminated by dihedral angles. In line with recent experiments, it is found that the free energy landscape of RNA hairpins is quite rugged and contains various metastable conformational states which may serve as an intermediate for unfolding.

The Biotin/Avidin complex adhesion force

NASA Astrophysics Data System (ADS)

Balsera, Manel A.; Izrailev, Sergei; Stepaniants, Sergey; Oono, Yoshitsugu; Schulten, Klaus

1997-03-01

The vitamin Biotin and the protein avidin form one of the strongest non-covalent bonds between biological molecules. We have performed molecular and stochastic dynamic modeling of the unbinding of this complex(Izrailev et al., Biophysical Journal, In press). These simulations provide insight into the effect of particular residues and water on the tight binding of the system. With the aid of simple phenomenological models we have related qualitatively our results to Atomic Force Microscopy adhesion force measurements (E.-L. Florin, V. T. Moy and H. E. Gaub Science) 264:415-417 and kinetic dissociation experiments( A. Chilcotti and P. S. Stayton, J. Am. Chem. Soc.) 117:10622-10628. We will discuss the difficulties preventing a more quantitative understanding of the unbinding force and kinetics.

Heading for the Hills: Risk Avoidance Drives Den Site Selection in African Wild Dogs

PubMed Central

Jackson, Craig R.; Power, R. John; Groom, Rosemary J.; Masenga, Emmanuel H.; Mjingo, Ernest E.; Fyumagwa, Robert D.; Røskaft, Eivin; Davies-Mostert, Harriet

2014-01-01

Compared to their main competitors, African wild dogs (Lycaon pictus) have inferior competitive abilities and interspecific competition is a serious fitness-limiting factor. Lions (Panthera leo) are the dominant large carnivore in African savannah ecosystems and wild dogs avoid them both spatially and temporally. Wild dog young are particularly vulnerable and suffer high rates of mortality from lions. Since lions do not utilize all parts of the landscape with an equal intensity, spatial variation in lion densities can be exploited by wild dogs both during their general ranging behaviour, but more specifically when they are confined to a den with vulnerable young. Since patches of rugged terrain are associated with lower lion densities, we hypothesized that these comparatively safe habitats should be selected by wild dogs for denning. We investigated the relationship between the distribution of 100 wild dog den sites and the occurrence of rugged terrain in four wild dog populations located in Tanzania, Zimbabwe and South Africa. A terrain ruggedness index was derived from a 90 m digital elevation model and used to map terrain ruggedness at each site. We compared characteristics of actual and potential (random) den sites to determine how wild dogs select den sites. The distributions of wild dog dens were strongly associated with rugged terrain and wild dogs actively selected terrain that was more rugged than that available on average. The likelihood of encountering lions is reduced in these habitats, minimizing the risk to both adults and pups. Our findings have important implications for the conservation management of the species, especially when assessing habitat suitability for potential reintroductions. The simple technique used to assess terrain ruggedness may be useful to investigate habitat suitability, and even predict highly suitable denning areas, across large landscapes. PMID:24918935

Heading for the hills: risk avoidance drives den site selection in African wild dogs.

PubMed

Jackson, Craig R; Power, R John; Groom, Rosemary J; Masenga, Emmanuel H; Mjingo, Ernest E; Fyumagwa, Robert D; Røskaft, Eivin; Davies-Mostert, Harriet

2014-01-01

Compared to their main competitors, African wild dogs (Lycaon pictus) have inferior competitive abilities and interspecific competition is a serious fitness-limiting factor. Lions (Panthera leo) are the dominant large carnivore in African savannah ecosystems and wild dogs avoid them both spatially and temporally. Wild dog young are particularly vulnerable and suffer high rates of mortality from lions. Since lions do not utilize all parts of the landscape with an equal intensity, spatial variation in lion densities can be exploited by wild dogs both during their general ranging behaviour, but more specifically when they are confined to a den with vulnerable young. Since patches of rugged terrain are associated with lower lion densities, we hypothesized that these comparatively safe habitats should be selected by wild dogs for denning. We investigated the relationship between the distribution of 100 wild dog den sites and the occurrence of rugged terrain in four wild dog populations located in Tanzania, Zimbabwe and South Africa. A terrain ruggedness index was derived from a 90 m digital elevation model and used to map terrain ruggedness at each site. We compared characteristics of actual and potential (random) den sites to determine how wild dogs select den sites. The distributions of wild dog dens were strongly associated with rugged terrain and wild dogs actively selected terrain that was more rugged than that available on average. The likelihood of encountering lions is reduced in these habitats, minimizing the risk to both adults and pups. Our findings have important implications for the conservation management of the species, especially when assessing habitat suitability for potential reintroductions. The simple technique used to assess terrain ruggedness may be useful to investigate habitat suitability, and even predict highly suitable denning areas, across large landscapes.

Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins

NASA Astrophysics Data System (ADS)

Egwolf, Bernhard; Tavan, Paul

2003-02-01

We present a continuum approach for efficient and accurate calculation of reaction field forces and energies in classical molecular-dynamics (MD) simulations of proteins in water. The derivation proceeds in two steps. First, we reformulate the electrostatics of an arbitrarily shaped molecular system, which contains partially charged atoms and is embedded in a dielectric continuum representing the water. A so-called fuzzy partition is used to exactly decompose the system into partial atomic volumes. The reaction field is expressed by means of dipole densities localized at the atoms. Since these densities cannot be calculated analytically for general systems, we introduce and carefully analyze a set of approximations in a second step. These approximations allow us to represent the dipole densities by simple dipoles localized at the atoms. We derive a system of linear equations for these dipoles, which can be solved numerically by iteration. After determining the two free parameters of our approximate method we check its quality by comparisons (i) with an analytical solution, which is available for a perfectly spherical system, (ii) with forces obtained from a MD simulation of a soluble protein in water, and (iii) with reaction field energies of small molecules calculated by a finite difference method.

Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

PubMed

Yong, Chin W

2016-08-22

DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.

A New Method for Unconstrained Heart Rate Monitoring

DTIC Science & Technology

2001-10-25

members. However, care of bedridden elderly persons are not easy task, and this caused severe psychological and financial problems for other family...physical and mental conditions of bedridden elderly people at home and patients at hospitals and to contribute to the labor saving of the care and the...not suitable for home care of bedridden elderly people. Our method provides very small, simple and mechanically rugged device suitable for home

Rugged Ozone Sterilization System Model M1 (ROSS M1)

DTIC Science & Technology

2017-07-13

water consumption , power requirements, and reliability). Special Forces personnel would benefit from the advantages of modern technology with the...chemical, heat, and radiation sterilization methods. At the end of the sterilization cycle, ozone and VHP are converted into oxygen and water vapor...chamber (Figure 7) was built to evaluate device operation over a range of environmental conditions ( temperature , humidity, pressure). Each component

Daniell method for power spectral density estimation in atomic force microscopy

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

Labuda, Aleksander

An alternative method for power spectral density (PSD) estimation—the Daniell method—is revisited and compared to the most prevalent method used in the field of atomic force microscopy for quantifying cantilever thermal motion—the Bartlett method. Both methods are shown to underestimate the Q factor of a simple harmonic oscillator (SHO) by a predictable, and therefore correctable, amount in the absence of spurious deterministic noise sources. However, the Bartlett method is much more prone to spectral leakage which can obscure the thermal spectrum in the presence of deterministic noise. By the significant reduction in spectral leakage, the Daniell method leads to amore » more accurate representation of the true PSD and enables clear identification and rejection of deterministic noise peaks. This benefit is especially valuable for the development of automated PSD fitting algorithms for robust and accurate estimation of SHO parameters from a thermal spectrum.« less

Investigation of static and dynamic behavior of functionally graded piezoelectric actuated Poly-Si micro cantilever probe

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

Pandey, Vibhuti Bhushan; Parashar, Sandeep Kumar, E-mail: skparashar@rtu.ac.in

In the present paper a novel functionally graded piezoelectric (FGP) actuated Poly-Si micro cantilever probe is proposed for atomic force microscope. The shear piezoelectric coefficient d{sub 15} has much higher value than coupling coefficients d{sub 31} and d{sub 33}, hence in the present work the micro cantilever beam actuated by d{sub 15} effect is utilized. The material properties are graded in the thickness direction of actuator by a simple power law. A three dimensional finite element analysis has been performed using COMSOL Multiphysics® (version 4.2) software. Tip deflection and free vibration analysis for the micro cantilever probe has been done.more » The results presented in the paper shall be useful in the design of micro cantilever probe and their subsequent utilization in atomic force microscopes.« less

Development of liquid-environment frequency modulation atomic force microscope with low noise deflection sensor for cantilevers of various dimensions

NASA Astrophysics Data System (ADS)

Fukuma, Takeshi; Jarvis, Suzanne P.

2006-04-01

We have developed a liquid-environment frequency modulation atomic force microscope (FM-AFM) with a low noise deflection sensor for a wide range of cantilevers with different dimensions. A simple yet accurate equation describing the theoretical limit of the optical beam deflection method in air and liquid is presented. Based on the equation, we have designed a low noise deflection sensor. Replaceable microscope objective lenses are utilized for providing a high magnification optical view (resolution: <3μm) as well as for focusing a laser beam (laser spot size: ˜10μm). Even for a broad range of cantilevers with lengths from 35to125μm, the sensor provides deflection noise densities of less than 11fm/√Hz in air and 16fm/√Hz in water. In particular, a cantilever with a length of 50μm gives the minimum deflection noise density of 5.7fm/√Hz in air and 7.3fm/√Hz in water. True atomic resolution of the developed FM-AFM is demonstrated by imaging mica in water.

Frustration-guided motion planning reveals conformational transitions in proteins

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

Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here in this paper, we present a new, robotics-inspired motion planning procedure called dCCRRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eightmore » proteins determined in two conformations separated by, on average, 7.5Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. Additionally, we then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions.Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/.« less

Frustration-guided motion planning reveals conformational transitions in proteins.

PubMed

Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid; van den Bedem, Henry

2017-10-01

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here, we present a new, robotics-inspired motion planning procedure called dCC-RRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5 Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. We then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25 Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions. Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/. © 2017 Wiley Periodicals, Inc.

Frustration-guided motion planning reveals conformational transitions in proteins

DOE PAGES

Budday, Dominik; Fonseca, Rasmus; Leyendecker, Sigrid; ...

2017-07-12

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here in this paper, we present a new, robotics-inspired motion planning procedure called dCCRRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eightmore » proteins determined in two conformations separated by, on average, 7.5Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. Additionally, we then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions.Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/.« less

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.

HIGH SENSITIVITY ELECTROSCOPE

DOEpatents

Shonka, F.R.; Okleshen, A.J.

1958-08-12

An electrometer with dependable and rugged construction for measuring cxtremely small charges is de scribed. The electrometer arrangement comprises an electrically conducting fiber totally disposed in a single plane in the absence of electrosthtic forces and affixed at both ends to fiber support means. The fiber is provided with a plurality of adjacent bends in opposite directions along its length..An electrode is disposed between two adjacent bends to apply an electrostatic force normal to the plane of the fiber whereby the fiber is caused to twist out of its plane in proportion to the potential apptied between the fiber and the electrode.

Investigating cell mechanics with atomic force microscopy

PubMed Central

Haase, Kristina; Pelling, Andrew E.

2015-01-01

Transmission of mechanical force is crucial for normal cell development and functioning. However, the process of mechanotransduction cannot be studied in isolation from cell mechanics. Thus, in order to understand how cells ‘feel’, we must first understand how they deform and recover from physical perturbations. Owing to its versatility, atomic force microscopy (AFM) has become a popular tool to study intrinsic cellular mechanical properties. Used to directly manipulate and examine whole and subcellular reactions, AFM allows for top-down and reconstitutive approaches to mechanical characterization. These studies show that the responses of cells and their components are complex, and largely depend on the magnitude and time scale of loading. In this review, we generally describe the mechanotransductive process through discussion of well-known mechanosensors. We then focus on discussion of recent examples where AFM is used to specifically probe the elastic and inelastic responses of single cells undergoing deformation. We present a brief overview of classical and current models often used to characterize observed cellular phenomena in response to force. Both simple mechanistic models and complex nonlinear models have been used to describe the observed cellular behaviours, however a unifying description of cell mechanics has not yet been resolved. PMID:25589563

Atomic force microscopy evaluation of aqueous interfaces of immobilized hyaluronan.

PubMed

Morra, Marco; Cassinelli, Clara; Pavesio, Alessandra; Renier, Davide

2003-03-15

Hyaluronan (HA) was immobilized on aminated glass surfaces in three different ways: by simple ionic interaction and by covalent linking at low density and at full density. In agreement with previous reports, in vitro experiments show that the outcome of fibroblast adhesion tests is markedly affected by the details of the coupling procedure, suggesting that different interfacial forces are operating at the aqueous/HA interface in the three cases investigated. The interfacial properties of the HA-coated surfaces were probed by force-distance curves obtained with the atomic force microscope (AFM). This approach readily shows significant differences among the tested samples, which are directly related to the coupling strategy and to results of cell adhesion tests. In particular, the range of interaction between the tip and the surface is much lower when HA is covalently linked than when it is ionically coupled, suggesting a more compact surface structure in the former case. Increasing HA surface density minimizes the interaction force between the surface and the AFM tip, likely reflecting more complete shielding by the HA chains of the underlying substrate. In summary, these measurements clearly show the different nature of the aqueous interfaces tested, and underline the role of this analytical approach in the development and control of finely tuned biomaterial surfaces.

PORPHOBILINOGEN DEAMINASE Deficiency Alters Vegetative and Reproductive Development and Causes Lesions in Arabidopsis

PubMed Central

Quesada, Víctor; Hricová, Andrea; Ponce, María Rosa; Micol, José Luis

2013-01-01

The Arabidopsis rugosa1 (rug1) mutant has irregularly shaped leaves and reduced growth. In the absence of pathogens, leaves of rug1 plants have spontaneous lesions reminiscent of those seen in lesion-mimic mutants; rug1 plants also express cytological and molecular markers associated with defence against pathogens. These rug1 phenotypes are made stronger by dark/light transitions. The rug1 mutant also has delayed flowering time, upregulation of the floral repressor FLOWERING LOCUS C (FLC) and downregulation of the flowering promoters FT and SOC1/AGL20. Vernalization suppresses the late flowering phenotype of rug1 by repressing FLC. Microarray analysis revealed that 280 nuclear genes are differentially expressed between rug1 and wild type; almost a quarter of these genes are involved in plant defence. In rug1, the auxin response is also affected and several auxin-responsive genes are downregulated. We identified the RUG1 gene by map-based cloning and found that it encodes porphobilinogen deaminase (PBGD), also known as hydroxymethylbilane synthase, an enzyme of the tetrapyrrole biosynthesis pathway, which produces chlorophyll, heme, siroheme and phytochromobilin in plants. PBGD activity is reduced in rug1 plants, which accumulate porphobilinogen. Our results indicate that Arabidopsis PBGD deficiency impairs the porphyrin pathway and triggers constitutive activation of plant defence mechanisms leading to leaf lesions and affecting vegetative and reproductive development. PMID:23308205

Note: Space qualified photon counting detector for laser time transfer with picosecond precision and stability

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

Prochazka, Ivan, E-mail: prochiva@gmail.com; Blazej, Josef; Kodet, Jan

2016-05-15

The laser time transfer link is under construction for the European Space Agency in the frame of Atomic Clock Ensemble in Space. We have developed and tested the flying unit of the photon counting detector optimized for this space mission. The results are summarized in this Note. An extreme challenge was to build a detector package, which is rugged, small and which provides long term detection delay stability on picosecond level. The device passed successfully all the tests required for space missions on the low Earth orbits. The detector is extremely rugged and compact. Its long term detection delay stabilitymore » is excellent, it is better than ±1 ps/day, in a sense of time deviation it is better than 0.5 ps for averaging times of 2000 s to several hours. The device is capable to operate in a temperature range of −55 °C up to +60 °C, the change of the detection delay with temperature is +0.5 ps/K. The device is ready for integration into the space structure now.« less

Note: Space qualified photon counting detector for laser time transfer with picosecond precision and stability.

PubMed

Prochazka, Ivan; Kodet, Jan; Blazej, Josef

2016-05-01

The laser time transfer link is under construction for the European Space Agency in the frame of Atomic Clock Ensemble in Space. We have developed and tested the flying unit of the photon counting detector optimized for this space mission. The results are summarized in this Note. An extreme challenge was to build a detector package, which is rugged, small and which provides long term detection delay stability on picosecond level. The device passed successfully all the tests required for space missions on the low Earth orbits. The detector is extremely rugged and compact. Its long term detection delay stability is excellent, it is better than ±1 ps/day, in a sense of time deviation it is better than 0.5 ps for averaging times of 2000 s to several hours. The device is capable to operate in a temperature range of -55 °C up to +60 °C, the change of the detection delay with temperature is +0.5 ps/K. The device is ready for integration into the space structure now.

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

PubMed Central

Allen, Lucy R.; Krivov, Sergei V.; Paci, Emanuele

2009-01-01

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical λ-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins. PMID:19593364

Rapid quantitative chemical mapping of surfaces with sub-2 nm resolution

NASA Astrophysics Data System (ADS)

Lai, Chia-Yun; Perri, Saverio; Santos, Sergio; Garcia, Ricardo; Chiesa, Matteo

2016-05-01

We present a theory that exploits four observables in bimodal atomic force microscopy to produce maps of the Hamaker constant H. The quantitative H maps may be employed by the broader community to directly interpret the high resolution of standard bimodal AFM images as chemical maps while simultaneously quantifying chemistry in the non-contact regime. We further provide a simple methodology to optimize a range of operational parameters for which H is in the closest agreement with the Lifshitz theory in order to (1) simplify data acquisition and (2) generalize the methodology to any set of cantilever-sample systems.We present a theory that exploits four observables in bimodal atomic force microscopy to produce maps of the Hamaker constant H. The quantitative H maps may be employed by the broader community to directly interpret the high resolution of standard bimodal AFM images as chemical maps while simultaneously quantifying chemistry in the non-contact regime. We further provide a simple methodology to optimize a range of operational parameters for which H is in the closest agreement with the Lifshitz theory in order to (1) simplify data acquisition and (2) generalize the methodology to any set of cantilever-sample systems. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr00496b

Analysis of the free-energy surface of proteins from reversible folding simulations.

PubMed

Allen, Lucy R; Krivov, Sergei V; Paci, Emanuele

2009-07-01

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

Multidomain proteins under force

NASA Astrophysics Data System (ADS)

Valle-Orero, Jessica; Andrés Rivas-Pardo, Jaime; Popa, Ionel

2017-04-01

Advancements in single-molecule force spectroscopy techniques such as atomic force microscopy and magnetic tweezers allow investigation of how domain folding under force can play a physiological role. Combining these techniques with protein engineering and HaloTag covalent attachment, we investigate similarities and differences between four model proteins: I10 and I91—two immunoglobulin-like domains from the muscle protein titin, and two α + β fold proteins—ubiquitin and protein L. These proteins show a different mechanical response and have unique extensions under force. Remarkably, when normalized to their contour length, the size of the unfolding and refolding steps as a function of force reduces to a single master curve. This curve can be described using standard models of polymer elasticity, explaining the entropic nature of the measured steps. We further validate our measurements with a simple energy landscape model, which combines protein folding with polymer physics and accounts for the complex nature of tandem domains under force. This model can become a useful tool to help in deciphering the complexity of multidomain proteins operating under force.

Quantum self-organization and nuclear collectivities

NASA Astrophysics Data System (ADS)

Otsuka, T.; Tsunoda, Y.; Togashi, T.; Shimizu, N.; Abe, T.

2018-02-01

The quantum self-organization is introduced as one of the major underlying mechanisms of the quantum many-body systems. In the case of atomic nuclei as an example, two types of the motion of nucleons, single-particle states and collective modes, dominate the structure of the nucleus. The outcome of the collective mode is determined basically by the balance between the effect of the mode-driving force (e.g., quadrupole force for the ellipsoidal deformation) and the resistance power against it. The single-particle energies are one of the sources to produce such resistance power: a coherent collective motion is more hindered by larger gaps between relevant single particle states. Thus, the single-particle state and the collective mode are “enemies” each other. However, the nuclear forces are demonstrated to be rich enough so as to enhance relevant collective mode by reducing the resistance power by changing singleparticle energies for each eigenstate through monopole interactions. This will be verified with the concrete example taken from Zr isotopes. Thus, when the quantum self-organization occurs, single-particle energies can be self-organized, being enhanced by (i) two quantum liquids, e.g., protons and neutrons, (ii) two major force components, e.g., quadrupole interaction (to drive collective mode) and monopole interaction (to control resistance). In other words, atomic nuclei are not necessarily like simple rigid vases containing almost free nucleons, in contrast to the naïve Fermi liquid picture. Type II shell evolution is considered to be a simple visible case involving excitations across a (sub)magic gap. The quantum self-organization becomes more important in heavier nuclei where the number of active orbits and the number of active nucleons are larger. The quantum self-organization is a general phenomenon, and is expected to be found in other quantum systems.

77 FR 44684 - General Dynamics Itronix Corporation; A Subsidiary of General Dynamics Corporation, Including...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-30

... program management services for rugged laptop computers and rugged mobile devices. The worker group... of program management services for rugged laptop computers and rugged mobile devices, meet the worker... threatened to become totally or partially separated. Section 222(a)(2)(A)(i) has been met because the sales...

Repulsive hydration forces between calcite surfaces and their effect on the brittle strength of calcite-bearing rocks

NASA Astrophysics Data System (ADS)

Røyne, Anja; Dalby, Kim N.; Hassenkam, Tue

2015-06-01

The long-term mechanical strength of calcite-bearing rocks is highly dependent on the presence and nature of pore fluids, and it has been suggested that the observed effects are due to changes in nanometer-scale surface forces near fracture tips and grain contacts. In this letter, we present measurements of forces between two calcite surfaces in air and water-glycol mixtures using the atomic force microscope. We show a time- and load-dependent adhesion at low water concentrations and a strong repulsion in the presence of water, which is most likely due to hydration of the strongly hydrophilic calcite surfaces. We argue that this hydration repulsion can explain the commonly observed water-induced decrease in strength in calcitic rocks and single calcite crystals. Furthermore, this relatively simple experimental setup may serve as a useful tool for analyzing surface forces in other mineral-fluid combinations.

A new solution chemical method to make low dimensional thermoelectric materials

NASA Astrophysics Data System (ADS)

Ding, Zhongfen

2001-11-01

Bismuth telluride and its alloys are currently the best thermoelectric materials known at room temperature and are therefore used for portable solid-state refrigeration. If the thermal electric figure of merit ZT could be improved by a factor of about 3, quiet and rugged solid-state devices could eventually replace conventional compressor based cooling systems. In order to test a theory that improved one-dimensional or two-dimensional materials could enhance ZT due to lower thermal conductivity, we are developing solution processing methods to make low dimensional materials. Bismuth telluride and its p-type and n-type alloys have layered structures consisting of 5 atom thick Te-Bi-Te-Bi-Te sheets, each sheet about 10 A thick. Lithium ions are intercalated into the layered materials using liquid ammonia. The lithium-intercalated materials are then exfoliated in water to form colloidal suspensions with narrow particle size distributions and are stable for more than 24 hours. The layers are then deposited on substrates, which after annealing at low temperatures, form highly c-axis oriented thin films. The exfoliated layers can potentially be restacked with other ions or layered materials in between the sheets to form novel structures. The restacked layers when treated with nitric acid and sonication form high yield nanorod structured materials. This new intercalation and exfoliation followed by sonication method could potentially be used for many other layered materials to make nanorod structured materials. The low dimensional materials are characterized by powder X-ray diffraction, atomic force microscopy (AFM), transmission electron microscopy (TEM), scanning electron microscopy (SEM), inductively coupled plasma (ICP) and dynamic light scattering.

Development of a quartz tuning-fork-based force sensor for measurements in the tens of nanoNewton force range during nanomanipulation experiments

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

Oiko, V. T. A., E-mail: oiko@ifi.unicamp.br; Rodrigues, V.; Ugarte, D.

2014-03-15

Understanding the mechanical properties of nanoscale systems requires new experimental and theoretical tools. In particular, force sensors compatible with nanomechanical testing experiments and with sensitivity in the nN range are required. Here, we report the development and testing of a tuning-fork-based force sensor for in situ nanomanipulation experiments inside a scanning electron microscope. The sensor uses a very simple design for the electronics and it allows the direct and quantitative force measurement in the 1–100 nN force range. The sensor response is initially calibrated against a nN range force standard, as, for example, a calibrated Atomic Force Microscopy cantilever; subsequently,more » applied force values can be directly derived using only the electric signals generated by the tuning fork. Using a homemade nanomanipulator, the quantitative force sensor has been used to analyze the mechanical deformation of multi-walled carbon nanotube bundles, where we analyzed forces in the 5–40 nN range, measured with an error bar of a few nN.« less

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

Basic Research in Electronics (JSEP).

DTIC Science & Technology

1981-09-30

These antennas can have a low profile or be flush-mounted, are inherently rugged, are simple to fabricate , and can be made conformal to the surface...made in. the " light flash" radiated by the plasma in front of the metal surface. D. High-Power Microwave-Atmosphere Interactions The original model...Scintillation," Ph.D. Thesis , Poly- technic Institute of New York (August 1980); also POLY-MRI Report No. 80-1410. 7. S.R. Barone, "Angular Momentum of Particles

MOEs for Drug Interdiction: Simple Tests Expose Critical Flaws

DTIC Science & Technology

1991-09-01

operations against illegal !rugs flowing into the U.S. Six candidate measures of effective (MOEs) are subjected to a structured assessment prcess that tests...supports spanning the decision space with a minimum number of MOEs. A small suite of MOEs reflecting relatively pure effects is preferred to long and...responds to changing consumer fashion--this year’s drug of choice may be overtaken by a new fad. Patterns of preference can vary widely by location as

Contributed Review: The feasibility of a fully miniaturized magneto-optical trap for portable ultracold quantum technology.

PubMed

Rushton, J A; Aldous, M; Himsworth, M D

2014-12-01

Experiments using laser cooled atoms and ions show real promise for practical applications in quantum-enhanced metrology, timing, navigation, and sensing as well as exotic roles in quantum computing, networking, and simulation. The heart of many of these experiments has been translated to microfabricated platforms known as atom chips whose construction readily lend themselves to integration with larger systems and future mass production. To truly make the jump from laboratory demonstrations to practical, rugged devices, the complex surrounding infrastructure (including vacuum systems, optics, and lasers) also needs to be miniaturized and integrated. In this paper we explore the feasibility of applying this approach to the Magneto-Optical Trap; incorporating the vacuum system, atom source and optical geometry into a permanently sealed micro-litre system capable of maintaining 10(-10) mbar for more than 1000 days of operation with passive pumping alone. We demonstrate such an engineering challenge is achievable using recent advances in semiconductor microfabrication techniques and materials.

Contributed Review: The feasibility of a fully miniaturized magneto-optical trap for portable ultracold quantum technology

NASA Astrophysics Data System (ADS)

Rushton, J. A.; Aldous, M.; Himsworth, M. D.

2014-12-01

Experiments using laser cooled atoms and ions show real promise for practical applications in quantum-enhanced metrology, timing, navigation, and sensing as well as exotic roles in quantum computing, networking, and simulation. The heart of many of these experiments has been translated to microfabricated platforms known as atom chips whose construction readily lend themselves to integration with larger systems and future mass production. To truly make the jump from laboratory demonstrations to practical, rugged devices, the complex surrounding infrastructure (including vacuum systems, optics, and lasers) also needs to be miniaturized and integrated. In this paper we explore the feasibility of applying this approach to the Magneto-Optical Trap; incorporating the vacuum system, atom source and optical geometry into a permanently sealed micro-litre system capable of maintaining 10-10 mbar for more than 1000 days of operation with passive pumping alone. We demonstrate such an engineering challenge is achievable using recent advances in semiconductor microfabrication techniques and materials.

Contributed Review: The feasibility of a fully miniaturized magneto-optical trap for portable ultracold quantum technology

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

Rushton, J. A.; Aldous, M.; Himsworth, M. D., E-mail: m.d.himsworth@soton.ac.uk

2014-12-15

Experiments using laser cooled atoms and ions show real promise for practical applications in quantum-enhanced metrology, timing, navigation, and sensing as well as exotic roles in quantum computing, networking, and simulation. The heart of many of these experiments has been translated to microfabricated platforms known as atom chips whose construction readily lend themselves to integration with larger systems and future mass production. To truly make the jump from laboratory demonstrations to practical, rugged devices, the complex surrounding infrastructure (including vacuum systems, optics, and lasers) also needs to be miniaturized and integrated. In this paper we explore the feasibility of applyingmore » this approach to the Magneto-Optical Trap; incorporating the vacuum system, atom source and optical geometry into a permanently sealed micro-litre system capable of maintaining 10{sup −10} mbar for more than 1000 days of operation with passive pumping alone. We demonstrate such an engineering challenge is achievable using recent advances in semiconductor microfabrication techniques and materials.« less

Simulations of the OKE Response in Simple Liquids Using a Polarizable and a Nonpolarizable Force Field.

PubMed

Polok, Kamil

2018-02-08

Recently polarizable force fields are becoming increasingly popular for molecular dynamics simulations. As the signal obtained in the optical Kerr effect (OKE) experiment is due to the polarizability dynamics of the investigated system, a study is conducted in order to compare the experimental results with those obtained with the polarizable AMOEBA force field. The comparison is made in the frequency domain; however, time domain data are also included. The selected molecular systems are the isotropic carbon tetrachloride molecule, the anisotropic chloroform, carbon disulfide and acetone molecules, and the hydrogen-bonded water and methanol molecules. Different dipole-induced-dipole (DID) method variants are used for calculation of the OKE response, showing the importance of use of the all-atom approach with preoptimized atomic polarizabilities. In order to obtain a good intermolecular to intramolecular components amplitude ratio, the isotropic polarizability in the Thole correction needs to be updated between iterations. The convergence of the spectra calculated with different DID variants is also considered, and the approach that appears to be the best gives a very good approximation after three iterations. The comparison of the experimental and simulated spectra shows a rather good agreement for the non-hydrogen-bonded molecules, although the contribution of the reorientation of anisotropic molecules is overestimated. In the case of the hydrogen-bonded molecules, the theoretical spectra are far from the experimental ones. The highly overestimated librational bands indicate excessive polarizability anisotropy introduced by the potential model. Finally, in order to verify the significance of different components of the AMOEBA model, it is gradually simplified and compared with a simple reference potential model. Removal of polarizability shows a tremendous change in the case of hydrogen-bonded liquids, whereas for the other molecules it is of minor importance. The non-hydrogen-bonded liquids are, however, more sensitive to the presence of atomic multipoles in the model.

Solution-processed flexible NiO resistive random access memory device

NASA Astrophysics Data System (ADS)

Kim, Soo-Jung; Lee, Heon; Hong, Sung-Hoon

2018-04-01

Non-volatile memories (NVMs) using nanocrystals (NCs) as active materials can be applied to soft electronic devices requiring a low-temperature process because NCs do not require a heat treatment process for crystallization. In addition, memory devices can be implemented simply by using a patterning technique using a solution process. In this study, a flexible NiO ReRAM device was fabricated using a simple NC patterning method that controls the capillary force and dewetting of a NiO NC solution at low temperature. The switching behavior of a NiO NC based memory was clearly observed by conductive atomic force microscopy (c-AFM).

The American Experience with Pacification in Vietnam. Volume 2: Elements of Pacification

DTIC Science & Technology

1972-03-01

Regiment elmnts conducted coordinated mortar /ground attacks throughout Dai Loc district--recently an area of CAP concern. At the time of the attack...essentially they should be very light infantry forces equipped with automatic weapons, light mortars , grenade launchers, and rugged but light com...it lasted, a signifi- cant part of USOMI- effort was channeled toward its direct support. Piai:ers and commodities, such as fertilizer and cement

Imaging and Quantitation of a Succession of Transient Intermediates Reveal the Reversible Self-Assembly Pathway of a Simple Icosahedral Virus Capsid.

PubMed

Medrano, María; Fuertes, Miguel Ángel; Valbuena, Alejandro; Carrillo, Pablo J P; Rodríguez-Huete, Alicia; Mateu, Mauricio G

2016-11-30

Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T = 1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T = 1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular self-assembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drug-encapsidating nanoparticle for anticancer targeted drug delivery.

Stable and rugged etalon for the Dynamics Explorer Fabry-Perot interferometer. I - Design and construction

NASA Astrophysics Data System (ADS)

Rees, D.; Fuller-Rowell, T. J.; Lyons, A.; Killeen, T. L.; Hays, P. B.

1982-11-01

The cemented etalons are shown to be rugged and highly stable for high-resolution spectroscopy and to be well suited to space applications. The etalons will be of considerable value as the tuning elements of dye laser systems and as the stable spectral disperser for pulse and CW laser spectroscopy. Even for etalons 15 cm in diameter, the strength of the cemented bond is greatly in excess of the maximum steady and impulsive forces experienced from the much larger etalon plate mass (2-4 kg rather than 200 g). It is thought that the small but systematic and significant positive increment in the thermal expansion coefficient which occurs when an etalon and its spacers are cemented may be linked to the cessation of the microscopic migration that occurs with an optically contacted bond under thermal or mechanical stress. The etalon comprises two flat plates of fused silica, with spacers constructed of Zerodur (a polycrystalline glass ceramic of extremely low expansion coefficient) which are cemented together using cyanoacrylic adhesives.

Applying Resource Utilization Groups (RUG-III) in Hong Kong Nursing Homes

ERIC Educational Resources Information Center

Chou, Kee-Lee; Chi, Iris; Leung, Joe C. B.

2008-01-01

Resource Utilization Groups III (RUG-III) is a case-mix system developed in the United States for categorization of nursing home residents and the financing of residential care services. In Hong Kong, RUG-III is based on several board groups of residents. The aim of this study was to examine the reliability and validity of the RUG-III in Hong Kong…

Single-particle states vs. collective modes: friends or enemies ?

NASA Astrophysics Data System (ADS)

Otsuka, T.; Tsunoda, Y.; Togashi, T.; Shimizu, N.; Abe, T.

2018-05-01

The quantum self-organization is introduced as one of the major underlying mechanisms of the quantum many-body systems. In the case of atomic nuclei as an example, two types of the motion of nucleons, single-particle states and collective modes, dominate the structure of the nucleus. The collective mode arises as the balance between the effect of the mode-driving force (e.g., quadrupole force for the ellipsoidal deformation) and the resistance power against it. The single-particle energies are one of the sources to produce such resistance power: a coherent collective motion is more hindered by larger spacings between relevant single particle states. Thus, the single-particle state and the collective mode are "enemies" against each other. However, the nuclear forces are rich enough so as to enhance relevant collective mode by reducing the resistance power by changing single-particle energies for each eigenstate through monopole interactions. This will be verified with the concrete example taken from Zr isotopes. Thus, the quantum self-organization occurs: single-particle energies can be self-organized by (i) two quantum liquids, e.g., protons and neutrons, (ii) monopole interaction (to control resistance). In other words, atomic nuclei are not necessarily like simple rigid vases containing almost free nucleons, in contrast to the naïve Fermi liquid picture. Type II shell evolution is considered to be a simple visible case involving excitations across a (sub)magic gap. The quantum self-organization becomes more important in heavier nuclei where the number of active orbits and the number of active nucleons are larger.

B-spline tight frame based force matching method

NASA Astrophysics Data System (ADS)

Yang, Jianbin; Zhu, Guanhua; Tong, Dudu; Lu, Lanyuan; Shen, Zuowei

2018-06-01

In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an ℓ1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach.

Modeling viscoelasticity through spring–dashpot models in intermittent-contact atomic force microscopy

PubMed Central

López-Guerra, Enrique A

2014-01-01

Summary We examine different approaches to model viscoelasticity within atomic force microscopy (AFM) simulation. Our study ranges from very simple linear spring–dashpot models to more sophisticated nonlinear systems that are able to reproduce fundamental properties of viscoelastic surfaces, including creep, stress relaxation and the presence of multiple relaxation times. Some of the models examined have been previously used in AFM simulation, but their applicability to different situations has not yet been examined in detail. The behavior of each model is analyzed here in terms of force–distance curves, dissipated energy and any inherent unphysical artifacts. We focus in this paper on single-eigenmode tip–sample impacts, but the models and results can also be useful in the context of multifrequency AFM, in which the tip trajectories are very complex and there is a wider range of sample deformation frequencies (descriptions of tip–sample model behaviors in the context of multifrequency AFM require detailed studies and are beyond the scope of this work). PMID:25551043

Manipulation of domain-wall solitons in bi- and trilayer graphene

NASA Astrophysics Data System (ADS)

Jiang, Lili; Wang, Sheng; Shi, Zhiwen; Jin, Chenhao; Utama, M. Iqbal Bakti; Zhao, Sihan; Shen, Yuen-Ron; Gao, Hong-Jun; Zhang, Guangyu; Wang, Feng

2018-01-01

Topological dislocations and stacking faults greatly affect the performance of functional crystalline materials1-3. Layer-stacking domain walls (DWs) in graphene alter its electronic properties and give rise to fascinating new physics such as quantum valley Hall edge states4-10. Extensive efforts have been dedicated to the engineering of dislocations to obtain materials with advanced properties. However, the manipulation of individual dislocations to precisely control the local structure and local properties of bulk material remains an outstanding challenge. Here we report the manipulation of individual layer-stacking DWs in bi- and trilayer graphene by means of a local mechanical force exerted by an atomic force microscope tip. We demonstrate experimentally the capability to move, erase and split individual DWs as well as annihilate or create closed-loop DWs. We further show that the DW motion is highly anisotropic, offering a simple approach to create solitons with designed atomic structures. Most artificially created DW structures are found to be stable at room temperature.

Elasticity of human embryonic stem cells as determined by atomic force microscopy.

PubMed

Kiss, Robert; Bock, Henry; Pells, Steve; Canetta, Elisabetta; Adya, Ashok K; Moore, Andrew J; De Sousa, Paul; Willoughby, Nicholas A

2011-10-01

The expansive growth and differentiation potential of human embryonic stem cells (hESCs) make them a promising source of cells for regenerative medicine. However, this promise is off set by the propensity for spontaneous or uncontrolled differentiation to result in heterogeneous cell populations. Cell elasticity has recently been shown to characterize particular cell phenotypes, with undifferentiated and differentiated cells sometimes showing significant differences in their elasticities. In this study, we determined the Young's modulus of hESCs by atomic force microscopy using a pyramidal tip. Using this method we are able to take point measurements of elasticity at multiple locations on a single cell, allowing local variations due to cell structure to be identified. We found considerable differences in the elasticity of the analyzed hESCs, reflected by a broad range of Young's modulus (0.05-10 kPa). This surprisingly high variation suggests that elasticity could serve as the basis of a simple and efficient large scale purification/separation technique to discriminate subpopulations of hESCs.

Perception, planning, and control for walking on rugged terrain

NASA Technical Reports Server (NTRS)

Simmons, Reid; Krotkov, Eric

1991-01-01

The CMU Planetary Rover project is developing a six-legged walking robot capable of autonomously navigating, exploring, and acquiring samples in rugged, unknown environments. To gain experience with the problems involved in walking on rugged terrain, a full-scale prototype leg was built and mounted on a carriage that rolls along overhead rails. Issues addressed in developing the software system to autonomously walk the leg through rugged terrain are described. In particular, the insights gained into perceiving and modeling rugged terrain, controlling the legged mechanism, interacting with the ground, choosing safe yet effective footfalls, and planning efficient leg moves through space are described.

Interplay between Switching Driven by the Tunneling Current and Atomic Force of a Bistable Four-Atom Si Quantum Dot.

PubMed

Yamazaki, Shiro; Maeda, Keisuke; Sugimoto, Yoshiaki; Abe, Masayuki; Zobač, Vladimír; Pou, Pablo; Rodrigo, Lucia; Mutombo, Pingo; Pérez, Ruben; Jelínek, Pavel; Morita, Seizo

2015-07-08

We assemble bistable silicon quantum dots consisting of four buckled atoms (Si4-QD) using atom manipulation. We demonstrate two competing atom switching mechanisms, downward switching induced by tunneling current of scanning tunneling microscopy (STM) and opposite upward switching induced by atomic force of atomic force microscopy (AFM). Simultaneous application of competing current and force allows us to tune switching direction continuously. Assembly of the few-atom Si-QDs and controlling their states using versatile combined AFM/STM will contribute to further miniaturization of nanodevices.

Fiber-Optic/Photoelastic Flow Sensors

NASA Technical Reports Server (NTRS)

Wesson, Laurence N.; Cabato, Nellie L.; Brooks, Edward F.

1995-01-01

Simple, rugged, lightweight transducers detect periodic vortices. Fiber-optic-coupled transducers developed to measure flows over wide dynamic ranges and over wide temperature ranges in severe environments. Used to measure flows of fuel in advanced aircraft engines. Feasibility of sensors demonstrated in tests of prototype sensor in water flowing at various temperatures and speeds. Particularly attractive for aircraft applications because optical fibers compact and make possible transmission of sensor signals at high rates with immunity from electromagnetic interference at suboptical frequencies. Sensors utilize optical-to-optical conversion via photoelastic effect.

Air-assisted liquid-liquid microextraction integrated with QuEChERS for determining endocrine-disrupting compounds in fish by high-performance liquid chromatography-tandem mass spectrometry.

PubMed

Luo, Zhoufei; Lu, Jing; Li, Haipu; Tu, Yi; Wan, Yuehao; Yang, Zhaoguang

2018-09-15

A new, sensitive, and rapid method based on the Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) approach and air-assisted liquid-liquid microextraction (AALLME) technology was developed for the determination of 20 endocrine-disrupting compounds (EDCs) in fish by high-performance liquid chromatography-tandem mass spectrometry. The method first integrates AALLME into QuEChERS to achieve clean-up and enrichment of the EDCs in one step. A self-made glass tube was enfolded with plasticine to withstand the high centrifugal force. The established method was developed by optimization of the parameters. High linearities (R 2  > 0.9924) and recoveries (78.2-118.6%) at three spiked levels (5, 10, and 20 ng g -1 ), and low relative standard deviation values (1.1-14.5%) and limits of detection (0.03-0.80 ng g -1 ) were obtained. The method comparison shows that the proposed method is superior as it involves less organic solvent usage, simple operation and high efficiency. This method was successfully applied to different fishes for analyzing EDCs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Adiabatic perturbation theory of electronic stopping in insulators

DOE PAGES

Horsfield, Andrew P.; Lim, Anthony; Foulkes, W. M. C.; ...

2016-06-02

A model able to explain the complicated structure of electronic stopping at low velocities in insulating materials is presented. It is shown to be in good agreement with results obtained from time-dependent density-functional theory for the stopping of a channeling Si atom in a Si crystal. If we define the repeat frequency f=v/λ, where λ is the periodic repeat length of the crystal along the direction the channeling atom is traveling, and v is the velocity of the channeling atom, we find that electrons experience a perturbing force that varies in time at integer multiples l of f. This enablesmore » electronic excitations at low atom velocity, but their contributions diminish rapidly with increasing values of l. The expressions for stopping power are derived using adiabatic perturbation theory for many-electron systems, and they are then specialized to the case of independent electrons. Lastly, a simple model for the nonadiabatic matrix elements is described, along with the procedure for determining its parameters.« less

Calculation of absolute protein-ligand binding free energy using distributed replica sampling.

PubMed

Rodinger, Tomas; Howell, P Lynne; Pomès, Régis

2008-10-21

Distributed replica sampling [T. Rodinger et al., J. Chem. Theory Comput. 2, 725 (2006)] is a simple and general scheme for Boltzmann sampling of conformational space by computer simulation in which multiple replicas of the system undergo a random walk in reaction coordinate or temperature space. Individual replicas are linked through a generalized Hamiltonian containing an extra potential energy term or bias which depends on the distribution of all replicas, thus enforcing the desired sampling distribution along the coordinate or parameter of interest regardless of free energy barriers. In contrast to replica exchange methods, efficient implementation of the algorithm does not require synchronicity of the individual simulations. The algorithm is inherently suited for large-scale simulations using shared or heterogeneous computing platforms such as a distributed network. In this work, we build on our original algorithm by introducing Boltzmann-weighted jumping, which allows moves of a larger magnitude and thus enhances sampling efficiency along the reaction coordinate. The approach is demonstrated using a realistic and biologically relevant application; we calculate the standard binding free energy of benzene to the L99A mutant of T4 lysozyme. Distributed replica sampling is used in conjunction with thermodynamic integration to compute the potential of mean force for extracting the ligand from protein and solvent along a nonphysical spatial coordinate. Dynamic treatment of the reaction coordinate leads to faster statistical convergence of the potential of mean force than a conventional static coordinate, which suffers from slow transitions on a rugged potential energy surface.

Calculation of absolute protein-ligand binding free energy using distributed replica sampling

NASA Astrophysics Data System (ADS)

Rodinger, Tomas; Howell, P. Lynne; Pomès, Régis

2008-10-01

Distributed replica sampling [T. Rodinger et al., J. Chem. Theory Comput. 2, 725 (2006)] is a simple and general scheme for Boltzmann sampling of conformational space by computer simulation in which multiple replicas of the system undergo a random walk in reaction coordinate or temperature space. Individual replicas are linked through a generalized Hamiltonian containing an extra potential energy term or bias which depends on the distribution of all replicas, thus enforcing the desired sampling distribution along the coordinate or parameter of interest regardless of free energy barriers. In contrast to replica exchange methods, efficient implementation of the algorithm does not require synchronicity of the individual simulations. The algorithm is inherently suited for large-scale simulations using shared or heterogeneous computing platforms such as a distributed network. In this work, we build on our original algorithm by introducing Boltzmann-weighted jumping, which allows moves of a larger magnitude and thus enhances sampling efficiency along the reaction coordinate. The approach is demonstrated using a realistic and biologically relevant application; we calculate the standard binding free energy of benzene to the L99A mutant of T4 lysozyme. Distributed replica sampling is used in conjunction with thermodynamic integration to compute the potential of mean force for extracting the ligand from protein and solvent along a nonphysical spatial coordinate. Dynamic treatment of the reaction coordinate leads to faster statistical convergence of the potential of mean force than a conventional static coordinate, which suffers from slow transitions on a rugged potential energy surface.

Southern California landslides-an overview

USGS Publications Warehouse

,

2005-01-01

Southern California lies astride a major tectonic plate boundary defined by the San Andreas Fault and numerous related faults that are spread across a broad region. This dynamic tectonic environment has created a spectacular landscape of rugged mountains and steep-walled valleys that compose much of the region’s scenic beauty. Unfortunately, this extraordinary landscape also presents serious geologic hazards. Just as tectonic forces are steadily pushing the landscape upward, gravity is relentlessly tugging it downward. When gravity prevails, landslides can occur.

Resource utilization groups (RUGs): defining chronic care, rehabilitation and nursing home case mix in Canada.

PubMed

Botz, C K; Bestard, S; Demaray, M; Molloy, G

1993-01-01

The two major purposes of this study were: (1) to evaluate Resource Utilization Groups (RUGs III) as a unified method for classifying all residential, chronic care and rehabilitation patients at the St. Joseph's Health Centre, London, and (2) to compare the potential funding implications of RUGs and other patient/resident classification systems. RUGs were used to classify a total of 336 patients/residents in residential, extended care, chronic care and rehabilitation beds at the Health Centre. Patients were also concurrently classified according to the Alberta Long Term Care Classification System and the Medicus Long Term Care System. Results show that RUGs provide relatively more credit for higher acuity patients than do the Alberta or Medicus systems. If used as a basis for funding, chronic care and rehabilitation hospitals would be entitled to more funding (relative to residential/nursing homes) under RUGs than under the other two patient classification mechanisms.

Complexity made simple

NASA Astrophysics Data System (ADS)

2010-02-01

With their passion for analysing the world by breaking it down into ever-smaller pieces, most physicists are "reductionists" at heart. Whether through tradition or instinct, our natural inclination is to reduce matter first to molecules and then to atoms and on to nuclei, nucleons, quarks and beyond. But this approach, while astonishingly successful in terms of understanding the fundamental particles and forces of nature, does not always work. In other words, the whole can often be more than the sum of the parts.

Molar volume and adsorption isotherm dependence of capillary forces in nanoasperity contacts.

PubMed

Asay, David B; Kim, Seong H

2007-11-20

The magnitude of the capillary force at any given temperature and adsorbate partial pressure depends primarily on four factors: the surface tension of the adsorbate, its liquid molar volume, its isothermal behavior, and the contact geometry. At large contacting radii, the adsorbate surface tension and the contact geometry are dominating. This is the case of surface force apparatus measurements and atomic force microscopy (AFM) experiments with micrometer-size spheres. However, as the size of contacting asperities decreases to the nanoscale as in AFM experiments with sharp tips, the molar volume and isotherm of the adsorbate become very important to capillary formation as well as capillary adhesion. This effect is experimentally and theoretically explored with simple alcohol molecules (ethanol, 1-butanol, and 1-pentanol) which have comparable surface tensions but differing liquid molar volumes. Adsorption isotherms for these alcohols on silicon oxide are also reported.

Morphological variation of stimuli-responsive polypeptide at air-water interface

NASA Astrophysics Data System (ADS)

Shin, Sungchul; Ahn, Sungmin; Cheng, Jie; Chang, Hyejin; Jung, Dae-Hong; Hyun, Jinho

2016-12-01

The morphological variation of stimuli-responsive polypeptide molecules at the air-water interface as a function of temperature and compression was described. The surface pressure-area (π-A) isotherms of an elastin-like polypeptide (ELP) monolayer were obtained under variable external conditions, and Langmuir-Blodgett (LB) monolayers were deposited onto a mica substrate for characterization. As the compression of the ELP monolayer increased, the surface pressure increased gradually, indicating that the ELP monolayer could be prepared with high stability at the air-water interface. The temperature in the subphase of the ELP monolayer was critical in the preparation of LB monolayers. The change in temperature induced a shift in the π-A isotherms as well as a change in ELP secondary structures. Surprisingly, the compression of the ELP monolayer influenced the ELP secondary structure due to the reduction in the phase transition temperature with decreasing temperature. The change in the ELP secondary structure formed at the air-water interface was investigated by surface-enhanced Raman scattering. Moreover, the morphology of the ELP monolayer was subsequently imaged using atomic force microscopy. The temperature responsive behavior resulted in changes in surface morphology from relatively flat structures to rugged labyrinth structures, which suggested conformational changes in the ELP monolayers.

Effect of cantilever geometry on the optical lever sensitivities and thermal noise method of the atomic force microscope.

PubMed

Sader, John E; Lu, Jianing; Mulvaney, Paul

2014-11-01

Calibration of the optical lever sensitivities of atomic force microscope (AFM) cantilevers is especially important for determining the force in AFM measurements. These sensitivities depend critically on the cantilever mode used and are known to differ for static and dynamic measurements. Here, we calculate the ratio of the dynamic and static sensitivities for several common AFM cantilevers, whose shapes vary considerably, and experimentally verify these results. The dynamic-to-static optical lever sensitivity ratio is found to range from 1.09 to 1.41 for the cantilevers studied - in stark contrast to the constant value of 1.09 used widely in current calibration studies. This analysis shows that accuracy of the thermal noise method for the static spring constant is strongly dependent on cantilever geometry - neglect of these dynamic-to-static factors can induce errors exceeding 100%. We also discuss a simple experimental approach to non-invasively and simultaneously determine the dynamic and static spring constants and optical lever sensitivities of cantilevers of arbitrary shape, which is applicable to all AFM platforms that have the thermal noise method for spring constant calibration.

Searching the Force Field Electrostatic Multipole Parameter Space.

PubMed

Jakobsen, Sofie; Jensen, Frank

2016-04-12

We show by tensor decomposition analyses that the molecular electrostatic potential for amino acid peptide models has an effective rank less than twice the number of atoms. This rank indicates the number of parameters that can be derived from the electrostatic potential in a statistically significant way. Using this as a guideline, we investigate different strategies for deriving a reduced set of atomic charges, dipoles, and quadrupoles capable of reproducing the reference electrostatic potential with a low error. A full combinatorial search of selected parameter subspaces for N-methylacetamide and a cysteine peptide model indicates that there are many different parameter sets capable of providing errors close to that of the global minimum. Among the different reduced multipole parameter sets that have low errors, there is consensus that atoms involved in π-bonding require higher order multipole moments. The possible correlation between multipole parameters is investigated by exhaustive searches of combinations of up to four parameters distributed in all possible ways on all possible atomic sites. These analyses show that there is no advantage in considering combinations of multipoles compared to a simple approach where the importance of each multipole moment is evaluated sequentially. When combined with possible weighting factors related to the computational efficiency of each type of multipole moment, this may provide a systematic strategy for determining a computational efficient representation of the electrostatic component in force field calculations.

Reference system for scanning probe tip fingerprinting

NASA Astrophysics Data System (ADS)

Turansky, Robert; Bamidele, Joseph; Sugawara, Yasuhiro; Kantorovitch, Lev; Stich, Ivan

2012-02-01

Knowledge of the chemical structure of the tip asperity in Non-Contact Atomic Force Microscopy (NC-AFM) is crucial as controlled manipulation of atoms and/or molecules on surfaces can only be performed if this information is available. However, a simple and robust protocol for ensuring a specific tip termination has not yet been developed. We propose a procedure for chemical tip finger printing and an example of a reference system, the oxygen-terminated Cu(110) surface, that enables one to ensure a specific tip termination with Si, Cu, or O atoms. To follow this up and unambiguously determine tip types, we performed a theoretical DFT study of the line scans with the tip models in question and found that the tip characterization made based on experimental results (Cu/O-terminated tip imaging Cu/O atoms) is in fact incorrect and the opposite is true (Cu/O-terminated tip imaging O/Cu atoms). This protocol allows the tip asperity's chemical structure to be verified and established both before as well as at any stage of the manipulation experiment when numerous tip changes may take place.

Non-contact lateral force microscopy.

PubMed

Weymouth, A J

2017-08-16

The goal of atomic force microscopy (AFM) is to measure the short-range forces that act between the tip and the surface. The signal recorded, however, includes long-range forces that are often an unwanted background. Lateral force microscopy (LFM) is a branch of AFM in which a component of force perpendicular to the surface normal is measured. If we consider the interaction between tip and sample in terms of forces, which have both direction and magnitude, then we can make a very simple yet profound observation: over a flat surface, long-range forces that do not yield topographic contrast have no lateral component. Short-range interactions, on the other hand, do. Although contact-mode is the most common LFM technique, true non-contact AFM techniques can be applied to perform LFM without the tip depressing upon the sample. Non-contact lateral force microscopy (nc-LFM) is therefore ideal to study short-range forces of interest. One of the first applications of nc-LFM was the study of non-contact friction. A similar setup is used in magnetic resonance force microscopy to detect spin flipping. More recently, nc-LFM has been used as a true microscopy technique to systems unsuitable for normal force microscopy.

Simple turbulence measurements with azopolymer thin films.

PubMed

Barillé, Regis; Pérez, Darío G; Morille, Yohann; Zielińska, Sonia; Ortyl, Ewelina

2013-04-01

A simple method to measure the influence on the laser beam propagation by a turbid medium is proposed. This measurement is based on the inscription of a surface relief grating (SRG) on an azopolymer thin film. The grating obtained with a single laser beam after propagation into a turbulent medium is perturbed and directly analyzed by a CCD camera through its diffraction pattern. Later, by scanning the surface pattern with an atomic force microscope, the inscribed SRG is analyzed with the Radon transform. This method has the advantage of using a single beam to remotely inscribe a grating detecting perturbations during the beam path. A method to evaluate the refractive index constant structure is developed.

Characterization of silicon carbide and diamond detectors for neutron applications

NASA Astrophysics Data System (ADS)

Hodgson, M.; Lohstroh, A.; Sellin, P.; Thomas, D.

2017-10-01

The presence of carbon atoms in silicon carbide and diamond makes these materials ideal candidates for direct fast neutron detectors. Furthermore the low atomic number, strong covalent bonds, high displacement energies, wide bandgap and low intrinsic carrier concentrations make these semiconductor detectors potentially suitable for applications where rugged, high-temperature, low-gamma-sensitivity detectors are required, such as active interrogation, electronic personal neutron dosimetry and harsh environment detectors. A thorough direct performance comparison of the detection capabilities of semi-insulating silicon carbide (SiC-SI), single crystal diamond (D-SC), polycrystalline diamond (D-PC) and a self-biased epitaxial silicon carbide (SiC-EP) detector has been conducted and benchmarked against a commercial silicon PIN (Si-PIN) diode, in a wide range of alpha (Am-241), beta (Sr/Y-90), ionizing photon (65 keV to 1332 keV) and neutron radiation fields (including 1.2 MeV to 16.5 MeV mono-energetic neutrons, as well as neutrons from AmBe and Cf-252 sources). All detectors were shown to be able to directly detect and distinguish both the different radiation types and energies by using a simple energy threshold discrimination method. The SiC devices demonstrated the best neutron energy discrimination ratio (E\\max (n=5 MeV)/E\\max (n=1 MeV)  ≈5), whereas a superior neutron/photon cross-sensitivity ratio was observed in the D-PC detector (E\\max (AmBe)/E\\max (Co-60)  ≈16). Further work also demonstrated that the cross-sensitivity ratios can be improved through use of a simple proton-recoil conversion layer. Stability issues were also observed in the D-SC, D-PC and SiC-SI detectors while under irradiation, namely a change of energy peak position and/or count rate with time (often referred to as the polarization effect). This phenomenon within the detectors was non-debilitating over the time period tested (> 5 h) and, as such, stable operation was possible. Furthermore, the D-SC, self-biased SiC-EP and semi-insulating SiC detectors were shown to operate over the temperature range -60 °C to +100 °C.

What Is a Simple Liquid?

NASA Astrophysics Data System (ADS)

Ingebrigtsen, Trond S.; Schrøder, Thomas B.; Dyre, Jeppe C.

2012-01-01

This paper is an attempt to identify the real essence of simplicity of liquids in John Locke’s understanding of the term. Simple liquids are traditionally defined as many-body systems of classical particles interacting via radially symmetric pair potentials. We suggest that a simple liquid should be defined instead by the property of having strong correlations between virial and potential-energy equilibrium fluctuations in the NVT ensemble. There is considerable overlap between the two definitions, but also some notable differences. For instance, in the new definition simplicity is not a direct property of the intermolecular potential because a liquid is usually only strongly correlating in part of its phase diagram. Moreover, not all simple liquids are atomic (i.e., with radially symmetric pair potentials) and not all atomic liquids are simple. The main part of the paper motivates the new definition of liquid simplicity by presenting evidence that a liquid is strongly correlating if and only if its intermolecular interactions may be ignored beyond the first coordination shell (FCS). This is demonstrated by NVT simulations of the structure and dynamics of several atomic and three molecular model liquids with a shifted-forces cutoff placed at the first minimum of the radial distribution function. The liquids studied are inverse power-law systems (r-n pair potentials with n=18,6,4), Lennard-Jones (LJ) models (the standard LJ model, two generalized Kob-Andersen binary LJ mixtures, and the Wahnstrom binary LJ mixture), the Buckingham model, the Dzugutov model, the LJ Gaussian model, the Gaussian core model, the Hansen-McDonald molten salt model, the Lewis-Wahnstrom ortho-terphenyl model, the asymmetric dumbbell model, and the single-point charge water model. The final part of the paper summarizes properties of strongly correlating liquids, emphasizing that these are simpler than liquids in general. Simple liquids, as defined here, may be characterized in three quite different ways: (1) chemically by the fact that the liquid’s properties are fully determined by interactions from the molecules within the FCS, (2) physically by the fact that there are isomorphs in the phase diagram, i.e., curves along which several properties like excess entropy, structure, and dynamics, are invariant in reduced units, and (3) mathematically by the fact that throughout the phase diagram the reduced-coordinate constant-potential-energy hypersurfaces define a one-parameter family of compact Riemannian manifolds. No proof is given that the chemical characterization follows from the strong correlation property, but we show that this FCS characterization is consistent with the existence of isomorphs in strongly correlating liquids’ phase diagram. Finally, we note that the FCS characterization of simple liquids calls into question the physical basis of standard perturbation theory, according to which the repulsive and attractive forces play fundamentally different roles for the physics of liquids.

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-01

We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ɛ(r) is close to one everywhere inside the protein. The Gaussian widths σi of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σi. A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by comparison with so-called generalized Born methods. A follow-up paper describes how the method enables Hamiltonian, efficient, and accurate MM molecular dynamics simulations of proteins in dielectric solvent continua.

Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description.

PubMed

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-14

We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ(i) of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ(i). A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by comparison with so-called generalized Born methods. A follow-up paper describes how the method enables Hamiltonian, efficient, and accurate MM molecular dynamics simulations of proteins in dielectric solvent continua.

A new force field including charge directionality for TMAO in aqueous solution

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

Usui, Kota; Nagata, Yuki, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de; Hunger, Johannes

We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (O{sub TMAO}) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O{sub TMAO} to mimic the O{sub TMAO} lone pairs and we migrate the negative charge on the O{sub TMAO} to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasingmore » TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.« less

Contact resonances of U-shaped atomic force microscope probes

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

Rezaei, E.; Turner, J. A., E-mail: jaturner@unl.edu

Recent approaches used to characterize the elastic or viscoelastic properties of materials with nanoscale resolution have focused on the contact resonances of atomic force microscope (CR-AFM) probes. The experiments for these CR-AFM methods involve measurement of several contact resonances from which the resonant frequency and peak width are found. The contact resonance values are then compared with the noncontact values in order for the sample properties to be evaluated. The data analysis requires vibration models associated with the probe during contact in order for the beam response to be deconvolved from the measured spectra. To date, the majority of CR-AFMmore » research has used rectangular probes that have a relatively simple vibration response. Recently, U-shaped AFM probes have created much interest because they allow local sample heating. However, the vibration response of these probes is much more complex such that CR-AFM is still in its infancy. In this article, a simplified analytical model of U-shaped probes is evaluated for contact resonance applications relative to a more complex finite element (FE) computational model. The tip-sample contact is modeled using three orthogonal Kelvin-Voigt elements such that the resonant frequency and peak width of each mode are functions of the contact conditions. For the purely elastic case, the frequency results of the simple model are within 8% of the FE model for the lowest six modes over a wide range of contact stiffness values. Results for the viscoelastic contact problem for which the quality factor of the lowest six modes is compared show agreement to within 13%. These results suggest that this simple model can be used effectively to evaluate CR-AFM experimental results during AFM scanning such that quantitative mapping of viscoelastic properties may be possible using U-shaped probes.« less

US Highway 395 Widen Median and Shoulder and Install Rumble Strips Project Environmental Assessment, Edwards Air Force Base, California

DTIC Science & Technology

2015-12-16

Topography of the area varies from rugged rocky mountaintops, surrounded by gravel-laden alluvial fans and aprons, to sand and clay deposits in flat valley...disposal practices resulted in releases or disposal of organic solvents that have affected groundwater. A sanitary landfill is also located in this...Great Basin scrub, Sonoran Desert scrub and desert dunes with sandy flats, dunes and sandy areas around clay slicks with Sarcobatus (greasewood

One-pot in situ mixed film formation by azo coupling and diazonium salt electrografting.

PubMed

Esnault, Charles; Delorme, Nicolas; Louarn, Guy; Pilard, Jean-François

2013-06-24

So simple: The in situ synthesis of an aryldiazonium salt and an azo-aryldiazonium salt by azo coupling from sulfanilic acid and aniline is reported. Formation of a mixed organic layer is monitored by cyclic voltammetry and atomic force microscopy. A compact mixed layer is obtained with a global roughness of 0.4 nm and 10-15 % vertical extension in the range 1.5-6 nm. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Urinary tract infection after retrograde urethrogram in children: A multicenter study.

PubMed

Malhotra, Neha R; Green, Jared R; Rigsby, Cynthia K; Holl, Jane L; Cheng, Earl Y; Johnson, Emilie K

2017-12-01

The risk of post-procedural urinary tract infection (ppUTI) after retrograde urethrogram (RUG) has not been well quantified. Prophylactic antibiotics may reduce the risk, but must be weighed against the risks of antibiotic resistance. Prior research has shown that this risk is variable after voiding cystourethrogram (0-42% reported ppUTI rate) and appears to be low after urodynamics (0-4.8%) but this risk has not been well documented for patients undergoing RUG. We aimed to (1) describe the rate of ppUTI after RUG, and (2) examine factors associated with use of antibiotics at the time of RUG. We conducted a retrospective cohort study of children undergoing RUG at two hospitals January 1, 2004, to December 31, 2014. ppUTI within 7 days was measured. Antibiotic prophylaxis was determined. Relationships between clinical characteristics and receipt of pre-procedure antibiotics were evaluated using univariate statistics. Forty-two patients (100% male, median age 11.7 years) underwent 47 RUGs. Indications included trauma (27%), hypospadias (17%), and non-hypospadias (27%) stricture. Study indication and antibiotic administration practices are illustrated in the Figure. Three patients (6.4%) had a history of posterior urethral valves (PUV); one had neurogenic bladder (NGB) (2.4%). Two (4%) studies were performed within 30 days of a clinical UTI and 11% had a positive urinalysis or culture within 30 days pre-RUG. UTI in the 30 days before RUG was not associated with antibiotic prescription (p > 0.99). One child (2.1%; 95% CI 0-6.3%) had a ppUTI: a 7-year-old, uncircumcised male with a history of PUV and voiding dysfunction who was asymptomatic at the time of RUG. Although the risk of ppUTI after RUG appears to be low, the rare occurrence of an iatrogenic UTI can lead to high cost and patient morbidity, particularly in cases similar to our patients who required inpatient admission for intravenous antibiotics. To help balance the risk of UTI with the associated healthcare costs and morbidity with the concerns about antibiotic overuse and potential exposure to drug reaction, data from this study may inform future development of evidence-based guidelines targeting only patients at highest risk for ppUTI with antibiotic prophylaxis. The risk of ppUTI after RUG is low. Antibiotic prophylaxis was unrelated pre-RUG UTI in our population. These results indicate the need for pre-procedural antibiotic prescribing guidelines, and suggest that routine antibiotics prior to RUG are not indicated unless the patient has another indication for antibiotics. Copyright © 2017 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.

Imaging latex–carbon nanotube composites by subsurface electrostatic force microscopy

DOE PAGES

Patel, Sajan; Petty, Clayton W.; Krafcik, Karen Lee; ...

2016-09-08

Electrostatic modes of atomic force microscopy have shown to be non-destructive and relatively simple methods for imaging conductors embedded in insulating polymers. Here we use electrostatic force microscopy to image the dispersion of carbon nanotubes in a latex-based conductive composite, which brings forth features not observed in previously studied systems employing linear polymer films. A fixed-potential model of the probe-nanotube electrostatics is presented which in principle gives access to the conductive nanoparticle's depth and radius, and the polymer film dielectric constant. Comparing this model to the data results in nanotube depths that appear to be slightly above the film–air interface.more » Furthermore, this result suggests that water-mediated charge build-up at the film–air interface may be the source of electrostatic phase contrast in ambient conditions.« less

Slipping and tripping: fall injuries in adults associated with rugs and carpets

PubMed Central

Rosen, Tony; Mack, Karin A.; Noonan, Rita K.

2013-01-01

Abstract: Background: Falls are a leading cause of unintentional injury among adults age 65 years and older. Loose, unsecured rugs and damaged carpets with curled edges, are recognized environmental hazards that may contribute to falls. To characterize nonfatal, unintentional fall-related injuries associated with rugs and carpets in adults aged 65 years and older. Methods: We conducted a retrospective analysis of surveillance data of injuries treated in hospital emergency departments (EDs) during 2001–2008. We used the National Electronic Injury Surveillance System-All Injury Program, which collects data from a nationally representative stratified probability sample of 66 U.S. hospital EDs. Sample weights were used to make national estimates. Results: Annually, an estimated 37,991 adults age 65 years or older were treated in U.S. EDs for falls associated with carpets (54.2%) and rugs (45.8%). Most falls (72.8%) occurred at home. Women represented 80.2% of fall injuries. The most common location for fall injuries in the home was the bathroom (35.7%). Frequent fall injuries occurred at the transition between carpet/rug and non-carpet/rug, on wet carpets or rugs, and while hurrying to the bathroom. Conclusions: Fall injuries associated with rugs and carpets are common and may cause potentially severe injuries. Older adults, their caregivers, and emergency and primary care physicians should be aware of the significant risk for fall injuries and of environmental modifications that may reduce that risk. PMID:22868399

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

PubMed Central

Ewen, James P.; Gattinoni, Chiara; Thakkar, Foram M.; Morgan, Neal; Spikes, Hugh A.; Dini, Daniele

2016-01-01

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed. PMID:28773773

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants.

PubMed

Ewen, James P; Gattinoni, Chiara; Thakkar, Foram M; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

2016-08-02

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n -hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n -hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n -hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed.

Subharmonic Oscillations and Chaos in Dynamic Atomic Force Microscopy

NASA Technical Reports Server (NTRS)

Cantrell, John H.; Cantrell, Sean A.

2015-01-01

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

Distributed force probe bending model of critical dimension atomic force microscopy bias

NASA Astrophysics Data System (ADS)

Ukraintsev, Vladimir A.; Orji, Ndubuisi G.; Vorburger, Theodore V.; Dixson, Ronald G.; Fu, Joseph; Silver, Rick M.

2013-04-01

Critical dimension atomic force microscopy (CD-AFM) is a widely used reference metrology technique. To characterize modern semiconductor devices, small and flexible probes, often 15 to 20 nm in diameter, are used. Recent studies have reported uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements. To understand the source of these variations, tip-sample interactions between high aspect ratio features and small flexible probes, and their influence on measurement bias, should be carefully studied. Using theoretical and experimental procedures, one-dimensional (1-D) and two-dimensional (2-D) models of cylindrical probe bending relevant to carbon nanotube (CNT) AFM probes were developed and tested. An earlier 1-D bending model was refined, and a new 2-D distributed force (DF) model was developed. Contributions from several factors were considered, including: probe misalignment, CNT tip apex diameter variation, probe bending before snapping, and distributed van der Waals-London force. A method for extracting Hamaker probe-surface interaction energy from experimental probe-bending data was developed. Comparison of the new 2-D model with 1-D single point force (SPF) model revealed a difference of about 28% in probe bending. A simple linear relation between biases predicted by the 1-D SPF and 2-D DF models was found. The results suggest that probe bending can be on the order of several nanometers and can partially explain the observed CD-AFM probe-to-probe variation. New 2-D and three-dimensional CD-AFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.

Adaptive enhanced sampling by force-biasing using neural networks

NASA Astrophysics Data System (ADS)

Guo, Ashley Z.; Sevgen, Emre; Sidky, Hythem; Whitmer, Jonathan K.; Hubbell, Jeffrey A.; de Pablo, Juan J.

2018-04-01

A machine learning assisted method is presented for molecular simulation of systems with rugged free energy landscapes. The method is general and can be combined with other advanced sampling techniques. In the particular implementation proposed here, it is illustrated in the context of an adaptive biasing force approach where, rather than relying on discrete force estimates, one can resort to a self-regularizing artificial neural network to generate continuous, estimated generalized forces. By doing so, the proposed approach addresses several shortcomings common to adaptive biasing force and other algorithms. Specifically, the neural network enables (1) smooth estimates of generalized forces in sparsely sampled regions, (2) force estimates in previously unexplored regions, and (3) continuous force estimates with which to bias the simulation, as opposed to biases generated at specific points of a discrete grid. The usefulness of the method is illustrated with three different examples, chosen to highlight the wide range of applicability of the underlying concepts. In all three cases, the new method is found to enhance considerably the underlying traditional adaptive biasing force approach. The method is also found to provide improvements over previous implementations of neural network assisted algorithms.

Development of a high-speed wavelength-agile CO2 local oscillator for heterodyne DIAL measurements

NASA Astrophysics Data System (ADS)

Senft, Daniel C.; Pierrottet, Diego F.

2002-06-01

A high repetition rate, wavelength agile CO2 laser has been developed at the Air Force Research Laboratory for use as a local oscillator in a heterodyne detection receiver. Fats wavelength selection is required for measurements of airborne chemical vapors using the differential absorption lidar (DIAL) technique. Acousto-optic modulator are used to tune between different wavelengths at high speeds without the need for moving mechanical parts. Other advantages obtained by the use of acousto-optic modulators are laser output power control per wavelength and rugged packaging for field applications. The local oscillator design is described, and the results from laboratory DIAL measurements are presented. The coherent remote optical sensor system is an internal research project being conducted by the Air Force Research Laboratory Directed Energy Directorate, Active Remote Sensing Branch. The objective of the project is to develop a new long-range standoff spectral sensor that takes advantage of the enhanced performance capabilities coherent detection can provide. Emphasis of the development is on a low cost, compact, and rugged active sensor exclusively designed for heterodyne detection using the differential absorption lidar technique. State of the art technologies in waveguide laser construction and acousto- optics make feasible the next generation of lasers capable of supporting coherent lidar system requirements. Issues addressed as part of the development include optoelectronic engineering of a low cost rugged system, and fast data throughput for real time chemical concentration measurements. All hardware used in this sensor are off-the- shelf items, so only minor hardware modifications were required for the system as it stands. This paper describes a high-speed heterodyne detection CO2 DIAL system that employs a wavelength agile, acousto-optically tuned local oscillator in the receiver. Sample experimental data collected in a controlled environment are presented as well. Chemical detection using 12 wavelengths at 200 pulses per second has been demonstrated. Initial progress on experiments to make a direct, simultaneous comparison of heterodyne and direct detection DIAL systems will also be described.

Subatomic Features on the Silicon (111)-(7x7) Surface Observed by Atomic Force Microscopy.

PubMed

Giessibl; Hembacher; Bielefeldt; Mannhart

2000-07-21

The atomic force microscope images surfaces by sensing the forces between a sharp tip and a sample. If the tip-sample interaction is dominated by short-range forces due to the formation of covalent bonds, the image of an individual atom should reflect the angular symmetry of the interaction. Here, we report on a distinct substructure in the images of individual adatoms on silicon (111)-(7x7), two crescents with a spherical envelope. The crescents are interpreted as images of two atomic orbitals of the front atom of the tip. Key for the observation of these subatomic features is a force-detection scheme with superior noise performance and enhanced sensitivity to short-range forces.

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

Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de; Lilienfeld, O. Anatole von

We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi tesselation approach instead of conventional density partitioning schemes. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular interaction model from dispersion and electrostatics for more than 1300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine—intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlightmore » the potential of this method and help to identify points of future improvement. The mean absolute error made by the combination of static electrostatics with many-body dispersion reduces at larger distances, while it plateaus for two-body dispersion, in conflict with the common assumption that the simple 1/R{sup 6} correction will yield proper dissociative tails. Overall, the method achieves an accuracy well within conventional molecular force fields while exhibiting a simple parametrization protocol.« less

Sb-Te alloy nanostructures produced on a graphite surface by a simple annealing process

NASA Astrophysics Data System (ADS)

Kuwahara, Masashi; Uratsuji, Hideaki; Abe, Maho; Sone, Hayato; Hosaka, Sumio; Sakai, Joe; Uehara, Yoichi; Endo, Rie; Tsuruoka, Tohru

2015-08-01

We have produced Sb-Te alloy nanostructures from a thin Sb2Te3 layer deposited on a highly oriented pyrolytic graphite substrate using a simple rf-magnetron sputtering and annealing technique. The size, shape, and chemical composition of the structures were investigated by scanning electron microscopy (SEM), atomic force microscopy (AFM), and energy dispersive X-ray spectrometry (EDX), respectively. The shape of the nanostructures was found to depend on the annealing temperature; nanoparticles appear on the substrate by annealing at 200 °C, while nanoneedles are formed at higher temperatures. Chemical composition analysis has revealed that all the structures were in the composition of Sb:Te = 1:3, Te rich compared to the target composition Sb2Te3, probably due to the higher movability of Te atoms on the substrate compared with Sb. We also tried to observe the production process of nanostructures in situ using SEM. Unfortunately, this was not possible because of evaporation in vacuum, suggesting that the formation of nanostructures is highly sensitive to the ambient pressure.

Clustering biomolecular complexes by residue contacts similarity.

PubMed

Rodrigues, João P G L M; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J

2012-07-01

Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions. Albeit widely used, these measures suffer from several theoretical and technical limitations (e.g., choice of regions for fitting) that impair their application in multicomponent systems (N > 2), large-scale studies (e.g., interactomes), and other time-critical scenarios. We present here a simple similarity measure for structural clustering based on atomic contacts--the fraction of common contacts--and compare it with the most used similarity measure of the protein docking community--interface backbone RMSD. We show that this method produces very compact clusters in remarkably short time when applied to a collection of binary and multicomponent protein-protein and protein-DNA complexes. Furthermore, it allows easy clustering of similar conformations of multicomponent symmetrical assemblies in which chain permutations can occur. Simple contact-based metrics should be applicable to other structural biology clustering problems, in particular for time-critical or large-scale endeavors. Copyright © 2012 Wiley Periodicals, Inc.

Patterning nanoparticles into rings by "2-D Pickering emulsions".

PubMed

Lee, Cheol Hee; Crosby, Alfred J; Hayward, Ryan C; Emrick, Todd

2014-04-09

We present a simple method for the two-dimensional self-assembly of CdSe/ZnS quantum dots (QDs) into well-defined rings at the air/water interface, through the formation of "2-D Pickering emulsions". Surfactant molecules assemble at the air/water interface into islands that are subsequently surrounded by adsorption of QDs from the aqueous subphase. The QD rings emanating from this process range from ∼100 nm to several micrometers in diameter, as characterized by atomic force microscopy, scanning electron microscopy, and fluorescence microscopy. The deposition and alignment of QD rings onto large areas (cm(2)) were demonstrated by dip-coating onto a substrate. This simple method produces rings of QDs without the need for any templating or fabrication steps.

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

Optical identification using imperfections in 2D materials

NASA Astrophysics Data System (ADS)

Cao, Yameng; Robson, Alexander J.; Alharbi, Abdullah; Roberts, Jonathan; Woodhead, Christopher S.; Noori, Yasir J.; Bernardo-Gavito, Ramón; Shahrjerdi, Davood; Roedig, Utz; Fal'ko, Vladimir I.; Young, Robert J.

2017-12-01

The ability to uniquely identify an object or device is important for authentication. Imperfections, locked into structures during fabrication, can be used to provide a fingerprint that is challenging to reproduce. In this paper, we propose a simple optical technique to read unique information from nanometer-scale defects in 2D materials. Imperfections created during crystal growth or fabrication lead to spatial variations in the bandgap of 2D materials that can be characterized through photoluminescence measurements. We show a simple setup involving an angle-adjustable transmission filter, simple optics and a CCD camera can capture spatially-dependent photoluminescence to produce complex maps of unique information from 2D monolayers. Atomic force microscopy is used to verify the origin of the optical signature measured, demonstrating that it results from nanometer-scale imperfections. This solution to optical identification with 2D materials could be employed as a robust security measure to prevent counterfeiting.

Dielectrophoretic immobilization of proteins: Quantification by atomic force microscopy.

PubMed

Laux, Eva-Maria; Knigge, Xenia; Bier, Frank F; Wenger, Christian; Hölzel, Ralph

2015-09-01

The combination of alternating electric fields with nanometer-sized electrodes allows the permanent immobilization of proteins by dielectrophoretic force. Here, atomic force microscopy is introduced as a quantification method, and results are compared with fluorescence microscopy. Experimental parameters, for example the applied voltage and duration of field application, are varied systematically, and the influence on the amount of immobilized proteins is investigated. A linear correlation to the duration of field application was found by atomic force microscopy, and both microscopical methods yield a square dependence of the amount of immobilized proteins on the applied voltage. While fluorescence microscopy allows real-time imaging, atomic force microscopy reveals immobilized proteins obscured in fluorescence images due to low S/N. Furthermore, the higher spatial resolution of the atomic force microscope enables the visualization of the protein distribution on single nanoelectrodes. The electric field distribution is calculated and compared to experimental results with very good agreement to atomic force microscopy measurements. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Simple Demonstration of Atomic and Molecular Orbitals Using Circular Magnets

ERIC Educational Resources Information Center

Chakraborty, Maharudra; Mukhopadhyay, Subrata; Das, Ranendu Sekhar

2014-01-01

A quite simple and inexpensive technique is described here to represent the approximate shapes of atomic orbitals and the molecular orbitals formed by them following the principles of the linear combination of atomic orbitals (LCAO) method. Molecular orbitals of a few simple molecules can also be pictorially represented. Instructors can employ the…

High-speed atomic force microscopy imaging of live mammalian cells

PubMed Central

Shibata, Mikihiro; Watanabe, Hiroki; Uchihashi, Takayuki; Ando, Toshio; Yasuda, Ryohei

2017-01-01

Direct imaging of morphological dynamics of live mammalian cells with nanometer resolution under physiological conditions is highly expected, but yet challenging. High-speed atomic force microscopy (HS-AFM) is a unique technique for capturing biomolecules at work under near physiological conditions. However, application of HS-AFM for imaging of live mammalian cells was hard to be accomplished because of collision between a huge mammalian cell and a cantilever during AFM scanning. Here, we review our recent improvements of HS-AFM for imaging of activities of live mammalian cells without significant damage to the cell. The improvement of an extremely long (~3 μm) AFM tip attached to a cantilever enables us to reduce severe damage to soft mammalian cells. In addition, a combination of HS-AFM with simple fluorescence microscopy allows us to quickly locate the cell in the AFM scanning area. After these improvements, we demonstrate that developed HS-AFM for live mammalian cells is possible to image morphogenesis of filopodia, membrane ruffles, pits open-close formations, and endocytosis in COS-7, HeLa cells as well as hippocampal neurons. PMID:28900590

Distortion in the thermal noise spectrum and quality factor of nanomechanical devices due to finite frequency resolution with applications to the atomic force microscope.

PubMed

Sader, John E; Sanelli, Julian; Hughes, Barry D; Monty, Jason P; Bieske, Evan J

2011-09-01

The thermal noise spectrum of nanomechanical devices is commonly used to characterize their mechanical properties and energy dissipation. This spectrum is measured from finite time series of Brownian motion of the device, which is windowed and Fourier transformed. Here, we present a theoretical and experimental investigation of the effect of such finite sampling on the measured device quality factor. We prove that if no spectral window is used, the thermal noise spectrum retains its original Lorentzian distribution but with a reduced quality factor, indicating an apparent enhancement in energy dissipation. A simple analytical formula is derived connecting the true and measured quality factors - this enables extraction of the true device quality factor from measured data. Common windows used to reduce spectral leakage are found to distort the (true) Lorentzian shape, potentially making fitting problematic. These findings are expected to be of particular importance for devices with high quality factors, where spectral resolution can be limited in practice. Comparison and validation using measurements on atomic force microscope cantilevers are presented. © 2011 American Institute of Physics

The binding domain of the HMGB1 inhibitor carbenoxolone: Theory and experiment

NASA Astrophysics Data System (ADS)

Mollica, Luca; Curioni, Alessandro; Andreoni, Wanda; Bianchi, Marco E.; Musco, Giovanna

2008-05-01

We present a combined computational and experimental study of the interaction of the Box A of the HMGB1 protein and carbenoxolone, an inhibitor of its pro-inflammatory activity. The computational approach consists of classical molecular dynamics (MD) simulations based on the GROMOS force field with quantum-refined (QRFF) atomic charges for the ligand. Experimental data consist of fluorescence intensities, chemical shift displacements, saturation transfer differences and intermolecular Nuclear Overhauser Enhancement signals. Good agreement is found between observations and the conformation of the ligand-protein complex resulting from QRFF-MD. In contrast, simple docking procedures and MD based on the unrefined force field provide models inconsistent with experiment. The ligand-protein binding is dominated by non-directional interactions.

Thermal Casimir-Polder forces on a V-type three-level atom

NASA Astrophysics Data System (ADS)

Xu, Chen-Ran; Xu, Jing-Ping; Al-amri, M.; Zhu, Cheng-Jie; Xie, Shuang-Yuan; Yang, Ya-Ping

2017-09-01

We study the thermal Casimir-Polder (CP) forces on a V-type three-level atom. The competition between the thermal effect and the quantum interference of the two transition dipoles on the force is investigated. To shed light onto the role of the quantum interference, we analyze two kinds of initial states of the atom, i.e., the superradiant state and the subradiant state. Considering the atom being in the thermal reservoir, the resonant CP force arising from the real photon emission dominates in the evolution of the CP force. Under the zero-temperature condition, the quantum interference can effectively modify the amplitude and the evolution of the force, leading to a long-time force or even the cancellation of the force. Our results reveal that in the finite-temperature case, the thermal photons can enhance the amplitude of all force elements, but have no influence on the net resonant CP force in the steady state, which means that the second law of thermodynamics still works. For the ideal degenerate V-type atom with parallel dipoles under the initial subradiant state, the robust destructive quantum interference overrides the thermal fluctuations, leading to the trapping of the atom in the subradiant state and the disappearance of the CP force. However, in terms of a realistic Zeeman atom, the thermal photons play a significant role during the evolution of the CP force. The thermal fluctuations can enhance the amplitude of the initial CP force by increasing the temperature, and weaken the influence of the quantum interference on the evolution of the CP force from the initial superradiant (subradiant) state to the steady state.

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/ .

Applying RUG-III in Japanese Long-Term Care Facilities.

ERIC Educational Resources Information Center

Ikegami, Naoki; And Others

1994-01-01

Tested U.S. nursing home case-mix system, Resource Utilization Groups, Version III (RUG-III) in Japanese long-term care facilities. Measured staff time and resident characteristics for 871 patients. Found acceptable reliability for items defining RUG-III, and system explained 44% of variance in wage-weighted staff time (cost). Japanese and U.S.…

16 CFR 1631.34 - Small carpets and rugs not meeting acceptance criterion.

Code of Federal Regulations, 2011 CFR

2011-01-01

... proximity to the edge of the small carpet or rug. (b) Such cautionary statements shall also appear in a... or effect the sale of small carpets or rugs shall be labeled with the information required by this... samples, swatches, or specimens used to promote or effect the sale thereof, which is not in compliance...

16 CFR 1631.34 - Small carpets and rugs not meeting acceptance criterion.

Code of Federal Regulations, 2014 CFR

2014-01-01

... proximity to the edge of the small carpet or rug. (b) Such cautionary statements shall also appear in a... or effect the sale of small carpets or rugs shall be labeled with the information required by this... samples, swatches, or specimens used to promote or effect the sale thereof, which is not in compliance...

16 CFR § 1631.34 - Small carpets and rugs not meeting acceptance criterion.

Code of Federal Regulations, 2013 CFR

2013-01-01

... proximity to the edge of the small carpet or rug. (b) Such cautionary statements shall also appear in a... or effect the sale of small carpets or rugs shall be labeled with the information required by this... samples, swatches, or specimens used to promote or effect the sale thereof, which is not in compliance...

16 CFR 1631.34 - Small carpets and rugs not meeting acceptance criterion.

Code of Federal Regulations, 2012 CFR

2012-01-01

... proximity to the edge of the small carpet or rug. (b) Such cautionary statements shall also appear in a... or effect the sale of small carpets or rugs shall be labeled with the information required by this... samples, swatches, or specimens used to promote or effect the sale thereof, which is not in compliance...

Diffraction-Based Density Restraints for Membrane and Membrane-Peptide Molecular Dynamics Simulations

PubMed Central

Benz, Ryan W.; Nanda, Hirsh; Castro-Román, Francisco; White, Stephen H.; Tobias, Douglas J.

2006-01-01

We have recently shown that current molecular dynamics (MD) atomic force fields are not yet able to produce lipid bilayer structures that agree with experimentally-determined structures within experimental errors. Because of the many advantages offered by experimentally validated simulations, we have developed a novel restraint method for membrane MD simulations that uses experimental diffraction data. The restraints, introduced into the MD force field, act upon specified groups of atoms to restrain their mean positions and widths to values determined experimentally. The method was first tested using a simple liquid argon system, and then applied to a neat dioleoylphosphatidylcholine (DOPC) bilayer at 66% relative humidity and to the same bilayer containing the peptide melittin. Application of experiment-based restraints to the transbilayer double-bond and water distributions of neat DOPC bilayers led to distributions that agreed with the experimental values. Based upon the experimental structure, the restraints improved the simulated structure in some regions while introducing larger differences in others, as might be expected from imperfect force fields. For the DOPC-melittin system, the experimental transbilayer distribution of melittin was used as a restraint. The addition of the peptide caused perturbations of the simulated bilayer structure, but which were larger than observed experimentally. The melittin distribution of the simulation could be fit accurately to a Gaussian with parameters close to the observed ones, indicating that the restraints can be used to produce an ensemble of membrane-bound peptide conformations that are consistent with experiments. Such ensembles pave the way for understanding peptide-bilayer interactions at the atomic level. PMID:16950837

High power laser source for atom cooling based on reliable telecoms technology with all fibre frequency stabilisation

NASA Astrophysics Data System (ADS)

Legg, Thomas; Farries, Mark

2017-02-01

Cold atom interferometers are emerging as important tools for metrology. Designed into gravimeters they can measure extremely small changes in the local gravitational field strength and be used for underground surveying to detect buried utilities, mineshafts and sinkholes prior to civil works. To create a cold atom interferometer narrow linewidth, frequency stabilised lasers are required to cool the atoms and to setup and measure the atom interferometer. These lasers are commonly either GaAs diodes, Ti Sapphire lasers or frequency doubled InGaAsP diodes and fibre lasers. The InGaAsP DFB lasers are attractive because they are very reliable, mass-produced, frequency controlled by injection current and simply amplified to high powers with fibre amplifiers. In this paper a laser system suitable for Rb atom cooling, based on a 1560nm DFB laser and erbium doped fibre amplifier, is described. The laser output is frequency doubled with fibre coupled periodically poled LiNbO3 to a wavelength of 780nm. The output power exceeds 1 W at 780nm. The laser is stabilised at 1560nm against a fibre Bragg resonator that is passively temperature compensated. Frequency tuning over a range of 1 GHz is achieved by locking the laser to sidebands of the resonator that are generated by a phase modulator. This laser design is attractive for field deployable rugged systems because it uses all fibre coupled components with long term proven reliability.

Spontaneous lateral atomic recoil force close to a photonic topological material

NASA Astrophysics Data System (ADS)

Hassani Gangaraj, S. Ali; Hanson, George W.; Antezza, Mauro; Silveirinha, Mário G.

2018-05-01

We investigate the quantum recoil force acting on an excited atom close to the surface of a nonreciprocal photonic topological insulator (PTI). The main atomic emission channel is the unidirectional surface plasmon propagating at the PTI-vacuum interface, and we show that it enables a spontaneous lateral recoil force that scales at short distances as 1 /d4 , where d is the atom-PTI separation. Remarkably, the sign of the recoil force is polarization and orientation independent, and it occurs in a translation-invariant homogeneous system in thermal equilibrium. Surprisingly, the recoil force persists for very small values of the gyration pseudovector, which, for a biased plasma, corresponds to very low cyclotron frequencies. The ultrastrong recoil force is rooted in the quasihyperbolic dispersion of the surface plasmons. We consider both an initially excited atom and a continuous pump scenario, the latter giving rise to a steady lateral force whose direction can be changed at will by simply varying the orientation of the biasing magnetic field. Our predictions may be tested in experiments with cold Rydberg atoms and superconducting qubits.

Research on the properties and interactions of simple atomic and ionic systems

NASA Technical Reports Server (NTRS)

Novick, R.

1972-01-01

Simple ionic systems were studied, such as metastable autoionizing states of the negative He ion, two-photon decay spectrum of metastable He ion, optical excitation with low energy ions, and lifetime measurements of singly ionized Li and metastable He ion. Simple atomic systems were also investigated. Metastable autoionizing atomic energy levels in alkali elements were included, along with lifetime measurements of Cr-53, group 2A isotopes, and alkali metal atoms using level crossing and optical double resonance spectroscopy.

A compressible multiphase framework for simulating supersonic atomization

NASA Astrophysics Data System (ADS)

Regele, Jonathan D.; Garrick, Daniel P.; Hosseinzadeh-Nik, Zahra; Aslani, Mohamad; Owkes, Mark

2016-11-01

The study of atomization in supersonic combustors is critical in designing efficient and high performance scramjets. Numerical methods incorporating surface tension effects have largely focused on the incompressible regime as most atomization applications occur at low Mach numbers. Simulating surface tension effects in high speed compressible flow requires robust numerical methods that can handle discontinuities caused by both material interfaces and shocks. A shock capturing/diffused interface method is developed to simulate high-speed compressible gas-liquid flows with surface tension effects using the five-equation model. This includes developments that account for the interfacial pressure jump that occurs in the presence of surface tension. A simple and efficient method for computing local interface curvature is developed and an acoustic non-dimensional scaling for the surface tension force is proposed. The method successfully captures a variety of droplet breakup modes over a range of Weber numbers and demonstrates the impact of surface tension in countering droplet deformation in both subsonic and supersonic cross flows.

Applying Resource Utilization Groups (RUG-III) in Hong Kong nursing homes.

PubMed

Chou, Kee-Lee; Chi, Iris; Leung, Joe C B

2008-01-01

Resource Utilization Groups III (RUG-III) is a case-mix system developed in the United States for categorization of nursing home residents and the financing of residential care services. In Hong Kong, RUG-III is based on several board groups of residents. The aim of this study was to examine the reliability and validity of the RUG-III in Hong Kong nursing homes. A cross-sectional survey was conducted in seven residential facilities operated by one agency. Residents ( N = 1,127) were assessed by the Minimum Data Set (MDS) and nursing as well as auxiliary staff care times were recorded within 2 weeks before or after the completion of MDS assessment. Forty-five out 1,127 residents were re-interviewed by an independent assessor to assess the inter-rater reliability. The inter-rater reliability of MDS assessment was excellent (kappa = 0.76) and the original RUG-III accounted for about 30 per cent of nursing staff time. Results provide preliminary evidence to support that RUG-III is a reliable and valid case-mix system for Hong Kong nursing homes, but future studies must be explored to reduce the variance of resource use explained by this case-mix system.

Monte Carlo based estimation of organ and effective doses to patients undergoing hysterosalpingography and retrograde urethrography fluoroscopy procedures

NASA Astrophysics Data System (ADS)

Ngaile, J. E.; Msaki, P. K.; Kazema, R. R.

2018-04-01

Contrast investigations of hysterosalpingography (HSG) and retrograde urethrography (RUG) fluoroscopy procedures remain the dominant diagnostic tools for the investigation of infertility in females and urethral strictures in males, respectively, owing to the scarcity and high cost of services of alternative diagnostic technologies. In light of the radiological risks associated with contrast based investigations of the genitourinary tract systems, there is a need to assess the magnitude of radiation burden imparted to patients undergoing HSG and RUG fluoroscopy procedures in Tanzania. The air kerma area product (KAP), fluoroscopy time, number of images, organ dose and effective dose to patients undergoing HSG and RUG procedures were obtained from four hospitals. The KAP was measured using a flat transmission ionization chamber, while the organ and effective doses were estimated using the knowledge of the patient characteristics, patient related exposure parameters, geometry of examination, KAP and Monte Carlo calculations (PCXMC). The median values of KAP for the HSG and RUG were 2.2 Gy cm2 and 3.3 Gy cm2, respectively. The median organ doses in the present study for the ovaries, urinary bladder and uterus for the HSG procedures, were 1.0 mGy, 4.0 mGy and 1.6 mGy, respectively, while for urinary bladder and testes of the RUG were 3.4 mGy and 5.9 mGy, respectively. The median values of effective doses for the HSG and RUG procedures were 0.65 mSv and 0.59 mSv, respectively. The median values of effective dose per hospital for the HSG and RUG procedures had a range of 1.6-2.8 mSv and 1.9-5.6 mSv, respectively, while the overall differences between individual effective doses across the four hospitals varied by factors of up to 22.0 and 46.7, respectively for the HSG and RUG procedures. The proposed diagnostic reference levels (DRLs) for the HSG and RUG were for KAP 2.8 Gy cm2 and 3.9 Gy cm2, for fluoroscopy time 0.8 min and 0.9 min, and for number of images 5 and 4, respectively. The suggested DRLs for the HSG and RUG procedures may be used by the radiology departments in Tanzania for management of attained dose levels until the national DRLs are established.

Quantitative force measurements using frequency modulation atomic force microscopy—theoretical foundations

NASA Astrophysics Data System (ADS)

Sader, John E.; Uchihashi, Takayuki; Higgins, Michael J.; Farrell, Alan; Nakayama, Yoshikazu; Jarvis, Suzanne P.

2005-03-01

Use of the atomic force microscope (AFM) in quantitative force measurements inherently requires a theoretical framework enabling conversion of the observed deflection properties of the cantilever to an interaction force. In this paper, the theoretical foundations of using frequency modulation atomic force microscopy (FM-AFM) in quantitative force measurements are examined and rigorously elucidated, with consideration being given to both 'conservative' and 'dissipative' interactions. This includes a detailed discussion of the underlying assumptions involved in such quantitative force measurements, the presentation of globally valid explicit formulae for evaluation of so-called 'conservative' and 'dissipative' forces, discussion of the origin of these forces, and analysis of the applicability of FM-AFM to quantitative force measurements in liquid.

Penicillin biosensor based on a capacitive field-effect structure functionalized with a dendrimer/carbon nanotube multilayer.

PubMed

Siqueira, José R; Abouzar, Maryam H; Poghossian, Arshak; Zucolotto, Valtencir; Oliveira, Osvaldo N; Schöning, Michael J

2009-10-15

Silicon-based sensors incorporating biomolecules are advantageous for processing and possible biological recognition in a small, reliable and rugged manufactured device. In this study, we report on the functionalization of field-effect (bio-)chemical sensors with layer-by-layer (LbL) films containing single-walled carbon nanotubes (SWNTs) and polyamidoamine (PAMAM) dendrimers. A capacitive electrolyte-insulator-semiconductor (EIS) structure modified with carbon nanotubes (EIS-NT) was built, which could be used as a penicillin biosensor. From atomic force microscopy (AFM) and field-emission scanning electron microscopy (FESEM) images, the LbL films were shown to be highly porous due to interpenetration of SWNTs into the dendrimer layers. Capacitance-voltage (C/V) measurements pointed to a high pH sensitivity of ca. 55 mV/pH for the EIS-NT structures. The biosensing ability towards penicillin of an EIS-NT-penicillinase biosensor was also observed as the flat-band voltage shifted to lower potentials at different penicillin concentrations. A dynamic response of penicillin concentrations, ranging from 5.0 microM to 25 mM, was evaluated for an EIS-NT with the penicillinase enzyme immobilized onto the surfaces, via constant-capacitance (ConCap) measurements, achieving a sensitivity of ca. 116 mV/decade. The presence of the nanostructured PAMAM/SWNT LbL film led to sensors with higher sensitivity and better performance.

3D display considerations for rugged airborne environments

NASA Astrophysics Data System (ADS)

Barnidge, Tracy J.; Tchon, Joseph L.

2015-05-01

The KC-46 is the next generation, multi-role, aerial refueling tanker aircraft being developed by Boeing for the United States Air Force. Rockwell Collins has developed the Remote Vision System (RVS) that supports aerial refueling operations under a variety of conditions. The system utilizes large-area, high-resolution 3D displays linked with remote sensors to enhance the operator's visual acuity for precise aerial refueling control. This paper reviews the design considerations, trade-offs, and other factors related to the selection and ruggedization of the 3D display technology for this military application.

Laser cooling by adiabatic transfer

NASA Astrophysics Data System (ADS)

Norcia, Matthew; Cline, Julia; Bartolotta, John; Holland, Murray; Thompson, James

2017-04-01

We have demonstrated a new method of laser cooling applicable to particles with narrow linewidth optical transitions. This simple and robust cooling mechanism uses a frequency-swept laser to adiabatically transfer atoms between internal and motional states. The role of spontaneous emission is reduced (though is still critical) compared to Doppler cooling. This allows us to achieve greater slowing forces than would be possible with Doppler cooling, and may make this an appealing technique for cooling molecules. In this talk, I will present a demonstration of this technique in a cold strontium system. DARPA QUASAR, NIST, NSF PFC.

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

Bowman, Adam J.; Scherrer, Joseph R.; Reiserer, Ronald S., E-mail: ron.reiserer@vanderbilt.edu

We present a simple apparatus for improved surface modification of polydimethylsiloxane (PDMS) microfluidic devices. A single treatment chamber for plasma activation and chemical/physical vapor deposition steps minimizes the time-dependent degradation of surface activation that is inherent in multi-chamber techniques. Contamination and deposition irregularities are also minimized by conducting plasma activation and treatment phases in the same vacuum environment. An inductively coupled plasma driver allows for interchangeable treatment chambers. Atomic force microscopy confirms that silane deposition on PDMS gives much better surface quality than standard deposition methods, which yield a higher local roughness and pronounced irregularities in the surface.

Evaluation of a new modified QuEChERS method for the monitoring of carbamate residues in high-fat cheeses by using UHPLC-MS/MS.

PubMed

Hamed, Ahmed M; Moreno-González, David; Gámiz-Gracia, Laura; García-Campaña, Ana M

2017-01-01

A simple and efficient method for the determination of 28 carbamates in high-fat cheeses is proposed. The methodology is based on a modified quick, easy, cheap, effective, rugged, and safe procedure as sample treatment using a new sorbent (Z-Sep + ) followed by ultra-high performance liquid chromatography with tandem mass spectrometry determination. The method has been validated in different kinds of cheese (Gorgonzola, Roquefort, and Camembert), achieving recoveries of 70-115%, relative standard deviations lower than 13% and limits of quantification lower than 5.4 μg/kg, below the maximum residue levels tolerated for these compounds by the European legislation. The matrix effect was lower than ±30% for all the studied pesticides. The combination of ultra-high performance liquid chromatography and tandem mass spectrometry with this modified quick, easy, cheap, effective, rugged, and safe procedure using Z-Sep + allowed a high sample throughput and an efficient cleaning of extracts for the control of these residues in cheeses with a high fat content. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2018-04-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

Effective particle size from molecular dynamics simulations in fluids

NASA Astrophysics Data System (ADS)

Ju, Jianwei; Welch, Paul M.; Rasmussen, Kim Ø.; Redondo, Antonio; Vorobieff, Peter; Kober, Edward M.

2017-12-01

We report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. This procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks-Chandler-Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ˜ 0.75σ , where σ defines the length scale of the force interaction (the LJ diameter). The effective "hydrodynamic" radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ , but agree with a value developed from the atomistic analysis of the viscosity of such systems.

Interfacial gas nanobubbles or oil nanodroplets?

PubMed

Wang, Xingya; Zhao, Binyu; Hu, Jun; Wang, Shuo; Tai, Renzhong; Gao, Xingyu; Zhang, Lijuan

2017-01-04

The existence of nanobubbles at a solid-liquid interface with high stability has been confirmed by myriad experimental studies, and their gaseous nature has also been extensively verified. However, nanodroplets of polydimethylsiloxane (PDMS) recently observed in the atomic force microscopy (AFM) measurement of nanobubbles plague the nanobubble community. It may easily lead to wrong interpretations of the AFM results and thus hinders further application of the already widely used AFM in nanobubble studies. Therefore, finding a direct experimental solution to distinguish nanobubbles from nanodroplets in AFM measurements is a matter of great urgency. Herein, we first developed an effective and reproducible method to produce PDMS nanodroplets at the highly ordered pyrolytic graphite (HOPG)/water interface. From their size, contact angle, and stiffness, the formed PDMS nanodroplets are not distinguishable from nanobubbles. However, the force curves on these two objects are strikingly different from each other, i.e., a peculiar plateau in both the approach and retraction curves was found on nanobubbles whereas they changed linearly between the jump-in and jump-off point on PDMS nanodroplets. Thus, the present study not only provided a simple and effective procedure to generate PDMS nanodroplets but also paved a simple practical and in situ way to discriminate nanobubbles from the PDMS nanodroplets by direct AFM force measurements.

Simple method of DNA stretching on glass substrate for fluorescence image and spectroscopy

NASA Astrophysics Data System (ADS)

Neupane, Guru P.; Dhakal, Krishna P.; Lee, Hyunsoo; Guthold, Martin; Joseph, Vincent S.; Hong, Jong-Dal; Kim, Jeongyong

2013-05-01

Study of biological molecule DNA has contributed to developing many breaking thoughts and wide applications in multidisciplinary fields, such as genomic, medical, sensing and forensic fields. Stretching of DNA molecules is an important supportive tool for AFM or spectroscopic studies of DNA in a single molecular level. In this article, we established a simple method of DNA stretching (to its full length) that occurred on a rotating negatively-charged surface of glass substrate. The isolation of a single DNA molecule was attained by the two competitive forces on DNA molecules, that is, the electrostatic attraction developed between the positively charged YOYO-1 stained DNA and the negatively charged substrate, and the centrifugal force of the rotating substrate, which separates the DNA aggregates into the single molecule. Density of stretched DNA molecules was controlled by selecting the specific parameters such as spinning time and rates, loading volume of DNA-dye complex solution etc. The atomic force microscopy image exhibited a single DNA molecule on the negatively-charged substrate in an isolated state. Further, the photoluminescence spectra of a single DNA molecule stained with YOYO-1 were achieved using the method developed in the present study, which is strongly believed to effectively support the spectroscopic analysis of DNA in a single molecular level.

AtomicJ: An open source software for analysis of force curves

NASA Astrophysics Data System (ADS)

Hermanowicz, Paweł; Sarna, Michał; Burda, Kvetoslava; Gabryś, Halina

2014-06-01

We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

A new look at the atomic level virial stress: on continuum-molecular system equivalence

NASA Astrophysics Data System (ADS)

Zhou, Min

2003-09-01

The virial stress is the most commonly used definition of stress in discrete particle systems. This quantity includes two parts. The first part depends on the mass and velocity (or, in some versions, the fluctuation part of the velocity) of atomic particles, reflecting an assertion that mass transfer causes mechanical stress to be applied on stationary spatial surfaces external to an atomic-particle system. The second part depends on interatomic forces and atomic positions, providing a continuum measure for the internal mechanical interactions between particles. Historic derivations of the virial stress include generalization from the virial theorem of Clausius (1870) for gas pressure and solution of the spatial equation of balance of momentum. The virial stress is stress-like a measure for momentum change in space. This paper shows that, contrary to the generally accepted view, the virial stress is not a measure for mechanical force between material points and cannot be regarded as a measure for mechanical stress in any sense. The lack of physical significance is both at the individual atom level in a time-resolved sense and at the system level in a statistical sense. It is demonstrated that the interatomic force term alone is a valid stress measure and can be identified with the Cauchy stress. The proof in this paper consists of two parts. First, for the simple conditions of rigid translation, uniform tension and tension with thermal oscillations, the virial stress yields clearly erroneous interpretations of stress. Second, the conceptual flaw in the generalization from the virial theorem for gas pressure to stress and the confusion over spatial and material equations of balance of momentum in theoretical derivations of the virial stress that led to its erroneous acceptance as the Cauchy stress are pointed out. Interpretation of the virial stress as a measure for mechanical force violates balance of momentum and is inconsistent with the basic definition of stress. The versions of the virial-stress formula that involve total particle velocity and the thermal fluctuation part of the velocity are demonstrated to be measures of spatial momentum flow relative to, respectively, a fixed reference frame and a moving frame with a velocity equal to the part of particle velocity not included in the virial formula. To further illustrate the irrelevance of mass transfer to the evaluation of stress, an equivalent continuum (EC) for dynamically deforming atomistic particle systems is defined. The equivalence of the continuum to discrete atomic systems includes (i) preservation of linear and angular momenta, (ii) conservation of internal, external and inertial work rates, and (iii) conservation of mass. This equivalence allows fields of work- and momentum-preserving Cauchy stress, surface traction, body force and deformation to be determined. The resulting stress field depends only on interatomic forces, providing an independent proof that as a measure for internal material interaction stress is independent of kinetic energy or mass transfer.

Visualization and quantification of magnetic nanoparticles into vesicular systems by combined atomic and magnetic force microscopy

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

Dong, C.; Department of Physics, SAPIENZA University of Rome, Piazzale A. Moro 5, 00185, Rome; Corsetti, S.

2015-06-23

We report a phenomenological approach for the quantification of the diameter of magnetic nanoparticles (MNPs) incorporated in non-ionic surfactant vesicles (niosomes) using magnetic force microscopy (MFM). After a simple specimen preparation, i.e., by putting a drop of solution containing MNPs-loaded niosomes on flat substrates, topography and MFM phase images are collected. To attempt the quantification of the diameter of entrapped MNPs, the method is calibrated on the sole MNPs deposited on the same substrates by analyzing the MFM signal as a function of the MNP diameter (at fixed tip-sample distance) and of the tip-sample distance (for selected MNPs). After calibration,more » the effective diameter of the MNPs entrapped in some niosomes is quantitatively deduced from MFM images.« less

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

Kim, Jong Hun; Park, Jeong Young, E-mail: jhjung@inha.ac.kr, E-mail: jeongypark@kaist.ac.kr; Graduate School of EEWS, Korea Advanced Institute of Science and Technology

Study of the triboelectric charging effect has recently gained much attraction by proposing a new potential technical application in the field of energy harvesting. Transparent polydimethylsiloxane (PDMS) has some advantages in employing the triboelectric effect due to good conformity at nanometer scale and the simple fabrication process. In this study, we demonstrate that UV irradiation can enhance the performance of a PDMS-based nanotribogenerator. Contact atomic force microscopy combined with Kelvin probe force microscopy enables an in-depth investigation of the effect of UV illumination on local triboelectric charge generation and its decay in PDMS. We found that UV exposure not onlymore » facilitates triboelectric charge generation but also enhances charge redistribution, which is related to the wettability of the PDMS surface. This study provides insights into the fundamental understanding and design of triboelectric generator devices.« less

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

Patel, Sajan; Petty, Clayton W.; Krafcik, Karen Lee

Electrostatic modes of atomic force microscopy have shown to be non-destructive and relatively simple methods for imaging conductors embedded in insulating polymers. Here we use electrostatic force microscopy to image the dispersion of carbon nanotubes in a latex-based conductive composite, which brings forth features not observed in previously studied systems employing linear polymer films. A fixed-potential model of the probe-nanotube electrostatics is presented which in principle gives access to the conductive nanoparticle's depth and radius, and the polymer film dielectric constant. Comparing this model to the data results in nanotube depths that appear to be slightly above the film–air interface.more » Furthermore, this result suggests that water-mediated charge build-up at the film–air interface may be the source of electrostatic phase contrast in ambient conditions.« less

Computational model for noncontact atomic force microscopy: energy dissipation of cantilever.

PubMed

Senda, Yasuhiro; Blomqvist, Janne; Nieminen, Risto M

2016-09-21

We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments. We attribute this dissipation to the hysteresis and nonconservative properties of the interatomic force that acts between the atoms in the tip and sample surface. The dissipation rate strongly depends on the parameters used in the computational model.

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.

Nonmonotonic velocity dependence of atomic friction.

PubMed

Reimann, Peter; Evstigneev, Mykhaylo

2004-12-03

We propose a theoretical model for friction force microscopy experiments with special emphasis on the realistic description of dissipation and inertia effects. Its main prediction is a nonmonotonic dependence of the friction force upon the sliding velocity of the atomic force microscope tip relative to an atomically flat surface. The region around the force maximum can be approximately described by a universal scaling law and should be observable under experimentally realistic conditions.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.

PubMed

Andrews, Casey T; Elcock, Adrian H

2014-11-11

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions-which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)-quantitatively reproduced all of the "target" MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic ( PLoS Comput. Biol. 2014 , 5 , e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP's nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

PubMed Central

2015-01-01

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins. PMID:25400526

16 CFR 1630.63 - Suspension of washing requirements for carpets and rugs with alumina trihydrate in the backing.

Code of Federal Regulations, 2010 CFR

2010-01-01

... of Carpets and Rugs (FF 1-70) at § 1630.4(b)(1)(ii) provides that if a carpet or rug has had a fire-retardant treatment, or is made of fibers which have had a fire-retardant treatment, the sample or oversized... specimens either 10 times under the washing and drying procedure prescribed in Method 124-1996 of the...

16 CFR 1630.63 - Suspension of washing requirements for carpets and rugs with alumina trihydrate in the backing.

Code of Federal Regulations, 2012 CFR

2012-01-01

... of Carpets and Rugs (FF 1-70) at § 1630.4(b)(1)(ii) provides that if a carpet or rug has had a fire-retardant treatment, or is made of fibers which have had a fire-retardant treatment, the sample or oversized... specimens either 10 times under the washing and drying procedure prescribed in Method 124-1996 of the...

16 CFR 1630.63 - Suspension of washing requirements for carpets and rugs with alumina trihydrate in the backing.

Code of Federal Regulations, 2014 CFR

2014-01-01

... of Carpets and Rugs (FF 1-70) at § 1630.4(b)(1)(ii) provides that if a carpet or rug has had a fire-retardant treatment, or is made of fibers which have had a fire-retardant treatment, the sample or oversized... specimens either 10 times under the washing and drying procedure prescribed in Method 124-1996 of the...

16 CFR 1630.63 - Suspension of washing requirements for carpets and rugs with alumina trihydrate in the backing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... of Carpets and Rugs (FF 1-70) at § 1630.4(b)(1)(ii) provides that if a carpet or rug has had a fire-retardant treatment, or is made of fibers which have had a fire-retardant treatment, the sample or oversized... specimens either 10 times under the washing and drying procedure prescribed in Method 124-1996 of the...

Development of a force sensor using atom interferometry to constrain theories on dark matter and dark energy

NASA Astrophysics Data System (ADS)

Schlupf, Chandler; Niederriter, Robert; Bohr, Eliot; Khamis, Sami; Park, Youna; Szwed, Erik; Hamilton, Paul

2017-04-01

Atom interferometry has been used in many precision measurements such as Newton's gravitational constant, the fine structure constant, and tests of the equivalence principle. We will perform atom interferometry in an optical lattice to measure the force felt by an atom due to a test mass in search of new forces suggested by dark matter and dark energy theories. We will be developing a new apparatus using laser-cooled ytterbium to continuously measure this force by observing their Bloch oscillations. Interfering atoms in an optical lattice allows continuous measurements in a small volume over a long period of time, enabling our device to be sensitive to time-varying forces while minimizing vibrational noise. We present the details of this experiment and the progress on it thus far.

Concept for room temperature single-spin tunneling force microscopy with atomic spatial resolution

NASA Astrophysics Data System (ADS)

Payne, Adam

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy (AFM) system noise. The results show that the approach could provide single-spin measurement of electrically isolated defect states with atomic spatial resolution at room temperature.

Atomic-resolution single-spin magnetic resonance detection concept based on tunneling force microscopy

NASA Astrophysics Data System (ADS)

Payne, A.; Ambal, K.; Boehme, C.; Williams, C. C.

2015-05-01

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single-electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy system noise. The results show that the approach could provide single-spin measurement of electrically isolated qubit states with atomic spatial resolution at room temperature.

Impact of centrality on cooperative processes

NASA Astrophysics Data System (ADS)

Reia, Sandro M.; Herrmann, Sebastian; Fontanari, José F.

2017-02-01

The solution of today's complex problems requires the grouping of task forces whose members are usually connected remotely over long physical distances and different time zones. Hence, understanding the effects of imposed communication patterns (i.e., who can communicate with whom) on group performance is important. Here we use an agent-based model to explore the influence of the betweenness centrality of the nodes on the time the group requires to find the global maxima of NK-fitness landscapes. The agents cooperate by broadcasting messages, informing on their fitness to their neighbors, and use this information to copy the more successful agents in their neighborhood. We find that for easy tasks (smooth landscapes), the topology of the communication network has no effect on the performance of the group, and that the more central nodes are the most likely to find the global maximum first. For difficult tasks (rugged landscapes), however, we find a positive correlation between the variance of the betweenness among the network nodes and the group performance. For these tasks, the performances of individual nodes are strongly influenced by the agents' dispositions to cooperate and by the particular realizations of the rugged landscapes.

Surface Biology of DNA by Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Hansma, Helen G.

2001-10-01

The atomic force microscope operates on surfaces. Since surfaces occupy much of the space in living organisms, surface biology is a valid and valuable form of biology that has been difficult to investigate in the past owing to a lack of good technology. Atomic force microscopy (AFM) of DNA has been used to investigate DNA condensation for gene therapy, DNA mapping and sizing, and a few applications to cancer research and to nanotechnology. Some of the most exciting new applications for atomic force microscopy of DNA involve pulling on single DNA molecules to obtain measurements of single-molecule mechanics and thermodynamics.

Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains.

PubMed

Sabater, Carlos; Untiedt, Carlos; van Ruitenbeek, Jan M

2015-01-01

This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a 'Berry force'. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose.

Phase modulation atomic force microscope with true atomic resolution

NASA Astrophysics Data System (ADS)

Fukuma, Takeshi; Kilpatrick, Jason I.; Jarvis, Suzanne P.

2006-12-01

We have developed a dynamic force microscope (DFM) working in a novel operation mode which is referred to as phase modulation atomic force microscopy (PM-AFM). PM-AFM utilizes a fixed-frequency excitation signal to drive a cantilever, which ensures stable imaging even with occasional tip crash and adhesion to the surface. The tip-sample interaction force is detected as a change of the phase difference between the cantilever deflection and excitation signals and hence the time response is not influenced by the Q factor of the cantilever. These features make PM-AFM more suitable for high-speed imaging than existing DFM techniques such as amplitude modulation and frequency modulation atomic force microscopies. Here we present the basic principle of PM-AFM and the theoretical limit of its performance. The design of the developed PM-AFM is described and its theoretically limited noise performance is demonstrated. Finally, we demonstrate the true atomic resolution imaging capability of the developed PM-AFM by imaging atomic-scale features of mica in water.

Unusual Features of Crystal Structures of Some Simple Copper Compounds

ERIC Educational Resources Information Center

Douglas, Bodie

2009-01-01

Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

On-Surface Synthesis and Characterization of 9-Atom Wide Armchair Graphene Nanoribbons

DOE PAGES

Talirz, Leopold; Söde, Hajo; Dumslaff, Tim; ...

2017-01-27

The bottom-up approach to synthesize graphene nanoribbons strives not only to introduce a band gap into the electronic structure of graphene but also to accurately tune its value by designing both the width and edge structure of the ribbons with atomic precision. Within this paper, we report the synthesis of an armchair graphene nanoribbon with a width of nine carbon atoms on Au(111) through surface-assisted aryl–aryl coupling and subsequent cyclodehydrogenation of a properly chosen molecular precursor. By combining high-resolution atomic force microscopy, scanning tunneling microscopy, and Raman spectroscopy, we demonstrate that the atomic structure of the fabricated ribbons is exactlymore » as designed. Angle-resolved photoemission spectroscopy and Fourier-transformed scanning tunneling spectroscopy reveal an electronic band gap of 1.4 eV and effective masses of ≈0.1 m e for both electrons and holes, constituting a substantial improvement over previous efforts toward the development of transistor applications. We use ab initio calculations to gain insight into the dependence of the Raman spectra on excitation wavelength as well as to rationalize the symmetry-dependent contribution of the ribbons’ electronic states to the tunneling current. Lastly, we propose a simple rule for the visibility of frontier electronic bands of armchair graphene nanoribbons in scanning tunneling spectroscopy.« less

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

PubMed Central

Neuman, Keir C.; Nagy, Attila

2012-01-01

Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. These techniques are described and illustrated with examples highlighting current capabilities and limitations. PMID:18511917

16 CFR § 1630.63 - Suspension of washing requirements for carpets and rugs with alumina trihydrate in the backing.

Code of Federal Regulations, 2013 CFR

2013-01-01

... of Carpets and Rugs (FF 1-70) at § 1630.4(b)(1)(ii) provides that if a carpet or rug has had a fire-retardant treatment, or is made of fibers which have had a fire-retardant treatment, the sample or oversized... specimens either 10 times under the washing and drying procedure prescribed in Method 124-1996 of the...

Optimization of classical nonpolarizable force fields for OH(-) and H3O(+).

PubMed

Bonthuis, Douwe Jan; Mamatkulov, Shavkat I; Netz, Roland R

2016-03-14

We optimize force fields for H3O(+) and OH(-) that reproduce the experimental solvation free energies and the activities of H3O(+) Cl(-) and Na(+) OH(-) solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of the optimized H3O(+) force field is 0.8 ± 0.1|e|--significantly higher than the value typically used for nonpolarizable water models and H3O(+) force fields. In contrast, the optimal partial charge on the hydrogen atom of OH(-) turns out to be zero. Standard combination rules can be used for H3O(+) Cl(-) solutions, while for Na(+) OH(-) solutions, we need to significantly increase the effective anion-cation Lennard-Jones radius. While highlighting the importance of intramolecular electrostatics, our results show that it is possible to generate thermodynamically consistent force fields without using atomic polarizability.

Measurements of Elastic Moduli of Silicone Gel Substrates with a Microfluidic Device

PubMed Central

Gutierrez, Edgar; Groisman, Alex

2011-01-01

Thin layers of gels with mechanical properties mimicking animal tissues are widely used to study the rigidity sensing of adherent animal cells and to measure forces applied by cells to their substrate with traction force microscopy. The gels are usually based on polyacrylamide and their elastic modulus is measured with an atomic force microscope (AFM). Here we present a simple microfluidic device that generates high shear stresses in a laminar flow above a gel-coated substrate and apply the device to gels with elastic moduli in a range from 0.4 to 300 kPa that are all prepared by mixing two components of a transparent commercial silicone Sylgard 184. The elastic modulus is measured by tracking beads on the gel surface under a wide-field fluorescence microscope without any other specialized equipment. The measurements have small and simple to estimate errors and their results are confirmed by conventional tensile tests. A master curve is obtained relating the mixing ratios of the two components of Sylgard 184 with the resulting elastic moduli of the gels. The rigidity of the silicone gels is less susceptible to effects from drying, swelling, and aging than polyacrylamide gels and can be easily coated with fluorescent tracer particles and with molecules promoting cellular adhesion. This work can lead to broader use of silicone gels in the cell biology laboratory and to improved repeatability and accuracy of cell traction force microscopy and rigidity sensing experiments. PMID:21980487

Mobile quantum gravity sensor with unprecedented stability

NASA Astrophysics Data System (ADS)

Leykauf, Bastian; Freier, Christian; Schkolnik, Vladimir; Krutzik, Markus; Peters, Achim

2017-04-01

The gravimetric atom interferometer GAIN is based on interfering ensembles of laser-cooled 87Rb atoms in a fountain setup, using stimulated Raman transitions. GAIN's rugged design allows for transports to sites of geodetic and geophysical interest while maintaining a high accuracy compatible with the best classical instruments. We compared our instrument's performance with falling corner-cube and superconducting gravimeters in two measurement campaigns at geodetic observatories in Wettzell, Germany and Onsala, Sweden. Our instrument's long-term stability of 0.5 nm/s2 is the best value for absolute gravimeters reported to date [1]. Our measured gravity value agrees with other state-of-the-art gravimeters on the 10-9 level in g, demonstrating effective control over systematics including wavefront distortions of the Raman beams [2]. By using the juggling technique [3], we are able to perform gravity measurements on two atomic clouds simultaneously. Advantages include the suppression of common mode phase noise, enabling differential phase shift extraction without the need for vibration isolation. We will present the results of our first gravity gradient measurements. [1] Freier, Hauth, Schkolnik, Leykauf, Schilling, Wziontek, Scherneck, Müller and Peters (2016). Mobile quantum gravity sensor with unprecedented stability. Journal of Physics: Conference Series, 8th Symposium on Frequency Standards and Metrology 2015, 723, 12050. [2] Schkolnik, Leykauf, Hauth, Freier and Peters (2015). The effect of wavefront aberrations in atom interferometry. Applied Physics B, 120(2), 311 - 316. [3] Legere and Gibble (1998). Quantum Scattering in a Juggling Atomic Fountain. Physical Review Letters, 81(1), 5780 - 5783.

Early Events in Insulin Fibrillization Studied by Time-Lapse Atomic Force Microscopy

PubMed Central

Podestà, Alessandro; Tiana, Guido; Milani, Paolo; Manno, Mauro

2006-01-01

The importance of understanding the mechanism of protein aggregation into insoluble amyloid fibrils lies not only in its medical consequences, but also in its more basic properties of self-organization. The discovery that a large number of uncorrelated proteins can form, under proper conditions, structurally similar fibrils has suggested that the underlying mechanism is a general feature of polypeptide chains. In this work, we address the early events preceding amyloid fibril formation in solutions of zinc-free human insulin incubated at low pH and high temperature. Here, we show by time-lapse atomic force microscopy that a steady-state distribution of protein oligomers with a quasiexponential tail is reached within a few minutes after heating. This metastable phase lasts for a few hours, until fibrillar aggregates are observable. Although for such complex systems different aggregation mechanisms can occur simultaneously, our results indicate that the prefibrillar phase is mainly controlled by a simple coagulation-evaporation kinetic mechanism, in which concentration acts as a critical parameter. These experimental facts, along with the kinetic model used, suggest a critical role for thermal concentration fluctuations in the process of fibril nucleation. PMID:16239333

Synthesis and characterization of novel 4-Tetra-4-Tolylsulfonyl ZnPc thin films for optoelectronic applications

NASA Astrophysics Data System (ADS)

Khalil, Salah; Tazarki, Helmi; Souli, Mehdi; Guasch, Cathy; Jamoussi, Bassem; Kamoun, Najoua

2017-11-01

Novel 4-Tetra-4-Tolylsulfonyl:zinc phthalocyanine and simple zinc phthalocyanine were synthesized. Our materials were grown on glass substrates by spin coating technique. Thin films were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electronic micrograph (SEM), atomic force microscopy (AFM), spectrophotometer and Hall effect measurement. X-ray spectra reveal that 4-Tetra-4-Tolylsulfonyl:zinc phthalocyanine (4T4TS:ZnPc) and zinc phthalocyanine (ZnPc) thin films have a monoclinic crystalline structure in β phase. The surface properties and chemical composition were detailed using XPS measurement. SEM were used to investigate the surface morphology for 4T4TS:ZnPc and ZnPc thin films. Atomic force microscopy images have shown a decrease in surface roughness after substitution. Optical properties were investigated by measuring transmission and reflection spectra. Electrical properties were studied and the different electrical parameters was measured and compared on glass, silicon and tin dioxide substrates by Hall Effect technique. All obtained results indicate an improvement in physical properties of 4T4TS:ZnPc which allows used it in optoelectronic applications.

Atomic force microscopy of chromatin arrays reveal non-monotonic salt dependence of array compaction in solution

PubMed Central

Krzemien, Katarzyna M.; Beckers, Maximilian; Quack, Salina; Michaelis, Jens

2017-01-01

Compaction of DNA in chromatin is a hallmark of the eukaryotic cell and unravelling its structure is required for an understanding of DNA involving processes. Despite strong experimental efforts, many questions concerning the DNA packing are open. In particular, it is heavily debated whether an ordered structure referred to as the “30 nm fibre” exist in vivo. Scanning probe microscopy has become a cutting edge technology for the high-resolution imaging of DNA- protein complexes. Here, we perform high-resolution atomic force microscopy of non-cross-linked chromatin arrays in liquid, under different salt conditions. A statistical analysis of the data reveals that array compaction is salt dependent in a non-monotonic fashion. A simple physical model can qualitatively explain the observed findings due to the opposing effects of salt dependent stiffening of DNA, nucleosome stability and histone-histone interactions. While for different salt concentrations different compaction states are observed, our data do not provide support for the existence of regular chromatin fibres. Our studies add new insights into chromatin structure, and with that contribute to a further understanding of the DNA condensation. PMID:28296908

Water: two liquids divided by a common hydrogen bond.

PubMed

Soper, Alan K

2011-12-08

The structure of water is the subject of a long and ongoing controversy. Unlike simpler liquids, where atomic interactions are dominated by strong repulsive forces at short distances and weaker attractive (van der Waals) forces at longer distances, giving rise to local atomic coordination numbers of order 12, water has pronounced and directional hydrogen bonds which cause the dense liquid close-packed structure to open out into a disordered and dynamic network, with coordination number 4-5. Here I show that water structure can be accurately represented as a mixture of two identical, interpenetrating, molecular species separated by common hydrogen bonds. Molecules of one type can form hydrogen bonds with molecules of the other type but cannot form hydrogen bonds with molecules of the same type. These hydrogen bonds are strong along the bond but weak with respect to changes in the angle between neighboring bonds. The observed pressure and temperature dependence of water structure and thermodynamic properties follow naturally from this choice of water model, and it also gives a simple explanation of the enduring claims based on spectroscopic evidence that water is a mixture of two components. © 2011 American Chemical Society

Novel and simple route to fabricate fully biocompatible plasmonic mushroom arrays adhered on silk biopolymer

NASA Astrophysics Data System (ADS)

Park, Joonhan; Choi, Yunkyoung; Lee, Myungjae; Jeon, Heonsu; Kim, Sunghwan

2014-12-01

A fully biocompatible plasmonic quasi-3D nanostructure is demonstrated by a simple and reliable fabrication method using strong adhesion between gold and silk fibroin. The quasi-3D nature gives rise to complex photonic responses in reflectance that are prospectively useful in bio/chemical sensing applications. Laser interference lithography is utilized to fabricate large-area plasmonic nanostructures.A fully biocompatible plasmonic quasi-3D nanostructure is demonstrated by a simple and reliable fabrication method using strong adhesion between gold and silk fibroin. The quasi-3D nature gives rise to complex photonic responses in reflectance that are prospectively useful in bio/chemical sensing applications. Laser interference lithography is utilized to fabricate large-area plasmonic nanostructures. Electronic supplementary information (ESI) available: The incident angle dependence of reflectance spectra and the atomic force microscopy image of the Au nanoparticle array on a silk film after 1 hour of ultrasonication. See DOI: 10.1039/c4nr05172f

Identification of registered nursing care of residents in English nursing homes using the Minimum Data Set Resident Assessment Instrument (MDS/RAI) and Resource Utilisation Groups version III (RUG-III).

PubMed

Carpenter, Iain; Perry, Michelle; Challis, David; Hope, Kevin

2003-05-01

to determine if a combination of Minimum Data Set/Resident Assessment Instrument (MDS/RAI) assessment variables and the Resource Utilisation Groups version III (RUG-III) case-mix system could be used as a method of identifying and reimbursing registered nursing care needs in long-term care. the sample included 193 nursing home residents from four nursing homes from three different locations and care providers in England. The study included assessments of residents' care needs using either the MDS/RAI assessments or RUG stand-alone questionnaires and a time study that recorded the amount of nursing time received by residents over a 24-h period. Validity of RUG-III for explaining the distribution of care time between residents in different RUG-III groups was tested. The difference in direct and indirect care provided by registered general nurses (RGN) and care assistants (CA) to residents in RUG-III clinical groups was compared. the RUG-III system explained 56% of the variance in care time (Eta2, P=0.0001). Residents in RUG-III groups associated with particular medical and nursing needs (enhanced RGN care) received more than twice as much indirect RGN care time (t-test, P<0.001) and 1.4 times as much direct RGN and direct CA time (t-test, P<0.01) than residents with primarily cognitive impairment or physical problems only (standard RGN care). Residents with enhanced RGN care received an average of 48.1 min of RGN care in 24 h (95% CI 4.1-55.2) compared with an average of 31.1 min (95% CI 26.8-35.5) for residents in the standard RGN care group. A third low RGN care group was created following publication of the Department of Health guidance on NHS Funded Nursing Care. With three levels, the enhanced care group receives about 38% more than the standard group, and the low group receives about 50% of the standard group. the RUG-III system effectively differentiated between nursing home residents who are receiving 'low', 'standard' and 'enhanced' RGN care time. The findings could provide the basis of a reimbursement system for registered nursing time in long-term care facilities in the UK.

Comparison of micellar extraction combined with ionic liquid based vortex-assisted liquid-liquid microextraction and modified quick, easy, cheap, effective, rugged, and safe method for the determination of difenoconazole in cowpea.

PubMed

Chen, Xiaochu; Bian, Yanli; Liu, Fengmao; Teng, Peipei; Sun, Pan

2017-10-06

Two simple sample pretreatment for the determination of difenoconazole in cowpea was developed including micellar extraction combined with ionic liquid based vortex-assisted liquid-liquid microextraction (ME-IL-VALLME) prior to high performance liquid chromatography (HPLC), and modified quick, easy, cheap, effective, rugged, and safe method (QuEChERS) coupled with HPLC-MS/MS. In ME-IL-VALLME method, the target analyte was extracted by surfactant Tween 20 micellar solution, then the supernatant was diluted with 3mL water to decrease the solubility of micellar solution. Subsequently, the vortex-assisted liquid-liquid microextraction (VALLME) procedure was performed in the diluted extraction solution by using the ionic liquid of 1-hexyl-3-methylimidazolium hexafluorophosphate ([HMIM]PF 6 ) as the extraction solvent and Tween 20 as an emulsifier to enhance the dispersion of the water-immiscible ionic liquid into the aqueous phase. Parameters that affect the extraction have been investigated in both methods Under the optimum conditions, the limits of quantitation were 0.10 and 0.05mgkg -1 , respectively. And good linearity was achieved with the correlation coefficient higher than 0.9941. The relative recoveries ranged from 78.6 to 94.8% and 92.0 to 118.0% with the relative standard deviations (RSD) of 7.9-9.6% and 1.2-3.2%, respectively. Both methods were quick, simple and inexpensive. However, the ME-IL-VALLME method provides higher enrichment factor compared with conventional QuEChERS method. The ME-IL-VALLME method has a strong potential for the determination of difenoconazole in complex vegetable matrices with HPLC. Copyright © 2017 Elsevier B.V. All rights reserved.

Removal of Covalent Heterogeneity Reveals Simple Folding Behavior for P4-P6 RNA*

PubMed Central

Greenfeld, Max; Solomatin, Sergey V.; Herschlag, Daniel

2011-01-01

RNA folding landscapes have been described alternately as simple and as complex. The limited diversity of RNA residues and the ability of RNA to form stable secondary structures prior to adoption of a tertiary structure would appear to simplify folding relative to proteins. Nevertheless, there is considerable evidence for long-lived misfolded RNA states, and these observations have suggested rugged energy landscapes. Recently, single molecule fluorescence resonance energy transfer (smFRET) studies have exposed heterogeneity in many RNAs, consistent with deeply furrowed rugged landscapes. We turned to an RNA of intermediate complexity, the P4-P6 domain from the Tetrahymena group I intron, to address basic questions in RNA folding. P4-P6 exhibited long-lived heterogeneity in smFRET experiments, but the inability to observe exchange in the behavior of individual molecules led us to probe whether there was a non-conformational origin to this heterogeneity. We determined that routine protocols in RNA preparation and purification, including UV shadowing and heat annealing, cause covalent modifications that alter folding behavior. By taking measures to avoid these treatments and by purifying away damaged P4-P6 molecules, we obtained a population of P4-P6 that gave near-uniform behavior in single molecule studies. Thus, the folding landscape of P4-P6 lacks multiple deep furrows that would trap different P4-P6 molecules in different conformations and contrasts with the molecular heterogeneity that has been seen in many smFRET studies of structured RNAs. The simplicity of P4-P6 allowed us to reliably determine the thermodynamic and kinetic effects of metal ions on folding and to now begin to build more detailed models for RNA folding behavior. PMID:21478155

As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

PubMed Central

Rottler, Jörg; Plotkin, Steven S.

2016-01-01

Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered. PMID:27898663

As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy.

PubMed

Habibi, Mona; Rottler, Jörg; Plotkin, Steven S

2016-11-01

Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered.

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.

Subatomic-scale force vector mapping above a Ge(001) dimer using bimodal atomic force microscopy

NASA Astrophysics Data System (ADS)

Naitoh, Yoshitaka; Turanský, Robert; Brndiar, Ján; Li, Yan Jun; Štich, Ivan; Sugawara, Yasuhiro

2017-07-01

Probing physical quantities on the nanoscale that have directionality, such as magnetic moments, electric dipoles, or the force response of a surface, is essential for characterizing functionalized materials for nanotechnological device applications. Currently, such physical quantities are usually experimentally obtained as scalars. To investigate the physical properties of a surface on the nanoscale in depth, these properties must be measured as vectors. Here we demonstrate a three-force-component detection method, based on multi-frequency atomic force microscopy on the subatomic scale and apply it to a Ge(001)-c(4 × 2) surface. We probed the surface-normal and surface-parallel force components above the surface and their direction-dependent anisotropy and expressed them as a three-dimensional force vector distribution. Access to the atomic-scale force distribution on the surface will enable better understanding of nanoscale surface morphologies, chemical composition and reactions, probing nanostructures via atomic or molecular manipulation, and provide insights into the behaviour of nano-machines on substrates.

Van der Waals interactions and the limits of isolated atom models at interfaces

PubMed Central

Kawai, Shigeki; Foster, Adam S.; Björkman, Torbjörn; Nowakowska, Sylwia; Björk, Jonas; Canova, Filippo Federici; Gade, Lutz H.; Jung, Thomas A.; Meyer, Ernst

2016-01-01

Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar–Xe, Kr–Xe and Xe–Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal–organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems. PMID:27174162

Classification of residents in nursing homes in Tuscany (Italy) using Resource Utilization Groups Version III (RUG-III).

PubMed

Francesconi, Paolo; Cantini, Elisabetta; Bavazzano, Emanuela; Lauretani, Fabrizio; Bandinelli, Stefania; Buiatti, Eva; Ferrucci, Luigi

2006-04-01

Samples of nursing homes in Tuscany (Italy) classify their residents and determine their case-mix according to the Resource Utilization Groups System, Version III (RUG-III). A large sample of nursing homes was selected, based on willingness to participate, representation of both public and private institutions, and wide geographic representation. Two registered nurses assessed all residents using the RUG questionnaire. The information collected was then used to group residents into 44 RUGs, and facility-specific case-mix indices were calculated using the RUG-specific weights previously validated in Italy. A total of 3981 residents from 93 nursing homes were assessed. Most residents were over 75 years old (87.4%) and women (68.6%). A large percentage was classified into RUGs within the following primary categories: reduced physical function (33.6%), impaired cognition (17.6%) and clinically complex (17.6%). The resulting nursing home case-mix indices ranged from 0.627 to 1.108 (mean 0.807+/-0.110). No significant association was found between type of facility, level of fees, or extent of staff in the nursing homes and their case-mix indices. RUGIII can provide information on types of nursing home residents and their care needs. This is useful for monitoring and evaluating long-term care services for the elderly, and allows for more effective planning and allocation of staffing and financial resources.

Taking Nanomedicine Teaching into Practice with Atomic Force Microscopy and Force Spectroscopy

ERIC Educational Resources Information Center

Carvalho, Filomena A.; Freitas, Teresa; Santos, Nuno C.

2015-01-01

Atomic force microscopy (AFM) is a useful and powerful tool to study molecular interactions applied to nanomedicine. The aim of the present study was to implement a hands-on atomic AFM course for graduated biosciences and medical students. The course comprises two distinct practical sessions, where students get in touch with the use of an atomic…

Molecular Simulations in Astrobiology

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.

2000-01-01

One of the main goals of astrobiology is to understand the origin of cellular life. The most direct approach to this problem is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing energy and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following questions about these proteins: (1) How do small proteins self-organize into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides form membrane-spanning structures (e.g. channels)? (3) By what mechanisms do such structures perform their functions? The simulations are performed using the molecular dynamics method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated in real space while long-range forces are evaluated in reciprocal space, using a particle-mesh algorithm which is of order O(NInN). With a time step of 2 femtoseconds, problems occurring on multi-nanosecond time scales (10(exp 6)-10(exp 8) time steps) are accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude, which requires algorithmic improvements and codes scalable to a large number of processors. Work in this direction is in progress. Two series of simulations are discussed. In one series, it is shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and fold into helical structures (see Figure). Once in the membrane, the peptides exhibit orientational flexibility with changing conditions, which may have provided a mechanism of transmitting signals between the protocell and its environment. In another series of simulations, the mechanism by which a simple protein channel efficiently mediates proton transport across membranes was investigated. This process is a key step in cellular bioenergetics. In the channel under study, proton transport is gated by four histidines that occlude the channel pore. The simulations identify the mechanisms by which protons move through the gate.

Using the RUG-III classification system for understanding the resource intensity of persons with intellectual disability residing in nursing homes.

PubMed

Martin, Lynn; Fries, Brant E; Hirdes, John P; James, Mary

2011-06-01

Since 1991, the Minimum Data Set 2.0 (MDS 2.0) has been the mandated assessment in US nursing homes. The Resource Utilization Groups III (RUG-III) case-mix system provides person-specific means of allocating resources based on the variable costs of caring for persons with different needs. Retrospective analyses of data collected on a sample of 9707 nursing home residents (2.4% had an intellectual disability) were used to examine the fit of the RUG-III case-mix system for determining the cost of supporting persons with intellectual disability (intellectual disability). The RUG-III system explained 33.3% of the variance in age-weighted nursing time among persons with intellectual disability compared to 29.6% among other residents, making it a good fit among persons with intellectual disability in nursing homes. The RUG-III may also serve as the basis for the development of a classification system that describes the resource intensity of persons with intellectual disability in other settings that provide similar types of support.

Densification and Devitrification of Fused Silica Induced by Ballistic Impact: A Computational Investigation

DTIC Science & Technology

2015-03-25

lime glass, the polyhedron -center atoms are all silicon and each silicon atom is surrounded by four oxygen atoms (while each oxygen atom is connected...of metallic force-field functions (in the pure metallic environment) within the force-field function database used in the present work. Consequently

Tactile Gloves for Autonomous Grasping With the NASA/DARPA Robonaut

NASA Technical Reports Server (NTRS)

Martin, T. B.; Ambrose, R. O.; Diftler, M. A.; Platt, R., Jr.; Butzer, M. J.

2004-01-01

Tactile data from rugged gloves are providing the foundation for developing autonomous grasping skills for the NASA/DARPA Robonaut, a dexterous humanoid robot. These custom gloves compliment the human like dexterity available in the Robonaut hands. Multiple versions of the gloves are discussed, showing a progression in using advanced materials and construction techniques to enhance sensitivity and overall sensor coverage. The force data provided by the gloves can be used to improve dexterous, tool and power grasping primitives. Experiments with the latest gloves focus on the use of tools, specifically a power drill used to approximate an astronaut's torque tool.

Boehmite nanostructures preparation by hydrothermal method from anodic aluminium oxide membrane.

PubMed

Yang, X; Wang, J Y; Pan, H Y

2009-02-01

Boehmite nanostructures were successfully synthesized from porous anodic aluminium oxide (AAO) membrane by a simple and efficient hydro-thermal method. The experiment used high purity alumina as raw material, and the whole reaction process avoided superfluous impurities to be introduced. Thus, the purity of Boehmite products was ensured. The examinations of the morphology and structure were carried out by atomic force microscope (AFM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Composition of the specimens was analyzed using energy dispersive X-ray spectroscope (EDX) and X-ray diffraction (XRD). Based on these observations the growth process was analyzed.

Quantum Gravitational Force Between Polarizable Objects.

PubMed

Ford, L H; Hertzberg, Mark P; Karouby, J

2016-04-15

Since general relativity is a consistent low energy effective field theory, it is possible to compute quantum corrections to classical forces. Here we compute a quantum correction to the gravitational potential between a pair of polarizable objects. We study two distant bodies and compute a quantum force from their induced quadrupole moments due to two-graviton exchange. The effect is in close analogy to the Casimir-Polder and London-van der Waals forces between a pair of atoms from their induced dipole moments due to two photon exchange. The new effect is computed from the shift in vacuum energy of metric fluctuations due to the polarizability of the objects. We compute the potential energy at arbitrary distances compared to the wavelengths in the system, including the far and near regimes. In the far distance, or retarded, regime, the potential energy takes on a particularly simple form: V(r)=-3987ℏcG^{2}α_{1S}α_{2S}/(4πr^{11}), where α_{1S}, α_{2S} are the static gravitational quadrupole polarizabilities of each object. We provide estimates of this effect.

Detection of cancerous cervical cells using physical adhesion of fluorescent silica particles and centripetal force

PubMed Central

Gaikwad, Ravi M.; Dokukin, Maxim E.; Iyer, K. Swaminathan; Woodworth, Craig D.; Volkov, Dmytro O.; Sokolov, Igor

2012-01-01

Here we describe a non-traditional method to identify cancerous human cervical epithelial cells in a culture dish based on physical interaction between silica beads and cells. It is a simple optical fluorescence-based technique which detects the relative difference in the amount of fluorescent silica beads physically adherent to surfaces of cancerous and normal cervical cells. The method utilizes the centripetal force gradient that occurs in a rotating culture dish. Due to the variation in the balance between adhesion and centripetal forces, cancerous and normal cells demonstrate clearly distinctive distributions of the fluorescent particles adherent to the cell surface over the culture dish. The method demonstrates higher adhesion of silica particles to normal cells compared to cancerous cells. The difference in adhesion was initially observed by atomic force microscopy (AFM). The AFM data were used to design the parameters of the rotational dish experiment. The optical method that we describe is much faster and technically simpler than AFM. This work provides proof of the concept that physical interactions can be used to accurately discriminate normal and cancer cells. PMID:21305062

Solidification of a liquid crystal: Morphologies and transitions. Ph.D. thesis, Simon Fraser University (Canada)

NASA Astrophysics Data System (ADS)

Hutter, Jeffrey Lee

When a material freezes, the form it takes depends on the solidification conditions. For instance, as the undercooling is increased, one typically sees solidification into less-ordered forms. The resulting growth modes appear to be generic, with qualitative similarities between systems whose microscopic details are quite dissimilar. I have used both optical and atomic-force microscopy to study the transitions between different growth morphologies during the solidification of a particular liquid crystal, 10 OCB. We have observed six different solidification modes, each with a distinct micro and meso structure. The front-velocity-vs.-undercooling curve has a discontinuity in its slope and, in some cases, in the curve itself at mode transitions, suggesting that these transitions are analogous to phase transitions. Such transitions have been seen in other systems, but no general rule has been found that can predict which morphology will be selected. We show that, contrary to intuition and widespread speculation, the fastest-growing mode is not always the one selected. One of the growth modes exhibited by 10 OCB is known as banded spherulitic growth. Spherulites have been seen in a wide variety of materials including minerals, pure elements, polymers, biomolecules, and metal alloys. However, despite a century of study, there is no generally accepted theory of spherulitic growth. In particular, the cause of the concentric banding seen in many spherulites remains a mystery. Our studies of banded spherulites in 10 OCB using both optical and atomic-force microscopy show that the bands are associated with a density modulation and thus are not merely the result of a birefringent effect, as is commonly believed. As the atomic-force microscope (AFM) is a relatively new tool, some time was spent studying its capabilities. We found that because the AFM resolution is largely determined by attractive forces between the tip of the probe and the sample, resolution can be improved by imaging in a suitable liquid medium. We also developed a simple method for calibrating AFM cantilevers--a crucial step in using the AFM to obtain quantitative force data. This work is presented in an appendix.

Quantitative force measurements in liquid using frequency modulation atomic force microscopy

NASA Astrophysics Data System (ADS)

Uchihashi, Takayuki; Higgins, Michael J.; Yasuda, Satoshi; Jarvis, Suzanne P.; Akita, Seiji; Nakayama, Yoshikazu; Sader, John E.

2004-10-01

The measurement of short-range forces with the atomic force microscope (AFM) typically requires implementation of dynamic techniques to maintain sensitivity and stability. While frequency modulation atomic force microscopy (FM-AFM) is used widely for high-resolution imaging and quantitative force measurements in vacuum, quantitative force measurements using FM-AFM in liquids have proven elusive. Here we demonstrate that the formalism derived for operation in vacuum can also be used in liquids, provided certain modifications are implemented. To facilitate comparison with previous measurements taken using surface forces apparatus, we choose a model system (octamethylcyclotetrasiloxane) that is known to exhibit short-ranged structural ordering when confined between two surfaces. Force measurements obtained are found to be in excellent agreement with previously reported results. This study therefore establishes FM-AFM as a powerful tool for the quantitative measurement of forces in liquid.

Effective Particle Size From Molecular Dynamics Simulations in Fluids

DOE PAGES

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov; ...

2017-12-08

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Ab initio simulations of bond breaking in sulfur crosslinked isoprene oligomer units

NASA Astrophysics Data System (ADS)

Gehrke, Sascha; Alznauer, Hans Tobias; Karimi-Varzaneh, Hossein Ali; Becker, Jörg August

2017-12-01

Sulfur crosslinked polyisoprene (rubber) is used in important material components for a number of technical tasks (e.g., in tires and sealings). If mechanical stress, like tension or shear, is applied on these material components, the sulfur crosslinks suffer from homolytic bond breaking. In this work, we have simulated the bond breaking mechanism of sulfur crosslinks between polyisoprene chains using Car-Parrinello molecular dynamic simulations and investigated the maximum forces which can be resisted by the crosslinks. Small model systems with crosslinks formed by chains of N = 1 to N = 6 sulfur atoms have been simulated with the slow growth-technique, known from the literature. The maximum force can be thereby determined from the calculated energies as a function of strain (elongation). The stability of the crosslink under strain is quantified in terms of the maximum force that can be resisted by the system before the crosslink breaks. As shown by our simulations, this maximum force decreases with the sulfur crosslink length N in a step like manner. Our findings indicate that in bridges with N = 1, 2, and 3 sulfur atoms predominantly, carbon-sulfur bonds break, while in crosslinks with N > 3, the breaking of a sulfur-sulfur bond is the dominant failure mechanism. The results are explained within a simple chemical bond model, which describes how the delocalization of the electrons in the generated radicals can lower their electronic energy and decrease the activation barriers. It is described which of the double bonds in the isoprene units are involved in the mechanochemistry of crosslinked rubber.

Tip localization of an atomic force microscope in transmission microscopy with nanoscale precision

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

Baumann, Fabian; Pippig, Diana A., E-mail: diana.pippig@physik.uni-muenchen.de; Gaub, Hermann E.

Since the atomic force microscope (AFM) has evolved into a general purpose platform for mechanical experiments at the nanoscale, the need for a simple and generally applicable localization of the AFM cantilever in the reference frame of an optical microscope has grown. Molecular manipulations like in single molecule cut and paste or force spectroscopy as well as tip mediated nanolithography are prominent examples for the broad variety of applications implemented to date. In contrast to the different kinds of superresolution microscopy where fluorescence is used to localize the emitter, we, here, employ the absorbance of the tip to localize itsmore » position in transmission microscopy. We show that in a low aperture illumination, the tip causes a significant reduction of the intensity in the image plane of the microscope objective when it is closer than a few hundred nm. By independently varying the z-position of the sample slide, we could verify that this diffraction limited image of the tip is not caused by a near field effect but is rather caused by the absorbance of the transmitted light in the low apex needle-like tip. We localized the centroid position of this tip image with a precision of better than 6 nm and used it in a feedback loop to position the tip into nano-apertures of 110 nm radius. Single-molecule force spectroscopy traces on the unfolding of individual green fluorescent proteins within the nano-apertures showed that their center positions were repeatedly approached with very high fidelity leaving the specific handle chemistry on the tip’s surface unimpaired.« less

Effective Particle Size From Molecular Dynamics Simulations in Fluids

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

Ju, Jianwei; Welch, Paul Michael Jr.; Rasmussen, Kim Orskov

Here, we report molecular dynamics simulations designed to investigate the effective size of colloidal particles suspended in a fluid in the vicinity of a rigid wall where all interactions are defined by smooth atomic potential functions. These simulations are used to assess how the behavior of this system at the atomistic length scale compares to continuum mechanics models. In order to determine the effective size of the particles, we calculate the solvent forces on spherical particles of different radii as a function of different positions near and overlapping with the atomistically defined wall and compare them to continuum models. Thismore » procedure also then determines the effective position of the wall. Our analysis is based solely on forces that the particles sense, ensuring self-consistency of the method. The simulations were carried out using both Weeks–Chandler–Andersen and modified Lennard-Jones (LJ) potentials to identify the different contributions of simple repulsion and van der Waals attractive forces. Upon correction for behavior arising the discreteness of the atomic system, the underlying continuum physics analysis appeared to be correct down to much less than the particle radius. For both particle types, the effective radius was found to be ~0.75σ, where σ defines the length scale of the force interaction (the LJ diameter). The effective “hydrodynamic” radii determined by this means are distinct from commonly assumed values of 0.5σ and 1.0σ, but agree with a value developed from the atomistic analysis of the viscosity of such systems.« less

Theoretical modeling of the catch-slip bond transition in biological adhesion

NASA Astrophysics Data System (ADS)

Gunnerson, Kim; Pereverzev, Yuriy; Prezhdo, Oleg

2006-05-01

The mechanism by which leukocytes leave the blood stream and enter inflamed tissue is called extravasation. This process is facilitated by the ability of selectin proteins, produced by the endothelial cells of blood vessels, to form transient bonds with the leukocytes. In the case of P-selectin, the protein bonds with P-selectin glycoprotein ligands (PSGL-1) produced by the leukocyte. Recent atomic force microscopy and flow chamber analyses of the binding of P-selectin to PSGL-1 provide evidence for an unusual biphasic catch-bond/slip-bond behavior in response to the strength of exerted force. This biphasic process is not well-understood. There are several theoretical models for describing this phenomenon. These models use different profiles for potential energy landscapes and how they change under forces. We are exploring these changes using molecular dynamics. We will present a simple theoretical model as well as share some of our early MD results for describing this phenomenon.

Dynamic Optical Tuning of Interlayer Interactions in the Transition Metal Dichalcogenides

DOE PAGES

Mannebach, Ehren M.; Nyby, Clara; Ernst, Friederike; ...

2017-11-09

Modulation of weak interlayer interactions between quasi-two-dimensional atomic planes in the transition metal dichalcogenides (TMDCs) provides avenues for tuning their functional properties. Here we show that above-gap optical excitation in the TMDCs leads to an unexpected large-amplitude, ultrafast compressive force between the two-dimensional layers, as probed by in situ measurements of the atomic layer spacing at femtosecond time resolution. We show that this compressive response arises from a dynamic modulation of the interlayer van der Waals interaction and that this represents the dominant light-induced stress at low excitation densities. A simple analytic model predicts the magnitude and carrier density dependencemore » of the measured strains. Furthermore, this work establishes a new method for dynamic, nonequilibrium tuning of correlation-driven dispersive interactions and of the optomechanical functionality of TMDC quasi-two-dimensional materials.« less

Radical Chemistry and Charge Manipulation with an Atomic Force Microscope

NASA Astrophysics Data System (ADS)

Gross, Leo

The fuctionalization of tips by atomic manipulation dramatically increased the resolution of atomic force microscopy (AFM). The combination of high-resolution AFM with atomic manipulation now offers the unprecedented possibility to custom-design individual molecules by making and breaking bonds with the tip of the microscope and directly characterizing the products on the atomic scale. We recently applied this technique to generate and study reaction intermediates and to investigate chemical reactions trigged by atomic manipulation. We formed diradicals by dissociating halogen atoms and then reversibly triggered ring-opening and -closing reactions via atomic manipulation, allowing us to switch and control the molecule's reactivity, magnetic and optical properties. Additional information about charge states and charge distributions can be obtained by Kelvin probe force spectroscopy. On multilayer insulating films we investigated single-electron attachment, detachment and transfer between individual molecules. EU ERC AMSEL (682144), EU project PAMS (610446).

MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

PubMed Central

Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

2011-01-01

We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

Proceedings of a pressure transducer-packer workshop, June 25-28, 1991

USGS Publications Warehouse

Latkovich, V. J.

1993-01-01

The U.S. Geological Survey conducted its first Pressure Transducer-Packer Workshop in Denver, Colorado, June 25-28, 1991. Nineteen attendees from the Survey, Environment Canada, academia, and the private sector presented papers concerning their experiences with the use of transducers and packers in hydrogeologic investigations. Workshop partici- pants concluded that fixed-head packers are generally more reliable than other types and that there is a need for a wet/wet transducer for deep wells. The group recommended that simple downhole technology be used, that only rugged commercially available packers be purchased, and that it is imperative electrical connections and transducer electronics be kept dry. (USGS)

Evaluation of the feasibility of using the data collection system to operate a network of hydrological and climatological stations at sites remote from normal communication links

NASA Technical Reports Server (NTRS)

Perrier, R. (Principal Investigator)

1974-01-01

The author has identified the following significant results. The General Electric DCP has proven to be a versatile, rugged piece of hardware and has surpassed original expectation; it is very simple to use and does not require skilled staff for its use, installation, and operation. It is well suited for use in remote sites where no power is available. From this experience, it is concluded that the data collection system will be very useful in operating a network of hydrometeorological stations situated in sites remote from normal communication links.

Quantum Chemical Topology: Knowledgeable atoms in peptides

NASA Astrophysics Data System (ADS)

Popelier, Paul L. A.

2012-06-01

The need to improve atomistic biomolecular force fields remains acute. Fortunately, the abundance of contemporary computing power enables an overhaul of the architecture of current force fields, which typically base their electrostatics on fixed atomic partial charges. We discuss the principles behind the electrostatics of a more realistic force field under construction, called QCTFF. At the heart of QCTFF lies the so-called topological atom, which is a malleable box, whose shape and electrostatics changes in response to a changing environment. This response is captured by a machine learning method called Kriging. Kriging directly predicts each multipole moment of a given atom (i.e. the output) from the coordinates of the nuclei surrounding this atom (i.e. the input). This procedure yields accurate interatomic electrostatic energies, which form the basis for future-proof progress in force field design.

Atomic force microscopy as a tool for the investigation of living cells.

PubMed

Morkvėnaitė-Vilkončienė, Inga; Ramanavičienė, Almira; Ramanavičius, Arūnas

2013-01-01

Atomic force microscopy is a valuable and useful tool for the imaging and investigation of living cells in their natural environment at high resolution. Procedures applied to living cell preparation before measurements should be adapted individually for different kinds of cells and for the desired measurement technique. Different ways of cell immobilization, such as chemical fixation on the surface, entrapment in the pores of a membrane, or growing them directly on glass cover slips or on plastic substrates, result in the distortion or appearance of artifacts in atomic force microscopy images. Cell fixation allows the multiple use of samples and storage for a prolonged period; it also increases the resolution of imaging. Different atomic force microscopy modes are used for the imaging and analysis of living cells. The contact mode is the best for cell imaging because of high resolution, but it is usually based on the following: (i) image formation at low interaction force, (ii) low scanning speed, and (iii) usage of "soft," low resolution cantilevers. The tapping mode allows a cell to behave like a very solid material, and destructive shear forces are minimized, but imaging in liquid is difficult. The force spectroscopy mode is used for measuring the mechanical properties of cells; however, obtained results strongly depend on the cell fixation method. In this paper, the application of 3 atomic force microscopy modes including (i) contact, (ii) tapping, and (iii) force spectroscopy for the investigation of cells is described. The possibilities of cell preparation for the measurements, imaging, and determination of mechanical properties of cells are provided. The applicability of atomic force microscopy to diagnostics and other biomedical purposes is discussed.

Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations.

PubMed

Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R; Shalashilin, Dmitrii V

2014-08-06

In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.

Principles and Applications of the qPlus Sensor

NASA Astrophysics Data System (ADS)

Giessibl, Franz J.

The concept of the atomic force microscope (AFM) is a very simple one: map the surface of a sample by a sharp probe that scans over the surface similar to the finger of a blind person that reads Braille characters. In AFM, the role of that finger is taken by the probe tip that senses the presence of the sample surface by detecting the force between the tip of the probe and a sample. The qPlus sensor is a self sensing cantilever based on a quartz tuning fork that supplements the traditional microfabricated cantilevers made of silicon. Quartz tuning forks are used in the watch industry in quantities of billions annually, with the positive effects on quality and perfection. Three properties of these quartz-based sensors simplify the AFM significantly: (1) the piezoelectricity of quartz allows simple self sensing, (2) the mechanical properties of quartz show very small variations with temperature, and (3) the given stiffness of many quartz tuning forks is close to the ideal stiffness of cantilevers. The key properties of the qPlus sensor are a large stiffness that allows small amplitude operation, the large size that allows to mount single-crystal probe tips, and the self-sensing piezoelectric detection mechanism.

Nanofrictional behavior of amorphous, polycrystalline and textured Y-Cr-O films

NASA Astrophysics Data System (ADS)

Gervacio-Arciniega, J. J.; Flores-Ruiz, F. J.; Diliegros-Godines, C. J.; Broitman, E.; Enriquez-Flores, C. I.; Espinoza-Beltrán, F. J.; Siqueiros, J.; Cruz, M. P.

2016-08-01

Differences in friction coefficients (μ) of ferroelectric YCrO3, textured and polycrystalline films, and non-ferroelectric Y-Cr-O films are analyzed. The friction coefficient was evaluated by atomic force microscopy using a simple quantitative procedure where the dependence of friction force with the applied load is obtained in only one topographical image. A simple code was developed with the MATLAB® software to analyze the experimental data. The code includes a correction of the hysteresis in the forward and backward scanning directions. The quantification of load exerted on the sample surface was obtained by finite element analysis of the AFM cantilever starting from its experimental dynamic information. The results show that the ferroelectric YCrO3 film deposited on a Pt(150 nm)/TiO2(30 nm)/SiO2/Si (100) substrate is polycrystalline and has a lower friction coefficient than the deposited on SrTiO3 (110), which is highly textured. From a viewpoint of industrial application in ferroelectric memories, where the writing process is electrical or mechanically achieved by sliding AFM tips on the sample, polycrystalline YCrO3 films seem to be the best candidates due to their lower μ.

Rugged switch responds to minute pressure differentials

NASA Technical Reports Server (NTRS)

Friend, L. C.; Shaub, K. D.

1967-01-01

Pressure responsive switching device exhibits high sensitivity but is extremely rugged and resistant to large amplitude shock and velocity loading. This snap-action, single pole-double throw switch operates over a wide temperature range.

Validation of Resource Utilization Groups version III for Home Care (RUG-III/HC): evidence from a Canadian home care jurisdiction.

PubMed

Poss, Jeffrey W; Hirdes, John P; Fries, Brant E; McKillop, Ian; Chase, Mary

2008-04-01

The case-mix system Resource Utilization Groups version III for Home Care (RUG-III/HC) was derived using a modest data sample from Michigan, but to date no comprehensive large scale validation has been done. This work examines the performance of the RUG-III/HC classification using a large sample from Ontario, Canada. Cost episodes over a 13-week period were aggregated from individual level client billing records and matched to assessment information collected using the Resident Assessment Instrument for Home Care, from which classification rules for RUG-III/HC are drawn. The dependent variable, service cost, was constructed using formal services plus informal care valued at approximately one-half that of a replacement worker. An analytic dataset of 29,921 episodes showed a skewed distribution with over 56% of cases falling into the lowest hierarchical level, reduced physical functions. Case-mix index values for formal and informal cost showed very close similarities to those found in the Michigan derivation. Explained variance for a function of combined formal and informal cost was 37.3% (20.5% for formal cost alone), with personal support services as well as informal care showing the strongest fit to the RUG-III/HC classification. RUG-III/HC validates well compared with the Michigan derivation work. Potential enhancements to the present classification should consider the large numbers of undifferentiated cases in the reduced physical function group, and the low explained variance for professional disciplines.

Theoretical Studies of the Structure and the Dynamics on Clean and Chemisorbed Metal Surfaces

NASA Astrophysics Data System (ADS)

Yang, Liqiu

Molecular dynamics (MD) and lattice dynamics (LD) techniques are employed to investigate several phenomena related to the structure and vibrations at metal surfaces. The MD simulations are performed with the many-body interaction potentials obtained using the Embedded-Atom Method (EAM). As specific examples, we present the results for Ag(100) at 300 K and Cu(100) at 150 K, 300 K, and 600 K. The calculated frequencies and polarizations of all surface modes and resonances at the high-symmetry points in the two-dimensional Brillouin zone are in good agreement with available data, as well as, existing lattice dynamics results with force constants obtained from first-principles calculations. Our calculated surface relaxation is also in reasonable agreement with the data. We also test a much simpler lattice dynamics model with nearest neighbor central force interactions, and conclude that it can reproduce the main features of the phonon modes, but only when adjustable surface parameters are used. Additionally, the temperature dependent studies of the phonon line-widths and the mean-square displacement (MSD) of surface atoms are indicative of enhanced surface anharmonicity. On several chemisorbed metal surfaces, for which force constants are not available from first-principles calculations or the EAM, we perform lattice dynamics studies of phonon dispersion curves using simple force-constant models. These studies provide reliable mean-square displacement of surface atoms and can distinguish between possible reconstruction patterns, the results being insensitive to the exact values of the surface parameters. On c(2 times 2)S-Ni(100), it is found that the parallel component of the mean-square displacement for sulfur is around 50% larger than the vertical component, but for the mean-square displacement of oxygen atoms in the system c(2 times 2)O-Ni(100), the opposite is the case. As regards surface reconstruction, for both p(2 times 1)O-Ag(110) and p(2 times 1)O-Ni(110) surfaces, it is concluded that a substrate missing-row type reconstruction is induced by the adsorbates, but the local symmetry is C_{2v} with oxygen atoms at the long-bridge sites for the former and C_{s} with (110) being the only symmetry axis for the latter. In the above theoretical analysis, close contacts are made to many available experimental results such as surface phonon dispersion curves, interlayer relaxations, and Debye -Waller factors and adsorbate-substrate bond lengths.

Elemental Identification by Combining Atomic Force Microscopy and Kelvin Probe Force Microscopy.

PubMed

Schulz, Fabian; Ritala, Juha; Krejčí, Ondrej; Seitsonen, Ari Paavo; Foster, Adam S; Liljeroth, Peter

2018-06-01

There are currently no experimental techniques that combine atomic-resolution imaging with elemental sensitivity and chemical fingerprinting on single molecules. The advent of using molecular-modified tips in noncontact atomic force microscopy (nc-AFM) has made it possible to image (planar) molecules with atomic resolution. However, the mechanisms responsible for elemental contrast with passivated tips are not fully understood. Here, we investigate elemental contrast by carrying out both nc-AFM and Kelvin probe force microscopy (KPFM) experiments on epitaxial monolayer hexagonal boron nitride (hBN) on Ir(111). The hBN overlayer is inert, and the in-plane bonds connecting nearest-neighbor boron and nitrogen atoms possess strong covalent character and a bond length of only ∼1.45 Å. Nevertheless, constant-height maps of both the frequency shift Δ f and the local contact potential difference exhibit striking sublattice asymmetry. We match the different atomic sites with the observed contrast by comparison with nc-AFM image simulations based on the density functional theory optimized hBN/Ir(111) geometry, which yields detailed information on the origin of the atomic-scale contrast.

Interpretation of frequency modulation atomic force microscopy in terms of fractional calculus

NASA Astrophysics Data System (ADS)

Sader, John E.; Jarvis, Suzanne P.

2004-07-01

It is widely recognized that small amplitude frequency modulation atomic force microscopy probes the derivative of the interaction force between tip and sample. For large amplitudes, however, such a physical connection is currently lacking, although it has been observed that the frequency shift presents a quantity intermediate to the interaction force and energy for certain force laws. Here we prove that these observations are a universal property of large amplitude frequency modulation atomic force microscopy, by establishing that the frequency shift is proportional to the half-fractional integral of the force, regardless of the force law. This finding indicates that frequency modulation atomic force microscopy can be interpreted as a fractional differential operator, where the order of the derivative/integral is dictated by the oscillation amplitude. We also establish that the measured frequency shift varies systematically from a probe of the force gradient for small oscillation amplitudes, through to the measurement of a quantity intermediate to the force and energy (the half-fractional integral of the force) for large oscillation amplitudes. This has significant implications to measurement sensitivity, since integrating the force will smooth its behavior, while differentiating it will enhance variations. This highlights the importance in choice of oscillation amplitude when wishing to optimize the sensitivity of force spectroscopy measurements to short-range interactions and consequently imaging with the highest possible resolution.

Friction on the Bond and the Vibrational Relaxation in Simple Liquids.

NASA Astrophysics Data System (ADS)

Mishra, Bimalendu Kumar

In chapter 1, the energy relaxation of a stiff Morse oscillator dissolved in a simple LJ fluid is calculated using a reversible integrator (r-RESPA) in molecular dynamics generated from the Trotter factorization of the classical propagator. We compare the "real" relaxation from full MD simulations with that predicted by the Generalized Langevin Equation (GLE) with memory friction determined from the full Molecular Dynamics for a series of fluid densities. It is found that the GLE gives very good agreement with MD for the vibrational energy relaxation for this nonlinear oscillator far from equilibrium only for high density fluids, but reduced densities rho < 0.5 the energy relaxation from the MD simulation becomes considered slower than that from the GLE. An analysis of the statistical properties of the random force shows that as the density is lowered the non-Gaussian behavior of the random force becomes more prominent. This behavior is consistent with a simple model in which the oscillator undergoes generalized Langevin dynamics between strong binary collisions with solvent atoms. In chapter 2, molecular hydrodynamics is used to calculate the memory friction on the intramolecular vibrational coordinate of a homonuclear diatomic molecule dissolved in a simple liquid. The predicted memory friction is then compared to recent computer experiments. Agreement with the experimental memory functions is obtained when the linearized hydrodynamics is modified to include gaussian viscoelasticity and compressibility. The hydrodynamic friction on the bond appears to agree qualitatively very well, although quantitative agreement is not found at high frequencies. Various limits of the hydrodynamic friction are discussed.

Functionalization of surfactant wrapped graphenenanosheets with alkylazides for enhanced dispersibility

NASA Astrophysics Data System (ADS)

Vadukumpully, Sajini; Gupta, Jhinuk; Zhang, Yongping; Xu, Guo Qin; Valiyaveettil, Suresh

2011-01-01

A facile and simple approach for the covalent functionalization of surfactant wrapped graphene sheets is described. The approach involves functionalization of dispersible graphene sheets with various alkylazides and 11-azidoundecanoic acid proved the best azide for enhanced dispersibility. The functionalization was confirmed by infrared spectroscopy and scanning tunneling microscopy. The free carboxylic acidgroups can bind to gold nanoparticles, which were introduced as markers for the reactive sites. The interaction between gold nanoparticles and the graphene sheets was followed by UV-vis spectroscopy. The gold nanoparticle-graphene composite was characterized by transmission electron microscopy and atomic force microscopy, demonstrating the uniform distribution of gold nanoparticles all over the surface. Our results open the possibility to control the functionalization on graphene in the construction of composite nanomaterials.A facile and simple approach for the covalent functionalization of surfactant wrapped graphene sheets is described. The approach involves functionalization of dispersible graphene sheets with various alkylazides and 11-azidoundecanoic acid proved the best azide for enhanced dispersibility. The functionalization was confirmed by infrared spectroscopy and scanning tunneling microscopy. The free carboxylic acidgroups can bind to gold nanoparticles, which were introduced as markers for the reactive sites. The interaction between gold nanoparticles and the graphene sheets was followed by UV-vis spectroscopy. The gold nanoparticle-graphene composite was characterized by transmission electron microscopy and atomic force microscopy, demonstrating the uniform distribution of gold nanoparticles all over the surface. Our results open the possibility to control the functionalization on graphene in the construction of composite nanomaterials. Electronic Supplementary Information (ESI) available: Synthesis and characterization details of dodecylazide, hexylazide, 11-azidoundecanol (AUO), micrographs (SEM and TEM images) of the various azide functionalized samples and the statistical analysis of the graphene thickness. See 10.1039/c0nr00547a.

Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains

PubMed Central

Sabater, Carlos; Untiedt, Carlos

2015-01-01

Summary This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a ‘Berry force’. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose. PMID:26734525

Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids

NASA Astrophysics Data System (ADS)

Chu, Huiying; Peng, Xiangda; Li, Yan; Zhang, Yuebin; Min, Hanyi; Li, Guohui

2018-04-01

A polarizable atomic multipole-based force field for the membrane bilayer models 1,2-dioleoyl-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) has been developed. The force field adopts the same framework as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) model, in which the charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments. Many-body polarization including the inter- and intra-molecular polarization is modelled in a consistent manner with distributed atomic polarizabilities. The van der Waals parameters were first transferred from existing AMOEBA parameters for small organic molecules and then optimised by fitting to ab initio intermolecular interaction energies between models and a water molecule. Molecular dynamics simulations of the two aqueous DOPC and POPE membrane bilayer systems, consisting of 72 model molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, etc. were consistent with experimental values.

Friction and Wear on the Atomic Scale

NASA Astrophysics Data System (ADS)

Gnecco, Enrico; Bennewitz, Roland; Pfeiffer, Oliver; Socoliuc, Anisoara; Meyer, Ernst

Friction has long been the subject of research: the empirical da Vinci-Amontons friction laws have been common knowledge for centuries. Macroscopic experiments performed by the school of Bowden and Tabor revealed that macroscopic friction can be related to the collective action of small asperities. Over the last 15 years, experiments performed with the atomic force microscope have provided new insights into the physics of single asperities sliding over surfaces. This development, together with the results from complementary experiments using surface force apparatus and the quartz microbalance, have led to the new field of nanotribology. At the same time, increasing computing power has permitted the simulation of processes that occur during sliding contact involving several hundreds of atoms. It has become clear that atomic processes cannot be neglected when interpreting nanotribology experiments. Even on well-defined surfaces, experiments have revealed that atomic structure is directly linked to friction force. This chapter will describe friction force microscopy experiments that reveal, more or less directly, atomic processes during sliding contact.

Nursing home case-mix instruments: validation of the RUG-III system in Italy.

PubMed

Brizioli, Enrico; Bernabei, Roberto; Grechi, Francesca; Masera, Filippo; Landi, Francesco; Bandinelli, Stefania; Cavazzini, Chiara; Gangemi, Salvatore; Ferrucci, Luigi

2003-06-01

The current Italian reimbursement system for long-term care does not adequately consider the great variability in the health and functional status of older persons who are admitted to long-term care institutions. Furthermore, no procedure is implemented to monitor the quality of care provided to older residents. We conducted this study to verify whether the RUG-III (Resource Utilization Groups-version III), a tool for assessing the case-mix of nursing home residents, which is widely used in the United States and in many European countries, can be effectively used in the Italian health care system. We administered an Italian version of the RUG-III to 1000 older residents of 11 intermediate- and long-term care institutions. We also collected objective information on the amount of care provided directly or indirectly to each resident by nurses, physical therapists, and other health professionals. The RUG-III 44 group classification system explained 61 and 44% of the variance in rehabilitative and nursing wage-adjusted care time, respectively. Our findings provide strong evidence that the RUG-III classification, applied to Italian intermediate- and long-term care institutions, provides a robust estimate of the amount of nursing and rehabilitation resources consumed by older residents.

Assessment of Simple Models for Molecular Simulation of Ethylene Carbonate and Propylene Carbonate as Solvents for Electrolyte Solutions.

PubMed

Chaudhari, Mangesh I; Muralidharan, Ajay; Pratt, Lawrence R; Rempe, Susan B

2018-02-12

Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples. The basic results discussed suggest that an empirically parameterized, non-polarizable force field can reproduce experimental structural, thermodynamic, and dielectric properties of EC and PC liquids with acceptable accuracy. More sophisticated force fields might include molecular polarizability and Buckingham-model description of inter-atomic overlap repulsions as extensions to Lennard-Jones models of van der Waals interactions. Simple approaches should be similarly successful also for applications to organic molecular ions in EC/PC solutions, but the important case of Li[Formula: see text] deserves special attention because of the particularly strong interactions of that small ion with neighboring solvent molecules. To treat the Li[Formula: see text] ions in liquid EC/PC solutions, we identify interaction models defined by empirically scaled partial charges for ion-solvent interactions. The empirical adjustments use more basic inputs, electronic structure calculations and ab initio molecular dynamics simulations, and also experimental results on Li[Formula: see text] thermodynamics and transport in EC/PC solutions. Application of such models to the mechanism of Li[Formula: see text] transport in glassy SEI models emphasizes the advantage of long time-scale molecular dynamics studies of these non-equilibrium materials.

MEAM interatomic force calculation subroutine for LAMMPS

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

Stukowski, A.

2010-10-25

Interatomic force and energy calculation subroutine tobe used with the molecular dynamics simulation code LAMMPS (Ref a.). The code evaluates the total energy and atomic forces (energy gradient) according to cubic spine-based variant (Ref b.) of the Modified Embedded Atom Method (MEAM).

Isolating and moving single atoms using silicon nanocrystals

DOEpatents

Carroll, Malcolm S.

2010-09-07

A method is disclosed for isolating single atoms of an atomic species of interest by locating the atoms within silicon nanocrystals. This can be done by implanting, on the average, a single atom of the atomic species of interest into each nanocrystal, and then measuring an electrical charge distribution on the nanocrystals with scanning capacitance microscopy (SCM) or electrostatic force microscopy (EFM) to identify and select those nanocrystals having exactly one atom of the atomic species of interest therein. The nanocrystals with the single atom of the atomic species of interest therein can be sorted and moved using an atomic force microscope (AFM) tip. The method is useful for forming nanoscale electronic and optical devices including quantum computers and single-photon light sources.

Final Technical Report for Award DESC0011912, "Trimodal Tapping Mode Atomic Force Microscopy: Simultaneous 4D Mapping of Conservative and Dissipative Probe-Sample Interactions of Energy-Relevant Materials”

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

Solares, Santiago D.

The final project report covering the period 7/1/14-6/30/17 provides an overview of the technical accomplishments in the areas of (i) fundamental viscoelasticity, (ii) multifrequency atomic force microscopy, and (iii) characterization of energy-relevant materials with atomic force microscopy. A list of publications supported by the project is also provided.

Excellent Resistive Switching Performance of Cu-Se-Based Atomic Switch Using Lanthanide Metal Nanolayer at the Cu-Se/Al2O3 Interface.

PubMed

Woo, Hyunsuk; Vishwanath, Sujaya Kumar; Jeon, Sanghun

2018-03-07

The next-generation electronic society is dependent on the performance of nonvolatile memory devices, which has been continuously improving. In the last few years, many memory devices have been introduced. However, atomic switches are considered to be a simple and reliable basis for next-generation nonvolatile devices. In general, atomic switch-based resistive switching is controlled by electrochemical metallization. However, excess ion injection from the entire area of the active electrode into the switching layer causes device nonuniformity and degradation of reliability. Here, we propose the fabrication of a high-performance atomic switch based on Cu x -Se 1- x by inserting lanthanide (Ln) metal buffer layers such as neodymium (Nd), samarium (Sm), dysprosium (Dy), or lutetium (Lu) between the active metal layer and the electrolyte. Current-atomic force microscopy results confirm that Cu ions penetrate through the Ln-buffer layer and form thin conductive filaments inside the switching layer. Compared with the Pt/Cu x -Se 1- x /Al 2 O 3 /Pt device, the optimized Pt/Cu x -Se 1- x /Ln/Al 2 O 3 /Pt devices show improvement in the on/off resistance ratio (10 2 -10 7 ), retention (10 years/85 °C), endurance (∼10 000 cycles), and uniform resistance state distribution.

Effects of 3D virtual haptics force feedback on brand personality perception: the mediating role of physical presence in advergames.

PubMed

Jin, Seung-A Annie

2010-06-01

This study gauged the effects of force feedback in the Novint Falcon haptics system on the sensory and cognitive dimensions of a virtual test-driving experience. First, in order to explore the effects of tactile stimuli with force feedback on users' sensory experience, feelings of physical presence (the extent to which virtual physical objects are experienced as actual physical objects) were measured after participants used the haptics interface. Second, to evaluate the effects of force feedback on the cognitive dimension of consumers' virtual experience, this study investigated brand personality perception. The experiment utilized the Novint Falcon haptics controller to induce immersive virtual test-driving through tactile stimuli. The author designed a two-group (haptics stimuli with force feedback versus no force feedback) comparison experiment (N = 238) by manipulating the level of force feedback. Users in the force feedback condition were exposed to tactile stimuli involving various force feedback effects (e.g., terrain effects, acceleration, and lateral forces) while test-driving a rally car. In contrast, users in the control condition test-drove the rally car using the Novint Falcon but were not given any force feedback. Results of ANOVAs indicated that (a) users exposed to force feedback felt stronger physical presence than those in the no force feedback condition, and (b) users exposed to haptics stimuli with force feedback perceived the brand personality of the car to be more rugged than those in the control condition. Managerial implications of the study for product trial in the business world are discussed.

A circularly polarized optical dipole trap and other developments in laser trapping of atoms

NASA Astrophysics Data System (ADS)

Corwin, Kristan Lee

Several innovations in laser trapping and cooling of alkali atoms are described. These topics share a common motivation to develop techniques for efficiently manipulating cold atoms. Such advances facilitate sensitive precision measurements such as parity non- conservation and 8-decay asymmetry in large trapped samples, even when only small quantities of the desired species are available. First, a cold, bright beam of Rb atoms is extracted from a magneto-optical trap (MOT) using a very simple technique. This beam has a flux of 5 × 109 atoms/s and a velocity of 14 m/s, and up to 70% of the atoms in the MOT were transferred to the atomic beam. Next, a highly efficient MOT for radioactive atoms is described, in which more than 50% of 221Fr atoms contained in a vapor cell are loaded into a MOT. Measurements were also made of the 221Fr 7 2P1/2 and 7 2P3/2 energies and hyperfine constants. To perform these experiments, two schemes for stabilizing the frequency of the light from a diode laser were developed and are described in detail. Finally, a new type of trap is described and a powerful cooling technique is demonstrated. The circularly polarized optical dipole trap provides large samples of highly spin-polarized atoms, suitable for many applications. Physical processes that govern the transfer of large numbers of atoms into the trap are described, and spin-polarization is measured to be 98(1)%. In addition, the trap breaks the degeneracy of the atomic spin states much like a magnetic trap does. This allows for RF and microwave cooling via both forced evaporation and a Sisyphus mechanism. Preliminary application of these techniques to the atoms in the circularly polarized dipole trap has successfully decreased the temperature by a factor of 4 while simultaneously increasing phase space density.

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin, E-mail: linlin@math.berkeley.edu; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE PAGES

Zhang, Gaigong; Lin, Lin; Hu, Wei; ...

2017-01-27

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin; Hu, Wei

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

2017-04-01

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

Dynamical Casimir-Polder force on a partially dressed atom near a conducting wall

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

Messina, Riccardo; Vasile, Ruggero; Passante, Roberto

2010-12-15

We study the time evolution of the Casimir-Polder force acting on a neutral atom in front of a perfectly conducting plate, when the system starts its unitary evolution from a partially dressed state. We solve the Heisenberg equations for both atomic and field quantum operators, exploiting a series expansion with respect to the electric charge and an iterative technique. After discussing the behavior of the time-dependent force on an initially partially dressed atom, we analyze a possible experimental scheme to prepare the partially dressed state and the observability of this new dynamical effect.

[On the Way to Culture-Sensitive Patient Information Materials: Results of a Focus Group Study].

PubMed

Ries, Zivile; Frank, Fabian; Bermejo, Isaac; Kalaitsidou, Chariklia; Zill, Jördis; Dirmaier, Jörg; Härter, Martin; Bengel, Jürgen; Hölzel, Lars

2018-06-01

This study was part of a double-blind randomised controlled trial aimed to evaluate the effects of culture-sensitive patient information materials (PIM) compared with standard translated material. The study aimed to obtain the data for the development of culture sensitive PIM about unipolar depression for the 4 largest migrant groups in Germany (Turkish, Polish, Russian and Italian migration background). A qualitative study using 4 manual-based focus groups (FG), one for each migrant group, with 29 participants (9 with a Turkish (TüG), 8 with a Polish (PoG), 5 with a Russian (RuG) and 7 with an Italian (ItG) migration background) was conducted. The discussions were recorded, transcribed and analyzed using qualitative content analysis. 7 categories were identified. For the (1.) development of a good culture-sensitive PIM an easy language, a clear structure, an assessable extent of information and the avoidance of stereotypes were highlighted cross-culturally in all four FG. RuG and PoG had the largest (2.) lack of information about the German health care system. Concerning the (3.) illness perception RuG named problems with recognizing and understanding depression. PoG, RuG and TüG thematized (4.) feared consequences of the illness and of professional helpseeking. ItG, PoG, RuG had fears concerning (5.) psychotropic drugs as a result from insufficient knowledge about medication. For (6.) doctor-patient relationship cultural specifics were identified in RuG and TüG and for (7.) migration or culture specific reasons for depression in RuG, ItG and TüG. Although the identified categories were relevant for all or for the majority of migrant groups, for most categories specific cultural aspects were discovered. These findings show the importance of a culture sensitive adaptation of PIM. © Georg Thieme Verlag KG Stuttgart · New York.

Rugged: an operational, open-source solution for Sentinel-2 mapping

NASA Astrophysics Data System (ADS)

Maisonobe, Luc; Seyral, Jean; Prat, Guylaine; Guinet, Jonathan; Espesset, Aude

2015-10-01

When you map the entire Earth every 5 days with the aim of generating high-quality time series over land, there is no room for geometrical error: the algorithms have to be stable, reliable, and precise. Rugged, a new open-source library for pixel geolocation, is at the geometrical heart of the operational processing for Sentinel-2. Rugged performs sensor-to-terrain mapping taking into account ground Digital Elevation Models, Earth rotation with all its small irregularities, on-board sensor pixel individual lines-of-sight, spacecraft motion and attitude, and all significant physical effects. It provides direct and inverse location, i.e. it allows the accurate computation of which ground point is viewed from a specific pixel in a spacecraft instrument, and conversely which pixel will view a specified ground point. Direct and inverse location can be used to perform full ortho-rectification of images and correlation between sensors observing the same area. Implemented as an add-on for Orekit (Orbits Extrapolation KIT; a low-level space dynamics library), Rugged also offers the possibility of simulating satellite motion and attitude auxiliary data using Orekit's full orbit propagation capability. This is a considerable advantage for test data generation and mission simulation activities. Together with the Orfeo ToolBox (OTB) image processing library, Rugged provides the algorithmic core of Sentinel-2 Instrument Processing Facilities. The S2 complex viewing model - with 12 staggered push-broom detectors and 13 spectral bands - is built using Rugged objects, enabling the computation of rectification grids for mapping between cartographic and focal plane coordinates. These grids are passed to the OTB library for further image resampling, thus completing the ortho-rectification chain. Sentinel-2 stringent operational requirements to process several terabytes of data per week represented a tough challenge, though one that was well met by Rugged in terms of the robustness and performance of the library.

Layer-by-layer assembled hydrophobic coatings for cellulose nanofibril films and textiles, made of polylysine and natural wax particles.

PubMed

Forsman, Nina; Lozhechnikova, Alina; Khakalo, Alexey; Johansson, Leena-Sisko; Vartiainen, Jari; Österberg, Monika

2017-10-01

Herein we present a simple method to render cellulosic materials highly hydrophobic while retaining their breathability and moisture buffering properties, thus allowing for their use as functional textiles. The surfaces are coated via layer-by-layer deposition of two natural components, cationic poly-l-lysine and anionic carnauba wax particles. The combination of multiscale roughness, open film structure, and low surface energy of wax colloids, resulted in long-lasting superhydrophobicity on cotton surface already after two bilayers. Atomic force microscopy, interference microscopy, scanning electron microscopy and X-ray photoelectron spectroscopy were used to decouple structural effects from changes in surface energy. Furthermore, the effect of thermal annealing on the coating was evaluated. The potential of this simple and green approach to enhance the use of natural cellulosic materials is discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Growth of tungsten oxide nanostructures by chemical solution deposition

NASA Astrophysics Data System (ADS)

Jin, L. H.; Bai, Y.; Li, C. S.; Wang, Y.; Feng, J. Q.; Lei, L.; Zhao, G. Y.; Zhang, P. X.

2018-05-01

Tungsten oxide nanostructures were fabricated on LaAlO3 (00l) substrates by a simple chemical solution deposition. The decomposition behavior and phase formation of ammonium tungstate precursor were characterized by thermal analysis and X-ray diffraction. Moreover, the morphology and chemical state of nanostructures were analyzed by scanning electron microscopy, atomic force microscopy and X-ray photoelectron spectra. The effects of crystallization temperature on the formation of nanodots and nanowires were investigated. The results indicated that the change of nanostructures had close relationship with the crystallization temperature during the chemical solution deposition process. Under higher crystallization temperature, the square-like dots transformed into the dome-like nanodots and nanowires. Moreover high density well-ordered nanodots could be obtained on the substrate with the further increase of crystallization temperature. It also suggested that this simple chemical solution process could be used to adjust the nanostructures of tungsten oxide compounds on substrate.

Neural-network quantum state tomography

NASA Astrophysics Data System (ADS)

Torlai, Giacomo; Mazzola, Guglielmo; Carrasquilla, Juan; Troyer, Matthias; Melko, Roger; Carleo, Giuseppe

2018-05-01

The experimental realization of increasingly complex synthetic quantum systems calls for the development of general theoretical methods to validate and fully exploit quantum resources. Quantum state tomography (QST) aims to reconstruct the full quantum state from simple measurements, and therefore provides a key tool to obtain reliable analytics1-3. However, exact brute-force approaches to QST place a high demand on computational resources, making them unfeasible for anything except small systems4,5. Here we show how machine learning techniques can be used to perform QST of highly entangled states with more than a hundred qubits, to a high degree of accuracy. We demonstrate that machine learning allows one to reconstruct traditionally challenging many-body quantities—such as the entanglement entropy—from simple, experimentally accessible measurements. This approach can benefit existing and future generations of devices ranging from quantum computers to ultracold-atom quantum simulators6-8.

Around Marshall

NASA Image and Video Library

1995-06-08

A rugged, highly accurate, low-temperature sensor is developed by NASA researchers. A new sensor allows accurate, quick low-temperature measurements in rugged environments. This is especially useful in piping with very cold liquids under high pressure, and high flow rate conditions.

A hacker's guide to catching a debris flow: Lessons learned from four years of chasing mud in Colorado and southern California

NASA Astrophysics Data System (ADS)

Kean, J. W.; McCoy, S. W.; Staley, D. M.; Coe, J.; Leeper, R.; Tucker, G. E.

2012-12-01

Direct measurements of natural debris flows provide valuable insights into debris-flow processes and hazards. Yet debris flows are difficult to "catch" because they live in rugged terrain, appear infrequently, and have an appetite for destroying monitoring equipment. We present an overview of some successful (and failed) techniques we have used over the past four years to obtain direct measurements of 40+ debris flows in Colorado and southern California. Following the "MacGyver" theme of the session, we focus on the improvised equipment and methods we use in our hunt for quality data. These include an inexpensive erosion sensor to measure rates of debris-flow entrainment, a custom load cell enclosure for measuring debris-flow normal force, tracer rocks implanted with passive integrated transponders, basic pressure transducers to measure debris-flow timing, and standard digital cameras adapted to obtain high-resolution (1936 x 1288 pixels) video footage of debris flows. These techniques are also suitable for catching data on elusive flash floods. In addition, we also share some practical solutions to the logistical problems associated with installing monitoring equipment in rugged debris-flow terrain, such as suspension of non-contact stage gages high above channels.

Motion of Cesium Atoms in the One-Dimensional Magneto-Optical Trap

NASA Technical Reports Server (NTRS)

Li, Yimin; Chen, Xuzong; Wang, Qingji; Wang, Yiqiu

1996-01-01

The force to which Cs atoms are subjected in the one-dimensional magneto-optical trap (lD-MOT) is calculated, and properties of this force are discussed. Several methods to increase the number of Cs atoms in the lD-MOT are presented on the basis of the analysis of the capture and escape of Cs atoms in the ID-MOT.

A universal strategy for the creation of machine learning-based atomistic force fields

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

2017-09-01

Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.

Perception for rugged terrain

NASA Technical Reports Server (NTRS)

Kweon, In SO; Hebert, Martial; Kanade, Takeo

1989-01-01

A three-dimensional perception system for building a geometrical description of rugged terrain environments from range image data is presented with reference to the exploration of the rugged terrain of Mars. An intermediate representation consisting of an elevation map that includes an explicit representation of uncertainty and labeling of the occluded regions is proposed. The locus method used to convert range image to an elevation map is introduced, along with an uncertainty model based on this algorithm. Both the elevation map and the locus method are the basis of a terrain matching algorithm which does not assume any correspondences between range images. The two-stage algorithm consists of a feature-based matching algorithm to compute an initial transform and an iconic terrain matching algorithm to merge multiple range images into a uniform representation. Terrain modeling results on real range images of rugged terrain are presented. The algorithms considered are a fundamental part of the perception system for the Ambler, a legged locomotor.

Upper Secondary Students' Understanding of the Basic Physical Interactions in Analogous Atomic and Solar Systems

ERIC Educational Resources Information Center

Taber, Keith S.

2013-01-01

Comparing the atom to a "tiny solar system" is a common teaching analogy, and the extent to which learners saw the systems as analogous was investigated. English upper secondary students were asked parallel questions about the physical interactions between the components of a simple atomic system and a simple solar system to investigate…

The Chemical Structure and Acid Deterioration of Paper.

ERIC Educational Resources Information Center

Hollinger, William K., Jr.

1984-01-01

Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

Dynamic-force spectroscopy measurement with precise force control using atomic-force microscopy probe

NASA Astrophysics Data System (ADS)

Takeuchi, Osamu; Miyakoshi, Takaaki; Taninaka, Atsushi; Tanaka, Katsunori; Cho, Daichi; Fujita, Machiko; Yasuda, Satoshi; Jarvis, Suzanne P.; Shigekawa, Hidemi

2006-10-01

The accuracy of dynamic-force spectroscopy (DFS), a promising technique of analyzing the energy landscape of noncovalent molecular bonds, was reconsidered in order to justify the use of an atomic-force microscopy (AFM) cantilever as a DFS force probe. The advantages and disadvantages caused, for example, by the force-probe hardness were clarified, revealing the pivotal role of the molecular linkage between the force probe and the molecular bonds. It was shown that the feedback control of the loading rate of tensile force enables us a precise DFS measurement using an AFM cantilever as the force probe.

Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways

PubMed Central

Sekhar, Ashok; Rumfeldt, Jessica AO; Broom, Helen R; Doyle, Colleen M; Bouvignies, Guillaume; Meiering, Elizabeth M; Kay, Lewis E

2015-01-01

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease involving cytotoxic conformations of Cu, Zn superoxide dismutase (SOD1). A major challenge in understanding ALS disease pathology has been the identification and atomic-level characterization of these conformers. Here, we use a combination of NMR methods to detect four distinct sparsely populated and transiently formed thermally accessible conformers in equilibrium with the native state of immature SOD1 (apoSOD12SH). Structural models of two of these establish that they possess features present in the mature dimeric protein. In contrast, the other two are non-native oligomers in which the native dimer interface and the electrostatic loop mediate the formation of aberrant intermolecular interactions. Our results show that apoSOD12SH has a rugged free energy landscape that codes for distinct kinetic pathways leading to either maturation or non-native association and provide a starting point for a detailed atomic-level understanding of the mechanisms of SOD1 oligomerization. DOI: http://dx.doi.org/10.7554/eLife.07296.001 PMID:26099300

Experimental Demonstration of a Synthetic Lorentz Force by Using Radiation Pressure.

PubMed

Šantić, N; Dubček, T; Aumiler, D; Buljan, H; Ban, T

2015-09-02

Synthetic magnetism in cold atomic gases opened the doors to many exciting novel physical systems and phenomena. Ubiquitous are the methods used for the creation of synthetic magnetic fields. They include rapidly rotating Bose-Einstein condensates employing the analogy between the Coriolis and the Lorentz force, and laser-atom interactions employing the analogy between the Berry phase and the Aharonov-Bohm phase. Interestingly, radiation pressure - being one of the most common forces induced by light - has not yet been used for synthetic magnetism. We experimentally demonstrate a synthetic Lorentz force, based on the radiation pressure and the Doppler effect, by observing the centre-of-mass motion of a cold atomic cloud. The force is perpendicular to the velocity of the cold atomic cloud, and zero for the cloud at rest. Our novel concept is straightforward to implement in a large volume, for a broad range of velocities, and can be extended to different geometries.

Note: Effect of the parasitic forced vibration in an atom gravimeter

NASA Astrophysics Data System (ADS)

Chen, Le-Le; Luo, Qin; Zhang, Heng; Duan, Xiao-Chun; Zhou, Min-Kang; Hu, Zhong-Kun

2018-06-01

The vibration isolator usually plays an important role in atom interferometry gravimeters to improve their sensitivity. We show that the parasitic forced vibration of the Raman mirror, which is induced by external forces acting on the vibration isolator, can cause a bias in atom gravimeters. The mechanism of how this effect induces an additional phase shift in our interferometer is analyzed. Moreover, modulation experiments are performed to measure the dominant part of this effect, which is caused by the magnetic force between the passive vibration isolator and the coil of the magneto-optic trap. In our current apparatus, this forced vibration contributes a systematic error of -2.3(2) × 10-7 m/s2 when the vibration isolator works in the passive isolation mode. Even suppressed with an active vibration isolator, this effect can still contribute -6(1) × 10-8 m/s2; thus, it should be carefully considered in precision atom gravimeters.

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

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

Visualizing the orientational dependence of an intermolecular potential

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip

2016-02-01

Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard-Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation.

Controlling Casimir force via coherent driving field

NASA Astrophysics Data System (ADS)

Ahmad, Rashid; Abbas, Muqaddar; Ahmad, Iftikhar; Qamar, Sajid

2016-04-01

A four level atom-field configuration is used to investigate the coherent control of Casimir force between two identical plates made up of chiral atomic media and separated by vacuum of width d. The electromagnetic chirality-induced negative refraction is obtained via atomic coherence. The behavior of Casimir force is investigated using Casimir-Lifshitz formula. It is noticed that Casimir force can be switched from repulsive to attractive and vice versa via coherent control of the driving field. This switching feature provides new possibilities of using the repulsive Casimir force in the development of new emerging technologies, such as, micro-electro-mechanical and nano-electro-mechanical systems, i.e., MEMS and NEMS, respectively.

Physicochemical characteristics of pristine and functionalized graphene.

PubMed

Bourdo, Shawn E; Al Faouri, Radwan; Sleezer, Robert; Nima, Zeid A; Lafont, Andersen; Chhetri, Bijay P; Benamara, Mourad; Martin, Betty; Salamo, Gregory J; Biris, Alexandru S

2017-11-01

Graphene-based nanomaterials have received significant attention in the last decade due to their interesting properties. Its electrical and thermal conductivity and strength make graphene well suited for a variety of applications, particularly for use as a composite material in plastics. Furthermore, much work is taking place to utilize graphene as a biomaterial for uses such as drug delivery and tissue regeneration scaffolds. Owing to the rapid progress of graphene and its potential in many marketplaces, the potential toxicity of these materials has garnered attention. Graphene, while simple in its purest form, can have many different chemical and physical properties. In this paper, we describe our toxicity evaluation of pristine graphene and a functionalized graphene sample that has been oxidized for enhanced hydrophilicity, which was synthesized from the pristine sample. The samples were characterized by X-ray photoelectron spectroscopy, Raman spectroscopy, infrared spectroscopy, thermogravimetric analysis, zeta-potential, atomic force microscopy and electron microscopy. We discuss the disagreement between the size of imaged samples analyzed by atomic force microscopy and by transmission electron microscopy. Furthermore, the samples each exhibit quite different surface chemistry and structure, which directly affects their interaction with aqueous environments and is important to consider when evaluating the toxicity of materials both in vitro and in vivo. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Structural mechanism of the ATP-induced dissociation of rigor myosin from actin

PubMed Central

Kühner, Sebastian; Fischer, Stefan

2011-01-01

Myosin is a true nanomachine, which produces mechanical force from ATP hydrolysis by cyclically interacting with actin filaments in a four-step cycle. The principle underlying each step is that structural changes in separate regions of the protein must be mechanically coupled. The step in which myosin dissociates from tightly bound actin (the rigor state) is triggered by the 30 Å distant binding of ATP. Large conformational differences between the crystal structures make it difficult to perceive the coupling mechanism. Energetically accessible transition pathways computed at atomic detail reveal a simple coupling mechanism for the reciprocal binding of ATP and actin. PMID:21518908

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

Attota, Ravikiran, E-mail: Ravikiran.attota@nist.gov; Dixson, Ronald G.

We experimentally demonstrate that the three-dimensional (3-D) shape variations of nanometer-scale objects can be resolved and measured with sub-nanometer scale sensitivity using conventional optical microscopes by analyzing 4-D optical data using the through-focus scanning optical microscopy (TSOM) method. These initial results show that TSOM-determined cross-sectional (3-D) shape differences of 30 nm–40 nm wide lines agree well with critical-dimension atomic force microscope measurements. The TSOM method showed a linewidth uncertainty of 1.22 nm (k = 2). Complex optical simulations are not needed for analysis using the TSOM method, making the process simple, economical, fast, and ideally suited for high volume nanomanufacturing process monitoring.

Surface enhanced Raman scattering of aged graphene: Effects of annealing in vacuum

NASA Astrophysics Data System (ADS)

Wang, Yingying; Ni, Zhenhua; Li, Aizhi; Zafar, Zainab; Zhang, Yan; Ni, Zhonghua; Qu, Shiliang; Qiu, Teng; Yu, Ting; Xiang Shen, Ze

2011-12-01

In this paper, we report a simple method to recover the surface enhanced Raman scattering activity of aged graphene. The Raman signals of Rhodamine molecules absorbed on aged graphene are dramatically increased after vacuum annealing and comparable to those on fresh graphene. Atomic force microscopy measurements indicate that residues on aged graphene surface can efficiently be removed by vacuum annealing, which makes target molecule closely contact with graphene. We also find that the hole doping in graphene will facilitate charge transfer between graphene and molecule. These results confirm the strong Raman enhancement of target molecule absorbed on graphene is due to the charge transfer mechanism.

Hydroxyethylated graphene oxide as potential carriers for methotrexate delivery

NASA Astrophysics Data System (ADS)

Du, Libo; Suo, Siqingaowa; Luo, Dan; Jia, Hongying; Sha, Yinlin; Liu, Yang

2013-06-01

In this study, we presented a simple approach to prepare hydroxyethylated graphene oxide (HE-GO) with high water solubility and physiological stability. The successful synthesis of HE-GO was confirmed by UV-Vis spectroscopy, Fourier transform infrared spectroscopy, and atomic force microscopy. The loading of anticancer drug methotrexate (MTX) onto this nanocarrier (MTX/HE-GO) was investigated. The results of in vitro drug release experiment showed that the rate of MTX release from MTX/HE-GO was pH dependent. Moreover, cell viability assay demonstrated that HE-GO loaded with MTX exhibits higher anticancer activity against human lung adenocarcinoma epithelial cell line than non-vehicle MTX.

The Analog Atomic Force Microscope: Measuring, Modeling, and Graphing for Middle School

ERIC Educational Resources Information Center

Goss, Valerie; Brandt, Sharon; Lieberman, Marya

2013-01-01

using an analog atomic force microscope (A-AFM) made from a cardboard box and mailing tubes. Varying numbers of ping pong balls inside the tubes mimic atoms on a surface. Students use a dowel to make macroscale measurements similar to those of a nanoscale AFM tip as it…

Connecting Fabric Families and Folk Art.

ERIC Educational Resources Information Center

Haussler-Mathews, Mary E.

2001-01-01

Discusses an art project in which students at the Quaker Farms School (Oxford, Connecticut) created a rag rug for the school bicentennial. Describes how the rag rug was created, stating that the students learned about their heritage in a cooperative way. (CMK)

Detection of cancerous cervical cells using physical adhesion of fluorescent silica particles and centripetal force.

PubMed

Gaikwad, Ravi M; Dokukin, Maxim E; Iyer, K Swaminathan; Woodworth, Craig D; Volkov, Dmytro O; Sokolov, Igor

2011-04-07

Here we describe a non-traditional method to identify cancerous human cervical epithelial cells in a culture dish based on physical adhesion between silica beads and cells. It is a simple optical fluorescence-based technique which detects the relative difference in the amount of fluorescent silica beads physically adherent to surfaces of cancerous and normal cervical cells. The method utilizes the centripetal force gradient that occurs in a rotating culture dish. Due to the variation in the balance between adhesion and centripetal forces, cancerous and normal cells demonstrate clearly distinctive distributions of the fluorescent particles adherent to the cell surface over the culture dish. The method demonstrates higher adhesion of silica particles to normal cells compared to cancerous cells. The difference in adhesion was initially observed by atomic force microscopy (AFM). The AFM data were used to design the parameters of the rotational dish experiment. The optical method that we describe is much faster and technically simpler than AFM. This work provides proof of the concept that physical interactions can be used to accurately discriminate normal and cancer cells. © The Royal Society of Chemistry 2011

Two-dimensional photon-counting detector arrays based on microchannel array plates

NASA Technical Reports Server (NTRS)

Timothy, J. G.; Bybee, R. L.

1975-01-01

The production of simple and rugged photon-counting detector arrays has been made possible by recent improvements in the performance of the microchannel array plate (MCP) and by the parallel development of compatible electronic readout systems. The construction of proximity-focused MCP arrays of novel design in which photometric information from (n x m) picture elements is read out with a total of (n + m) amplifier and discriminator circuits is described. Results obtained with a breadboard (32 x 32)-element array employing 64 charge-sensitive amplifiers are presented, and the application of systems of this type in spectrometers and cameras for use with ground-based telescopes and on orbiting spacecraft discussed.

Variable speed induction motor operation from a 20-kHz power bus

NASA Technical Reports Server (NTRS)

Hansen, Irving G.

1989-01-01

Induction motors are recognized for their simple rugged construction. To date, however, their application to variable speed or servo drives was hampered by limitations on their control. Induction motor drives tend to be complex and to display troublesome low speed characteristics due in part to nonsinusoidal driving voltages. A technique was developed which involves direct synthesis of sinusoidal driving voltages from a high frequency power bus and independent control of frequency and voltages. Separation of frequency and voltage allows independent control of rotor and stator flux, full four quadrant operation, and instantaneous torque control. Recent test results, current status of the technology, and proposed aerospace applications will be discussed.

Variable speed induction motor operation from a 20-kHz power bus

NASA Technical Reports Server (NTRS)

Hansen, Irving G.

1989-01-01

Induction motors are recognized for their simple rugged construction to date, however, their application to variable speed or servo drives has been hampered by limitations on their control. Induction motor drives tend to be complex and to display troublesome low speed characteristics due in part to nonsinusoidal driving voltages. A technique was developed which involves direct synthesis of sinusoidal driving voltages from a high frequency power bus and independent control of frequency and voltages. Separation offrequency and voltage allows independent control of rotor and stator flux, full four-quadrant operation, and instantaneous torque control. Recent test results, current status of the technology, and proposed aerospace applications will be discussed.

Optical design of low cost imaging systems for mobile medical applications

NASA Astrophysics Data System (ADS)

Kass, Alexander; Slyper, Ronit; Levitz, David

2015-03-01

Colposcopes, the gold standard devices for imaging the cervix at high magnfication, are expensive and sparse in low resource settings. Using a lens attachment, any smartphone camera can be turned into an imaging device for tissues such as the cervix. We create a smartphone-based colposcope using a simple lens design for high magnification. This particular design is useful because it allows parameters such as F-number, depth of field, and magnification to be controlled easily. We were therefore able to determine a set of design steps which are general to mobile medical imaging devices and allow them to maintain requisite image quality while still being rugged and affordable.

Low-Power Architecture for an Optical Life Gas Analyzer

NASA Technical Reports Server (NTRS)

Pilgrim, Jeffrey; Vakhtin, Andrei

2012-01-01

Analog and digital electronic control architecture has been combined with an operating methodology for an optical trace gas sensor platform that allows very low power consumption while providing four independent gas measurements in essentially real time, as well as a user interface and digital data storage and output. The implemented design eliminates the cross-talk between the measurement channels while maximizing the sensitivity, selectivity, and dynamic range for each measured gas. The combination provides for battery operation on a simple camcorder battery for as long as eight hours. The custom, compact, rugged, self-contained design specifically targets applications of optical major constituent and trace gas detection for multiple gases using multiple lasers and photodetectors in an integrated package.

Patient-reported quality indicators for osteoarthritis: a patient and public generated self-report measure for primary care.

PubMed

Blackburn, Steven; Higginbottom, Adele; Taylor, Robert; Bird, Jo; Østerås, Nina; Hagen, Kåre Birger; Edwards, John J; Jordan, Kelvin P; Jinks, Clare; Dziedzic, Krysia

2016-01-01

People with osteoarthritis desire high quality care, support and information. However, the quality of care for people with OA in general practice is not routinely collected. Quality Indicators can be used to benefit patients by measuring whether minimum standards of quality care are being met from a patient perspective. The aim of this study was to describe how a Research User Group (RUG) worked alongside researchers to co-produce a set of self-reported quality indicators for people with osteoarthritis when visiting their general practitioner or practice nurse (primary care). These were required in the MOSAICS study, which developed and evaluated a new model of supported self-management of OA to implement the NICE quality standards for OA. This article describes the public involvement in the MOSAICS study. This was 1) the co-development by RUG members and researchers of an Osteoarthritis Quality Indicators United Kingdom (OA QI (UK)) questionnaire for use in primary care, and 2) the comparison of the OA QI (UK) with a similar questionnaire developed in Norway. This study shows how important and effective a research user group can be in working with researchers in developing quality care indicators for osteoarthritis for use in a research study and, potentially, routine use in primary care. The questionnaire is intended to benefit patients by enabling the assessment of the quality of primary care for osteoarthritis from a patient's perspective. The OA QI (UK) has been used to examine differences in the quality of osteoarthritis care in four European countries. Background People with osteoarthritis (OA) desire high quality care, support and information about OA. However, the quality of care for people with OA in general practice is not routinely collected. Quality Indicators (QI) can be used to benefit patients by measuring whether minimum standards of quality care (e.g. NICE quality standards) are being met from a patient perspective. A Research User Group (RUG) worked with researchers to co-produce a set of self-report, patient-generated QIs for OA. The QIs were intended for use in the MOSAICS study, which developed and evaluated a new model of supported self-management of OA to implement the NICE guidelines. We report on 1) the co-development of the OA QI (UK) questionnaire for primary care; and 2) the comparison of the content of the OA QI (UK) questionnaire with a parallel questionnaire developed in Norway for the Musculoskeletal Pain in Ullensaker (MUST) study. Methods Researchers were invited to OA RUG meetings. Firstly, RUG members were asked to consider factors important to patients consulting their general practitioner (GP) for OA and then each person rated their five most important. RUG members then discussed these in relation to a systematic review of OA QIs in order to form a list of OA QIs from a patient perspective. RUG members suggested wording and response options for a draft OA QI (UK) questionnaire to assess the QIs. Finally RUG members commented on draft and final versions of the questionnaire and how it compared with a translated Norwegian OA-QI questionnaire. Results RUG members (5 males, 5 females; aged 52-80 years) attended up to four meetings. RUG members ranked 20 factors considered most important to patients consulting their GP for joint pain. Following discussion, a list of eleven patient-reported QIs for OA consultations were formed. RUG members then suggested the wording and response options of 16 draft items - four QIs were split into two or more questionnaire items to avoid multiple dimensions of care quality within a single item. On comparison of this to the Norwegian OA-QI questionnaire, RUG members commented that both questionnaires contained seven similar QIs. The RUG members and researchers agreed to adopt the Norwegian OA-QI wording for four of these items. RUG members also recommended adopting an additional seven items from the Norwegian OA-QI with some minor word changes to improve their suitability for patients in the UK. One other item from the draft OA QI (UK) questionnaire was retained and eight items were excluded, resulting in a 15-item final version. Conclusions This study describes the development of patient-reported quality indicators for OA primary care derived by members of a RUG group, working in partnership with the research team throughout the study. The OA QI (UK) supports the NICE quality standards for OA and they have been successfully used to assess the quality of OA consultations in primary care in the MOSAICS study. The OA QI (UK) has the potential for routine use in primary care to assess the quality of OA care provided to patients. Ongoing research using both the UK and Norwegian OA-QI questionnaires is assessing the self-reported quality of OA care in different European populations.

Characterization of Akiyama probe applied to dual-probes atomic force microscope

NASA Astrophysics Data System (ADS)

Wang, Hequn; Gao, Sitian; Li, Wei; Shi, Yushu; Li, Qi; Li, Shi; Zhu, Zhendong

2016-10-01

The measurement of nano-scale line-width has always been important and difficult in the field of nanometer measurements, while the rapid development of integrated circuit greatly raises the demand again. As one kind of scanning probe microscope (SPM), atomic force microscope (AFM) can realize quasi three-dimensional measurement, which is widely used in nanometer scale line-width measurement. Our team researched a dual-probes atomic force microscope, which can eliminate the prevalent effect of probe width on measurement results. In dual-probes AFM system, a novel head are newly designed. A kind of self-sensing and self-exciting probes which is Nanosensors cooperation's patented probe—Akiyama probe, is used in this novel head. The Akiyama probe applied to dual-probe atomic force microscope is one of the most important issues. The characterization of Akiyama probe would affect performance and accuracy of the whole system. The fundamental features of the Akiyama probe are electrically and optically characterized in "approach-withdraw" experiments. Further investigations include the frequency response of an Akiyama probe to small mechanical vibrations externally applied to the tip and the effective loading force yielding between the tip and the sample during the periodic contact. We hope that the characterization of the Akiyama probe described in this paper will guide application for dual-probe atomic force microscope.

Resonant difference-frequency atomic force ultrasonic microscope

NASA Technical Reports Server (NTRS)

Cantrell, John H. (Inventor); Cantrell, Sean A. (Inventor)

2010-01-01

A scanning probe microscope and methodology called resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), employs an ultrasonic wave launched from the bottom of a sample while the cantilever of an atomic force microscope, driven at a frequency differing from the ultrasonic frequency by one of the contact resonance frequencies of the cantilever, engages the sample top surface. The nonlinear mixing of the oscillating cantilever and the ultrasonic wave in the region defined by the cantilever tip-sample surface interaction force generates difference-frequency oscillations at the cantilever contact resonance. The resonance-enhanced difference-frequency signals are used to create images of nanoscale near-surface and subsurface features.

Nonlinear Dynamics of Cantilever-Sample Interactions in Atomic Force Microscopy

NASA Technical Reports Server (NTRS)

Cantrell, John H.; Cantrell, Sean A.

2010-01-01

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

Van der Waals forces in pNRQED

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

Shtabovenko, Vladyslav

2016-01-22

We report on the calculation of electromagnetic van der Waals forces [1] between two hydrogen atoms using non-relativistic effective field theories (EFTs) of QED for large and small momentum transfers with respect to the intrinsic energy scale of the hydrogen atom. Our results reproduce the well known London and Casimir-Polder forces.

Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

PubMed Central

2015-01-01

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations. PMID:25290376

Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

PubMed

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

2014-10-16

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations.

The Indeterminate Case of Classical Static Friction When Coupled with Tension

NASA Astrophysics Data System (ADS)

Hahn, Kenneth D.; Russell, Jacob M.

2018-02-01

It has been noted that the static friction force poses challenges for students and, at times, even their instructors. Unlike the gravitational force, which has a precise and unambiguous magnitude (FG = mg), the magnitude and direction of the static friction force depend on other forces at play. Friction can be understood rather well in terms of complicated atomic-scale interactions between surfaces. Ringlein and Robbins survey aspects of the atomic origins of friction, and Folkerts explores factors that affect the value of static friction. However, what students typically encounter in an introductory course ignores the atomic origins of friction (beyond perhaps a brief overview of the atomic model). The rules of dry friction (i.e., non-lubricated surfaces in contact) taught in introductory physics were originally published in 1699 by Guillaume Amontons. Amontons's first law states that the force of friction is directly proportional to the applied load, i.e., f = μFN, where FN is the normal force and μ is the coefficient of friction. His second law states that the force of friction is independent of the macroscopic area of contact. These laws were verified by Coulomb in 1781.

Self-assembled monolayers of alkyl-thiols on InAs: A Kelvin probe force microscopy study

NASA Astrophysics Data System (ADS)

Szwajca, A.; Wei, J.; Schukfeh, M. I.; Tornow, M.

2015-03-01

We report on the preparation and characterization of self-assembled monolayers from aliphatic thiols with different chain length and termination on InAs (100) planar surfaces. This included as first step the development and investigation of a thorough chemical InAs surface preparation step using a dedicated bromine/NH4OH-based etching process. Ellipsometry, contact angle measurements and atomic force microscopy (AFM) indicated the formation of smooth, surface conforming monolayers. The molecular tilt angles were obtained as 30 ± 10° with respect to the surface normal. Kelvin probe force microscopy (KPFM) measurements in hand with Parameterized Model number 5 (PM5) calculations of the involved molecular dipoles allowed for an estimation of the molecular packing densities on the surface. We obtained values of up to n = 1014 cm- 2 for the SAMs under study. These are close to what is predicted from a simple geometrical model that would calculate a maximum density of about n = 2.7 × 1014 cm- 2. We take this as additional conformation of the substrate smoothness and quality of our InAs-SAM hybrid layer systems.

Interactions of hyaluronan grafted on protein surfaces studied using a quartz crystal microbalance and a surface force balance.

PubMed

Jiang, Lei; Han, Juan; Yang, Limin; Ma, Hongchao; Huang, Bo

2015-10-07

Vocal folds are complex and multilayer-structured where the main layer is widely composed of hyaluronan (HA). The viscoelasticity of HA is key to voice production in the vocal fold as it affects the initiation and maintenance of phonation. In this study a simple layer-structured surface model was set up to mimic the structure of the vocal folds. The interactions between two opposing surfaces bearing HA were measured and characterised to analyse HA's response to the normal and shear compression at a stress level similar to that in the vocal fold. From the measurements of the quartz crystal microbalance, atomic force microscopy and the surface force balance, the osmotic pressure, normal interactions, elasticity change, volume fraction, refractive index and friction of both HA and the supporting protein layer were obtained. These findings may shed light on the physical mechanism of HA function in the vocal fold and the specific role of HA as an important component in the effective treatment of the vocal fold disease.

DNA combing on low-pressure oxygen plasma modified polysilsesquioxane substrates for single-molecule studies

PubMed Central

Sriram, K. K.; Chang, Chun-Ling; Rajesh Kumar, U.; Chou, Chia-Fu

2014-01-01

Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versatility of microfluidics regarding robustness, buffer exchange capability, and molecule manipulation using external forces for single molecule studies. Here, we demonstrate a simple one-step combing process involving only low-pressure oxygen (O2) plasma modified polysilsesquioxane (PSQ) polymer layer to facilitate both room temperature microfluidic device bonding and immobilization of stretched single DNA molecules without molecular functionalization step. Atomic force microscopy and Kelvin probe force microscopy experiments revealed a significant increase in surface roughness and surface potential on low-pressure O2 plasma treated PSQ, in contrast to that with high-pressure O2 plasma treatment, which are proposed to be responsible for enabling effective DNA immobilization. We further demonstrate the use of our platform to observe DNA-RNA polymerase complexes and cancer drug cisplatin induced DNA condensation using wide-field fluorescence imaging. PMID:25332730

X-ray Device Makes Scrubbing Rugs Clean a Spotless Effort

NASA Technical Reports Server (NTRS)

2006-01-01

If "pulling the rug out from under" means suddenly withdrawing support and assistance, then NASA is pretty good at "putting the rug under" when it comes to offering technical support and assistance to private industry. In the case of a new X-ray fluorescence (XRF) sensor featuring enhancements compliments of NASA, the Space Agency not only provided the rug, but helped give private industry a means to ensure it keeps clean. This sensor, utilized by NASA to read chemical bar codes concealed by paint and other coatings, perform on-the-spot chemical analyses in field conditions, and detect difficult-to-identify contaminants, has found another use as a tool that can measure how much soil is removed from household and commercial carpets. The original technology was developed in 2002 to conduct quality control for critical aluminum alloy parts destined for the space shuttle. Evaluation of these parts is critical for the Space Agency, as any signs of contamination, corrosion, or material deviation could compromise a shuttle mission.

Probing Long-Range Neutrino-Mediated Forces with Atomic and Nuclear Spectroscopy.

PubMed

Stadnik, Yevgeny V

2018-06-01

The exchange of a pair of low-mass neutrinos between electrons, protons, and neutrons produces a "long-range" 1/r^{5} potential, which can be sought for in phenomena originating on the atomic and subatomic length scales. We calculate the effects of neutrino-pair exchange on transition and binding energies in atoms and nuclei. In the case of atomic s-wave states, there is a large enhancement of the induced energy shifts due to the lack of a centrifugal barrier and the highly singular nature of the neutrino-mediated potential. We derive limits on neutrino-mediated forces from measurements of the deuteron binding energy and transition energies in positronium, muonium, hydrogen, and deuterium, as well as isotope-shift measurements in calcium ions. Our limits improve on existing constraints on neutrino-mediated forces from experiments that search for new macroscopic forces by 18 orders of magnitude. Future spectroscopy experiments have the potential to probe long-range forces mediated by the exchange of pairs of standard-model neutrinos and other weakly charged particles.

Probing Long-Range Neutrino-Mediated Forces with Atomic and Nuclear Spectroscopy

NASA Astrophysics Data System (ADS)

Stadnik, Yevgeny V.

2018-06-01

The exchange of a pair of low-mass neutrinos between electrons, protons, and neutrons produces a "long-range" 1 /r5 potential, which can be sought for in phenomena originating on the atomic and subatomic length scales. We calculate the effects of neutrino-pair exchange on transition and binding energies in atoms and nuclei. In the case of atomic s -wave states, there is a large enhancement of the induced energy shifts due to the lack of a centrifugal barrier and the highly singular nature of the neutrino-mediated potential. We derive limits on neutrino-mediated forces from measurements of the deuteron binding energy and transition energies in positronium, muonium, hydrogen, and deuterium, as well as isotope-shift measurements in calcium ions. Our limits improve on existing constraints on neutrino-mediated forces from experiments that search for new macroscopic forces by 18 orders of magnitude. Future spectroscopy experiments have the potential to probe long-range forces mediated by the exchange of pairs of standard-model neutrinos and other weakly charged particles.

Remarkable effect of halogenation of aromatic compounds on efficiency of nanowire formation through polymerization/crosslinking by high-energy single particle irradiation

NASA Astrophysics Data System (ADS)

Horio, Akifumi; Sakurai, Tsuneaki; Kayama, Kazuto; Lakshmi, G. B. V. S.; Kumar Avasthi, Devesh; Sugimoto, Masaki; Yamaki, Tetsuya; Chiba, Atsuya; Saito, Yuichi; Seki, Shu

2018-01-01

Irradiation of high-energy ion particles on organic films induced solid-state polymerization and crosslinking reactions of the materials along the ion trajectories, resulting in the formation of insoluble uniform nanowires with a precise diameter. The nanowires were isolated by the development process i.e. the irradiated film was immersed in organic solvents, and their morphology was visualized by atomic force microscopy. The target organic materials are 4-vinyltriphenylamine, poly(4-vinyltriphenylamine), and polystyrene derivatives with/without the partial substitutions by halogen atoms. It was found that 4-vinyltriphenylamines, in spite of their small molecular sizes, afforded nanowires more clearly than poly(4-vinyltriphenylamine)s. Moreover, the efficiency of demonstrated polymerization/crosslinking reactions obviously depends on the substituted halogen atom species. The averaged diameters of nanowires from bromo- or iodo- substituted 4-vinyltriphenylamine (9.3 and 9.4 nm, respectively) were larger than that obtained from simple 4-vinyltriphenylamine (6.8 nm). The remarkable effect of halogenation of aromatic compounds on the efficiency of the radiation-induced reactions was also observed for polystyrene derivatives. This contrast was considered to originate from the sum of the efficiency of elementary reactions including dissociative electron attachment.

Visualization of Electrostatic Dipoles in Molecular Dynamics of Metal Oxides.

PubMed

Grottel, S; Beck, P; Muller, C; Reina, G; Roth, J; Trebin, H-R; Ertl, T

2012-12-01

Metal oxides are important for many technical applications. For example alumina (aluminum oxide) is the most commonly-used ceramic in microelectronic devices thanks to its excellent properties. Experimental studies of these materials are increasingly supplemented with computer simulations. Molecular dynamics (MD) simulations can reproduce the material behavior very well and are now reaching time scales relevant for interesting processes like crack propagation. In this work we focus on the visualization of induced electric dipole moments on oxygen atoms in crack propagation simulations. The straightforward visualization using glyphs for the individual atoms, simple shapes like spheres or arrows, is insufficient for providing information about the data set as a whole. As our contribution we show for the first time that fractional anisotropy values computed from the local neighborhood of individual atoms of MD simulation data depict important information about relevant properties of the field of induced electric dipole moments. Iso surfaces in the field of fractional anisotropy as well as adjustments of the glyph representation allow the user to identify regions of correlated orientation. We present novel and relevant findings for the application domain resulting from these visualizations, like the influence of mechanical forces on the electrostatic properties.

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

Bonthuis, Douwe Jan, E-mail: douwe.bonthuis@physics.ox.ac.uk; Mamatkulov, Shavkat I.; Netz, Roland R.

We optimize force fields for H{sub 3}O{sup +} and OH{sup −} that reproduce the experimental solvation free energies and the activities of H{sub 3}O{sup +} Cl{sup −} and Na{sup +} OH{sup −} solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of the optimized H{sub 3}O{sup +} force field is 0.8 ± 0.1|e|—significantly higher than the value typically used for nonpolarizable water models and H{sub 3}O{sup +} force fields. In contrast,more » the optimal partial charge on the hydrogen atom of OH{sup −} turns out to be zero. Standard combination rules can be used for H{sub 3}O{sup +} Cl{sup −} solutions, while for Na{sup +} OH{sup −} solutions, we need to significantly increase the effective anion-cation Lennard-Jones radius. While highlighting the importance of intramolecular electrostatics, our results show that it is possible to generate thermodynamically consistent force fields without using atomic polarizability.« less

Manipulating Si(100) at 5 K using qPlus frequency modulated atomic force microscopy: Role of defects and dynamics in the mechanical switching of atoms

NASA Astrophysics Data System (ADS)

Sweetman, A.; Jarvis, S.; Danza, R.; Bamidele, J.; Kantorovich, L.; Moriarty, P.

2011-08-01

We use small-amplitude qPlus frequency modulated atomic force microscopy (FM-AFM), at 5 K, to investigate the atomic-scale mechanical stability of the Si(100) surface. By operating at zero applied bias the effect of tunneling electrons is eliminated, demonstrating that surface manipulation can be performed by solely mechanical means. Striking differences in surface response are observed between different regions of the surface, most likely due to variations in strain associated with the presence of surface defects. We investigate the variation in local energy surface by ab initio simulation, and comment on the dynamics observed during force spectroscopy.

Frequency modulation atomic force microscopy: a dynamic measurement technique for biological systems

NASA Astrophysics Data System (ADS)

Higgins, Michael J.; Riener, Christian K.; Uchihashi, Takayuki; Sader, John E.; McKendry, Rachel; Jarvis, Suzanne P.

2005-03-01

Frequency modulation atomic force microscopy (FM-AFM) has been modified to operate in a liquid environment within an atomic force microscope specifically designed for investigating biological samples. We demonstrate the applicability of FM-AFM to biological samples using the spectroscopy mode to measure the unbinding forces of a single receptor-ligand (biotin-avidin) interaction. We show that quantitative adhesion force measurements can only be obtained provided certain modifications are made to the existing theory, which is used to convert the detected frequency shifts to an interaction force. Quantitative force measurements revealed that the unbinding forces for the biotin-avidin interaction were greater than those reported in previous studies. This finding was due to the use of high average tip velocities, which were calculated to be two orders of magnitude greater than those typically used in unbinding receptor-ligand experiments. This study therefore highlights the potential use of FM-AFM to study a range of biological systems, including living cells and/or single biomolecule interactions.

Rugged Metropolis sampling with simultaneous updating of two dynamical variables

NASA Astrophysics Data System (ADS)

Berg, Bernd A.; Zhou, Huan-Xiang

2005-07-01

The rugged Metropolis (RM) algorithm is a biased updating scheme which aims at directly hitting the most likely configurations in a rugged free-energy landscape. Details of the one-variable (RM1) implementation of this algorithm are presented. This is followed by an extension to simultaneous updating of two dynamical variables (RM2) . In a test with the brain peptide Met-Enkephalin in vacuum RM2 improves conventional Metropolis simulations by a factor of about 4. Correlations between three or more dihedral angles appear to prevent larger improvements at low temperatures. We also investigate a multihit Metropolis scheme, which spends more CPU time on variables with large autocorrelation times.

High-resolution imaging of silicene on an Ag(111) surface by atomic force microscopy

NASA Astrophysics Data System (ADS)

Onoda, Jo; Yabuoshi, Keisuke; Miyazaki, Hiroki; Sugimoto, Yoshiaki

2017-12-01

Silicene, a two-dimensional (2D) honeycomb arrangement of Si atoms, is expected to have better electronic properties than graphene and has been mostly synthesized on Ag surfaces. Although scanning tunneling microscopy (STM) has been used for visualizing its atomic structure in real space, the interpretation of STM contrast is not straightforward and only the topmost Si atoms were observed on the (4 ×4 ) silicene/Ag(111) surface. Here, we demonstrate that high-resolution atomic force microscopy (AFM) can resolve all constituent Si atoms in the buckled honeycomb arrangement of the (4 ×4 ) silicene. Site-specific force spectroscopy attributes the origin of the high-resolution AFM images to chemical bonds between the AFM probe apex and the individual Si atoms on the (4 ×4 ) silicene. A detailed analysis of the geometric parameters suggests that the pulling up of lower-buckled Si atoms by the AFM tip could be a key for high-resolution AFM, implying a weakening of the Si-Ag interactions at the interface. We expect that high-resolution AFM will also unveil atomic structures of edges and defects of silicene, or other emerging 2D materials.

Manipulator Performance Evaluation Using Fitts' Taping Task

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

Draper, J.V.; Jared, B.C.; Noakes, M.W.

1999-04-25

Metaphorically, a teleoperator with master controllers projects the user's arms and hands into a re- mote area, Therefore, human users interact with teleoperators at a more fundamental level than they do with most human-machine systems. Instead of inputting decisions about how the system should func- tion, teleoperator users input the movements they might make if they were truly in the remote area and the remote machine must recreate their trajectories and impedance. This intense human-machine inter- action requires displays and controls more carefully attuned to human motor capabilities than is neces- sary with most systems. It is important for teleoperatedmore » manipulators to be able to recreate human trajectories and impedance in real time. One method for assessing manipulator performance is to observe how well a system be- haves while a human user completes human dexterity tasks with it. Fitts' tapping task has been, used many times in the past for this purpose. This report describes such a performance assessment. The International Submarine Engineering (ISE) Autonomous/Teleoperated Operations Manipulator (ATOM) servomanipulator system was evalu- ated using a generic positioning accuracy task. The task is a simple one but has the merits of (1) pro- ducing a performance function estimate rather than a point estimate and (2) being widely used in the past for human and servomanipulator dexterity tests. Results of testing using this task may, therefore, allow comparison with other manipulators, and is generically representative of a broad class of tasks. Results of the testing indicate that the ATOM manipulator is capable of performing the task. Force reflection had a negative impact on task efficiency in these data. This was most likely caused by the high resistance to movement the master controller exhibited with the force reflection engaged. Measurements of exerted forces were not made, so it is not possible to say whether the force reflection helped partici- pants control force during testing.« less

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

PubMed Central

Stark, Austin C.; Andrews, Casey T.

2013-01-01

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods – especially with regard to using them to model, for example, intracellular environments – is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields. PMID:24223529

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

PubMed

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

2013-09-10

Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.

Interplay between Mechanics, Electronics, and Energetics in Atomic-Scale Junctions

NASA Astrophysics Data System (ADS)

Aradhya, Sriharsha V.

The physical properties of materials at the nanoscale are controlled to a large extent by their interfaces. While much knowledge has been acquired about the properties of material in the bulk, there are many new and interesting phenomena at the interfaces that remain to be better understood. This is especially true at the scale of their constituent building blocks - atoms and molecules. Studying materials at this intricate level is a necessity at this point in time because electronic devices are rapidly approaching the limits of what was once thought possible, both in terms of their miniaturization as well as our ability to design their behavior. In this thesis I present our explorations of the interplay between mechanical properties, electronic transport and binding energetics of single atomic contacts and single-molecule junctions. Experimentally, we use a customized conducting atomic force microscope (AFM) that simultaneously measures the current and force across atomic-scale junctions. We use this instrument to study single atomic contacts of gold and silver and single-molecule junctions formed in the gap between two gold metallic point contacts, with molecules with a variety of backbones and chemical linker groups. Combined with density functional theory based simulations and analytical modeling, these experiments provide insight into the correlations between mechanics and electronic structure at the atomic level. In carrying out these experimental studies, we repeatedly form and pull apart nanoscale junctions between a metallized AFM cantilever tip and a metal-coated substrate. The force and conductance of the contact are simultaneously measured as each junction evolves through a series of atomic-scale rearrangements and bond rupture events, frequently resulting in single atomic contacts before rupturing completely. The AFM is particularly optimized to achieve high force resolution with stiff probes that are necessary to create and measure forces across atomic-size junctions that are otherwise difficult to fabricate using conventional lithographic techniques. In addition to the instrumentation, we have developed new algorithmic routines to perform statistical analyses of force data, with varying degrees of reliance on the conductance signatures. The key results presented in this thesis include our measurements with gold metallic contacts, through which we are able to rigorously characterize the stiffness and maximum forces sustained by gold single atomic contacts and many different gold-molecule-gold single-molecule junctions. In our experiments with silver metallic contacts we use statistical correlations in conductance to distinguish between pristine and oxygen-contaminated silver single atomic contacts. This allows us to separately obtain mechanical information for each of these structural motifs. The independently measured force data also provides new insights about atomic-scale junctions that are not possible to obtain through conductance measurements alone. Using a systematically designed set of molecules, we are able to demonstrate that quantum interference is not quenched in single-molecule junctions even at room temperature and ambient conditions. We have also been successful in conducting one of the first quantitative measurements of van der Waals forces at the metal-molecule interface at the single-molecule level. Finally, towards the end of this thesis, we present a general analytical framework to quantitatively reconstruct the binding energy curves of atomic-scale junctions directly from experiments, thereby unifying all of our mechanical measurements. I conclude with a summary of the work presented in this thesis, and an outlook for potential future studies that could be guided by this work.

Midinfrared absorption measured at a lambda/400 resolution with an atomic force microscope.

PubMed

Houel, Julien; Homeyer, Estelle; Sauvage, Sébastien; Boucaud, Philippe; Dazzi, Alexandre; Prazeres, Rui; Ortéga, Jean-Michel

2009-06-22

Midinfrared absorption can be locally measured using a detection combining an atomic force microscope and a pulsed excitation. This is illustrated for the midinfrared bulk GaAs phonon absorption and for the midinfrared absorption of thin SiO(2) microdisks. We show that the signal given by the cantilever oscillation amplitude of the atomic force microscope follows the spectral dependence of the bulk material absorption. The absorption spatial resolution achieved with microdisks is around 50 nanometer for an optical excitation around 22 micrometer wavelength.

The P-factor and atomic mass systematics: Application to medium mass nuclei

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

Brenner, D.S.; Haustein, P.E.; Casten, R.F.

1988-01-01

The P formalism was applied to atomic mass systematics for medium and heavy nuclei. The P-factor linearizes the structure-dependent part of the nuclear mass in those regions which are free from subshell effects indicating that the attractive quadrupole p-n force plays an important role in determining the binding of valence nucleons. Where marked non-linearities occur, the P-factor provides a means for recognizing subshell closures and/or other structural features not embodied in the simple assumptions of abrupt shell or subshell changes. These are thought to be regions where the monopole part of the p-n interaction is highly orbit dependent and altersmore » the underlying single-particle structure as a function of A, N or Z. Finally, in those regions where the systematics are smooth and subshells are absent, the P-factor provides a means for predicting masses of some nuclei far-from-stability by interpolation rather than by extrapolation. 5 figs.« less

A simple structural hydrazide-based gelator as a fluoride ion colorimetric sensor.

PubMed

Bai, Binglian; Ma, Jie; Wei, Jue; Song, Jianxi; Wang, Haitao; Li, Min

2014-06-07

A 4-nitrobenzohydrazide derivative, N-(3,4,5-octyloxybenzoyl)-N'-(4'-nitrobenzoyl)hydrazine (C8), was synthesized. It could form stable gels in some of the tested organic solvents. The wide-angle X-ray diffraction analysis showed that the xerogels exhibited a layered structure. SEM images revealed that the molecules self-assembled into fibrous aggregates in the xerogels. FT-IR studies confirmed that the intermolecular hydrogen bonding between C=O and N-H groups was the major driving force for the formation of self-assembling gel processes. The gel is utilized for a 'naked eye' detection of fluoride ions, through a reversible gel-sol transition, which is associated with a color change from colorless to red. An extended conjugated system formed through the phenyl group and a five-membered ring based on intramolecular hydrogen bonding between the oxygen atom near the deprotonation nitrogen atom and the other NH, which is responsible for the dramatic color change upon addition of fluoride ions.

Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model.

PubMed

Pulawski, Wojciech; Jamroz, Michal; Kolinski, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2016-11-28

The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics, and interactions). Here we introduce an extension of the CABS representation and force field (CABS-membrane) to the modeling of the effect of the biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane. In the resulting trajectories, we have found models close to the experimental membrane structures. We also attempted to select the correctly folded models using simple filtering followed by structural clustering combined with reconstruction to the all-atom representation and all-atom scoring. The CABS-membrane model is a promising approach for further development toward modeling of large protein-membrane systems.

GaAs MOEMS Technology

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

SPAHN, OLGA B.; GROSSETETE, GRANT D.; CICH, MICHAEL J.

2003-03-01

Many MEMS-based components require optical monitoring techniques using optoelectronic devices for converting mechanical position information into useful electronic signals. While the constituent piece-parts of such hybrid opto-MEMS components can be separately optimized, the resulting component performance, size, ruggedness and cost are substantially compromised due to assembly and packaging limitations. GaAs MOEMS offers the possibility of monolithically integrating high-performance optoelectronics with simple mechanical structures built in very low-stress epitaxial layers with a resulting component performance determined only by GaAs microfabrication technology limitations. GaAs MOEMS implicitly integrates the capability for radiation-hardened optical communications into the MEMS sensor or actuator component, a vitalmore » step towards rugged integrated autonomous microsystems that sense, act, and communicate. This project establishes a new foundational technology that monolithically combines GaAs optoelectronics with simple mechanics. Critical process issues addressed include selectivity, electrochemical characteristics, and anisotropy of the release chemistry, and post-release drying and coating processes. Several types of devices incorporating this novel technology are demonstrated.« less

Control and Analysis for a Self-Excited Induction Generator for Wind Turbine and Electrolyzer Applications

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

Muljadi, Eduard; Na, Woonki; Leighty, Bill

Self-Excited Induction Generation(SEIG) is very rugged, simple, lightweight, and it is easy and inexpensive to implement, very simple to control, and requires a very little maintenance. In this variable-speed operation, the SEIG needs a power electronics interface to convert from the variable frequency output voltage of the generator to a DC output voltage for battery or other DC applications. In our study, a SEIG is connected to the power electronics interface such as diode rectifier and DC/DC converter and then an electrolyzer is connected as a final DC load for fuel cell applications. An equivalent circuit model for an electrolyzermore » is utilized for our application. The control and analysis for the proposed system is carried out by using PSCAD and MATLAB software. This study would be useful for designing and control analysis of power interface circuits for SEIG for a variable speed wind turbine generation with fuel cell applications before the actual implementation.« less

Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations.

PubMed

Buslaev, Pavel; Gordeliy, Valentin; Grudinin, Sergei; Gushchin, Ivan

2016-03-08

Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14, and Slipids and united-atom Berger, GROMOS43A1-S3, and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the time scales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers.

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

PubMed Central

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

2012-01-01

The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS), it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of AFS, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution. PMID:23202925

Performing the Millikan experiment at the molecular scale: Determination of atomic Millikan-Thomson charges by computationally measuring atomic forces.

PubMed

Rogers, T Ryan; Wang, Feng

2017-10-28

An atomic version of the Millikan oil drop experiment is performed computationally. It is shown that for planar molecules, the atomic version of the Millikan experiment can be used to define an atomic partial charge that is free from charge flow contributions. We refer to this charge as the Millikan-Thomson (MT) charge. Since the MT charge is directly proportional to the atomic forces under a uniform electric field, it is the most relevant charge for force field developments. The MT charge shows good stability with respect to different choices of the basis set. In addition, the MT charge can be easily calculated even at post-Hartree-Fock levels of theory. With the MT charge, it is shown that for a planar water dimer, the charge transfer from the proton acceptor to the proton donor is about -0.052 e. While both planar hydrated cations and anions show signs of charge transfer, anions show a much more significant charge transfer to the hydration water than the corresponding cations. It might be important to explicitly model the ion charge transfer to water in a force field at least for the anions.

Energy shift and Casimir-Polder force for an atom out of thermal equilibrium near a dielectric substrate

NASA Astrophysics Data System (ADS)

Zhou, Wenting; Yu, Hongwei

2014-09-01

We study the energy shift and the Casimir-Polder force of an atom out of thermal equilibrium near the surface of a dielectric substrate. We first generalize, adopting the local source hypothesis, the formalism proposed by Dalibard, Dupont-Roc, and Cohen-Tannoudji [J. Phys. (Paris) 43, 1617 (1982), 10.1051/jphys:0198200430110161700; J. Phys. (Paris) 45, 637 (1984), 10.1051/jphys:01984004504063700], which separates the contributions of thermal fluctuations and radiation reaction to the energy shift and allows a distinct treatment of atoms in the ground and excited states, to the case out of thermal equilibrium, and then we use the generalized formalism to calculate the energy shift and the Casimir-Polder force of an isotropically polarizable neutral atom. We identify the effects of the thermal fluctuations that originate from the substrate and the environment and discuss in detail how the Casimir-Polder force out of thermal equilibrium behaves in three different distance regions in both the low-temperature limit and the high-temperature limit for both the ground-state and excited-state atoms, with special attention devoted to the distinctive features as opposed to thermal equilibrium. In particular, we recover the distinctive behavior of the atom-wall force out of thermal equilibrium at large distances in the low-temperature limit recently found in a different theoretical framework, and furthermore we give a concrete region where this behavior holds.

A classical mechanics model for the interpretation of piezoelectric property data

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

Bell, Andrew J., E-mail: a.j.bell@leeds.ac.uk

2015-12-14

In order to provide a means of understanding, the relationship between the primary electromechanical coefficients and simple crystal chemistry parameters for piezoelectric materials, a static analysis of a 3 atom, dipolar molecule has been undertaken to derive relationships for elastic compliance s{sup E}, dielectric permittivity ε{sup X}, and piezoelectric charge coefficient d in terms of an effective ionic charge and two inter-atomic force constants. The relationships demonstrate the mutual interdependence of the three coefficients, in keeping with experimental evidence from a large dataset of commercial piezoelectric materials. It is shown that the electromechanical coupling coefficient k is purely an expressionmore » of the asymmetry in the two force constants or bond compliances. The treatment is extended to show that the quadratic electrostriction relation between strain and polarization, in both centrosymmetric and non-centrosymmetric systems, is due to the presence of a non-zero 2nd order term in the bond compliance. Comparison with experimental data explains the counter-intuitive, positive correlation of k with s{sup E} and ε{sup X} and supports the proposition that high piezoelectric activity in single crystals is dominated by large compliance coupled with asymmetry in the sub-cell force constants. However, the analysis also shows that in polycrystalline materials, the dielectric anisotropy of the constituent crystals can be more important for attaining large charge coefficients. The model provides a completely new methodology for the interpretation of piezoelectric and electrostrictive property data and suggests methods for rapid screening for high activity in candidate piezoelectric materials, both experimentally and by novel interrogation of ab initio calculations.« less

Measuring Roughnesses Of Optical Surfaces

NASA Technical Reports Server (NTRS)

Coulter, Daniel R.; Al-Jumaily, Gahnim A.; Raouf, Nasrat A.; Anderson, Mark S.

1994-01-01

Report discusses use of scanning tunneling microscopy and atomic force microscopy to measure roughnesses of optical surfaces. These techniques offer greater spatial resolution than other techniques. Report notes scanning tunneling microscopes and atomic force microscopes resolve down to 1 nm.

Chemical bond imaging using higher eigenmodes of tuning fork sensors in atomic force microscopy

NASA Astrophysics Data System (ADS)

Ebeling, Daniel; Zhong, Qigang; Ahles, Sebastian; Chi, Lifeng; Wegner, Hermann A.; Schirmeisen, André

2017-05-01

We demonstrate the ability of resolving the chemical structure of single organic molecules using non-contact atomic force microscopy with higher normal eigenmodes of quartz tuning fork sensors. In order to achieve submolecular resolution, CO-functionalized tips at low temperatures are used. The tuning fork sensors are operated in ultrahigh vacuum in the frequency modulation mode by exciting either their first or second eigenmode. Despite the high effective spring constant of the second eigenmode (on the order of several tens of kN/m), the force sensitivity is sufficiently high to achieve atomic resolution above the organic molecules. This is observed for two different tuning fork sensors with different tip geometries (small tip vs. large tip). These results represent an important step towards resolving the chemical structure of single molecules with multifrequency atomic force microscopy techniques where two or more eigenmodes are driven simultaneously.

A review of demodulation techniques for amplitude-modulation atomic force microscopy

PubMed Central

Harcombe, David M; Ragazzon, Michael R P; Moheimani, S O Reza; Fleming, Andrew J

2017-01-01

In this review paper, traditional and novel demodulation methods applicable to amplitude-modulation atomic force microscopy are implemented on a widely used digital processing system. As a crucial bandwidth-limiting component in the z-axis feedback loop of an atomic force microscope, the purpose of the demodulator is to obtain estimates of amplitude and phase of the cantilever deflection signal in the presence of sensor noise or additional distinct frequency components. Specifically for modern multifrequency techniques, where higher harmonic and/or higher eigenmode contributions are present in the oscillation signal, the fidelity of the estimates obtained from some demodulation techniques is not guaranteed. To enable a rigorous comparison, the performance metrics tracking bandwidth, implementation complexity and sensitivity to other frequency components are experimentally evaluated for each method. Finally, the significance of an adequate demodulator bandwidth is highlighted during high-speed tapping-mode atomic force microscopy experiments in constant-height mode. PMID:28900596

The deflection of carbon composite carbon nanotube / graphene using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Kolesnikova, A. S.; Kirillova, I. V.; Kossovich, L. U.

2018-02-01

For the first time, the dependence of the bending force on the transverse displacement of atoms in the center of the composite material consisting of graphene and parallel oriented zigzag nanotubes was studied. Mathematical modeling of the action of the needle of the atomic force microscope was carried out using the single-layer armchair carbon nanotube. Armchair nanotubes are convenient for using them as a needle of an atomic force microscope, because their edges are not sharpened (unlike zigzag tubes). Consequently, armchair nanotubes will cause minimal damage upon contact with the investigation object. The geometric parameters of the composite was revealed under the action of the bending force of 6μN.

Toggling Bistable Atoms via Mechanical Switching of Bond Angle

NASA Astrophysics Data System (ADS)

Sweetman, Adam; Jarvis, Sam; Danza, Rosanna; Bamidele, Joseph; Gangopadhyay, Subhashis; Shaw, Gordon A.; Kantorovich, Lev; Moriarty, Philip

2011-04-01

We reversibly switch the state of a bistable atom by direct mechanical manipulation of bond angle using a dynamic force microscope. Individual buckled dimers at the Si(100) surface are flipped via the formation of a single covalent bond, actuating the smallest conceivable in-plane toggle switch (two atoms) via chemical force alone. The response of a given dimer to a flip event depends critically on both the local and nonlocal environment of the target atom—an important consideration for future atomic scale fabrication strategies.

Noncontact atomic force microscopy in liquid environment with quartz tuning fork and carbon nanotube probe

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Jensenius, Henriette; Dienwiebel, Martin; Nakayama, Yoshikazu; Tokumoto, Hiroshi; Jarvis, Suzanne P.; Oosterkamp, Tjerk H.

2002-03-01

A force sensor for noncontact atomic force microscopy in liquid environment was developed by combining a multiwalled carbon nanotube (MWNT) probe with a quartz tuning fork. Solvation shells of octamethylcyclotetrasiloxane on a graphite surface were detected both in the frequency shift and dissipation. Due to the high aspect ratio of the CNT probe, the long-range background force was barely detectable in the solvation region.

Rugged, portable tungsten coil atomic emission spectrometer.

PubMed

Gu, Jiyan; Oliveira, Silvana R; Donati, George L; Gomes Neto, José Anchieta; Jones, Bradley T

2011-04-01

Tungsten coil atomic emission spectrometry is an ideal technique for field applications because of its simplicity, low cost, low power requirement, and independence from cooling systems. A new, portable, compact design is reported here. The tungsten coil is extracted from an inexpensive 24 V, 250 W commercial light bulb. The coil is housed in a small, aluminum cell. The emission signal exits from a small aperture in the cell, while the bulk of the blackbody emission from the tungsten coil is blocked. The resulting spectra exhibit extremely low background signals. The atomization cell, a single lens, and a hand-held charge coupled device (CCD) spectrometer are fixed on a 1 × 6 × 30 cm ceramic base. The resulting system is robust and easily transported. A programmable, miniature 400 W solid-state constant current power supply controls the temperature of the coil. Fifteen elements are determined with the system (Ba, Cs, Li, Rb, Cr, Sr, Eu, Yb, Mn, Fe, Cu, Mg, V, Al, and Ga). The precision ranges from 4.3% to 8.4% relative standard deviation for repetitive measurements of the same solution. Detection limits are in the 0.04 to 1500 μg/L range. Accuracy is tested using standard reference materials for polluted water, peach leaves, and tomato leaves. For those elements present above the detection limit, recoveries range from 72% to 147%.

A compact, rugged, high repetition rate CO2 laser incorporating catalyst

NASA Technical Reports Server (NTRS)

Schwarzenberger, P. M.; Matzangou, X.

1990-01-01

The principal design features and operating characteristics of a high repetition rate CO2 laser are outlined. The laser is a compact, rugged unit, completely sealed and incorporating an unheated solid catalyst. Stable operation has been successfully demonstrated over a temperature range of -35 C to 65 C.

Electronegativity determination of individual surface atoms by atomic force microscopy.

PubMed

Onoda, Jo; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

2017-04-26

Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Pauling's equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale.

Electronegativity determination of individual surface atoms by atomic force microscopy

PubMed Central

Onoda, Jo; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

2017-01-01

Electronegativity is a fundamental concept in chemistry. Despite its importance, the experimental determination has been limited only to ensemble-averaged techniques. Here, we report a methodology to evaluate the electronegativity of individual surface atoms by atomic force microscopy. By measuring bond energies on the surface atoms using different tips, we find characteristic linear relations between the bond energies of different chemical species. We show that the linear relation can be rationalized by Pauling's equation for polar covalent bonds. This opens the possibility to characterize the electronegativity of individual surface atoms. Moreover, we demonstrate that the method is sensitive to variation of the electronegativity of given atomic species on a surface due to different chemical environments. Our findings open up ways of analysing surface chemical reactivity at the atomic scale. PMID:28443645

A Novel Method to Reconstruct the Force Curve by Higher Harmonics of the First Two Flexural Modes in Frequency Modulation Atomic Force Microscope (FM-AFM).

PubMed

Zhang, Suoxin; Qian, Jianqiang; Li, Yingzi; Zhang, Yingxu; Wang, Zhenyu

2018-06-04

Atomic force microscope (AFM) is an idealized tool to measure the physical and chemical properties of the sample surfaces by reconstructing the force curve, which is of great significance to materials science, biology, and medicine science. Frequency modulation atomic force microscope (FM-AFM) collects the frequency shift as feedback thus having high force sensitivity and it accomplishes a true noncontact mode, which means great potential in biological sample detection field. However, it is a challenge to establish the relationship between the cantilever properties observed in practice and the tip-sample interaction theoretically. Moreover, there is no existing method to reconstruct the force curve in FM-AFM combining the higher harmonics and the higher flexural modes. This paper proposes a novel method that a full force curve can be reconstructed by any order higher harmonics of the first two flexural modes under any vibration amplitude in FM-AFM. Moreover, in the small amplitude regime, short range forces are reconstructed more accurately by higher harmonics analysis compared with fundamental harmonics using the Sader-Jarvis formula.

A Simple Relativistic Bohr Atom

ERIC Educational Resources Information Center

Terzis, Andreas F.

2008-01-01

A simple concise relativistic modification of the standard Bohr model for hydrogen-like atoms with circular orbits is presented. As the derivation requires basic knowledge of classical and relativistic mechanics, it can be taught in standard courses in modern physics and introductory quantum mechanics. In addition, it can be shown in a class that…

Innovative technology summary report: Houdini{trademark} I and II remotely operated vehicle

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

NONE

1998-07-01

The US Department of Energy (DOE) is responsible for cleaning up and closing 273 large, aging, underground tanks the department has used for storing approximately 1 million gal of high- and low-level radioactive and mixed waste. The waste`s radioactivity precludes humans from working in the tanks. A remote-controlled retrieval method must be used. The Houdini robot addresses the need for vehicle-based, rugged, remote manipulation systems that can perform waste retrieval, characterization, and inspection tasks. Houdini-I was delivered to ORNL in September 1996, deployed in a cold test facility in November, and first deployed in the gunite tanks in June 1997.more » Since then, it has seen continuous (still on-going) service at ORNL, providing a critical role in the cleanup of two gunite tanks, W-3 and W-4, in the GAAT NTF. Houdini-I has proven rugged, capable of waste retrieval, and able to withstand high reaction force operations such as wall core sampling. It`s even able to operate while hanging, which was the case when Houdini was used to cut and remove cables and steel pipes hanging below manways in Tank W-3. Based upon the lessons learned at ORNL, Houdini`s design has been completely overhauled. A second generation system, Houdini-II, is now being built.« less

Atomic scale study of nanocontacts

NASA Astrophysics Data System (ADS)

Buldum, A.; Ciraci, S.; Batra, Inder P.; Fong, C. Y.

1998-03-01

Nanocontact and subsequent pulling off a sharp Ni(111) tip on a Cu(110) surface are investigated by using molecular dynamics method with embedded atom model. As the contact is formed, the sharp tip experiences multiple jump to contact in the attractive force range. The contact interface develops discontinuously mainly due to disorder-order transformations which lead to disappearance of a layer and hence abrupt changes in the normal force variation. Atom exchange occurs in the repulsive range. The connective neck is reduced also discontinuously by pulling off the tip. The novel atomic structure of the neck under the tensile force is analyzed. We also presented a comperative study for the contact by a Si(111) tip on Si(111)-(2x1) surface.

Minor Corrections to Physics for Optimizing Homeland Security by Our Pal Asija

NASA Astrophysics Data System (ADS)

Asija, Pal

2008-04-01

To optimize Homeland security it must be based on correct physics. There is But ONE Reality of Physics and finding that rugged reality requires identifying and expunging erroneous knowledge. Six examples are included. *Lighter Bodies Travel Faster. (Aristotle got it backwards) *Faster Objects Become Lighter. (Einstein got it backwards) *Two Minor Corrections to Newton's First Law of Motion. *Three D or No D (Any theory based on other than 3 D is fantastic) *Gravity is A Local and Physical Contact Force *Light is never Waves and Photons at the Same Instant. These corrections are then further delineated by several examples for leading and driving innovations in homeland security.

CVD synthesis of large-area, highly crystalline MoSe2 atomic layers on diverse substrates and application to photodetectors.

PubMed

Xia, Jing; Huang, Xing; Liu, Ling-Zhi; Wang, Meng; Wang, Lei; Huang, Ben; Zhu, Dan-Dan; Li, Jun-Jie; Gu, Chang-Zhi; Meng, Xiang-Min

2014-08-07

Synthesis of large-area, atomically thin transition metal dichalcogenides (TMDs) on diverse substrates is of central importance for the large-scale fabrication of flexible devices and heterojunction-based devices. In this work, we successfully synthesized a large area of highly-crystalline MoSe2 atomic layers on SiO2/Si, mica and Si substrates using a simple chemical vapour deposition (CVD) method at atmospheric pressure. Atomic force microscopy (AFM) and Raman spectroscopy reveal that the as-grown ultrathin MoSe2 layers change from a single layer to a few layers. Photoluminescence (PL) spectroscopy demonstrates that while the multi-layer MoSe2 shows weak emission peaks, the monolayer has a much stronger emission peak at ∼ 1.56 eV, indicating the transition from an indirect to a direct bandgap. Transmission electron microscopy (TEM) analysis confirms the single-crystallinity of MoSe2 layers with a hexagonal structure. In addition, the photoresponse performance of photodetectors based on MoSe2 monolayer was studied for the first time. The devices exhibit a rapid response of ∼ 60 ms and a good photoresponsivity of ∼ 13 mA/W (using a 532 nm laser at an intensity of 1 mW mm(-2) and a bias of 10 V), suggesting that MoSe2 monolayer is a promising material for photodetection applications.

Dynamics-Enabled Nanoelectromechanical Systems (NEMS) Oscillators

DTIC Science & Technology

2014-06-01

it becomes strongly nonlinear, and thus constitutes an archetypal candidate for nonlinear engineering • its fundamental resonant frequency...width of spectral peaks of atomic force microscopy (AFM) resonators as they are brought close to a surface. 39 Approved for public release...alternating current AD Allan Deviation AFM atomic force microscopy AFRL Air Force Research Laboratory AlN aluminum nitride APN Anomalous Phase

Fabrication of electron beam deposited tip for atomic-scale atomic force microscopy in liquid.

PubMed

Miyazawa, K; Izumi, H; Watanabe-Nakayama, T; Asakawa, H; Fukuma, T

2015-03-13

Recently, possibilities of improving operation speed and force sensitivity in atomic-scale atomic force microscopy (AFM) in liquid using a small cantilever with an electron beam deposited (EBD) tip have been intensively explored. However, the structure and properties of an EBD tip suitable for such an application have not been well-understood and hence its fabrication process has not been established. In this study, we perform atomic-scale AFM measurements with a small cantilever and clarify two major problems: contaminations from a cantilever and tip surface, and insufficient mechanical strength of an EBD tip having a high aspect ratio. To solve these problems, here we propose a fabrication process of an EBD tip, where we attach a 2 μm silica bead at the cantilever end and fabricate a 500-700 nm EBD tip on the bead. The bead height ensures sufficient cantilever-sample distance and enables to suppress long-range interaction between them even with a short EBD tip having high mechanical strength. After the tip fabrication, we coat the whole cantilever and tip surface with Si (30 nm) to prevent the generation of contamination. We perform atomic-scale AFM imaging and hydration force measurements at a mica-water interface using the fabricated tip and demonstrate its applicability to such an atomic-scale application. With a repeated use of the proposed process, we can reuse a small cantilever for atomic-scale measurements for several times. Therefore, the proposed method solves the two major problems and enables the practical use of a small cantilever in atomic-scale studies on various solid-liquid interfacial phenomena.

Tungsten devices in analytical atomic spectrometry

NASA Astrophysics Data System (ADS)

Hou, Xiandeng; Jones, Bradley T.

2002-04-01

Tungsten devices have been employed in analytical atomic spectrometry for approximately 30 years. Most of these atomizers can be electrically heated up to 3000 °C at very high heating rates, with a simple power supply. Usually, a tungsten device is employed in one of two modes: as an electrothermal atomizer with which the sample vapor is probed directly, or as an electrothermal vaporizer, which produces a sample aerosol that is then carried to a separate atomizer for analysis. Tungsten devices may take various physical shapes: tubes, cups, boats, ribbons, wires, filaments, coils and loops. Most of these orientations have been applied to many analytical techniques, such as atomic absorption spectrometry, atomic emission spectrometry, atomic fluorescence spectrometry, laser excited atomic fluorescence spectrometry, metastable transfer emission spectroscopy, inductively coupled plasma optical emission spectrometry, inductively coupled plasma mass spectrometry and microwave plasma atomic spectrometry. The analytical figures of merit and the practical applications reported for these techniques are reviewed. Atomization mechanisms reported for tungsten atomizers are also briefly summarized. In addition, less common applications of tungsten devices are discussed, including analyte preconcentration by adsorption or electrodeposition and electrothermal separation of analytes prior to analysis. Tungsten atomization devices continue to provide simple, versatile alternatives for analytical atomic spectrometry.

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

PubMed Central

Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

PubMed

Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

Single ricin detection by atomic force microscopy chemomechanical mapping

NASA Astrophysics Data System (ADS)

Chen, Guojun; Zhou, Jianfeng; Park, Bosoon; Xu, Bingqian

2009-07-01

The authors report on a study of detecting ricin molecules immobilized on chemically modified Au (111) surface by chemomechanically mapping the molecular interactions with a chemically modified atomic force microscopy (AFM) tip. AFM images resolved the different fold-up conformations of single ricin molecule as well as their intramolecule structure of A- and B-chains. AFM force spectroscopy study of the interaction indicates that the unbinding force has a linear relation with the logarithmic force loading rate, which agrees well with calculations using one-barrier bond dissociation model.

Simple, reliable, and nondestructive method for the measurement of vacuum pressure without specialized equipment.

PubMed

Yuan, Jin-Peng; Ji, Zhong-Hua; Zhao, Yan-Ting; Chang, Xue-Fang; Xiao, Lian-Tuan; Jia, Suo-Tang

2013-09-01

We present a simple, reliable, and nondestructive method for the measurement of vacuum pressure in a magneto-optical trap. The vacuum pressure is verified to be proportional to the collision rate constant between cold atoms and the background gas with a coefficient k, which can be calculated by means of the simple ideal gas law. The rate constant for loss due to collisions with all background gases can be derived from the total collision loss rate by a series of loading curves of cold atoms under different trapping laser intensities. The presented method is also applicable for other cold atomic systems and meets the miniaturization requirement of commercial applications.

Vibrational properties of TaW alloy using modified embedded atom method potential

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

Chand, Manesh, E-mail: maneshchand@gmail.com; Uniyal, Shweta; Joshi, Subodh

2016-05-06

Force-constants up to second neighbours of pure transition metal Ta and TaW alloy are determined using the modified embedded atom method (MEAM) potential. The obtained force-constants are used to calculate the phonon dispersion of pure Ta and TaW alloy. As a further application of MEAM potential, the force-constants are used to calculate the local vibrational density of states and mean square thermal displacements of pure Ta and W impurity atoms with Green’s function method. The calculated results are found to be in agreement with the experimental measurements.

Combined Atomic Force Microscope-Based Topographical Imaging and Nanometer Scale Resolved Proximal Probe Thermal Desorption/Electrospray Ionization-Mass Spectrometry

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

Ovchinnikova, Olga S; Nikiforov, Maxim; Bradshaw, James A

2011-01-01

Nanometer scale proximal probe thermal desorption/electrospray ionization mass spectrometry (TD/ESI-MS) was demonstrated for molecular surface sampling of caffeine from a thin film using a 30 nm diameter nano-thermal analysis (nano-TA) probe tip in an atomic force microscope (AFM) coupled via a vapor transfer line and ESI interface to a MS detection platform. Using a probe temperature of 350 C and a spot sampling time of 30 s, conical desorption craters 250 nm in diameter and 100 nm deep were created as shown through subsequent topographical imaging of the surface within the same system. Automated sampling of a 5 x 2more » array of spots, with 2 m spacing between spots, and real time selective detection of the desorbed caffeine using tandem mass spectrometry was also demonstrated. Estimated from the crater volume (~2x106 nm3), only about 10 amol (2 fg) of caffeine was liberated from each thermal desorption crater in the thin film. These results illustrate a relatively simple experimental setup and means to acquire in automated fashion sub-micrometer scale spatial sampling resolution and mass spectral detection of materials amenable to TD. The ability to achieve MS-based chemical imaging with 250 nm scale spatial resolution with this system is anticipated.« less

Controlled manipulation of flexible carbon nanotubes through shape-dependent pushing by atomic force microscopy.

PubMed

Yang, Seung-Cheol; Qian, Xiaoping

2013-09-17

A systematic approach to manipulating flexible carbon nanotubes (CNTs) has been developed on the basis of atomic force microscope (AFM) based pushing. Pushing CNTs enables efficient transport and precise location of individual CNTs. A key issue for pushing CNTs is preventing defective distortion in repetitive bending and unbending deformation. The approach presented here controls lateral movement of an AFM tip to bend CNTs without permanent distortion. The approach investigates possible defects caused by tensile strain of the outer tube under uniform bending and radial distortion by kinking. Using the continuum beam model and experimental bending tests, dependency of maximum bending strain on the length of bent CNTs and radial distortion on bending angles at a bent point have been demonstrated. Individual CNTs are manipulated by limiting the length of bent CNTs and the bending angle. In our approach, multiwalled CNTs with 5-15 nm diameter subjected to bending deformation produce no outer tube breakage under uniform bending and reversible radial deformation with bending angles less than 110°. The lateral tip movement is determined by a simple geometric model that relies on the shape of multiwalled CNTs. The model effectively controls deforming CNT length and bending angle for given CNT shape. Experimental results demonstrate successful manipulation of randomly dispersed CNTs without visual defects. This approach to pushing can be extended to develop a wide range of CNT based nanodevice applications.

The Goat in the Rug.

ERIC Educational Resources Information Center

Blood, Charles L.; Link, Martin

Based on the activities of the real Window Rock weaver, Glenmae, and her goat, Geraldine, this illustrated story incorporates authentic details relative to the Navajo art of rug weaving and is designed for children aged four to eight. Capitalizing on the humor inherent in Geraldine's point of view, the story centers on the goat's observation of…

Rugged microelectronic module package supports circuitry on heat sink

NASA Technical Reports Server (NTRS)

Johnson, A. L.

1966-01-01

Rugged module package for thin film hybrid microcircuits incorporated a rigid, thermally conductive support structure, which serves as a heat sink, and a lead wire block in which T-shaped electrical connectors are potted. It protects the circuitry from shock and vibration loads, dissipates internal heat, and simplifies electrical connections between adjacent modules.

46 CFR 116.423 - Furniture and furnishings.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Systems Using a Radiant Heat Energy Source,” and with a specific optical density not to exceed 450 in both...) “Specific Optical Density of Smoke generated by Solid Materials.” Also: (i) Rugs and carpets shall not extend up bulkheads or vertical surfaces more than 10 centimeters (4 inches) above the deck. (ii) Rugs...

46 CFR 116.423 - Furniture and furnishings.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Systems Using a Radiant Heat Energy Source,” and with a specific optical density not to exceed 450 in both...) “Specific Optical Density of Smoke generated by Solid Materials.” Also: (i) Rugs and carpets shall not extend up bulkheads or vertical surfaces more than 10 centimeters (4 inches) above the deck. (ii) Rugs...

46 CFR 116.423 - Furniture and furnishings.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Systems Using a Radiant Heat Energy Source,” and with a specific optical density not to exceed 450 in both...) “Specific Optical Density of Smoke generated by Solid Materials.” Also: (i) Rugs and carpets shall not extend up bulkheads or vertical surfaces more than 10 centimeters (4 inches) above the deck. (ii) Rugs...

Lenz's Law: Feel the Force.

ERIC Educational Resources Information Center

Sawicki, Charles A.

1996-01-01

Describes a simple, inexpensive system that allows students to have hands-on contact with simple experiments involving forces generated by induced currents. Discusses the use of a dynamic force sensor in making quantitative measurements of the forces generated. (JRH)

Effect of the tip state during qPlus noncontact atomic force microscopy of Si(100) at 5 K: Probing the probe

PubMed Central

Jarvis, Sam; Danza, Rosanna; Moriarty, Philip

2012-01-01

Summary Background: Noncontact atomic force microscopy (NC-AFM) now regularly produces atomic-resolution images on a wide range of surfaces, and has demonstrated the capability for atomic manipulation solely using chemical forces. Nonetheless, the role of the tip apex in both imaging and manipulation remains poorly understood and is an active area of research both experimentally and theoretically. Recent work employing specially functionalised tips has provided additional impetus to elucidating the role of the tip apex in the observed contrast. Results: We present an analysis of the influence of the tip apex during imaging of the Si(100) substrate in ultra-high vacuum (UHV) at 5 K using a qPlus sensor for noncontact atomic force microscopy (NC-AFM). Data demonstrating stable imaging with a range of tip apexes, each with a characteristic imaging signature, have been acquired. By imaging at close to zero applied bias we eliminate the influence of tunnel current on the force between tip and surface, and also the tunnel-current-induced excitation of silicon dimers, which is a key issue in scanning probe studies of Si(100). Conclusion: A wide range of novel imaging mechanisms are demonstrated on the Si(100) surface, which can only be explained by variations in the precise structural configuration at the apex of the tip. Such images provide a valuable resource for theoreticians working on the development of realistic tip structures for NC-AFM simulations. Force spectroscopy measurements show that the tip termination critically affects both the short-range force and dissipated energy. PMID:22428093

Key issues review: evolution on rugged adaptive landscapes

NASA Astrophysics Data System (ADS)

Obolski, Uri; Ram, Yoav; Hadany, Lilach

2018-01-01

Adaptive landscapes represent a mapping between genotype and fitness. Rugged adaptive landscapes contain two or more adaptive peaks: allele combinations with higher fitness than any of their neighbors in the genetic space. How do populations evolve on such rugged landscapes? Evolutionary biologists have struggled with this question since it was first introduced in the 1930s by Sewall Wright. Discoveries in the fields of genetics and biochemistry inspired various mathematical models of adaptive landscapes. The development of landscape models led to numerous theoretical studies analyzing evolution on rugged landscapes under different biological conditions. The large body of theoretical work suggests that adaptive landscapes are major determinants of the progress and outcome of evolutionary processes. Recent technological advances in molecular biology and microbiology allow experimenters to measure adaptive values of large sets of allele combinations and construct empirical adaptive landscapes for the first time. Such empirical landscapes have already been generated in bacteria, yeast, viruses, and fungi, and are contributing to new insights about evolution on adaptive landscapes. In this Key Issues Review we will: (i) introduce the concept of adaptive landscapes; (ii) review the major theoretical studies of evolution on rugged landscapes; (iii) review some of the recently obtained empirical adaptive landscapes; (iv) discuss recent mathematical and statistical analyses motivated by empirical adaptive landscapes, as well as provide the reader with instructions and source code to implement simulations of evolution on adaptive landscapes; and (v) discuss possible future directions for this exciting field.

Antibacterial Activity Of ternary semiconductor compounds AgInSe2 Nanoparticles Synthesized by Simple Chemical Method

NASA Astrophysics Data System (ADS)

Shehab, A. A.; Fadaam, S. A.; Abd, A. N.; Mustafa, M. H.

2018-05-01

In this objective AgInSe2Nanoparticles (AgInSe2 NPs) were prepared by a simple chemical method (SCM). The optica structural l and morphological properties of the synthesized AgInSe2 NPs swere investigated by using UVVI absorption atomic force microscopy AFMmf, Fourier Transform Infrared Spectroscopy and x-ray diffraction. The resistance of bacteria represents a trouble and the outlook for the use of antibiotics in the future until now uncertain. Measures must be taken to decrease this problem. Antibacterial activity of the AgInSe2 nanoparticles were exposed against several pathogenic bacteriaa including Klebsiella pneumonia KPa, Staphylococcus aureus, Bacillus subtili, Enterobacter Cloacae and Esherichia Coliby. Using a good spread method the results showed that AgInSe2 NPs had inhibitory effect versus some pathogenic bacteria with suppression area 18, 14 and 17 mm for SAgInSe2 NPs had an inhibitory effect against S Bacillus Subtilis 11 mm K EnterobactercCloacae 12 mm.

Binding of an adatom to a simple metal surface

NASA Technical Reports Server (NTRS)

Huntington, H. B.; Turk, L. A.; White, W. W., III

1975-01-01

The density functional formalism of Hohenberg and Kohn is used to investigate the energies, charge densities and forces which hold an adatom on the surface of a simple metal. The valence wavefunction of the adatom is fitted to the Herman-Skillman solutions at large distance and is simplified somewhat in the core region. The field of the ion is represented by the Ashcroft pseudopotential. For the metal the jellium model is used. Detailed calculations are carried out for a sodium adatom on a sodium surface. Simply juxtaposing adatom and surface gives a binding energy of about 1/3 eV. This value is approximately twice the surface energy per atom in the close-packed plane. Charge redistributions as determined variationally increase the binding energy by about 10%. The equilibrium distance for the adatom turns out to be 1.66 A from the surface, as compared with 1.52 A, the observed value for one-half the distance between the close-packed planes.

Visible high-power laser sources for today and beyond

NASA Astrophysics Data System (ADS)

Smolka, Gregory L.

1995-04-01

The diversity and proliferation of 'real-world' laser applications continues to put increasing demand on laser technology. New system constraints, often dictated by the operation environment, stretch the capabilities of conventional laboratory lasers. As the applications proliferate, so too do the users. Today's laser user is often not a laser engineer, but rather views the laser simply as a tool to help him perform his job. For lasers to reach their true market potential, laser designers must respond to these user-mandated requirements with simple, compact, rugged devices. Traditional commercial lasers are far too large, bulky and complex for many of these new applications. Design techniques for shrinking, simplifying the ruggedizing solid-state lasers for today's applications will be discussed.

Pressure Measurement Sensor

NASA Technical Reports Server (NTRS)

1997-01-01

FFPI Industries Inc. is the manufacturer of fiber-optic sensors that furnish accurate pressure measurements in internal combustion chambers. Such an assessment can help reduce pollution emitted by these engines. A chief component in the sensor owes its seven year- long development to Lewis Research Center funding to embed optical fibers and sensors in metal parts. NASA support to Texas A&M University played a critical role in developing this fiber optic technology and led to the formation of FFPI Industries and the production of fiber sensor products. The simple, rugged design of the sensor offers the potential for mass production at low cost. Widespread application of the new technology is forseen, from natural gas transmission, oil refining and electrical power generation to rail transport and the petrochemical paper product industry.

REFRIGERATION ESPECIALLY FOR VERY LOW TEMPERATURES

DOEpatents

Kennedy, P.B.; Smith, H.R. Jr.

1960-09-13

A refrigeration system for producing very low temperatures is described. The system of the invention employs a binary mixture refrigerant in a closed constant volume, e.g., Freon and ethylene. Such mixture is compressed in the gaseous state and is then separated in a fractionating column element of the system. Thenceforth, the first liquid to separate is employed stagewise to cool and liq uefy successive portions of the refrigerant at successively lower temperatures by means of heat exchangers coupled between the successive stages. When shut down, all of the volumes of the system are interconnected and a portion of the refrigerant remains liquid at ambient temperatures so that no dangerous overpressures develop. The system is therefore rugged, simple and dependable in operation.

Effect of dispersion forces on squeezing with Rydberg atoms

NASA Technical Reports Server (NTRS)

Ng, S. K.; Muhamad, M. R.; Wahiddin, M. R. B.

1994-01-01

We report exact results concerning the effect of dipole-dipole interaction (dispersion forces) on dynamic and steady-state characteristics of squeezing in the emitted fluorescent field from two identical coherently driven two-level atoms. The atomic system is subjected to three different damping baths in particular the normal vacuum, a broad band thermal field and a broad band squeezed vacuum. The atomic model is the Dicke model, hence possible experiments are most likely to agree with theory when performed on systems of Rydberg atoms making microwave transitions. The presence of dipole-dipole interaction can enhance squeezing for realizable values of the various parameters involved.

Adhesion Forces between Lewis(X) Determinant Antigens as Measured by Atomic Force Microscopy.

PubMed

Tromas, C; Rojo, J; de la Fuente, J M; Barrientos, A G; García, R; Penadés, S

2001-01-01

The adhesion forces between individual molecules of Lewis(X) trisaccharide antigen (Le(X) ) have been measured in water and in calcium solution by using atomic force microscopy (AFM, see graph). These results demonstrate the self-recognition capability of this antigen, and reinforce the hypothesis that carbohydrate-carbohydrate interaction could be considered as the first step in the cell-adhesion process in nature. Copyright © 2001 WILEY-VCH Verlag GmbH, Weinheim, Fed. Rep. of Germany.

Topological Structures and Membrane Nanostructures of Erythrocytes after Splenectomy in Hereditary Spherocytosis Patients via Atomic Force Microscopy.

PubMed

Li, Ying; Lu, Liyuan; Li, Juan

2016-09-01

Hereditary spherocytosis is an inherited red blood cell membrane disorder resulting from mutations of genes encoding erythrocyte membrane and cytoskeletal proteins. Few equipments can observe the structural characteristics of hereditary spherocytosis directly expect for atomic force microscopy In our study, we proved atomic force microscopy is a powerful and sensitive instrument to describe the characteristics of hereditary spherocytosis. Erythrocytes from hereditary spherocytosis patients were small spheroidal, lacking a well-organized lattice on the cell membrane, with smaller cell surface particles and had reduced valley to peak distance and average cell membrane roughness vs. those from healthy individuals. These observations indicated defects in the certain cell membrane structural proteins such as α- and β-spectrin, ankyrin, etc. Until now, splenectomy is still the most effective treatment for symptoms relief for hereditary spherocytosis. In this study, we further solved the mysteries of membrane nanostructure changes of erythrocytes before and after splenectomy in hereditary spherocytosis by atomic force microscopy. After splenectomy, the cells were larger, but still spheroidal-shaped. The membrane ultrastructure was disorganized and characterized by a reduced surface particle size and lower than normal Ra values. These observations indicated that although splenectomy can effectively relieve the symptoms of hereditary spherocytosis, it has little effect on correction of cytoskeletal membrane defects of hereditary spherocytosis. We concluded that atomic force microscopy is a powerful tool to investigate the pathophysiological mechanisms of hereditary spherocytosis and to monitor treatment efficacy in clinical practices. To the best of our knowledge, this is the first report to study hereditary spherocytosis with atomic force microscopy and offers important mechanistic insight into the underlying role of splenectomy.

Simple display system of mechanical properties of cells and their dispersion.

PubMed

Shimizu, Yuji; Kihara, Takanori; Haghparast, Seyed Mohammad Ali; Yuba, Shunsuke; Miyake, Jun

2012-01-01

The mechanical properties of cells are unique indicators of their states and functions. Though, it is difficult to recognize the degrees of mechanical properties, due to small size of the cell and broad distribution of the mechanical properties. Here, we developed a simple virtual reality system for presenting the mechanical properties of cells and their dispersion using a haptic device and a PC. This system simulates atomic force microscopy (AFM) nanoindentation experiments for floating cells in virtual environments. An operator can virtually position the AFM spherical probe over a round cell with the haptic handle on the PC monitor and feel the force interaction. The Young's modulus of mesenchymal stem cells and HEK293 cells in the floating state was measured by AFM. The distribution of the Young's modulus of these cells was broad, and the distribution complied with a log-normal pattern. To represent the mechanical properties together with the cell variance, we used log-normal distribution-dependent random number determined by the mode and variance values of the Young's modulus of these cells. The represented Young's modulus was determined for each touching event of the probe surface and the cell object, and the haptic device-generating force was calculated using a Hertz model corresponding to the indentation depth and the fixed Young's modulus value. Using this system, we can feel the mechanical properties and their dispersion in each cell type in real time. This system will help us not only recognize the degrees of mechanical properties of diverse cells but also share them with others.

Simple Display System of Mechanical Properties of Cells and Their Dispersion

PubMed Central

Shimizu, Yuji; Kihara, Takanori; Haghparast, Seyed Mohammad Ali; Yuba, Shunsuke; Miyake, Jun

2012-01-01

The mechanical properties of cells are unique indicators of their states and functions. Though, it is difficult to recognize the degrees of mechanical properties, due to small size of the cell and broad distribution of the mechanical properties. Here, we developed a simple virtual reality system for presenting the mechanical properties of cells and their dispersion using a haptic device and a PC. This system simulates atomic force microscopy (AFM) nanoindentation experiments for floating cells in virtual environments. An operator can virtually position the AFM spherical probe over a round cell with the haptic handle on the PC monitor and feel the force interaction. The Young's modulus of mesenchymal stem cells and HEK293 cells in the floating state was measured by AFM. The distribution of the Young's modulus of these cells was broad, and the distribution complied with a log-normal pattern. To represent the mechanical properties together with the cell variance, we used log-normal distribution-dependent random number determined by the mode and variance values of the Young's modulus of these cells. The represented Young's modulus was determined for each touching event of the probe surface and the cell object, and the haptic device-generating force was calculated using a Hertz model corresponding to the indentation depth and the fixed Young's modulus value. Using this system, we can feel the mechanical properties and their dispersion in each cell type in real time. This system will help us not only recognize the degrees of mechanical properties of diverse cells but also share them with others. PMID:22479595

Continuous Liquid-Sample Introduction for Bunsen Burner Atomic Emission Spectrometry.

ERIC Educational Resources Information Center

Smith, Gregory D.; And Others

1995-01-01

Describes a laboratory-constructed atomic emission spectrometer with modular instrumentation components and a simple Bunsen burner atomizer with continuous sample introduction. A schematic diagram and sample data are provided. (DDR)

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

PubMed Central

2016-01-01

We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

Force-induced desorption of 3-star polymers: a self-avoiding walk model

NASA Astrophysics Data System (ADS)

Janse van Rensburg, E. J.; Whittington, S. G.

2018-05-01

We consider a simple cubic lattice self-avoiding walk model of 3-star polymers adsorbed at a surface and then desorbed by pulling with an externally applied force. We determine rigorously the free energy of the model in terms of properties of a self-avoiding walk, and show that the phase diagram includes four phases, namely a ballistic phase where the extension normal to the surface is linear in the length, an adsorbed phase and a mixed phase, in addition to the free phase where the model is neither adsorbed nor ballistic. In the adsorbed phase all three branches or arms of the star are adsorbed at the surface. In the ballistic phase two arms of the star are pulled into a ballistic phase, while the remaining arm is in a free phase. In the mixed phase two arms in the star are adsorbed while the third arm is ballistic. The phase boundaries separating the ballistic and mixed phases, and the adsorbed and mixed phases, are both first order phase transitions. The presence of the mixed phase is interesting because it does not occur for pulled, adsorbed self-avoiding walks. In an atomic force microscopy experiment it would appear as an additional phase transition as a function of force.

Evolution of optical force on two-level atom by ultrashort time-domain dark hollow Gaussian pulse

NASA Astrophysics Data System (ADS)

Cao, Xiaochao; Wang, Zhaoying; Lin, Qiang

2017-09-01

Based on the analytical expression of the ultrashort time-domain dark hollow Gaussian (TDHG) pulse, the optical force on two-level atoms induced by a TDHG pulse is calculated in this paper. The phenomena of focusing or defocusing of the light force is numerical analyzed for different detuning, various duration time, and different order of the ultrashort pulse. The transverse optical force can change from a focusing force to a defocusing force depending on the spatial-temporal coupling effect as the TDHG pulses propagating in free space. Our results also show that the initial phase of the TDHG pulse can significantly changes the envelope of the optical force.

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

Solares, Santiago D.

This study introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretationmore » of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tappingmode imaging, for both of which the force curves exhibit the expected features. Lastly, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.« less

Athermalization in atomic force microscope based force spectroscopy using matched microstructure coupling.

PubMed

Torun, H; Finkler, O; Degertekin, F L

2009-07-01

The authors describe a method for athermalization in atomic force microscope (AFM) based force spectroscopy applications using microstructures that thermomechanically match the AFM probes. The method uses a setup where the AFM probe is coupled with the matched structure and the displacements of both structures are read out simultaneously. The matched structure displaces with the AFM probe as temperature changes, thus the force applied to the sample can be kept constant without the need for a separate feedback loop for thermal drift compensation, and the differential signal can be used to cancel the shift in zero-force level of the AFM.

The use of atomic force microscopy to evaluate warm mix asphalt.

DOT National Transportation Integrated Search

2013-01-01

The main objective of this study was to use the Atomic Force Microscopy (AFM) to examine the moisture susceptibility : and healing characteristics of Warm Mix Asphalt (WMA) and compare it with those of conventional Hot Mix Asphalt (HMA). To : this en...

Antibacterial isoeugenol coating on stainless steel and polyethylene surfaces prevents biofilm growth.

PubMed

Nielsen, C K; Subbiahdoss, G; Zeng, G; Salmi, Z; Kjems, J; Mygind, T; Snabe, T; Meyer, R L

2018-01-01

Pathogenic bacteria can spread between individuals or between food items via the surfaces they share. Limiting the survival of pathogens on surfaces, therefore, presents an opportunity to limit at least one route of how pathogens spread. In this study, we propose that a simple coating with the essential oil isoeugenol can be used to circumvent the problem of bacterial transfer via surfaces. Two commonly used materials, stainless steel and polyethylene, were coated by physical adsorption, and the coatings were characterized by Raman spectroscopy, atomic force microscopy and water contact angle measurements. We quantified and visualized the colonization of coated and uncoated surfaces by three bacteria: Staphylococcus aureus, Listeria monocytogenes and Pseudomonas fluorescens. No viable cells were detected on surfaces coated with isoeugenol. The isoeugenol coating prepared with simple adsorption proved effective in preventing biofilm formation on stainless steel and polyethylene surfaces. The result was caused by the antibacterial effect of isoeugenol, as the coating did not diminish the adhesive properties of the surface. Our study demonstrates that a simple isoeugenol coating can prevent biofilm formation of S. aureus, L. monocytogenes and P. fluorescens on two commonly used surfaces. © 2017 The Society for Applied Microbiology.

First-principles calculation of the polarization-dependent force driving the Eg mode in bismuth under optical excitation.

NASA Astrophysics Data System (ADS)

Murray, Eamonn; Fahy, Stephen

2014-03-01

Using first principles electronic structure methods, we calculate the induced force on the Eg (zone centre transverse optical) phonon mode in bismuth immediately after absorption of polarized light. When radiation with polarization perpendicular to the c-axis is absorbed in bismuth, the distribution of excited electrons and holes breaks the three-fold rotational symmetry and leads to a net force on the atoms in the direction perpendicular to the axis. We calculate the initial excited electronic distribution as a function of photon energy and polarization and find the resulting transverse and longitudinal forces experienced by the atoms. Using the measured, temperature-dependent rate of decay of the transverse force[2], we predict the approximate amplitude of induced atomic motion in the Eg mode as a function of temperature and optical fluence. This work is supported by Science Foundation Ireland and a Marie Curie International Incoming Fellowship.

Balancing Force Field Protein–Lipid Interactions To Capture Transmembrane Helix–Helix Association

PubMed Central

2018-01-01

Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold globular proteins and have provided insights into folding mechanisms. Gaining similar understanding from simulations of membrane protein folding and association would be of great medical interest. All-atom simulations of the folding and assembly of transmembrane protein domains are much more challenging, not least due to very slow diffusion within the lipid bilayer membrane. Here, we focus on a simple and well-characterized prototype of membrane protein folding and assembly, namely the dimerization of glycophorin A, a homodimer of single transmembrane helices. We have determined the free energy landscape for association of the dimer using the CHARMM36 force field. We find that the native structure is a metastable state, but not stable as expected from experimental estimates of the dissociation constant and numerous experimental structures obtained under a variety of conditions. We explore two straightforward approaches to address this problem and demonstrate that they result in stable dimers with dissociation constants consistent with experimental data. PMID:29424543

16 CFR 1630.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2010 CFR

2010-01-01

... normally used for that type of carpet or rug in service. (b) On February 10, 1972 (37 FR 3010) the Federal... 2″ in diameter and 9″ long composed of nonabsorbant material such as glass or plastic. (4) Select... remove all excess water and wrap around the operating applicator. (7) Immediately with light pressure...

16 CFR 1631.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2010 CFR

2010-01-01

... normally used for that type of carpet or rug in service. (b) On February 10, 1972 (37 FR 3010) the Federal... 2″ in diameter and 9″ long composed of nonabsorbent material such as glass or plastic. (4) Select... remove all excess water and wrap around the operating applicator. (7) Immediately, with light pressure...

16 CFR 1630.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2011 CFR

2011-01-01

... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 1-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...

16 CFR 1630.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2014 CFR

2014-01-01

... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 1-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...

16 CFR 1630.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2012 CFR

2012-01-01

... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 1-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...

16 CFR 1631.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2011 CFR

2011-01-01

... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 2-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...

16 CFR 1631.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2014 CFR

2014-01-01

... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 2-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...

16 CFR 1631.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2012 CFR

2012-01-01

... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 2-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...

75 FR 42315 - Third Party Testing for Certain Children's Products; Carpets and Rugs: Requirements for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-21

... samples that are identical in all material respects to the product. The Commission also emphasizes that... Small Carpets and Rugs (FF 2-70). A true copy, in English, of the accreditation and scope documents... status must submit to the Commission copies, in English, of their training documents showing how...

16 CFR 1631.34 - Small carpets and rugs not meeting acceptance criterion.

Code of Federal Regulations, 2010 CFR

2010-01-01

... acceptance criterion of such standard, it shall, prior to its introduction into commerce, be legibly and.... DEPARTMENT OF COMMERCE STANDARD FF 2-70): SHOULD NOT BE USED NEAR SOURCES OF IGNITION.” The required... section, in addition to the label required to be affixed to the small carpets or rugs. (e) Where small...

Mathematics Student Teachers' Modelling Approaches While Solving the Designed Esme Rug Problem

ERIC Educational Resources Information Center

Hidiroglu, Çaglar Naci; Dede, Ayse Tekin; Ünver, Semiha Kula; Güzel, Esra Bukova

2017-01-01

The purpose of the study is to analyze the mathematics student teachers' solutions on the Esme Rug Problem through 7-stage mathematical modelling process. This problem was designed by the researchers by considering the modelling problems' main properties. The study was conducted with twenty one secondary mathematics student teachers. The data were…

Development of high-performance low-reflection rugged resistive touch screens for military displays

NASA Astrophysics Data System (ADS)

Wang, Raymond; Wang, Minshine; Thomas, John; Wang, Lawrence; Chang, Victor

2010-04-01

Just as iPhones with sophisticated touch interfaces have revolutionised the human interface for the ubiquitous cell phone, the Military is rapidly adopting touch-screens as a primary interface to their computers and vehicle systems. This paper describes the development of a true military touch interface solution from an existing industrial design. We will report on successful development of 10.4" and 15.4" high performance rugged resistive touch panels using IAD sputter coating. Low reflectance (specular < 1% and diffuse < 0.07%) was achieved with high impact, dust, and chemical resistant surface finishes. These touch panels were qualified over a wide operational temperature range, -51°C to +80°C specifically for military and rugged industrial applications.

Universal aspects of adhesion and atomic force microscopy

NASA Technical Reports Server (NTRS)

Banerjea, Amitava; Smith, John R.; Ferrante, John

1990-01-01

Adhesive energies are computed for flat and atomically sharp tips as a function of the normal distance to the substrate. The dependence of binding energies on tip shape is investigated. The magnitudes of the binding energies for the atomic force microscope are found to depend sensitively on tip material, tip shape and the sample site being probed. The form of the energy-distance curve, however, is universal and independent of these variables, including tip shape.

Scanning ion-conductance and atomic force microscope with specialized sphere-shaped nanopippettes

NASA Astrophysics Data System (ADS)

Zhukov, M. V.; Sapozhnikov, I. D.; Golubok, A. O.; Chubinskiy-Nadezhdin, V. I.; Komissarenko, F. E.; Lukashenko, S. Y.

2017-11-01

A scanning ion-conductance microscope was designed on the basis of scanning probe microscope NanoTutor. The optimal parameters of nanopipettes fabrication were found according to scanning electron microscopy diagnostics, current-distance I (Z) and current-voltage characteristics. A comparison of images of test objects, including biological samples, was carried out in the modes of optical microscopy, atomic force microscopy and scanning ion-conductance microscopy. Sphere-shaped nanopippettes probes were developed and tested to increase the stability of pipettes, reduce invasiveness and improve image quality of atomic force microscopy in tapping mode. The efficiency of sphere-shaped nanopippettes is shown.

Length-extension resonator as a force sensor for high-resolution frequency-modulation atomic force microscopy in air.

PubMed

Beyer, Hannes; Wagner, Tino; Stemmer, Andreas

2016-01-01

Frequency-modulation atomic force microscopy has turned into a well-established method to obtain atomic resolution on flat surfaces, but is often limited to ultra-high vacuum conditions and cryogenic temperatures. Measurements under ambient conditions are influenced by variations of the dew point and thin water layers present on practically every surface, complicating stable imaging with high resolution. We demonstrate high-resolution imaging in air using a length-extension resonator operating at small amplitudes. An additional slow feedback compensates for changes in the free resonance frequency, allowing stable imaging over a long period of time with changing environmental conditions.

Analysis of the physical atomic forces between noble gas atoms, alkali ions and halogen ions

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Heinbockel, J. H.; Outlaw, R. A.

1986-01-01

The physical forces between atoms and molecules are important in a number of processes of practical importance, including line broadening in radiative processes, gas and crystal properties, adhesion, and thin films. The components of the physical forces between noble gas atoms, alkali ions, and halogen ions are analyzed and a data base for the dispersion forces is developed from the literature based on evaluations with the harmonic oscillator dispersion model for higher order coefficients. The Zener model of the repulsive core is used in the context of the recent asymptotic wave functions of Handler and Smith; and an effective ionization potential within the Handler and Smith wave functions is defined to analyze the two body potential data of Waldman and Gordon, the alkali-halide molecular data, and the noble gas crystal and salt crystal data. A satisfactory global fit to this molecular and crystal data is then reproduced by the model to within several percent. Surface potentials are evaluated for noble gas atoms on noble gas and salt crystal surfaces with surface tension neglected. Within this context, the noble gas surface potentials on noble gas and salt crystals are considered to be accurate to within several percent.

Minimizing pulling geometry errors in atomic force microscope single molecule force spectroscopy.

PubMed

Rivera, Monica; Lee, Whasil; Ke, Changhong; Marszalek, Piotr E; Cole, Daniel G; Clark, Robert L

2008-10-01

In atomic force microscopy-based single molecule force spectroscopy (AFM-SMFS), it is assumed that the pulling angle is negligible and that the force applied to the molecule is equivalent to the force measured by the instrument. Recent studies, however, have indicated that the pulling geometry errors can drastically alter the measured force-extension relationship of molecules. Here we describe a software-based alignment method that repositions the cantilever such that it is located directly above the molecule's substrate attachment site. By aligning the applied force with the measurement axis, the molecule is no longer undergoing combined loading, and the full force can be measured by the cantilever. Simulations and experimental results verify the ability of the alignment program to minimize pulling geometry errors in AFM-SMFS studies.

Rugged, Portable, Real-Time Optical Gaseous Analyzer for Hydrogen Fluoride

NASA Technical Reports Server (NTRS)

Pilgrim, Jeffrey; Gonzales, Paula

2012-01-01

Hydrogen fluoride (HF) is a primary evolved combustion product of fluorinated and perfluorinated hydrocarbons. HF is produced during combustion by the presence of impurities and hydrogen- containing polymers including polyimides. This effect is especially dangerous in closed occupied volumes like spacecraft and submarines. In these systems, combinations of perfluorinated hydrocarbons and polyimides are used for insulating wiring. HF is both highly toxic and short-lived in closed environments due to its reactivity. The high reactivity also makes HF sampling problematic. An infrared optical sensor can detect promptly evolving HF with minimal sampling requirements, while providing both high sensitivity and high specificity. A rugged optical path length enhancement architecture enables both high HF sensitivity and rapid environmental sampling with minimal gaseous contact with the low-reactivity sensor surfaces. The inert optical sample cell, combined with infrared semiconductor lasers, is joined with an analog and digital electronic control architecture that allows for ruggedness and compactness. The combination provides both portability and battery operation on a simple camcorder battery for up to eight hours. Optical detection of gaseous HF is confounded by the need for rapid sampling with minimal contact between the sensor and the environmental sample. A sensor is required that must simultaneously provide the required sub-parts-permillion detection limits, but with the high specificity and selectivity expected of optical absorption techniques. It should also be rugged and compact for compatibility with operation onboard spacecraft and submarines. A new optical cell has been developed for which environmental sampling is accomplished by simply traversing the few mm-thick cell walls into an open volume where the measurement is made. A small, low-power fan or vacuum pump may be used to push or pull the gaseous sample into the sample volume for a response time of a few seconds. The optical cell simultaneously provides for an enhanced optical interaction path length between the environmental sample and the infrared laser. Further, the optical cell itself is comprised of inert materials that render it immune to attack by HF. In some cases, the sensor may be configured so that the optoelectronic devices themselves are protected and isolated from HF by the optical cell. The optical sample cell is combined with custom-developed analog and digital control electronics that provide rugged, compact operation on a platform that can run on a camcorder battery. The sensor is inert with respect to acidic gases like HF, while providing the required sensitivity, selectivity, and response time. Certain types of combustion events evolve copious amounts of HF, very little of other gases typically associated with combustion (e.g., carbon monoxide), and very low levels of aerosols and particulates (which confound traditional smoke detectors). The new sensor platform could warn occupants early enough to take the necessary countermeasures.

VEDA: a web-based virtual environment for dynamic atomic force microscopy.

PubMed

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy

NASA Astrophysics Data System (ADS)

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Three-dimensional atomic force microscopy mapping at the solid-liquid interface with fast and flexible data acquisition

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

Söngen, Hagen, E-mail: soengen@uni-mainz.de; Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz; Nalbach, Martin

2016-06-15

We present the implementation of a three-dimensional mapping routine for probing solid-liquid interfaces using frequency modulation atomic force microscopy. Our implementation enables fast and flexible data acquisition of up to 20 channels simultaneously. The acquired data can be directly synchronized with commercial atomic force microscope controllers, making our routine easily extendable for related techniques that require additional data channels, e.g., Kelvin probe force microscopy. Moreover, the closest approach of the tip to the sample is limited by a user-defined threshold, providing the possibility to prevent potential damage to the tip. The performance of our setup is demonstrated by visualizing themore » hydration structure above the calcite (10.4) surface in water.« less

Imaging contrast and tip-sample interaction of non-contact amplitude modulation atomic force microscopy with Q-control

NASA Astrophysics Data System (ADS)

Shi, Shuai; Guo, Dan; Luo, Jianbin

2017-10-01

Active quality factor (Q) exhibits many promising properties in dynamic atomic force microscopy. Energy dissipation and image contrasts are investigated in the non-contact amplitude modulation atomic force microscopy (AM-AFM) with an active Q-control circuit in the ambient air environment. Dissipated power and virial were calculated to compare the highly nonlinear interaction of tip-sample and image contrasts with different Q gain values. Greater free amplitudes and lower effective Q values show better contrasts for the same setpoint ratio. Active quality factor also can be employed to change tip-sample interaction force in non-contact regime. It is meaningful that non-destructive and better contrast images can be realized in non-contact AM-AFM by applying an active Q-control to the dynamic system.

Taking nanomedicine teaching into practice with atomic force microscopy and force spectroscopy.

PubMed

Carvalho, Filomena A; Freitas, Teresa; Santos, Nuno C

2015-12-01

Atomic force microscopy (AFM) is a useful and powerful tool to study molecular interactions applied to nanomedicine. The aim of the present study was to implement a hands-on atomic AFM course for graduated biosciences and medical students. The course comprises two distinct practical sessions, where students get in touch with the use of an atomic force microscope by performing AFM scanning images of human blood cells and force spectroscopy measurements of the fibrinogen-platelet interaction. Since the beginning of this course, in 2008, the overall rating by the students was 4.7 (out of 5), meaning a good to excellent evaluation. Students were very enthusiastic and produced high-quality AFM images and force spectroscopy data. The implementation of the hands-on AFM course was a success, giving to the students the opportunity of contact with a technique that has a wide variety of applications on the nanomedicine field. In the near future, nanomedicine will have remarkable implications in medicine regarding the definition, diagnosis, and treatment of different diseases. AFM enables students to observe single molecule interactions, enabling the understanding of molecular mechanisms of different physiological and pathological processes at the nanoscale level. Therefore, the introduction of nanomedicine courses in bioscience and medical school curricula is essential. Copyright © 2015 The American Physiological Society.

Images of Atoms.

ERIC Educational Resources Information Center

Wright, Tony

2003-01-01

Recommends using a simple image, such as the fuzzy atom ball to help students develop a useful understanding of the molecular world. Explains that the image helps students easily grasp ideas about atoms and molecules and leads naturally to more advanced ideas of atomic structure, chemical bonding, and quantum physics. (Author/NB)

Linker Dependent Bond Rupture Force Measurements in Single-Molecule Junctions

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

Frei M.; Hybertsen M.; Aradhya S.V.

We use a modified conducting atomic force microscope to simultaneously probe the conductance of a single-molecule junction and the force required to rupture the junction formed by alkanes terminated with four different chemical link groups which vary in binding strength and mechanism to the gold electrodes. Molecular junctions with amine, methylsulfide, and diphenylphosphine terminated molecules show clear conductance signatures and rupture at a force that is significantly smaller than the measured 1.4 nN force required to rupture the single-atomic gold contact. In contrast, measurements with a thiol terminated alkane which can bind covalently to the gold electrode show conductance andmore » force features unlike those of the other molecules studied. Specifically, the strong Au-S bond can cause structural rearrangements in the electrodes, which are accompanied by substantial conductance changes. Despite the strong Au-S bond and the evidence for disruption of the Au structure, the experiments show that on average these junctions also rupture at a smaller force than that measured for pristine single-atom gold contacts.« less

The Effects of Orthophosphate in Drinking Water on the Initial Copper Corrosion Using Atomic Force Microscopy

EPA Science Inventory

Corroding of copper piping used in household drinking water plumbing may potentially impacts consumer’s health and economics. Copper corrosion studies conducted on newly corroding material with atomic force microscopy (AFM) may be particularly useful in understanding the impact ...

Helium cluster isolation spectroscopy

NASA Astrophysics Data System (ADS)

Higgins, John Paul

Clusters of helium, each containing ~103- 104 atoms, are produced in a molecular beam and are doped with alkali metal atoms (Li, Na, and K) and large organic molecules. Electronic spectroscopy in the visible and UV regions of the spectrum is carried out on the dopant species. Since large helium clusters are liquid and attain an equilibrium internal temperature of 0.4 K, they interact weakly with atoms or molecules absorbed on their surface or resident inside the cluster. The spectra that are obtained are characterized by small frequency shifts from the positions of the gas phase transitions, narrow lines, and cold vibrational temperatures. Alkali atoms aggregate on the helium cluster surface to form dimers and trimers. The spectra of singlet alkali dimers exhibit the presence of elementary excitations in the superfluid helium cluster matrix. It is found that preparation of the alkali molecules on the surface of helium clusters leads to the preferential formation of high-spin, van der Waals bound, triplet dimers and quartet trimers. Four bound-bound and two bound-free transitions are observed in the triplet manifold of the alkali dimers. The quartet trimers serve as an ideal system for the study of a simple unimolecular reaction in the cold helium cluster environment. Analysis of the lowest quartet state provides valuable insight into three-body forces in a van der Waals trimer. The wide range of atomic and molecular systems studied in this thesis constitutes a preliminary step in the development of helium cluster isolation spectroscopy, a hybrid technique combining the advantages of high resolution spectroscopy with the synthetic, low temperature environment of matrices.

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

Trapped atom number in millimeter-scale magneto-optical traps

NASA Astrophysics Data System (ADS)

Hoth, Gregory W.; Donley, Elizabeth A.; Kitching, John

2012-06-01

For compact cold-atom instruments, it is desirable to trap a large number of atoms in a small volume to maximize the signal-to-noise ratio. In MOTs with beam diameters of a centimeter or larger, the slowing force is roughly constant versus velocity and the trapped atom number scales as d^4. For millimeter-scale MOTs formed from pyramidal reflectors, a d^6 dependence has been observed [Pollack et al., Opt. Express 17, 14109 (2009)]. A d^6 scaling is expected for small MOTs, where the slowing force is proportional to the atom velocity. For a 1 mm diameter MOT, a d^6 scaling results in 10 atoms, and the difference between a d^4 and a d^6 dependence corresponds to a factor of 1000 in atom number and a factor of 30 in the signal-to-noise ratio. We have observed >10^4 atoms in 1 mm diameter MOTs, consistent with a d^4 dependence. We are currently performing measurements for sub-mm MOTs to determine where the d^4 to d^6 crossover occurs in our system. We are also exploring MOTs based on linear polarization, which can potentially produce stronger slowing forces due to stimulated emission [Emile et al., Europhys. Lett. 20, 687 (1992)]. It may be possible to trap more atoms in small volumes with this method, since high intensities can be easily achieved.

Direct quantitative measurement of the C═O⋅⋅⋅H–C bond by atomic force microscopy

PubMed Central

Kawai, Shigeki; Nishiuchi, Tomohiko; Kodama, Takuya; Spijker, Peter; Pawlak, Rémy; Meier, Tobias; Tracey, John; Kubo, Takashi; Meyer, Ernst; Foster, Adam S.

2017-01-01

The hydrogen atom—the smallest and most abundant atom—is of utmost importance in physics and chemistry. Although many analysis methods have been applied to its study, direct observation of hydrogen atoms in a single molecule remains largely unexplored. We use atomic force microscopy (AFM) to resolve the outermost hydrogen atoms of propellane molecules via very weak C═O⋅⋅⋅H–C hydrogen bonding just before the onset of Pauli repulsion. The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs and polymers, building the capabilities of AFM toward quantitative probing of local chemical reactivity. PMID:28508080

Atom-Pair Kinetics with Strong Electric-Dipole Interactions.

PubMed

Thaicharoen, N; Gonçalves, L F; Raithel, G

2016-05-27

Rydberg-atom ensembles are switched from a weakly to a strongly interacting regime via adiabatic transformation of the atoms from an approximately nonpolar into a highly dipolar quantum state. The resultant electric dipole-dipole forces are probed using a device akin to a field ion microscope. Ion imaging and pair-correlation analysis reveal the kinetics of the interacting atoms. Dumbbell-shaped pair-correlation images demonstrate the anisotropy of the binary dipolar force. The dipolar C_{3} coefficient, derived from the time dependence of the images, agrees with the value calculated from the permanent electric-dipole moment of the atoms. The results indicate many-body dynamics akin to disorder-induced heating in strongly coupled particle systems.

Stretching of short monatomic gold chains-some model calculations

NASA Astrophysics Data System (ADS)

Sumali, Priyanka, Verma, Veena; Dharamvir, Keya

2012-06-01

The Mechanical properties of zig-zag monatomic gold chains containing 5 and 7 atoms were studied using the Siesta Code (SC), which works within the framework of DFT formalism and Gupta Potential (GP), which is an effective atom-atom potential. The zig-zag chains were stretched by keeping the end atoms fixed while rest of the atoms were relaxed till minimum energy is obtained. Energy, Force and Young's Modulus found using GP and SC were plotted as functions of total length. It is found that the breaking force in case of GP is of order of 1.6nN while for SIESTA is of the order of 2.9nN for both the chains.

Imaging powders with the atomic force microscope: from biominerals to commercial materials.

PubMed

Friedbacher, G; Hansma, P K; Ramli, E; Stucky, G D

1991-09-13

Atomically resolved images of pressed powder samples have been obtained with the atomic force microscope (AFM). The technique was successful in resolving the particle, domain, and atomic structure of pismo clam (Tivela stultorum) and sea urchin (Strongylocentrotus purpuratus) shells and of commercially available calcium carbonate (CaCO(3)) and strontium carbonate (SrCO(3)) powders. Grinding and subsequent pressing of the shells did not destroy the microstructure of these materials. The atomic-resolution imaging capabilities of AFM can be applied to polycrystalline samples by means of pressing powders with a grain size as small as 50 micrometers. These results illustrate that the AFM is a promising tool for material science and the study of biomineralization.

Nanoscale charge transfer and diffusion at the MoS2/SiO2 interface by atomic force microscopy: contact injection versus triboelectrification.

PubMed

Xu, Rui; Ye, Shili; Xu, Kunqi; Lei, Le; Hussain, Sabir; Zheng, Zhiyue; Pang, Fei; Xing, Shuya; Liu, Xinmeng; Ji, Wei; Cheng, Zhihai

2018-08-31

Understanding the process of charge generation, transfer, and diffusion between two-dimensional (2D) materials and their supporting substrates is very important for potential applications of 2D materials. Compared with the systematic studies of triboelectric charging in a bulk sample, a fundamental understanding of the triboelectrification of the 2D material/insulator system is rather limited. Here, the charge transfer and diffusion of both the SiO 2 surface and MoS 2 /SiO 2 interface through contact electrification and frictional electrification are investigated systematically in situ by scanning Kelvin probe microscopy and dual-harmonic electrostatic force microscopy. Different from the simple static charge transfer between SiO 2 and the PtSi alloy atomic force microscope (AFM) tip, the charge transfer between the tip and the MoS 2 /SiO 2 system is complicated. Triboelectric charges, generated by contact or frictional electrification with the AFM tip, are trapped at the MoS 2 /SiO 2 interface and act as floating gates. The local charge discharge processes can be obtained by monitoring the surface potential. The charge decay time (τ) of the MoS 2 /SiO 2 interface is one (or two) orders of magnitude larger than the decay time τ of the SiO 2 surface. This work facilitates an understanding of the triboelectric and de-electrification of the interface between 2D materials and substrates. In addition to the charge transfer and diffusion, we demonstrate the nanopatterns of surface and interfacial charges, which have great potential for the application of self-assembly of charged nanostructures.

Shear-induced partial translational ordering of a colloidal solid

NASA Astrophysics Data System (ADS)

Ackerson, B. J.; Clark, N. A.

1984-08-01

Highly charged submicrometer plastic spheres suspended in water at low ionic strength will order spontaneously into bcc crystals or polycrystals. A simple linear shear orients and disorders these crystals by forcing (110) planes to stack normal to the shear gradient and to slide relative to each other with a <111> direction parallel to the solvent flow. In this paper we analyze in detail the disordering and flow processes occurring beyond the intrinsic elastic limit of the bcc crystal. We are led to a model in which the flow of a colloidal crystal is interpreted as a fundamentally different process from that found in atomic crystals. In the colloidal crystal the coupling of particle motion to the background fluid forces a homogeneous flow, where every layer is in motion relative to its neighboring layers. In contrast, the plastic flow in an atomic solid is defect mediated flow. At the lowest applied stress, the local bcc order in the colloidal crystal exhibits shear strains both parallel and perpendicular to the direction of the applied stress. The magnitude of these deformations is estimated using the configurational energy for bcc and distorted bcc crystals, assuming a screened Coulomb pair interaction between colloidal particles. As the applied stress is increased, the intrinsic elastic limit of the crystal is exceeded and the crystal begins to flow with adjacent layers executing an oscillatory path governed by the balance of viscous and screened Coulomb forces. The path takes the structure from the bcc1 and bcc2 twins observed at zero shear to a distorted two-dimensional hcp structure at moderate shear rates, with a loss of interlayer registration as the shear is increased. This theoretical model is consistent with other experimental observations, as well.

A finite-volume HLLC-based scheme for compressible interfacial flows with surface tension

NASA Astrophysics Data System (ADS)

Garrick, Daniel P.; Owkes, Mark; Regele, Jonathan D.

2017-06-01

Shock waves are often used in experiments to create a shear flow across liquid droplets to study secondary atomization. Similar behavior occurs inside of supersonic combustors (scramjets) under startup conditions, but it is challenging to study these conditions experimentally. In order to investigate this phenomenon further, a numerical approach is developed to simulate compressible multiphase flows under the effects of surface tension forces. The flow field is solved via the compressible multicomponent Euler equations (i.e., the five equation model) discretized with the finite volume method on a uniform Cartesian grid. The solver utilizes a total variation diminishing (TVD) third-order Runge-Kutta method for time-marching and second order TVD spatial reconstruction. Surface tension is incorporated using the Continuum Surface Force (CSF) model. Fluxes are upwinded with a modified Harten-Lax-van Leer Contact (HLLC) approximate Riemann solver. An interface compression scheme is employed to counter numerical diffusion of the interface. The present work includes modifications to both the HLLC solver and the interface compression scheme to account for capillary force terms and the associated pressure jump across the gas-liquid interface. A simple method for numerically computing the interface curvature is developed and an acoustic scaling of the surface tension coefficient is proposed for the non-dimensionalization of the model. The model captures the surface tension induced pressure jump exactly if the exact curvature is known and is further verified with an oscillating elliptical droplet and Mach 1.47 and 3 shock-droplet interaction problems. The general characteristics of secondary atomization at a range of Weber numbers are also captured in a series of simulations.

A finite-volume HLLC-based scheme for compressible interfacial flows with surface tension

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

Garrick, Daniel P.; Owkes, Mark; Regele, Jonathan D., E-mail: jregele@iastate.edu

Shock waves are often used in experiments to create a shear flow across liquid droplets to study secondary atomization. Similar behavior occurs inside of supersonic combustors (scramjets) under startup conditions, but it is challenging to study these conditions experimentally. In order to investigate this phenomenon further, a numerical approach is developed to simulate compressible multiphase flows under the effects of surface tension forces. The flow field is solved via the compressible multicomponent Euler equations (i.e., the five equation model) discretized with the finite volume method on a uniform Cartesian grid. The solver utilizes a total variation diminishing (TVD) third-order Runge–Kuttamore » method for time-marching and second order TVD spatial reconstruction. Surface tension is incorporated using the Continuum Surface Force (CSF) model. Fluxes are upwinded with a modified Harten–Lax–van Leer Contact (HLLC) approximate Riemann solver. An interface compression scheme is employed to counter numerical diffusion of the interface. The present work includes modifications to both the HLLC solver and the interface compression scheme to account for capillary force terms and the associated pressure jump across the gas–liquid interface. A simple method for numerically computing the interface curvature is developed and an acoustic scaling of the surface tension coefficient is proposed for the non-dimensionalization of the model. The model captures the surface tension induced pressure jump exactly if the exact curvature is known and is further verified with an oscillating elliptical droplet and Mach 1.47 and 3 shock-droplet interaction problems. The general characteristics of secondary atomization at a range of Weber numbers are also captured in a series of simulations.« less

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

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

Nemchinsky, V.; Khrabry, A.

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Effect of polarization forces on carbon deposition on a non-spherical nanoparticle. Monte Carlo simulations [Effect of polarization forces on atom deposition on a non-spherical nanoparticle. Monte Carlo simulations

DOE PAGES

Nemchinsky, V.; Khrabry, A.

2018-02-01

Trajectories of a polarizable species (atoms or molecules) in the vicinity of a negatively charged nanoparticle (at a floating potential) are considered. The atoms are pulled into regions of strong electric field by polarization forces. The polarization increases the deposition rate of the atoms and molecules at the nanoparticle. The effect of the non-spherical shape of the nanoparticle is investigated by the Monte Carlo method. The shape of the non-spherical nanoparticle is approximated by an ellipsoid. The total deposition rate and its flux density distribution along the nanoparticle surface are calculated. As a result, it is shown that the fluxmore » density is not uniform along the surface. It is maximal at the nanoparticle tips.« less

Refined tip preparation by electrochemical etching and ultrahigh vacuum treatment to obtain atomically sharp tips for scanning tunneling microscope and atomic force microscope.

PubMed

Hagedorn, Till; El Ouali, Mehdi; Paul, William; Oliver, David; Miyahara, Yoichi; Grütter, Peter

2011-11-01

A modification of the common electrochemical etching setup is presented. The described method reproducibly yields sharp tungsten tips for usage in the scanning tunneling microscope and tuning fork atomic force microscope. In situ treatment under ultrahigh vacuum (p ≤10(-10) mbar) conditions for cleaning and fine sharpening with minimal blunting is described. The structure of the microscopic apex of these tips is atomically resolved with field ion microscopy and cross checked with field emission. © 2011 American Institute of Physics

Radiation pressure excitation of a low temperature atomic force/magnetic force microscope for imaging in 4-300 K temperature range

NASA Astrophysics Data System (ADS)

Ćelik, Ümit; Karcı, Özgür; Uysallı, Yiǧit; Özer, H. Özgür; Oral, Ahmet

2017-01-01

We describe a novel radiation pressure based cantilever excitation method for imaging in dynamic mode atomic force microscopy (AFM) for the first time. Piezo-excitation is the most common method for cantilever excitation, however it may cause spurious resonance peaks. Therefore, the direct excitation of the cantilever plays a crucial role in AFM imaging. A fiber optic interferometer with a 1310 nm laser was used both for the excitation of the cantilever at the resonance and the deflection measurement of the cantilever in a commercial low temperature atomic force microscope/magnetic force microscope (AFM/MFM) from NanoMagnetics Instruments. The laser power was modulated at the cantilever's resonance frequency by a digital Phase Locked Loop (PLL). The laser beam is typically modulated by ˜500 μW, and ˜141.8 nmpp oscillation amplitude is obtained in moderate vacuum levels between 4 and 300 K. We have demonstrated the performance of the radiation pressure excitation in AFM/MFM by imaging atomic steps in graphite, magnetic domains in CoPt multilayers between 4 and 300 K and Abrikosov vortex lattice in BSCCO(2212) single crystal at 4 K for the first time.

Radiation pressure excitation of a low temperature atomic force/magnetic force microscope for imaging in 4-300 K temperature range.

PubMed

Çelik, Ümit; Karcı, Özgür; Uysallı, Yiğit; Özer, H Özgür; Oral, Ahmet

2017-01-01

We describe a novel radiation pressure based cantilever excitation method for imaging in dynamic mode atomic force microscopy (AFM) for the first time. Piezo-excitation is the most common method for cantilever excitation, however it may cause spurious resonance peaks. Therefore, the direct excitation of the cantilever plays a crucial role in AFM imaging. A fiber optic interferometer with a 1310 nm laser was used both for the excitation of the cantilever at the resonance and the deflection measurement of the cantilever in a commercial low temperature atomic force microscope/magnetic force microscope (AFM/MFM) from NanoMagnetics Instruments. The laser power was modulated at the cantilever's resonance frequency by a digital Phase Locked Loop (PLL). The laser beam is typically modulated by ∼500 μW, and ∼141.8 nm pp oscillation amplitude is obtained in moderate vacuum levels between 4 and 300 K. We have demonstrated the performance of the radiation pressure excitation in AFM/MFM by imaging atomic steps in graphite, magnetic domains in CoPt multilayers between 4 and 300 K and Abrikosov vortex lattice in BSCCO(2212) single crystal at 4 K for the first time.

Thermodynamic forces in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Noid, William

Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.

PubMed

Yao, Kun; Herr, John E; Toth, David W; Mckintyre, Ryker; Parkhill, John

2018-02-28

Traditional force fields cannot model chemical reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab initio accuracy at low cost. However a data-driven approach is naturally inefficient for long-range interatomic forces that have simple physical formulas. In this manuscript we construct a hybrid model chemistry consisting of a nearsighted neural network potential with screened long-range electrostatic and van der Waals physics. This trained potential, simply dubbed "TensorMol-0.1", is offered in an open-source Python package capable of many of the simulation types commonly used to study chemistry: geometry optimizations, harmonic spectra, open or periodic molecular dynamics, Monte Carlo, and nudged elastic band calculations. We describe the robustness and speed of the package, demonstrating its millihartree accuracy and scalability to tens-of-thousands of atoms on ordinary laptops. We demonstrate the performance of the model by reproducing vibrational spectra, and simulating the molecular dynamics of a protein. Our comparisons with electronic structure theory and experimental data demonstrate that neural network molecular dynamics is poised to become an important tool for molecular simulation, lowering the resource barrier to simulating chemistry.

Design and validation of a novel learning tool, the "Anato-Rug," for teaching equine topographical anatomy.

PubMed

Braid, Francesca; Williams, Sarah B; Weller, Renate

2012-01-01

Recognition of anatomical landmarks in live animals (and humans) is key for clinical practice, but students often find it difficult to translate knowledge from dissection-based anatomy onto the live animal and struggle to acquire this vital skill. The purpose of this study was to create and evaluate the use of an equine anatomy rug ("Anato-Rug") depicting topographical anatomy and key areas of lung, heart, and gastrointestinal auscultation, which could be used together with a live horse to aid learning of "live animal" anatomy. Over the course of 2 weeks, 38 third year veterinary students were randomly allocated into an experimental group, revising topographical anatomy from the "Anato-Rug," or a control group, learning topographical anatomy from a textbook. Immediately post activity, both groups underwent a test on live anatomy knowledge and were retested 1 week later. Both groups then completed a questionnaire to ascertain their perceptions of their learning experiences. Results showed that the experimental groups scored significantly higher than the control group at the first testing session, experienced more enjoyment during the activity and gained more confidence in identifying anatomical landmarks than the control group. There was not a significant difference in scores between groups at the second testing session. The findings indicate that the anatomy rug is an effective learning tool that aids understanding, confidence, and enjoyment in learning equine thorax and abdominal anatomy; however it was not better than traditional methods with regards to longer term memory recall. Copyright © 2012 American Association of Anatomists.

Explaining direct care resource use of nursing home residents: findings from time studies in four states.

PubMed

Arling, Greg; Kane, Robert L; Mueller, Christine; Lewis, Teresa

2007-04-01

To explain variation in direct care resource use (RU) of nursing home residents based on the Resource Utilization Groups III (RUG-III) classification system and other resident- and unit-level explanatory variables. Primary data were collected on 5,314 nursing home residents in 156 nursing units in 105 facilities from four states (CO, IN, MN, MS) from 1998 to 2004. Study Design. Nurses and other direct care staff recorded resident-specific and other time caring for all residents on sampled nursing units. Care time was linked to resident data from the Minimum Data Set assessment instrument. Major variables were: RUG-III group (34-group), other health and functional conditions, licensed and other professional minutes per day, unlicensed minutes per day, and direct care RU (wage-weighted minutes). Resident- and unit-level relationships were examined through hierarchical linear modeling. Time study data were recorded with hand-held computers, verified for accuracy by project staff at the data collection sites and then merged into resident and unit-level data sets. Resident care time and RU varied between and within nursing units. RUG-III group was related to RU; variables such as length of stay and unit percentage of high acuity residents also were significantly related. Case-mix indices (CMIs) constructed from study data displayed much less variation across RUG-III groups than CMIs from earlier time studies. Results from earlier time studies may not be representative of care patterns of Medicaid and private pay residents. New RUG-III CMIs should be developed to better reflect the relative costs of caring for these residents.

Observation of DNA Molecules Using Fluorescence Microscopy and Atomic Force Microscopy

ERIC Educational Resources Information Center

Ito, Takashi

2008-01-01

This article describes experiments for an undergraduate instrumental analysis laboratory that aim to observe individual double-stranded DNA (dsDNA) molecules using fluorescence microscopy and atomic force microscopy (AFM). dsDNA molecules are observed under several different conditions to discuss their chemical and physical properties. In…

Conductive Atomic Force Microscopy | Materials Science | NREL

Science.gov Websites

electrical measurement techniques is the high spatial resolution. For example, C-AFM measurements on : High-resolution image of a sample semiconductor device; the image shows white puff-like clusters on a dark background and was obtained using atomic force microscopy. Bottom: High-resolution image of the

Atomic force microscope with combined FTIR-Raman spectroscopy having a micro thermal analyzer

DOEpatents

Fink, Samuel D [Aiken, SC; Fondeur, Fernando F [North Augusta, SC

2011-10-18

An atomic force microscope is provided that includes a micro thermal analyzer with a tip. The micro thermal analyzer is configured for obtaining topographical data from a sample. A raman spectrometer is included and is configured for use in obtaining chemical data from the sample.

Uncertainty quantification in nanomechanical measurements using the atomic force microscope

Treesearch

Ryan Wagner; Robert Moon; Jon Pratt; Gordon Shaw; Arvind Raman

2011-01-01

Quantifying uncertainty in measured properties of nanomaterials is a prerequisite for the manufacture of reliable nanoengineered materials and products. Yet, rigorous uncertainty quantification (UQ) is rarely applied for material property measurements with the atomic force microscope (AFM), a widely used instrument that can measure properties at nanometer scale...

Combinatorial structures to modeling simple games and applications

NASA Astrophysics Data System (ADS)

Molinero, Xavier

2017-09-01

We connect three different topics: combinatorial structures, game theory and chemistry. In particular, we establish the bases to represent some simple games, defined as influence games, and molecules, defined from atoms, by using combinatorial structures. First, we characterize simple games as influence games using influence graphs. It let us to modeling simple games as combinatorial structures (from the viewpoint of structures or graphs). Second, we formally define molecules as combinations of atoms. It let us to modeling molecules as combinatorial structures (from the viewpoint of combinations). It is open to generate such combinatorial structures using some specific techniques as genetic algorithms, (meta-)heuristics algorithms and parallel programming, among others.

Note: Thermal analog to atomic force microscopy force-displacement measurements for nanoscale interfacial contact resistance.

PubMed

Iverson, Brian D; Blendell, John E; Garimella, Suresh V

2010-03-01

Thermal diffusion measurements on polymethylmethacrylate-coated Si substrates using heated atomic force microscopy tips were performed to determine the contact resistance between an organic thin film and Si. The measurement methodology presented demonstrates how the thermal contrast signal obtained during a force-displacement ramp is used to quantify the resistance to heat transfer through an internal interface. The results also delineate the interrogation thickness beyond which thermal diffusion in the organic thin film is not affected appreciably by the underlying substrate.

77 FR 42483 - Application(s) for Duty-Free Entry of Scientific Instruments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-19

... creating artificial nanoscale structures on an atom-by- atom basis using nascent atom manipulation techniques. The instrument will be used to investigate the amount of force required to move one atom on a materials surface while simultaneously measuring local electronic structural changes during atom movement...

16 CFR § 1630.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2013 CFR

2013-01-01

... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 1-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...

16 CFR § 1631.61 - Hide carpets and rugs-alternative washing procedure.

Code of Federal Regulations, 2013 CFR

2013-01-01

... natural “lay” of the hair structure for ten complete strokes. (8) Place test specimen in a circulating... procedure under FF 2-70 for testing the flammability of shearling and hide rugs that (1) consist of natural wool or hair attached to the hide with no synthetic fibers and (2) have been treated with a fire...

DelPhiForce web server: electrostatic forces and energy calculations and visualization.

PubMed

Li, Lin; Jia, Zhe; Peng, Yunhui; Chakravorty, Arghya; Sun, Lexuan; Alexov, Emil

2017-11-15

Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software. Here we demonstrate the usage of the server for various biological problems including protein-cofactor, domain-domain, protein-protein, protein-DNA and protein-RNA interactions. The DelPhiForce web server is available at: http://compbio.clemson.edu/delphi-force. delphi@clemson.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

[Study on the modeling of earth-atmosphere coupling over rugged scenes for hyperspectral remote sensing].

PubMed

Zhao, Hui-Jie; Jiang, Cheng; Jia, Guo-Rui

2014-01-01

Adjacency effects may introduce errors in the quantitative applications of hyperspectral remote sensing, of which the significant item is the earth-atmosphere coupling radiance. However, the surrounding relief and shadow induce strong changes in hyperspectral images acquired from rugged terrain, which is not accurate to describe the spectral characteristics. Furthermore, the radiative coupling process between the earth and the atmosphere is more complex over the rugged scenes. In order to meet the requirements of real-time processing in data simulation, an equivalent reflectance of background was developed by taking into account the topography and the geometry between surroundings and targets based on the radiative transfer process. The contributions of the coupling to the signal at sensor level were then evaluated. This approach was integrated to the sensor-level radiance simulation model and then validated through simulating a set of actual radiance data. The results show that the visual effect of simulated images is consistent with that of observed images. It was also shown that the spectral similarity is improved over rugged scenes. In addition, the model precision is maintained at the same level over flat scenes.

Rugged sensor window materials for harsh environments

NASA Astrophysics Data System (ADS)

Bayya, Shyam; Villalobos, Guillermo; Kim, Woohong; Sanghera, Jasbinger; Hunt, Michael; Aggarwal, Ishwar D.

2014-09-01

There are several military or commercial systems operating in very harsh environments that require rugged windows. On some of these systems, windows become the single point of failure. These applications include sensor or imaging systems, high-energy laser weapons systems, submarine photonic masts, IR countermeasures and missiles. Based on the sea or land or air based platforms the window or dome on these systems must withstand wave slap, underwater or ground based explosions, or survive flight through heavy rain and sand storms while maintaining good optical transmission in the desired wavelength range. Some of these applications still use softer ZnS or fused silica windows because of lack of availability of rugged materials in shapes or sizes required. Sapphire, ALON and spinel are very rugged materials with significantly higher strengths compared to ZnS and fused silica. There have been recent developments in spinel, ALON and sapphire materials to fabricate in large sizes and conformal shapes. We have been developing spinel ceramics for several of these applications. We are also developing β-SiC as a transparent window material as it has higher hardness, strength, and toughness than sapphire, ALON and spinel. This paper gives a summary of our recent findings.

Refining a case-mix measure for nursing homes: Resource Utilization Groups (RUG-III).

PubMed

Fries, B E; Schneider, D P; Foley, W J; Gavazzi, M; Burke, R; Cornelius, E

1994-07-01

A case-mix classification system for nursing home residents is developed, based on a sample of 7,658 residents in seven states. Data included a broad assessment of resident characteristics, corresponding to items of the Minimum Data Set, and detailed measurement of nursing staff care time over a 24-hour period and therapy staff time over a 1-week period. The Resource Utilization Groups, Version III (RUG-III) system, with 44 distinct groups, achieves 55.5% variance explanation of total (nursing and therapy) per diem cost and meets goals of clinical validity and payment incentives. The mean resource use (case-mix index) of groups spans a nine-fold range. The RUG-III system improves on an earlier version not only by increasing the variance explanation (from 43%), but, more importantly, by identifying residents with "high tech" procedures (e.g., ventilators, respirators, and parenteral feeding) and those with cognitive impairments; by using better multiple activities of daily living; and by providing explicit qualifications for the Medicare nursing home benefit. RUG-III is being implemented for nursing home payment in 11 states (six as part of a federal multistate demonstration) and can be used in management, staffing level determination, and quality assurance.

The resource utilization group system: its effect on nursing home case mix and costs.

PubMed

Thorpe, K E; Gertler, P J; Goldman, P

1991-01-01

Using data from 1985 and 1986, we examine how New York state's prospective payment system affected nursing homes. The system, called Resource Utilization Group (RUG-II), aimed to limit nursing home cost growth and improve access to nursing homes by "heavy-care" patients. As in Medicare's prospective hospital reimbursement system, payments to nursing homes were based on a "price," rather than facility-specific rates. With respect to cost growth, we observed considerable diversity among homes. Specifically, those nursing homes most financially constrained by the RUG-II methodology exhibited the slowest rates of cost growth; we observed higher cost growth among the homes least constrained. This higher rate of cost growth raises a question about the desirability of using a pricing methodology to determine nursing home payment rates. In addition to moderating cost growth, we also observed a significant change in the mix of patients admitted to nursing homes. During the first year of the RUG-II program, nursing homes admitted more heavy-care patients and reduced days of care to lighter-care patients. Thus, through 1986, the RUG-II program appeared to satisfy at least one of its major policy objectives.